Query psy7454
Match_columns 103
No_of_seqs 115 out of 2006
Neff 11.2
Searched_HMMs 46136
Date Fri Aug 16 18:44:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7454.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7454hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 9.1E-24 2E-28 123.6 5.5 87 10-99 159-245 (279)
2 KOG2462|consensus 99.9 4.1E-24 9E-29 125.1 3.6 85 4-91 181-265 (279)
3 KOG3623|consensus 99.7 2.4E-19 5.2E-24 116.5 1.2 80 10-90 892-971 (1007)
4 KOG3576|consensus 99.7 7.1E-19 1.5E-23 99.6 0.5 87 9-96 114-200 (267)
5 KOG1074|consensus 99.7 2.9E-17 6.2E-22 108.1 3.7 58 42-100 881-938 (958)
6 KOG1074|consensus 99.6 1.2E-16 2.7E-21 105.2 1.9 56 42-98 607-662 (958)
7 KOG3576|consensus 99.6 1.5E-16 3.2E-21 90.3 1.7 95 3-97 136-240 (267)
8 KOG3623|consensus 99.6 5.4E-16 1.2E-20 101.3 1.9 80 11-91 239-331 (1007)
9 PHA00733 hypothetical protein 99.4 2.8E-13 6.1E-18 73.2 3.6 82 10-94 38-124 (128)
10 KOG3608|consensus 99.4 3.4E-13 7.3E-18 82.3 4.2 95 3-98 198-320 (467)
11 PHA02768 hypothetical protein; 99.2 4.6E-12 9.9E-17 58.1 1.7 43 12-56 5-47 (55)
12 KOG3608|consensus 99.2 3.3E-11 7.1E-16 73.9 4.1 89 4-93 284-376 (467)
13 PHA02768 hypothetical protein; 99.1 3E-11 6.5E-16 55.4 1.9 43 40-85 5-47 (55)
14 PLN03086 PRLI-interacting fact 99.0 1.3E-09 2.8E-14 71.2 6.7 83 10-99 451-543 (567)
15 PHA00733 hypothetical protein 99.0 7.1E-10 1.5E-14 60.1 4.6 51 8-60 69-119 (128)
16 PF13465 zf-H2C2_2: Zinc-finge 99.0 5.3E-10 1.2E-14 44.2 2.2 23 28-50 2-24 (26)
17 PF13465 zf-H2C2_2: Zinc-finge 98.9 2.8E-09 6.1E-14 42.1 2.5 26 55-81 1-26 (26)
18 PHA00616 hypothetical protein 98.9 1.4E-09 3.1E-14 47.7 1.7 31 69-99 1-31 (44)
19 PLN03086 PRLI-interacting fact 98.8 7.7E-09 1.7E-13 67.7 5.3 78 11-93 477-564 (567)
20 KOG3993|consensus 98.8 5.4E-10 1.2E-14 69.9 -0.2 82 13-95 268-382 (500)
21 PHA00616 hypothetical protein 98.8 1.7E-09 3.7E-14 47.4 0.7 34 12-45 1-34 (44)
22 PF05605 zf-Di19: Drought indu 98.5 3.6E-07 7.8E-12 42.3 4.6 50 41-93 3-53 (54)
23 PHA00732 hypothetical protein 98.4 2.6E-07 5.6E-12 46.0 3.0 42 12-59 1-43 (79)
24 PHA00732 hypothetical protein 98.4 3E-07 6.6E-12 45.8 2.9 46 40-92 1-47 (79)
25 PF00096 zf-C2H2: Zinc finger, 98.4 2.8E-07 6.1E-12 35.1 1.8 22 13-34 1-22 (23)
26 PF00096 zf-C2H2: Zinc finger, 98.4 4E-07 8.7E-12 34.7 2.2 23 70-92 1-23 (23)
27 PF13894 zf-C2H2_4: C2H2-type 98.2 2.4E-06 5.1E-11 32.6 2.6 24 70-93 1-24 (24)
28 PF05605 zf-Di19: Drought indu 98.1 7.1E-06 1.5E-10 38.0 3.9 46 12-60 2-49 (54)
29 PF13912 zf-C2H2_6: C2H2-type 98.1 3.5E-06 7.5E-11 33.3 2.1 25 12-36 1-25 (27)
30 PF13912 zf-C2H2_6: C2H2-type 98.1 3.4E-06 7.5E-11 33.3 2.0 25 69-93 1-25 (27)
31 COG5189 SFP1 Putative transcri 98.0 2.4E-06 5.2E-11 52.4 1.0 53 38-90 347-419 (423)
32 PF12756 zf-C2H2_2: C2H2 type 98.0 7.9E-06 1.7E-10 42.2 2.8 73 14-92 1-73 (100)
33 PF13894 zf-C2H2_4: C2H2-type 98.0 7.7E-06 1.7E-10 31.1 2.0 23 13-35 1-23 (24)
34 PF09237 GAGA: GAGA factor; I 97.9 2.7E-05 5.9E-10 35.1 3.2 26 12-37 24-49 (54)
35 KOG3993|consensus 97.9 1E-05 2.2E-10 51.4 2.2 53 12-65 295-380 (500)
36 COG5189 SFP1 Putative transcri 97.8 9.2E-06 2E-10 49.9 1.1 50 10-59 347-417 (423)
37 PF09237 GAGA: GAGA factor; I 97.8 5E-05 1.1E-09 34.2 3.1 32 66-97 21-52 (54)
38 smart00355 ZnF_C2H2 zinc finge 97.6 7.2E-05 1.6E-09 28.7 2.3 24 70-93 1-24 (26)
39 PRK04860 hypothetical protein; 97.6 8.2E-05 1.8E-09 42.0 3.1 37 40-81 119-155 (160)
40 smart00355 ZnF_C2H2 zinc finge 97.5 7.3E-05 1.6E-09 28.7 1.7 23 13-35 1-23 (26)
41 PF12874 zf-met: Zinc-finger o 97.5 0.0001 2.3E-09 28.3 1.8 22 13-34 1-22 (25)
42 PF13909 zf-H2C2_5: C2H2-type 97.3 0.00022 4.8E-09 27.2 1.9 23 70-93 1-23 (24)
43 PRK04860 hypothetical protein; 97.3 0.00033 7.2E-09 39.6 3.1 38 11-52 118-155 (160)
44 PF12874 zf-met: Zinc-finger o 97.3 0.00024 5.3E-09 27.3 1.9 22 70-91 1-22 (25)
45 PF12171 zf-C2H2_jaz: Zinc-fin 97.1 0.00021 4.5E-09 28.1 0.7 22 13-34 2-23 (27)
46 PF13909 zf-H2C2_5: C2H2-type 96.8 0.0011 2.4E-08 25.1 1.6 21 13-34 1-21 (24)
47 PF12171 zf-C2H2_jaz: Zinc-fin 96.6 0.00069 1.5E-08 26.6 0.2 22 70-91 2-23 (27)
48 PF13913 zf-C2HC_2: zinc-finge 96.2 0.0061 1.3E-07 23.5 1.9 19 71-90 4-22 (25)
49 smart00451 ZnF_U1 U1-like zinc 96.0 0.0071 1.5E-07 25.0 1.9 23 12-34 3-25 (35)
50 COG4049 Uncharacterized protei 95.8 0.0049 1.1E-07 28.4 1.0 30 64-93 12-41 (65)
51 COG4049 Uncharacterized protei 95.6 0.0062 1.3E-07 28.0 0.9 28 6-33 11-38 (65)
52 PF09538 FYDLN_acid: Protein o 95.4 0.012 2.7E-07 31.1 1.8 30 13-53 10-39 (108)
53 cd00350 rubredoxin_like Rubred 95.3 0.019 4.2E-07 23.6 1.9 10 13-22 2-11 (33)
54 KOG1146|consensus 95.2 0.0098 2.1E-07 43.3 1.2 79 8-91 461-540 (1406)
55 COG5048 FOG: Zn-finger [Genera 94.9 0.0067 1.5E-07 38.7 -0.2 58 40-98 289-352 (467)
56 PF12756 zf-C2H2_2: C2H2 type 94.7 0.049 1.1E-06 27.8 2.8 25 39-64 49-73 (100)
57 COG5048 FOG: Zn-finger [Genera 94.7 0.01 2.2E-07 37.9 0.3 62 11-73 288-355 (467)
58 TIGR00622 ssl1 transcription f 94.5 0.094 2E-06 27.9 3.6 80 11-93 14-105 (112)
59 PF13719 zinc_ribbon_5: zinc-r 94.1 0.079 1.7E-06 22.4 2.3 12 68-79 24-35 (37)
60 KOG2186|consensus 94.1 0.036 7.7E-07 33.6 1.6 44 13-59 4-47 (276)
61 PF09986 DUF2225: Uncharacteri 94.0 0.019 4.1E-07 34.1 0.4 44 10-53 3-61 (214)
62 TIGR02300 FYDLN_acid conserved 93.6 0.063 1.4E-06 29.1 1.9 32 13-55 10-41 (129)
63 KOG2231|consensus 93.5 0.12 2.6E-06 35.7 3.4 77 23-100 125-213 (669)
64 TIGR02098 MJ0042_CXXC MJ0042 f 93.4 0.12 2.6E-06 21.8 2.3 10 70-79 26-35 (38)
65 COG2888 Predicted Zn-ribbon RN 93.2 0.1 2.2E-06 24.4 2.0 33 39-77 26-58 (61)
66 PF13717 zinc_ribbon_4: zinc-r 93.1 0.17 3.7E-06 21.2 2.5 12 42-53 4-15 (36)
67 KOG2186|consensus 92.8 0.095 2.1E-06 31.8 2.0 54 41-98 4-57 (276)
68 cd00729 rubredoxin_SM Rubredox 92.4 0.15 3.2E-06 21.1 1.8 11 12-22 2-12 (34)
69 COG1592 Rubrerythrin [Energy p 92.1 0.13 2.7E-06 29.5 1.8 24 40-77 134-157 (166)
70 TIGR02605 CxxC_CxxC_SSSS putat 92.1 0.072 1.6E-06 24.1 0.7 31 11-48 4-34 (52)
71 smart00659 RPOLCX RNA polymera 92.0 0.22 4.8E-06 21.9 2.2 26 13-49 3-28 (44)
72 PRK00398 rpoP DNA-directed RNA 91.9 0.22 4.7E-06 22.0 2.2 10 13-22 4-13 (46)
73 KOG2893|consensus 91.7 0.059 1.3E-06 32.5 0.3 47 15-65 13-59 (341)
74 TIGR00373 conserved hypothetic 91.2 0.17 3.8E-06 28.6 1.8 35 35-79 104-138 (158)
75 smart00834 CxxC_CXXC_SSSS Puta 90.8 0.12 2.6E-06 22.0 0.7 30 12-48 5-34 (41)
76 PRK14890 putative Zn-ribbon RN 90.6 0.31 6.7E-06 22.9 2.0 33 39-77 24-56 (59)
77 PRK06266 transcription initiat 90.4 0.18 3.9E-06 29.2 1.4 33 37-79 114-146 (178)
78 smart00531 TFIIE Transcription 90.4 0.72 1.6E-05 25.8 3.8 39 37-80 96-134 (147)
79 PF09723 Zn-ribbon_8: Zinc rib 89.8 0.21 4.5E-06 21.7 1.0 30 12-48 5-34 (42)
80 PF05191 ADK_lid: Adenylate ki 89.7 0.24 5.3E-06 20.8 1.2 9 14-22 3-11 (36)
81 PF05443 ROS_MUCR: ROS/MUCR tr 89.4 0.21 4.6E-06 27.5 1.1 28 67-97 70-97 (132)
82 PHA00626 hypothetical protein 89.2 0.37 8E-06 22.3 1.6 15 38-52 21-35 (59)
83 PF12013 DUF3505: Protein of u 88.9 0.48 1E-05 25.0 2.3 26 69-94 80-109 (109)
84 COG5236 Uncharacterized conser 88.5 0.72 1.6E-05 29.6 3.1 75 14-94 222-306 (493)
85 PF02892 zf-BED: BED zinc fing 87.9 0.58 1.3E-05 20.3 1.9 23 68-90 15-41 (45)
86 PF08790 zf-LYAR: LYAR-type C2 87.3 0.15 3.2E-06 20.2 -0.2 9 42-50 2-10 (28)
87 COG4530 Uncharacterized protei 86.8 0.67 1.5E-05 24.6 1.9 26 14-50 11-36 (129)
88 COG1996 RPC10 DNA-directed RNA 86.3 0.72 1.6E-05 20.8 1.6 11 12-22 6-16 (49)
89 PF14353 CpXC: CpXC protein 86.1 0.11 2.4E-06 28.2 -1.2 47 13-59 2-57 (128)
90 PRK00464 nrdR transcriptional 85.9 0.19 4E-06 28.4 -0.4 15 41-55 29-43 (154)
91 smart00614 ZnF_BED BED zinc fi 85.6 1.3 2.8E-05 19.9 2.4 21 70-90 19-44 (50)
92 smart00734 ZnF_Rad18 Rad18-lik 85.1 1.1 2.4E-05 17.2 1.8 19 71-90 3-21 (26)
93 KOG2593|consensus 84.6 0.91 2E-05 29.9 2.1 33 12-47 128-160 (436)
94 KOG4173|consensus 83.7 0.32 6.9E-06 28.8 -0.1 78 13-93 80-170 (253)
95 PF03604 DNA_RNApol_7kD: DNA d 83.4 1.9 4.1E-05 17.6 2.2 10 13-22 1-10 (32)
96 COG4957 Predicted transcriptio 83.3 0.77 1.7E-05 25.3 1.2 25 70-97 77-101 (148)
97 PF08271 TF_Zn_Ribbon: TFIIB z 82.6 1.2 2.5E-05 19.3 1.5 12 38-49 17-28 (43)
98 KOG2893|consensus 82.6 0.29 6.4E-06 29.7 -0.5 41 43-88 13-53 (341)
99 KOG4173|consensus 82.3 0.69 1.5E-05 27.5 0.9 50 39-92 78-129 (253)
100 PF13878 zf-C2H2_3: zinc-finge 81.9 1.3 2.9E-05 19.1 1.5 24 13-36 14-39 (41)
101 PF08274 PhnA_Zn_Ribbon: PhnA 81.8 0.94 2E-05 18.2 1.0 9 39-47 18-26 (30)
102 PF07754 DUF1610: Domain of un 81.8 0.83 1.8E-05 17.4 0.8 9 12-20 16-24 (24)
103 PF02176 zf-TRAF: TRAF-type zi 80.5 1.5 3.3E-05 20.2 1.6 34 11-45 8-43 (60)
104 KOG1280|consensus 80.4 2.3 5E-05 27.3 2.7 37 11-47 78-116 (381)
105 KOG4167|consensus 80.3 0.33 7.1E-06 34.0 -1.0 27 10-36 790-816 (907)
106 PF13451 zf-trcl: Probable zin 80.1 1.6 3.5E-05 19.7 1.5 13 12-24 4-16 (49)
107 KOG1146|consensus 79.6 0.21 4.6E-06 37.0 -2.1 75 13-93 1261-1352(1406)
108 COG1655 Uncharacterized protei 79.5 0.4 8.7E-06 28.9 -0.7 25 10-34 17-41 (267)
109 KOG2785|consensus 79.3 2.3 5E-05 27.7 2.5 80 12-91 3-90 (390)
110 COG1997 RPL43A Ribosomal prote 79.2 1.1 2.4E-05 22.8 0.9 32 38-80 33-64 (89)
111 KOG3408|consensus 79.0 1.3 2.9E-05 24.0 1.2 26 9-34 54-79 (129)
112 PF10571 UPF0547: Uncharacteri 78.7 1.1 2.4E-05 17.3 0.7 11 13-23 15-25 (26)
113 PF12013 DUF3505: Protein of u 77.8 2.5 5.3E-05 22.3 2.1 24 12-35 80-107 (109)
114 PF15269 zf-C2H2_7: Zinc-finge 77.8 4.6 0.0001 17.8 2.5 23 12-34 20-42 (54)
115 COG3091 SprT Zn-dependent meta 77.6 2 4.4E-05 24.3 1.7 33 39-77 116-148 (156)
116 COG1198 PriA Primosomal protei 77.1 2 4.3E-05 30.5 1.9 34 13-47 436-469 (730)
117 PF06524 NOA36: NOA36 protein; 77.0 2 4.4E-05 26.6 1.7 81 9-91 139-231 (314)
118 PRK03824 hypA hydrogenase nick 76.9 1.5 3.3E-05 24.2 1.2 13 12-24 70-82 (135)
119 PF04959 ARS2: Arsenite-resist 76.2 2.3 5E-05 25.5 1.8 26 39-64 76-101 (214)
120 KOG2593|consensus 76.0 3.8 8.2E-05 27.2 2.8 38 36-77 124-161 (436)
121 TIGR01206 lysW lysine biosynth 75.4 2.9 6.2E-05 19.3 1.6 10 13-22 3-12 (54)
122 KOG4167|consensus 74.5 0.68 1.5E-05 32.6 -0.7 25 69-93 792-816 (907)
123 PRK09678 DNA-binding transcrip 74.1 1.4 3.1E-05 21.6 0.5 42 13-56 2-45 (72)
124 KOG2785|consensus 73.6 5.8 0.00013 25.9 3.2 50 41-91 167-242 (390)
125 PF04959 ARS2: Arsenite-resist 73.1 1.9 4.2E-05 25.8 1.0 29 67-95 75-103 (214)
126 PF01780 Ribosomal_L37ae: Ribo 72.5 0.91 2E-05 23.3 -0.4 31 39-80 34-64 (90)
127 PF10013 DUF2256: Uncharacteri 71.9 1.5 3.3E-05 19.1 0.3 14 71-84 10-23 (42)
128 COG4888 Uncharacterized Zn rib 71.4 1.1 2.3E-05 23.5 -0.3 37 12-52 22-58 (104)
129 TIGR00100 hypA hydrogenase nic 71.4 3.1 6.8E-05 22.3 1.5 10 13-22 71-80 (115)
130 PTZ00255 60S ribosomal protein 71.1 1.9 4.1E-05 22.2 0.6 32 38-80 34-65 (90)
131 smart00440 ZnF_C2C2 C2C2 Zinc 70.3 0.93 2E-05 19.4 -0.6 8 41-48 29-36 (40)
132 PRK12380 hydrogenase nickel in 69.1 4.1 8.8E-05 21.8 1.6 10 13-22 71-80 (113)
133 COG2331 Uncharacterized protei 68.5 2.9 6.3E-05 20.7 0.9 33 10-49 10-42 (82)
134 TIGR00280 L37a ribosomal prote 68.4 1.9 4.2E-05 22.2 0.3 32 38-80 33-64 (91)
135 smart00154 ZnF_AN1 AN1-like Zi 68.4 3.3 7.1E-05 17.6 0.9 13 12-24 12-24 (39)
136 COG3357 Predicted transcriptio 68.1 3.5 7.6E-05 21.2 1.1 14 39-52 57-70 (97)
137 COG4391 Uncharacterized protei 67.7 2 4.3E-05 20.4 0.2 45 31-80 15-59 (62)
138 PF07295 DUF1451: Protein of u 67.7 4 8.7E-05 23.0 1.4 8 41-48 113-120 (146)
139 PRK00432 30S ribosomal protein 67.2 4.9 0.00011 18.2 1.4 10 69-78 37-46 (50)
140 PF13453 zf-TFIIB: Transcripti 66.5 4.8 0.0001 17.1 1.3 18 40-57 19-36 (41)
141 KOG2482|consensus 66.1 4 8.7E-05 26.4 1.3 23 69-91 195-217 (423)
142 COG1773 Rubredoxin [Energy pro 65.8 3.6 7.8E-05 19.1 0.8 13 69-81 3-15 (55)
143 PF04423 Rad50_zn_hook: Rad50 64.9 3.1 6.8E-05 18.9 0.6 11 14-24 22-32 (54)
144 COG4896 Uncharacterized protei 64.2 5.8 0.00013 18.8 1.4 40 14-53 4-44 (68)
145 PRK03976 rpl37ae 50S ribosomal 63.6 2.6 5.7E-05 21.6 0.2 32 38-80 34-65 (90)
146 KOG2807|consensus 63.1 11 0.00024 24.3 2.8 26 68-93 344-369 (378)
147 PF07282 OrfB_Zn_ribbon: Putat 62.9 7.5 0.00016 18.5 1.7 15 67-81 44-58 (69)
148 PF01428 zf-AN1: AN1-like Zinc 62.3 4.1 8.9E-05 17.6 0.7 14 11-24 12-25 (43)
149 COG3364 Zn-ribbon containing p 62.3 6.5 0.00014 20.7 1.5 13 12-24 2-14 (112)
150 PF01155 HypA: Hydrogenase exp 62.0 5.2 0.00011 21.4 1.1 11 13-23 71-81 (113)
151 KOG1280|consensus 61.8 9 0.00019 24.9 2.3 25 41-65 80-104 (381)
152 PRK00564 hypA hydrogenase nick 61.3 5.6 0.00012 21.4 1.2 10 13-22 72-81 (117)
153 PRK04351 hypothetical protein; 61.2 7.9 0.00017 21.9 1.8 33 40-81 112-144 (149)
154 TIGR00595 priA primosomal prot 60.0 6.9 0.00015 26.6 1.7 13 35-47 235-247 (505)
155 PF03811 Zn_Tnp_IS1: InsA N-te 59.9 3.8 8.3E-05 17.2 0.3 14 33-46 22-35 (36)
156 PF13824 zf-Mss51: Zinc-finger 59.7 8 0.00017 18.0 1.4 11 38-48 12-22 (55)
157 COG5151 SSL1 RNA polymerase II 59.6 5 0.00011 25.6 0.9 49 42-93 364-412 (421)
158 PF04810 zf-Sec23_Sec24: Sec23 59.4 2.9 6.4E-05 17.8 -0.0 12 67-78 22-33 (40)
159 PRK14873 primosome assembly pr 58.9 14 0.0003 26.3 3.0 13 35-47 405-417 (665)
160 PF04780 DUF629: Protein of un 58.8 9.7 0.00021 25.8 2.2 26 68-93 56-81 (466)
161 PF07975 C1_4: TFIIH C1-like d 58.0 2.2 4.7E-05 19.5 -0.6 24 69-92 21-44 (51)
162 PLN02294 cytochrome c oxidase 57.8 6.7 0.00014 22.7 1.2 15 67-81 139-153 (174)
163 PF15135 UPF0515: Uncharacteri 55.9 15 0.00032 22.8 2.4 11 10-20 110-120 (278)
164 cd00924 Cyt_c_Oxidase_Vb Cytoc 55.6 8.3 0.00018 20.1 1.2 18 62-80 73-90 (97)
165 cd00730 rubredoxin Rubredoxin; 55.3 6.3 0.00014 17.9 0.7 12 70-81 2-13 (50)
166 COG1998 RPS31 Ribosomal protei 55.0 15 0.00032 16.7 1.8 9 69-77 37-45 (51)
167 PRK03681 hypA hydrogenase nick 54.9 6.8 0.00015 21.0 0.9 7 42-48 72-78 (114)
168 PF10263 SprT-like: SprT-like 54.1 6.8 0.00015 21.9 0.8 32 40-80 123-154 (157)
169 KOG0227|consensus 53.9 7.6 0.00017 23.0 1.0 28 3-32 46-73 (222)
170 PF10276 zf-CHCC: Zinc-finger 53.5 7 0.00015 16.8 0.6 11 69-79 29-39 (40)
171 COG1675 TFA1 Transcription ini 53.5 12 0.00025 21.9 1.7 32 36-77 109-140 (176)
172 PF14787 zf-CCHC_5: GAG-polypr 53.4 6.1 0.00013 16.6 0.4 15 71-85 4-18 (36)
173 COG0068 HypF Hydrogenase matur 53.0 2.7 5.9E-05 29.7 -1.0 29 42-77 153-181 (750)
174 PF12230 PRP21_like_P: Pre-mRN 53.0 4.5 9.8E-05 24.4 0.0 32 69-101 168-199 (229)
175 COG4338 Uncharacterized protei 52.7 2.8 6E-05 18.8 -0.7 13 71-83 14-26 (54)
176 PF12760 Zn_Tnp_IS1595: Transp 52.6 6 0.00013 17.3 0.4 11 67-77 35-45 (46)
177 KOG2907|consensus 52.2 9.8 0.00021 20.5 1.1 13 69-81 102-114 (116)
178 PF00301 Rubredoxin: Rubredoxi 52.2 7.9 0.00017 17.3 0.7 13 70-82 2-14 (47)
179 PF14311 DUF4379: Domain of un 51.8 16 0.00035 16.6 1.8 12 41-52 29-40 (55)
180 PF11672 DUF3268: Protein of u 51.6 13 0.00028 19.7 1.5 12 12-23 2-13 (102)
181 PF02591 DUF164: Putative zinc 51.2 19 0.00041 16.4 2.0 32 42-78 24-55 (56)
182 KOG0696|consensus 50.7 4 8.6E-05 27.5 -0.5 41 10-59 71-111 (683)
183 COG4306 Uncharacterized protei 50.6 5.5 0.00012 21.8 0.1 18 66-83 65-82 (160)
184 smart00731 SprT SprT homologue 50.4 14 0.00031 20.6 1.7 33 40-80 112-144 (146)
185 KOG0717|consensus 49.9 12 0.00025 25.4 1.5 21 13-33 293-313 (508)
186 KOG3507|consensus 49.7 14 0.00031 17.4 1.3 9 69-77 37-45 (62)
187 PF06397 Desulfoferrod_N: Desu 49.6 9.7 0.00021 16.0 0.7 12 11-22 5-16 (36)
188 KOG2482|consensus 49.5 11 0.00025 24.4 1.3 23 12-34 195-217 (423)
189 COG1571 Predicted DNA-binding 49.5 13 0.00027 24.9 1.6 13 40-52 367-379 (421)
190 PF01363 FYVE: FYVE zinc finge 48.6 14 0.00031 17.4 1.4 12 12-23 9-20 (69)
191 PF04780 DUF629: Protein of un 48.6 14 0.00031 25.0 1.7 26 12-37 57-83 (466)
192 PF09845 DUF2072: Zn-ribbon co 48.2 9.9 0.00021 21.0 0.8 14 12-25 1-14 (131)
193 PTZ00448 hypothetical protein; 48.2 13 0.00027 24.4 1.4 24 12-35 314-337 (373)
194 PHA02998 RNA polymerase subuni 48.1 5.6 0.00012 23.2 -0.1 11 70-80 172-182 (195)
195 KOG2231|consensus 48.1 48 0.001 23.8 4.1 17 43-59 185-201 (669)
196 PRK05580 primosome assembly pr 47.6 24 0.00053 25.1 2.8 8 14-21 383-390 (679)
197 COG1326 Uncharacterized archae 47.3 35 0.00076 20.4 3.0 13 39-51 29-41 (201)
198 TIGR00686 phnA alkylphosphonat 46.8 17 0.00037 19.4 1.5 13 39-51 18-30 (109)
199 PF01286 XPA_N: XPA protein N- 46.4 11 0.00025 15.6 0.7 12 13-24 4-15 (34)
200 KOG2071|consensus 45.0 19 0.0004 25.2 1.9 27 67-93 416-442 (579)
201 PRK00420 hypothetical protein; 45.0 25 0.00054 18.9 2.0 7 71-77 42-48 (112)
202 PF00130 C1_1: Phorbol esters/ 44.9 9.1 0.0002 17.0 0.3 10 12-21 11-20 (53)
203 PF03966 Trm112p: Trm112p-like 44.5 11 0.00024 18.0 0.6 14 10-23 51-64 (68)
204 PF09963 DUF2197: Uncharacteri 44.3 23 0.00049 16.6 1.6 11 38-48 29-39 (56)
205 KOG0717|consensus 43.9 16 0.00034 24.9 1.4 22 70-91 293-314 (508)
206 KOG3183|consensus 43.7 19 0.0004 22.2 1.6 41 12-52 23-67 (250)
207 COG5216 Uncharacterized conser 43.5 20 0.00044 16.9 1.4 13 65-77 40-52 (67)
208 KOG0782|consensus 43.3 2.9 6.4E-05 29.0 -1.9 51 26-83 239-290 (1004)
209 KOG1940|consensus 43.3 24 0.00051 22.3 2.0 8 41-48 197-204 (276)
210 COG2879 Uncharacterized small 41.2 37 0.0008 16.3 2.0 19 81-99 24-42 (65)
211 PF08209 Sgf11: Sgf11 (transcr 41.1 31 0.00066 14.2 1.9 20 12-32 4-23 (33)
212 KOG1088|consensus 40.2 16 0.00034 19.9 0.8 19 7-25 93-111 (124)
213 PF12773 DZR: Double zinc ribb 40.2 17 0.00038 15.9 0.9 8 41-48 30-37 (50)
214 PF08792 A2L_zn_ribbon: A2L zi 40.0 18 0.00038 14.8 0.8 12 12-23 21-32 (33)
215 COG1779 C4-type Zn-finger prot 40.0 7.8 0.00017 23.0 -0.3 35 13-53 15-56 (201)
216 COG1594 RPB9 DNA-directed RNA 40.0 10 0.00022 20.4 0.1 16 10-25 20-35 (113)
217 COG3677 Transposase and inacti 40.0 15 0.00033 20.2 0.8 16 10-25 51-66 (129)
218 PRK14892 putative transcriptio 39.9 18 0.00039 19.0 1.0 8 12-19 21-28 (99)
219 KOG4727|consensus 39.8 24 0.00052 20.6 1.5 22 11-32 74-95 (193)
220 PF11789 zf-Nse: Zinc-finger o 39.7 27 0.00058 16.2 1.5 32 38-74 22-53 (57)
221 KOG2636|consensus 39.6 26 0.00056 23.8 1.8 27 33-59 394-421 (497)
222 PF10058 DUF2296: Predicted in 39.2 34 0.00075 15.7 1.8 10 68-77 43-52 (54)
223 KOG1842|consensus 39.2 19 0.00041 24.4 1.2 29 39-67 14-42 (505)
224 PRK05978 hypothetical protein; 39.1 12 0.00025 21.3 0.3 11 71-81 54-64 (148)
225 PF01927 Mut7-C: Mut7-C RNAse 39.1 17 0.00037 20.3 0.9 44 41-84 92-139 (147)
226 PTZ00043 cytochrome c oxidase 38.5 17 0.00038 22.2 0.9 15 67-81 179-193 (268)
227 PRK12722 transcriptional activ 38.5 27 0.00058 20.7 1.7 9 69-77 154-162 (187)
228 PF08882 Acetone_carb_G: Aceto 38.3 23 0.0005 19.0 1.3 17 18-34 29-46 (112)
229 PRK05452 anaerobic nitric oxid 37.6 20 0.00044 24.3 1.2 14 39-52 424-437 (479)
230 COG5246 PRP11 Splicing factor 37.4 29 0.00063 20.5 1.6 27 4-32 47-73 (222)
231 PRK12860 transcriptional activ 37.2 27 0.00059 20.7 1.6 11 41-51 135-145 (189)
232 PF04438 zf-HIT: HIT zinc fing 37.0 22 0.00047 14.1 0.8 11 12-22 13-23 (30)
233 PRK00762 hypA hydrogenase nick 36.9 26 0.00056 19.1 1.4 6 71-76 94-99 (124)
234 PRK10220 hypothetical protein; 36.7 37 0.00079 18.3 1.8 13 40-52 20-32 (111)
235 PF02148 zf-UBP: Zn-finger in 35.8 13 0.00029 17.4 0.1 16 67-82 9-24 (63)
236 COG0675 Transposase and inacti 35.7 30 0.00066 21.7 1.7 15 68-82 321-335 (364)
237 PF14803 Nudix_N_2: Nudix N-te 35.6 25 0.00054 14.5 0.9 12 11-22 21-32 (34)
238 TIGR03831 YgiT_finger YgiT-typ 35.6 19 0.00042 15.2 0.6 12 13-24 33-44 (46)
239 cd00974 DSRD Desulforedoxin (D 35.5 25 0.00054 14.2 0.9 11 12-22 4-14 (34)
240 TIGR00319 desulf_FeS4 desulfof 35.3 24 0.00053 14.2 0.9 12 11-22 6-17 (34)
241 cd00065 FYVE FYVE domain; Zinc 35.1 37 0.0008 15.2 1.6 10 14-23 4-13 (57)
242 KOG2923|consensus 34.8 31 0.00067 16.6 1.3 10 67-76 42-51 (67)
243 PF01215 COX5B: Cytochrome c o 34.6 16 0.00034 20.5 0.3 18 63-81 107-124 (136)
244 smart00064 FYVE Protein presen 34.2 34 0.00075 16.0 1.5 12 12-23 10-21 (68)
245 PF15616 TerY-C: TerY-C metal 34.2 15 0.00031 20.4 0.1 13 66-78 102-114 (131)
246 KOG4118|consensus 33.8 23 0.00049 17.1 0.7 29 70-98 39-67 (74)
247 PF04606 Ogr_Delta: Ogr/Delta- 33.7 14 0.00031 16.2 0.1 6 75-80 33-38 (47)
248 PLN03238 probable histone acet 32.5 65 0.0014 20.6 2.7 24 67-90 46-69 (290)
249 KOG1994|consensus 32.4 25 0.00055 21.5 0.9 25 66-90 236-260 (268)
250 PF05180 zf-DNL: DNL zinc fing 31.8 18 0.00039 17.5 0.2 34 12-48 4-37 (66)
251 TIGR00627 tfb4 transcription f 31.6 45 0.00099 21.1 2.0 25 40-79 255-279 (279)
252 PF05741 zf-nanos: Nanos RNA b 31.5 21 0.00046 16.6 0.4 10 12-21 33-42 (55)
253 PF02748 PyrI_C: Aspartate car 30.9 28 0.0006 15.9 0.8 15 66-80 32-46 (52)
254 smart00132 LIM Zinc-binding do 30.9 8.8 0.00019 15.4 -0.9 6 42-47 29-34 (39)
255 KOG0978|consensus 30.5 24 0.00052 25.3 0.7 13 71-83 680-692 (698)
256 PF14369 zf-RING_3: zinc-finge 30.4 24 0.00052 14.6 0.5 10 14-23 23-32 (35)
257 PF00412 LIM: LIM domain; Int 30.2 7.2 0.00016 17.6 -1.3 14 39-52 25-38 (58)
258 PF06676 DUF1178: Protein of u 29.9 40 0.00086 19.2 1.4 10 39-48 31-40 (148)
259 COG5188 PRP9 Splicing factor 3 29.8 22 0.00047 23.4 0.4 22 12-33 238-259 (470)
260 smart00109 C1 Protein kinase C 29.8 40 0.00087 14.2 1.2 10 12-21 11-20 (49)
261 PF01096 TFIIS_C: Transcriptio 29.4 28 0.0006 14.7 0.6 9 41-49 29-37 (39)
262 KOG2272|consensus 29.2 66 0.0014 20.2 2.3 19 64-82 216-234 (332)
263 PF10083 DUF2321: Uncharacteri 29.1 20 0.00044 20.5 0.2 21 66-86 65-85 (158)
264 smart00661 RPOL9 RNA polymeras 29.1 33 0.00071 15.1 0.8 13 12-24 20-32 (52)
265 PHA02942 putative transposase; 29.1 39 0.00085 22.3 1.5 16 67-82 340-355 (383)
266 TIGR03829 YokU_near_AblA uncha 28.5 39 0.00085 17.4 1.1 18 12-29 35-52 (89)
267 PF02891 zf-MIZ: MIZ/SP-RING z 27.9 42 0.00092 15.0 1.1 9 69-77 41-49 (50)
268 PRK11032 hypothetical protein; 27.7 48 0.001 19.1 1.5 8 41-48 125-132 (160)
269 PF14255 Cys_rich_CPXG: Cystei 27.7 30 0.00065 15.8 0.6 10 71-80 2-11 (52)
270 PLN02748 tRNA dimethylallyltra 27.3 48 0.001 22.7 1.7 23 12-34 418-441 (468)
271 TIGR01384 TFS_arch transcripti 27.1 15 0.00032 19.1 -0.6 37 41-80 63-101 (104)
272 PRK01343 zinc-binding protein; 26.4 62 0.0013 15.2 1.5 11 12-22 9-19 (57)
273 TIGR00244 transcriptional regu 26.2 31 0.00067 19.6 0.6 13 70-82 29-41 (147)
274 PF14690 zf-ISL3: zinc-finger 25.5 36 0.00078 14.6 0.6 8 12-19 2-9 (47)
275 CHL00174 accD acetyl-CoA carbo 25.3 27 0.00059 22.2 0.3 13 41-53 58-70 (296)
276 PF14354 Lar_restr_allev: Rest 24.9 37 0.0008 15.6 0.6 10 12-21 3-12 (61)
277 KOG3214|consensus 24.8 22 0.00048 18.7 -0.2 12 41-52 48-59 (109)
278 PF02146 SIR2: Sir2 family; I 24.8 1.3E+02 0.0029 17.2 3.0 11 41-51 106-116 (178)
279 COG5112 UFD2 U1-like Zn-finger 24.6 36 0.00078 18.2 0.6 24 10-33 53-76 (126)
280 COG1656 Uncharacterized conser 24.4 42 0.00091 19.5 0.9 45 41-86 98-147 (165)
281 PF03884 DUF329: Domain of unk 24.4 38 0.00081 15.9 0.6 12 13-24 3-14 (57)
282 PF13821 DUF4187: Domain of un 24.2 41 0.00089 15.5 0.7 23 65-87 23-45 (55)
283 TIGR00515 accD acetyl-CoA carb 24.2 30 0.00066 21.9 0.3 13 41-53 46-58 (285)
284 TIGR01385 TFSII transcription 23.8 27 0.00058 22.3 0.0 10 70-79 287-296 (299)
285 PF09082 DUF1922: Domain of un 23.5 48 0.001 16.2 0.8 26 13-50 4-29 (68)
286 PLN00104 MYST -like histone ac 23.3 75 0.0016 21.7 2.0 25 67-91 196-220 (450)
287 PRK05654 acetyl-CoA carboxylas 23.0 32 0.0007 21.8 0.3 32 13-53 28-59 (292)
288 PRK03564 formate dehydrogenase 22.7 52 0.0011 21.2 1.1 11 11-21 186-196 (309)
289 PF09855 DUF2082: Nucleic-acid 22.4 36 0.00077 16.3 0.3 9 13-21 1-9 (64)
290 KOG3277|consensus 22.3 56 0.0012 18.8 1.1 33 12-47 79-111 (165)
291 PF03107 C1_2: C1 domain; Int 22.2 49 0.0011 12.9 0.7 8 71-78 2-9 (30)
292 PRK08222 hydrogenase 4 subunit 22.0 61 0.0013 18.9 1.3 18 12-29 114-131 (181)
293 TIGR03830 CxxCG_CxxCG_HTH puta 21.9 88 0.0019 16.6 1.8 18 12-29 31-48 (127)
294 PF14446 Prok-RING_1: Prokaryo 21.8 25 0.00055 16.3 -0.3 26 13-50 6-31 (54)
295 KOG3352|consensus 21.7 48 0.0011 18.9 0.8 13 68-80 132-144 (153)
296 PF06220 zf-U1: U1 zinc finger 21.7 86 0.0019 13.2 1.5 10 41-50 4-13 (38)
297 smart00290 ZnF_UBP Ubiquitin C 21.7 49 0.0011 14.3 0.7 10 70-79 12-21 (50)
298 PF11931 DUF3449: Domain of un 21.6 31 0.00067 20.6 0.0 23 11-33 100-123 (196)
299 COG5539 Predicted cysteine pro 21.5 92 0.002 20.0 2.0 24 8-31 271-294 (306)
300 PF05280 FlhC: Flagellar trans 21.4 42 0.0009 19.6 0.5 12 41-52 135-146 (175)
301 COG1327 Predicted transcriptio 21.4 43 0.00093 19.2 0.5 13 70-82 29-41 (156)
302 PF14375 Cys_rich_CWC: Cystein 21.1 49 0.0011 14.8 0.6 9 15-23 1-9 (50)
303 KOG3014|consensus 21.1 84 0.0018 19.7 1.7 23 14-36 39-63 (257)
304 PTZ00064 histone acetyltransfe 20.9 1E+02 0.0022 21.5 2.2 25 67-91 278-302 (552)
305 COG5109 Uncharacterized conser 20.8 85 0.0018 20.5 1.7 45 36-84 347-391 (396)
306 PRK06260 threonine synthase; V 20.7 1.1E+02 0.0024 20.2 2.4 10 13-22 4-13 (397)
307 COG1885 Uncharacterized protei 20.6 49 0.0011 17.6 0.6 13 12-24 49-61 (115)
308 COG1579 Zn-ribbon protein, pos 20.6 1.1E+02 0.0024 19.0 2.1 35 41-80 198-232 (239)
309 PLN03239 histone acetyltransfe 20.2 79 0.0017 20.8 1.6 25 67-91 104-128 (351)
310 PF05876 Terminase_GpA: Phage 20.1 48 0.001 23.1 0.7 12 13-24 201-212 (557)
No 1
>KOG2462|consensus
Probab=99.89 E-value=9.1e-24 Score=123.63 Aligned_cols=87 Identities=23% Similarity=0.456 Sum_probs=69.1
Q ss_pred CCceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHHH
Q psy7454 10 RYKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALKVHT 89 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H~ 89 (103)
++.+.|+.||+.|.....|..|+++|+ -+.+|.+||+.|..+=.|+.| +++|+|||||.|..|++.|..+++|..|+
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGH-iRTHTGEKPF~C~hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGH-IRTHTGEKPFSCPHCGKAFADRSNLRAHM 235 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcc-cccccCCCCccCCcccchhcchHHHHHHH
Confidence 456777777777777777777777775 567788888888887778887 78888888888888888888888888888
Q ss_pred HhhCCCCCcc
Q psy7454 90 KRYHPKMYDV 99 (103)
Q Consensus 90 ~~~~~~~~~~ 99 (103)
++|.+.++|.
T Consensus 236 QTHS~~K~~q 245 (279)
T KOG2462|consen 236 QTHSDVKKHQ 245 (279)
T ss_pred HhhcCCcccc
Confidence 8888888774
No 2
>KOG2462|consensus
Probab=99.89 E-value=4.1e-24 Score=125.06 Aligned_cols=85 Identities=26% Similarity=0.440 Sum_probs=78.9
Q ss_pred CCCCCCCCceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcH
Q psy7454 4 PRPNAYRYKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQ 83 (103)
Q Consensus 4 ~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~ 83 (103)
.|+|+ -+..|.+||+.|...=-|+.|+|+|+||+||.|..|+++|...++|+.| +.+|.+.++|.|..|++.|...+
T Consensus 181 irTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAH-mQTHS~~K~~qC~~C~KsFsl~S 257 (279)
T KOG2462|consen 181 IRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAH-MQTHSDVKKHQCPRCGKSFALKS 257 (279)
T ss_pred hhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHH-HHhhcCCccccCcchhhHHHHHH
Confidence 44555 6799999999999888899999999999999999999999999999998 89999999999999999999999
Q ss_pred HHHHHHHh
Q psy7454 84 ALKVHTKR 91 (103)
Q Consensus 84 ~l~~H~~~ 91 (103)
.|.+|.-.
T Consensus 258 yLnKH~ES 265 (279)
T KOG2462|consen 258 YLNKHSES 265 (279)
T ss_pred HHHHhhhh
Confidence 99999754
No 3
>KOG3623|consensus
Probab=99.75 E-value=2.4e-19 Score=116.52 Aligned_cols=80 Identities=24% Similarity=0.559 Sum_probs=76.7
Q ss_pred CCceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHHH
Q psy7454 10 RYKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALKVHT 89 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H~ 89 (103)
...|.|+.|++.|...+.|.+|...|+|.+||.|.+|.++|+.+-.|..| ++.|.|++||.|..|++.|.++..+..||
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEH-kRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEH-KRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhh-hhhccCCCcchhhhhhhhcccccchHhhh
Confidence 45799999999999999999999999999999999999999999999998 99999999999999999999999999987
Q ss_pred H
Q psy7454 90 K 90 (103)
Q Consensus 90 ~ 90 (103)
-
T Consensus 971 N 971 (1007)
T KOG3623|consen 971 N 971 (1007)
T ss_pred c
Confidence 5
No 4
>KOG3576|consensus
Probab=99.72 E-value=7.1e-19 Score=99.61 Aligned_cols=87 Identities=28% Similarity=0.467 Sum_probs=80.9
Q ss_pred CCCceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHH
Q psy7454 9 YRYKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALKVH 88 (103)
Q Consensus 9 ~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H 88 (103)
+...|.|.+|++.|.....|.+|++.|...+.+.|..||++|...-.|++| .++|+|-+||+|..|++.|++..+|..|
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh-~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRH-TRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhh-hccccCccccchhhhhHHHHhhccHHHH
Confidence 345799999999999999999999999999999999999999999999998 8999999999999999999999999999
Q ss_pred HHhhCCCC
Q psy7454 89 TKRYHPKM 96 (103)
Q Consensus 89 ~~~~~~~~ 96 (103)
++..+|..
T Consensus 193 l~kvhgv~ 200 (267)
T KOG3576|consen 193 LKKVHGVQ 200 (267)
T ss_pred HHHHcCch
Confidence 99877654
No 5
>KOG1074|consensus
Probab=99.68 E-value=2.9e-17 Score=108.10 Aligned_cols=58 Identities=28% Similarity=0.513 Sum_probs=54.8
Q ss_pred ecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHHHHhhCCCCCccc
Q psy7454 42 TCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALKVHTKRYHPKMYDVE 100 (103)
Q Consensus 42 ~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~ 100 (103)
.|.+||+.|...+.|+.| +++|++++||.|.+|++.|....+|+.||.+|.+..|..+
T Consensus 881 ~C~vCgk~FsSSsALqiH-~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~sr 938 (958)
T KOG1074|consen 881 VCNVCGKQFSSSAALEIH-MRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSR 938 (958)
T ss_pred hhccchhcccchHHHHHh-hhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCcc
Confidence 799999999999999998 9999999999999999999999999999999998887643
No 6
>KOG1074|consensus
Probab=99.62 E-value=1.2e-16 Score=105.20 Aligned_cols=56 Identities=25% Similarity=0.459 Sum_probs=40.7
Q ss_pred ecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHHHHhhCCCCCc
Q psy7454 42 TCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALKVHTKRYHPKMYD 98 (103)
Q Consensus 42 ~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~ 98 (103)
.|.+|.+...-.+.|+.| -++|+||+||+|.+||+.|.++.+|+.|+..|....|+
T Consensus 607 qCiiC~rVlSC~saLqmH-yrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~ 662 (958)
T KOG1074|consen 607 QCIICLRVLSCPSALQMH-YRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPA 662 (958)
T ss_pred ceeeeeecccchhhhhhh-hhcccCcCccccccccchhccccchhhcccccccCccc
Confidence 677777777777777776 67777777777777777777777777777777554443
No 7
>KOG3576|consensus
Probab=99.62 E-value=1.5e-16 Score=90.32 Aligned_cols=95 Identities=25% Similarity=0.460 Sum_probs=83.4
Q ss_pred CCCCCCCCCceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcC----------CCCCeeC
Q psy7454 3 MPRPNAYRYKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHT----------GQKPYPC 72 (103)
Q Consensus 3 ~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~----------~~~~~~c 72 (103)
|+.-|+..+.+.|..||+.|.+...|++|+++|+|.+||.|..|+++|.....|..|...+|. .++.|.|
T Consensus 136 h~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vc 215 (267)
T KOG3576|consen 136 HLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVC 215 (267)
T ss_pred HhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeee
Confidence 455677778899999999999999999999999999999999999999999999999666664 3577999
Q ss_pred CCCCccccCcHHHHHHHHhhCCCCC
Q psy7454 73 RYCDYKARETQALKVHTKRYHPKMY 97 (103)
Q Consensus 73 ~~C~~~f~~~~~l~~H~~~~~~~~~ 97 (103)
..||........+..|+..++..-|
T Consensus 216 edcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 216 EDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred cccCCCCCChhHHHHHHHhcCCCCH
Confidence 9999999999999999999886544
No 8
>KOG3623|consensus
Probab=99.58 E-value=5.4e-16 Score=101.28 Aligned_cols=80 Identities=24% Similarity=0.595 Sum_probs=71.1
Q ss_pred CceeeCCCCCcccCchhHHHHHhhcCC-------------CCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCc
Q psy7454 11 YKYVCFACKFYTYNTGNIKRHLGMHLG-------------EKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDY 77 (103)
Q Consensus 11 ~~~~C~~C~~~f~~~~~l~~h~~~h~~-------------~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~ 77 (103)
..|.|..|..+|..+..|.+|+.+|.. -+.|+|.+||++|+.+-.|+.| +++|.|++||.|+.|++
T Consensus 239 ~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEH-lRIHSGEKPfeCpnCkK 317 (1007)
T KOG3623|consen 239 PNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEH-LRIHSGEKPFECPNCKK 317 (1007)
T ss_pred CCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhh-heeecCCCCcCCccccc
Confidence 358899999999999999999988742 2458999999999999999998 89999999999999999
Q ss_pred cccCcHHHHHHHHh
Q psy7454 78 KARETQALKVHTKR 91 (103)
Q Consensus 78 ~f~~~~~l~~H~~~ 91 (103)
.|.++..+..|+..
T Consensus 318 RFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 318 RFSHSGSYSSHMSS 331 (1007)
T ss_pred ccccCCcccccccc
Confidence 99999999999764
No 9
>PHA00733 hypothetical protein
Probab=99.40 E-value=2.8e-13 Score=73.25 Aligned_cols=82 Identities=21% Similarity=0.364 Sum_probs=67.8
Q ss_pred CCceeeCCCCCcccCchhHHHH--H---hhcCCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHH
Q psy7454 10 RYKYVCFACKFYTYNTGNIKRH--L---GMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQA 84 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~~~l~~h--~---~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~ 84 (103)
++++.|.+|...|.....|..+ . ..+.+.++|.|..||+.|.....|..| ++.+ +.++.|..|++.|.....
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H-~r~h--~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQH-IRYT--EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHH-HhcC--CcCccCCCCCCccCCHHH
Confidence 5678999999888877666554 1 123458899999999999999999998 6655 457999999999999999
Q ss_pred HHHHHHhhCC
Q psy7454 85 LKVHTKRYHP 94 (103)
Q Consensus 85 l~~H~~~~~~ 94 (103)
|..|+...++
T Consensus 115 L~~H~~~~h~ 124 (128)
T PHA00733 115 TLDHVCKKHN 124 (128)
T ss_pred HHHHHHHhcC
Confidence 9999998775
No 10
>KOG3608|consensus
Probab=99.40 E-value=3.4e-13 Score=82.33 Aligned_cols=95 Identities=20% Similarity=0.382 Sum_probs=69.8
Q ss_pred CCCCCCCCCceeeCCCCCcccCchhHHHHHhhcCC----------------------------CCCeecCCCCccccCch
Q psy7454 3 MPRPNAYRYKYVCFACKFYTYNTGNIKRHLGMHLG----------------------------EKPFTCNMCEFKCRDNR 54 (103)
Q Consensus 3 ~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~----------------------------~~~~~c~~C~~~~~~~~ 54 (103)
|.++|++++.--|+.||..|.....|-.|.+..+. ...|+|+.|..+....+
T Consensus 198 H~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~s 277 (467)
T KOG3608|consen 198 HIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSAS 277 (467)
T ss_pred HHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChH
Confidence 34566666666666666666666666555432110 24578999999999999
Q ss_pred HHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHHHHhhCCCCCc
Q psy7454 55 TLKAHHINIHTGQKPYPCRYCDYKARETQALKVHTKRYHPKMYD 98 (103)
Q Consensus 55 ~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~ 98 (103)
.|..|++..|..++||+|..|+..+...++|.+|...|. +..|
T Consensus 278 sL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y 320 (467)
T KOG3608|consen 278 SLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVY 320 (467)
T ss_pred HHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccce
Confidence 999986667888999999999999999999999999776 4434
No 11
>PHA02768 hypothetical protein; Provisional
Probab=99.23 E-value=4.6e-12 Score=58.12 Aligned_cols=43 Identities=16% Similarity=0.226 Sum_probs=30.4
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHH
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTL 56 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l 56 (103)
.|.|+.||+.|...++|..|+++|+ +++.|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 3677777777777777777777776 567777777776655554
No 12
>KOG3608|consensus
Probab=99.18 E-value=3.3e-11 Score=73.87 Aligned_cols=89 Identities=19% Similarity=0.510 Sum_probs=56.3
Q ss_pred CCCCCCCCceeeCCCCCcccCchhHHHHHhhcCCCCCeecCC--CCccccCchHHHHHHHHhcCC--CCCeeCCCCCccc
Q psy7454 4 PRPNAYRYKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNM--CEFKCRDNRTLKAHHINIHTG--QKPYPCRYCDYKA 79 (103)
Q Consensus 4 ~~~h~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~--C~~~~~~~~~l~~h~~~~h~~--~~~~~c~~C~~~f 79 (103)
+-.|...+||+|+.|++.|...+.|..|..+|. +..|.|.. |...+.+...+.+|.+..|.| ..+|.|-.|++.|
T Consensus 284 r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~f 362 (467)
T KOG3608|consen 284 RYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFF 362 (467)
T ss_pred HhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhh
Confidence 334555666777777766666666776766665 55566655 666666666666664444433 3457777777777
Q ss_pred cCcHHHHHHHHhhC
Q psy7454 80 RETQALKVHTKRYH 93 (103)
Q Consensus 80 ~~~~~l~~H~~~~~ 93 (103)
++-.+|.+|+..-+
T Consensus 363 t~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 363 TSGKSLSAHLMKKH 376 (467)
T ss_pred ccchhHHHHHHHhh
Confidence 77777777766543
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.13 E-value=3e-11 Score=55.42 Aligned_cols=43 Identities=14% Similarity=0.331 Sum_probs=38.7
Q ss_pred CeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHH
Q psy7454 40 PFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQAL 85 (103)
Q Consensus 40 ~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l 85 (103)
.|.|+.||+.|...+.|..| ++.|+ ++++|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H-~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITH-LRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHH-HHhcC--CcccCCcccceeccccee
Confidence 47899999999999999998 89998 689999999999977665
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.02 E-value=1.3e-09 Score=71.19 Aligned_cols=83 Identities=14% Similarity=0.358 Sum_probs=65.1
Q ss_pred CCceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc---------
Q psy7454 10 RYKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR--------- 80 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~--------- 80 (103)
+..+.|+.|+..|. ...|..|+.++. +++.|+ ||..+ ....|..| +..+..++++.|..|+..+.
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H-~~thCp~Kpi~C~fC~~~v~~g~~~~d~~ 524 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQH-QASTCPLRLITCRFCGDMVQAGGSAMDVR 524 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhh-hhccCCCCceeCCCCCCccccCccccchh
Confidence 44678999998885 577899988874 788999 99755 56788887 78889999999999998884
Q ss_pred -CcHHHHHHHHhhCCCCCcc
Q psy7454 81 -ETQALKVHTKRYHPKMYDV 99 (103)
Q Consensus 81 -~~~~l~~H~~~~~~~~~~~ 99 (103)
..+.|..|.... |.+++.
T Consensus 525 d~~s~Lt~HE~~C-G~rt~~ 543 (567)
T PLN03086 525 DRLRGMSEHESIC-GSRTAP 543 (567)
T ss_pred hhhhhHHHHHHhc-CCcceE
Confidence 235788888874 666653
No 15
>PHA00733 hypothetical protein
Probab=99.02 E-value=7.1e-10 Score=60.09 Aligned_cols=51 Identities=22% Similarity=0.389 Sum_probs=45.4
Q ss_pred CCCCceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHH
Q psy7454 8 AYRYKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHH 60 (103)
Q Consensus 8 ~~~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~ 60 (103)
.+..+|.|+.|++.|.....|..|++.+ ..++.|..|++.|.....|..|.
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~ 119 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHV 119 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHH
Confidence 3477999999999999999999999876 45789999999999999999983
No 16
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.97 E-value=5.3e-10 Score=44.20 Aligned_cols=23 Identities=39% Similarity=0.947 Sum_probs=11.6
Q ss_pred HHHHHhhcCCCCCeecCCCCccc
Q psy7454 28 IKRHLGMHLGEKPFTCNMCEFKC 50 (103)
Q Consensus 28 l~~h~~~h~~~~~~~c~~C~~~~ 50 (103)
|..|+++|++++||.|+.|++.|
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEE
T ss_pred HHHHhhhcCCCCCCCCCCCcCee
Confidence 44455555555555555555444
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.86 E-value=2.8e-09 Score=42.10 Aligned_cols=26 Identities=42% Similarity=0.974 Sum_probs=22.8
Q ss_pred HHHHHHHHhcCCCCCeeCCCCCccccC
Q psy7454 55 TLKAHHINIHTGQKPYPCRYCDYKARE 81 (103)
Q Consensus 55 ~l~~h~~~~h~~~~~~~c~~C~~~f~~ 81 (103)
.|..| ++.|++++||.|+.|++.|..
T Consensus 1 ~l~~H-~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRH-MRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHH-HHHHSSSSSEEESSSSEEESS
T ss_pred CHHHH-hhhcCCCCCCCCCCCcCeeCc
Confidence 36788 889999999999999999863
No 18
>PHA00616 hypothetical protein
Probab=98.86 E-value=1.4e-09 Score=47.68 Aligned_cols=31 Identities=19% Similarity=0.228 Sum_probs=22.9
Q ss_pred CeeCCCCCccccCcHHHHHHHHhhCCCCCcc
Q psy7454 69 PYPCRYCDYKARETQALKVHTKRYHPKMYDV 99 (103)
Q Consensus 69 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~ 99 (103)
||.|+.||+.|...+.|..|++.|++++++.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 4677777777777777777777777777763
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.84 E-value=7.7e-09 Score=67.66 Aligned_cols=78 Identities=19% Similarity=0.390 Sum_probs=62.6
Q ss_pred CceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccC----------chHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 11 YKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRD----------NRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 11 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~----------~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
.++.|+ ||..+ ....|..|+.+|..++++.|..|+..+.. .+.|..| .... +.+++.|..||+.+.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~H-E~~C-G~rt~~C~~Cgk~Vr 552 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEH-ESIC-GSRTAPCDSCGRSVM 552 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHH-HHhc-CCcceEccccCCeee
Confidence 578999 99755 56889999999999999999999988842 3478887 6664 889999999998766
Q ss_pred CcHHHHHHHHhhC
Q psy7454 81 ETQALKVHTKRYH 93 (103)
Q Consensus 81 ~~~~l~~H~~~~~ 93 (103)
. ..+..|+...|
T Consensus 553 l-rdm~~H~~~~h 564 (567)
T PLN03086 553 L-KEMDIHQIAVH 564 (567)
T ss_pred e-hhHHHHHHHhh
Confidence 4 46677776644
No 20
>KOG3993|consensus
Probab=98.83 E-value=5.4e-10 Score=69.89 Aligned_cols=82 Identities=20% Similarity=0.335 Sum_probs=65.5
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcCC--------------------------
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHTG-------------------------- 66 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~-------------------------- 66 (103)
|.|..|...|.+...|.+|.-.-.-..-|.|++|++.|.-+.+|..| ++.|--
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASH-RRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASH-RRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhh-hcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 78888988888888888886444444568899999999999999888 776621
Q ss_pred -------CCCeeCCCCCccccCcHHHHHHHHhhCCC
Q psy7454 67 -------QKPYPCRYCDYKARETQALKVHTKRYHPK 95 (103)
Q Consensus 67 -------~~~~~c~~C~~~f~~~~~l~~H~~~~~~~ 95 (103)
+-.|.|..|++.|++...|+.|+.+|+..
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhcc
Confidence 12489999999999999999998887643
No 21
>PHA00616 hypothetical protein
Probab=98.79 E-value=1.7e-09 Score=47.45 Aligned_cols=34 Identities=18% Similarity=0.249 Sum_probs=24.9
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCCCCCeecCC
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNM 45 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~ 45 (103)
||.|+.||+.|...+.|..|++.|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 4677777777777777777777777777766653
No 22
>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=98.53 E-value=3.6e-07 Score=42.34 Aligned_cols=50 Identities=26% Similarity=0.458 Sum_probs=23.6
Q ss_pred eecCCCCccccCchHHHHHHHHhcCCC-CCeeCCCCCccccCcHHHHHHHHhhC
Q psy7454 41 FTCNMCEFKCRDNRTLKAHHINIHTGQ-KPYPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 41 ~~c~~C~~~~~~~~~l~~h~~~~h~~~-~~~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
|.|+.|++ ......|..|....|..+ +.+.|++|...+. .+|..|+...+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 45555555 233344555544444433 2355555554322 25555555443
No 23
>PHA00732 hypothetical protein
Probab=98.44 E-value=2.6e-07 Score=46.02 Aligned_cols=42 Identities=29% Similarity=0.502 Sum_probs=34.4
Q ss_pred ceeeCCCCCcccCchhHHHHHhh-cCCCCCeecCCCCccccCchHHHHH
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGM-HLGEKPFTCNMCEFKCRDNRTLKAH 59 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~-h~~~~~~~c~~C~~~~~~~~~l~~h 59 (103)
||.|+.|++.|.+...|..|++. |.+ +.|+.|++.|.. +..|
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~---l~~H 43 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRR---LNQH 43 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCC---hhhh
Confidence 57899999999999999999874 553 479999999874 5666
No 24
>PHA00732 hypothetical protein
Probab=98.41 E-value=3e-07 Score=45.77 Aligned_cols=46 Identities=30% Similarity=0.472 Sum_probs=37.6
Q ss_pred CeecCCCCccccCchHHHHHHHH-hcCCCCCeeCCCCCccccCcHHHHHHHHhh
Q psy7454 40 PFTCNMCEFKCRDNRTLKAHHIN-IHTGQKPYPCRYCDYKARETQALKVHTKRY 92 (103)
Q Consensus 40 ~~~c~~C~~~~~~~~~l~~h~~~-~h~~~~~~~c~~C~~~f~~~~~l~~H~~~~ 92 (103)
||.|..|++.|...+.|..| ++ .|.+ +.|..||+.|. .+..|..+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H-~r~~H~~---~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQH-ARRNHTL---TKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHH-hhcccCC---CccCCCCCEeC---Chhhhhccc
Confidence 57899999999999999998 66 4653 58999999998 477777544
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.38 E-value=2.8e-07 Score=35.15 Aligned_cols=22 Identities=32% Similarity=0.548 Sum_probs=16.0
Q ss_pred eeeCCCCCcccCchhHHHHHhh
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGM 34 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~ 34 (103)
|.|+.|++.|.....|..|++.
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 5677777777777777777665
No 26
>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=98.37 E-value=4e-07 Score=34.69 Aligned_cols=23 Identities=30% Similarity=0.583 Sum_probs=16.9
Q ss_pred eeCCCCCccccCcHHHHHHHHhh
Q psy7454 70 YPCRYCDYKARETQALKVHTKRY 92 (103)
Q Consensus 70 ~~c~~C~~~f~~~~~l~~H~~~~ 92 (103)
|.|..|++.|.....|..|++.|
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 56777777777777777777653
No 27
>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=98.19 E-value=2.4e-06 Score=32.59 Aligned_cols=24 Identities=25% Similarity=0.614 Sum_probs=16.7
Q ss_pred eeCCCCCccccCcHHHHHHHHhhC
Q psy7454 70 YPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 70 ~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
|.|+.|++.|.....|..|+.+++
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 567788888888888888877664
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.13 E-value=7.1e-06 Score=37.96 Aligned_cols=46 Identities=20% Similarity=0.465 Sum_probs=34.5
Q ss_pred ceeeCCCCCcccCchhHHHHHh-hcCC-CCCeecCCCCccccCchHHHHHH
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLG-MHLG-EKPFTCNMCEFKCRDNRTLKAHH 60 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~-~h~~-~~~~~c~~C~~~~~~~~~l~~h~ 60 (103)
.|.||.|++ ..+...|..|.. .|.. .+.+.|++|...+. ..|..|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHL 49 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHH
Confidence 589999999 456788999954 4554 35799999997543 4788873
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=98.09 E-value=3.5e-06 Score=33.30 Aligned_cols=25 Identities=16% Similarity=0.299 Sum_probs=18.2
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcC
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHL 36 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~ 36 (103)
+|.|..|++.|.....|..|++.|.
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 4677777777777777777776653
No 30
>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=98.07 E-value=3.4e-06 Score=33.32 Aligned_cols=25 Identities=24% Similarity=0.523 Sum_probs=18.1
Q ss_pred CeeCCCCCccccCcHHHHHHHHhhC
Q psy7454 69 PYPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 69 ~~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
+|.|..|++.|.....|..|++.|.
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 4677777777777777777776654
No 31
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.98 E-value=2.4e-06 Score=52.38 Aligned_cols=53 Identities=36% Similarity=0.763 Sum_probs=38.1
Q ss_pred CCCeecCC--CCccccCchHHHHHHHHhc------------------CCCCCeeCCCCCccccCcHHHHHHHH
Q psy7454 38 EKPFTCNM--CEFKCRDNRTLKAHHINIH------------------TGQKPYPCRYCDYKARETQALKVHTK 90 (103)
Q Consensus 38 ~~~~~c~~--C~~~~~~~~~l~~h~~~~h------------------~~~~~~~c~~C~~~f~~~~~l~~H~~ 90 (103)
++||.|++ |.+.|+....|+.|.+..| ...+||.|.+|++.+.....|+-|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 46677754 6677777777766633333 23589999999999999999887765
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.98 E-value=7.9e-06 Score=42.16 Aligned_cols=73 Identities=18% Similarity=0.287 Sum_probs=21.7
Q ss_pred eeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHHHHhh
Q psy7454 14 VCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALKVHTKRY 92 (103)
Q Consensus 14 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H~~~~ 92 (103)
.|..|+..|.....|..|+....+...-.. ..+.....+... .... ....+.|..|++.|.....|..|+..+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~----~~l~~~~~~~~~-~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQ----KYLVDPNRLLNY-LRKK-VKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccccc----cccccccccccc-cccc-cCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 488999999999999999865433221111 111122222222 2221 223689999999999999999999974
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.96 E-value=7.7e-06 Score=31.09 Aligned_cols=23 Identities=17% Similarity=0.496 Sum_probs=13.8
Q ss_pred eeeCCCCCcccCchhHHHHHhhc
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMH 35 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h 35 (103)
|.|+.|+..|.+...|..|+..+
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 46677777777777777766543
No 34
>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=97.88 E-value=2.7e-05 Score=35.08 Aligned_cols=26 Identities=23% Similarity=0.374 Sum_probs=11.0
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCC
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLG 37 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~ 37 (103)
|.+|++|+..+.+..+|.+|+....+
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCCCcchhhccchhhHHHHHHHHhc
Confidence 45555555555555555555544333
No 35
>KOG3993|consensus
Probab=97.86 E-value=1e-05 Score=51.37 Aligned_cols=53 Identities=26% Similarity=0.437 Sum_probs=44.2
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCC---------------------------------CCCeecCCCCccccCchHHHH
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLG---------------------------------EKPFTCNMCEFKCRDNRTLKA 58 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~---------------------------------~~~~~c~~C~~~~~~~~~l~~ 58 (103)
-|.|+.|++.|.-..+|..|.|=|.. +..|.|..|++.|.....|+.
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 49999999999999999999875521 123899999999999999999
Q ss_pred HHHHhcC
Q psy7454 59 HHINIHT 65 (103)
Q Consensus 59 h~~~~h~ 65 (103)
| +.+|.
T Consensus 375 H-qlthq 380 (500)
T KOG3993|consen 375 H-QLTHQ 380 (500)
T ss_pred h-HHhhh
Confidence 8 66654
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.78 E-value=9.2e-06 Score=49.92 Aligned_cols=50 Identities=26% Similarity=0.522 Sum_probs=42.0
Q ss_pred CCceeeCC--CCCcccCchhHHHHHhhcC-------------------CCCCeecCCCCccccCchHHHHH
Q psy7454 10 RYKYVCFA--CKFYTYNTGNIKRHLGMHL-------------------GEKPFTCNMCEFKCRDNRTLKAH 59 (103)
Q Consensus 10 ~~~~~C~~--C~~~f~~~~~l~~h~~~h~-------------------~~~~~~c~~C~~~~~~~~~l~~h 59 (103)
++||+|++ |++.+...-.|+.|+.-.. ..+||.|.+|++.|+....|+.|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYH 417 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYH 417 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceec
Confidence 47999998 9999999989999864311 24899999999999999999887
No 37
>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=97.77 E-value=5e-05 Score=34.24 Aligned_cols=32 Identities=25% Similarity=0.442 Sum_probs=19.9
Q ss_pred CCCCeeCCCCCccccCcHHHHHHHHhhCCCCC
Q psy7454 66 GQKPYPCRYCDYKARETQALKVHTKRYHPKMY 97 (103)
Q Consensus 66 ~~~~~~c~~C~~~f~~~~~l~~H~~~~~~~~~ 97 (103)
.+.|-.|++|+..+.+..+|.+|+.+.++.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45577788888888888888888877776665
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.62 E-value=7.2e-05 Score=28.69 Aligned_cols=24 Identities=29% Similarity=0.502 Sum_probs=16.4
Q ss_pred eeCCCCCccccCcHHHHHHHHhhC
Q psy7454 70 YPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 70 ~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
|.|..|++.|.....+..|+..|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 356777777777777777776543
No 39
>PRK04860 hypothetical protein; Provisional
Probab=97.60 E-value=8.2e-05 Score=41.96 Aligned_cols=37 Identities=27% Similarity=0.659 Sum_probs=22.2
Q ss_pred CeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccC
Q psy7454 40 PFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARE 81 (103)
Q Consensus 40 ~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~ 81 (103)
+|.|. |+. ....+..| .+.+.++++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH-~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRH-NRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHH-HHHhcCCccEECCCCCceeEE
Confidence 46665 664 34445555 566666666667666665553
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.53 E-value=7.3e-05 Score=28.67 Aligned_cols=23 Identities=26% Similarity=0.521 Sum_probs=14.3
Q ss_pred eeeCCCCCcccCchhHHHHHhhc
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMH 35 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h 35 (103)
|.|+.|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35666666666666666666544
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.48 E-value=0.0001 Score=28.35 Aligned_cols=22 Identities=18% Similarity=0.454 Sum_probs=15.3
Q ss_pred eeeCCCCCcccCchhHHHHHhh
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGM 34 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~ 34 (103)
|.|..|+..|.+...|..|++.
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 4677777777777777777654
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.34 E-value=0.00022 Score=27.18 Aligned_cols=23 Identities=43% Similarity=0.833 Sum_probs=15.1
Q ss_pred eeCCCCCccccCcHHHHHHHHhhC
Q psy7454 70 YPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 70 ~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
|.|..|+.... ...|..|++.++
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 56777777776 777777777754
No 43
>PRK04860 hypothetical protein; Provisional
Probab=97.30 E-value=0.00033 Score=39.55 Aligned_cols=38 Identities=24% Similarity=0.498 Sum_probs=28.3
Q ss_pred CceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccC
Q psy7454 11 YKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRD 52 (103)
Q Consensus 11 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~ 52 (103)
.+|.|. |+. ....+..|.+++.++++|.|..|+..+..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 468887 875 45567788888888888888888876654
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.30 E-value=0.00024 Score=27.28 Aligned_cols=22 Identities=18% Similarity=0.546 Sum_probs=14.8
Q ss_pred eeCCCCCccccCcHHHHHHHHh
Q psy7454 70 YPCRYCDYKARETQALKVHTKR 91 (103)
Q Consensus 70 ~~c~~C~~~f~~~~~l~~H~~~ 91 (103)
|.|..|+..|.....+..|++.
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 4566777777777777776654
No 45
>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=97.09 E-value=0.00021 Score=28.13 Aligned_cols=22 Identities=27% Similarity=0.629 Sum_probs=15.8
Q ss_pred eeeCCCCCcccCchhHHHHHhh
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGM 34 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~ 34 (103)
|.|..|++.|.+...+..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5677777777777777777654
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.80 E-value=0.0011 Score=25.15 Aligned_cols=21 Identities=43% Similarity=0.803 Sum_probs=11.7
Q ss_pred eeeCCCCCcccCchhHHHHHhh
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGM 34 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~ 34 (103)
|.|+.|+.... ...|..|++.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 45666766655 5566666654
No 47
>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=96.56 E-value=0.00069 Score=26.60 Aligned_cols=22 Identities=32% Similarity=0.534 Sum_probs=13.5
Q ss_pred eeCCCCCccccCcHHHHHHHHh
Q psy7454 70 YPCRYCDYKARETQALKVHTKR 91 (103)
Q Consensus 70 ~~c~~C~~~f~~~~~l~~H~~~ 91 (103)
|.|..|++.|.....+..|+.+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 4566666666666666665543
No 48
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.17 E-value=0.0061 Score=23.50 Aligned_cols=19 Identities=37% Similarity=0.739 Sum_probs=10.5
Q ss_pred eCCCCCccccCcHHHHHHHH
Q psy7454 71 PCRYCDYKARETQALKVHTK 90 (103)
Q Consensus 71 ~c~~C~~~f~~~~~l~~H~~ 90 (103)
.|+.||+.| ....|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 466666666 4445555543
No 49
>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=96.00 E-value=0.0071 Score=24.99 Aligned_cols=23 Identities=17% Similarity=0.348 Sum_probs=16.8
Q ss_pred ceeeCCCCCcccCchhHHHHHhh
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGM 34 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~ 34 (103)
+|.|+.|+..|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 47788888888877777777643
No 50
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.83 E-value=0.0049 Score=28.38 Aligned_cols=30 Identities=20% Similarity=0.411 Sum_probs=22.8
Q ss_pred cCCCCCeeCCCCCccccCcHHHHHHHHhhC
Q psy7454 64 HTGQKPYPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 64 h~~~~~~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
-.||.-+.|+.||..|....++.+|.-..+
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 346777788888888888888888876544
No 51
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.60 E-value=0.0062 Score=28.04 Aligned_cols=28 Identities=14% Similarity=0.157 Sum_probs=21.6
Q ss_pred CCCCCCceeeCCCCCcccCchhHHHHHh
Q psy7454 6 PNAYRYKYVCFACKFYTYNTGNIKRHLG 33 (103)
Q Consensus 6 ~h~~~~~~~C~~C~~~f~~~~~l~~h~~ 33 (103)
+..|+..+.|+.||..|.....+..|..
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 4567777888888888888877877754
No 52
>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=95.40 E-value=0.012 Score=31.12 Aligned_cols=30 Identities=23% Similarity=0.588 Sum_probs=19.6
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCc
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDN 53 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~ 53 (103)
-.|+.||..|+. .+..|.+|+.||..|...
T Consensus 10 R~Cp~CG~kFYD-----------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD-----------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc-----------CCCCCccCCCCCCccCcc
Confidence 467777777764 224666777777766655
No 53
>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=95.34 E-value=0.019 Score=23.60 Aligned_cols=10 Identities=40% Similarity=1.062 Sum_probs=6.0
Q ss_pred eeeCCCCCcc
Q psy7454 13 YVCFACKFYT 22 (103)
Q Consensus 13 ~~C~~C~~~f 22 (103)
|.|.+||..+
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 5666666554
No 54
>KOG1146|consensus
Probab=95.16 E-value=0.0098 Score=43.34 Aligned_cols=79 Identities=20% Similarity=0.416 Sum_probs=47.4
Q ss_pred CCCCceeeCCCCCcccCchhHHHHHhhcC-CCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHH
Q psy7454 8 AYRYKYVCFACKFYTYNTGNIKRHLGMHL-GEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALK 86 (103)
Q Consensus 8 ~~~~~~~C~~C~~~f~~~~~l~~h~~~h~-~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~ 86 (103)
.-.+-+.|+.|+..|.....|..|+++-. ..+. .+|.-+-.... +.+- ...-.+.++|.|..|...+.....|.
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~~gq~~~~-~arg-~~~~~~~~p~~C~~C~~stttng~Ls 535 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCKAGQNHPR-LARG-EVYRCPGKPYPCRACNYSTTTNGNLS 535 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccch---hHhHhcccccc-cccc-ccccCCCCcccceeeeeeeecchHHH
Confidence 33456888888888888888888887632 2221 22211100000 0000 11123457889999999999989999
Q ss_pred HHHHh
Q psy7454 87 VHTKR 91 (103)
Q Consensus 87 ~H~~~ 91 (103)
+|+..
T Consensus 536 ihlqS 540 (1406)
T KOG1146|consen 536 IHLQS 540 (1406)
T ss_pred HHHHH
Confidence 99775
No 55
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.88 E-value=0.0067 Score=38.71 Aligned_cols=58 Identities=24% Similarity=0.464 Sum_probs=33.0
Q ss_pred CeecCCCCccccCchHHHHHHHH--hcCCC--CCeeCC--CCCccccCcHHHHHHHHhhCCCCCc
Q psy7454 40 PFTCNMCEFKCRDNRTLKAHHIN--IHTGQ--KPYPCR--YCDYKARETQALKVHTKRYHPKMYD 98 (103)
Q Consensus 40 ~~~c~~C~~~~~~~~~l~~h~~~--~h~~~--~~~~c~--~C~~~f~~~~~l~~H~~~~~~~~~~ 98 (103)
++.|..|...+.....+..| .. .|.++ +++.|. .|++.|.+...+..|..++.+..++
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~-~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRH-LRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred CCCCccccCCcccccccccc-ccccccccccCCceeeeccCCCccccccccccCCcccccCCCcc
Confidence 34555566666666555555 44 45555 566665 4666666666666665555554443
No 56
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.68 E-value=0.049 Score=27.78 Aligned_cols=25 Identities=24% Similarity=0.624 Sum_probs=19.7
Q ss_pred CCeecCCCCccccCchHHHHHHHHhc
Q psy7454 39 KPFTCNMCEFKCRDNRTLKAHHINIH 64 (103)
Q Consensus 39 ~~~~c~~C~~~~~~~~~l~~h~~~~h 64 (103)
..+.|..|+..|.+...|..| ++.+
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~H-m~~~ 73 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEH-MRSK 73 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHH-HHHT
T ss_pred CCCCCCccCCCCcCHHHHHHH-HcCc
Confidence 478999999999999999998 5543
No 57
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.67 E-value=0.01 Score=37.87 Aligned_cols=62 Identities=32% Similarity=0.536 Sum_probs=52.6
Q ss_pred CceeeCCCCCcccCchhHHHHHh--hcCCC--CCeecC--CCCccccCchHHHHHHHHhcCCCCCeeCC
Q psy7454 11 YKYVCFACKFYTYNTGNIKRHLG--MHLGE--KPFTCN--MCEFKCRDNRTLKAHHINIHTGQKPYPCR 73 (103)
Q Consensus 11 ~~~~C~~C~~~f~~~~~l~~h~~--~h~~~--~~~~c~--~C~~~~~~~~~l~~h~~~~h~~~~~~~c~ 73 (103)
.++.|..|...|.....+..|.+ .|.++ +++.|+ .|++.+.....+..| ...|.+..+..+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRH-ILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCC-cccccCCCccccc
Confidence 36889999999999999999998 79999 999999 799999999998887 7778776655544
No 58
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.50 E-value=0.094 Score=27.94 Aligned_cols=80 Identities=14% Similarity=0.131 Sum_probs=51.6
Q ss_pred CceeeCCCCCcccCchhHHHHHhhc-----CCC-------CCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcc
Q psy7454 11 YKYVCFACKFYTYNTGNIKRHLGMH-----LGE-------KPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYK 78 (103)
Q Consensus 11 ~~~~C~~C~~~f~~~~~l~~h~~~h-----~~~-------~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~ 78 (103)
-|..|+.||-.......|.+....- ..+ ....|-.|...|........ ..-.....|.|..|...
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~---~~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF---DELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc---cccccccceeCCCCCCc
Confidence 4788999998888887777542110 011 11247788877765432111 00122347999999999
Q ss_pred ccCcHHHHHHHHhhC
Q psy7454 79 ARETQALKVHTKRYH 93 (103)
Q Consensus 79 f~~~~~l~~H~~~~~ 93 (103)
|-..-+.-.|...|.
T Consensus 91 FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 91 FCVDCDVFVHESLHC 105 (112)
T ss_pred cccccchhhhhhccC
Confidence 999999889988875
No 59
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.11 E-value=0.079 Score=22.38 Aligned_cols=12 Identities=17% Similarity=0.390 Sum_probs=6.4
Q ss_pred CCeeCCCCCccc
Q psy7454 68 KPYPCRYCDYKA 79 (103)
Q Consensus 68 ~~~~c~~C~~~f 79 (103)
....|..|+..|
T Consensus 24 ~~vrC~~C~~~f 35 (37)
T PF13719_consen 24 RKVRCPKCGHVF 35 (37)
T ss_pred cEEECCCCCcEe
Confidence 344566665554
No 60
>KOG2186|consensus
Probab=94.09 E-value=0.036 Score=33.57 Aligned_cols=44 Identities=18% Similarity=0.398 Sum_probs=30.2
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHH
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAH 59 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h 59 (103)
|.|.+||.... +..+..|+....+ .-|.|..|+..|... ....|
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~~~-sYknH 47 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFERV-SYKNH 47 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccC-CeeEEeecccccccc-hhhhh
Confidence 77888887764 3456678766555 668888888888773 34454
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=94.00 E-value=0.019 Score=34.10 Aligned_cols=44 Identities=16% Similarity=0.354 Sum_probs=27.8
Q ss_pred CCceeeCCCCCcccCchhHHHHHhh---c-------CCCCC-----eecCCCCccccCc
Q psy7454 10 RYKYVCFACKFYTYNTGNIKRHLGM---H-------LGEKP-----FTCNMCEFKCRDN 53 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~~~l~~h~~~---h-------~~~~~-----~~c~~C~~~~~~~ 53 (103)
++...||+|+..|..+.......+. . .+..| .+|+.||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 3468999999999876554444332 1 12333 3788898766544
No 62
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=93.63 E-value=0.063 Score=29.14 Aligned_cols=32 Identities=13% Similarity=0.185 Sum_probs=21.7
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchH
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRT 55 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~ 55 (103)
..|+.||+.|+. .++.|..|+.||..+.....
T Consensus 10 r~Cp~cg~kFYD-----------Lnk~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 10 RICPNTGSKFYD-----------LNRRPAVSPYTGEQFPPEEA 41 (129)
T ss_pred ccCCCcCccccc-----------cCCCCccCCCcCCccCcchh
Confidence 478888888764 23467788888877655533
No 63
>KOG2231|consensus
Probab=93.47 E-value=0.12 Score=35.71 Aligned_cols=77 Identities=14% Similarity=0.086 Sum_probs=43.3
Q ss_pred cCchhHHHHHh-hcCCCCCe-------ecCCCCccccCchHHHHHHHHhcCCCCC----eeCCCCCccccCcHHHHHHHH
Q psy7454 23 YNTGNIKRHLG-MHLGEKPF-------TCNMCEFKCRDNRTLKAHHINIHTGQKP----YPCRYCDYKARETQALKVHTK 90 (103)
Q Consensus 23 ~~~~~l~~h~~-~h~~~~~~-------~c~~C~~~~~~~~~l~~h~~~~h~~~~~----~~c~~C~~~f~~~~~l~~H~~ 90 (103)
.....|+.|++ .|..-... .+..+.+. -....|..|++....+++. -.|..|...|.....+.+|++
T Consensus 125 ~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~-Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 125 KSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKL-YTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLR 203 (669)
T ss_pred hHHHHHHHHHHHhhhhhccccccccceeeeeeeeh-ehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhc
Confidence 35677888874 34221111 12222333 3445566664443332221 357788888888888888888
Q ss_pred hhCCCCCccc
Q psy7454 91 RYHPKMYDVE 100 (103)
Q Consensus 91 ~~~~~~~~~~ 100 (103)
..+...-|++
T Consensus 204 ~~h~~chfC~ 213 (669)
T KOG2231|consen 204 FDHEFCHFCD 213 (669)
T ss_pred cceeheeecC
Confidence 7765555554
No 64
>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=93.44 E-value=0.12 Score=21.78 Aligned_cols=10 Identities=20% Similarity=0.351 Sum_probs=4.9
Q ss_pred eeCCCCCccc
Q psy7454 70 YPCRYCDYKA 79 (103)
Q Consensus 70 ~~c~~C~~~f 79 (103)
..|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4455555443
No 65
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.21 E-value=0.1 Score=24.45 Aligned_cols=33 Identities=21% Similarity=0.419 Sum_probs=19.3
Q ss_pred CCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCc
Q psy7454 39 KPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDY 77 (103)
Q Consensus 39 ~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~ 77 (103)
-.|.|+.||........- .-....+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~~------CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAK------CRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhhh------HHHcCCceECCCcCc
Confidence 347788888554443321 111345788888874
No 66
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=93.12 E-value=0.17 Score=21.22 Aligned_cols=12 Identities=33% Similarity=0.648 Sum_probs=6.1
Q ss_pred ecCCCCccccCc
Q psy7454 42 TCNMCEFKCRDN 53 (103)
Q Consensus 42 ~c~~C~~~~~~~ 53 (103)
.|+.|+..|.-.
T Consensus 4 ~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 4 TCPNCQAKYEID 15 (36)
T ss_pred ECCCCCCEEeCC
Confidence 455555555443
No 67
>KOG2186|consensus
Probab=92.79 E-value=0.095 Score=31.82 Aligned_cols=54 Identities=22% Similarity=0.398 Sum_probs=36.1
Q ss_pred eecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHHHHhhCCCCCc
Q psy7454 41 FTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALKVHTKRYHPKMYD 98 (103)
Q Consensus 41 ~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~ 98 (103)
|.|.+||.....+. +.+| +....+ .-|.|.-|+..|-. -++..|....+....|
T Consensus 4 FtCnvCgEsvKKp~-vekH-~srCrn-~~fSCIDC~k~F~~-~sYknH~kCITEaQKY 57 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKH-MSRCRN-AYFSCIDCGKTFER-VSYKNHTKCITEAQKY 57 (276)
T ss_pred Eehhhhhhhccccc-hHHH-HHhccC-CeeEEeeccccccc-chhhhhhhhcchHHHh
Confidence 67888887666554 4556 555544 56788888888877 6777777766655444
No 68
>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=92.41 E-value=0.15 Score=21.13 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=6.9
Q ss_pred ceeeCCCCCcc
Q psy7454 12 KYVCFACKFYT 22 (103)
Q Consensus 12 ~~~C~~C~~~f 22 (103)
.|.|..||..+
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 36677777554
No 69
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=92.10 E-value=0.13 Score=29.46 Aligned_cols=24 Identities=29% Similarity=0.917 Sum_probs=15.5
Q ss_pred CeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCc
Q psy7454 40 PFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDY 77 (103)
Q Consensus 40 ~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~ 77 (103)
-++|.+||.. +.++.|..|+.||-
T Consensus 134 ~~vC~vCGy~--------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT--------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc--------------ccCCCCCcCCCCCC
Confidence 5778888742 22466777888873
No 70
>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=92.06 E-value=0.072 Score=24.14 Aligned_cols=31 Identities=26% Similarity=0.418 Sum_probs=18.0
Q ss_pred CceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCc
Q psy7454 11 YKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEF 48 (103)
Q Consensus 11 ~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~ 48 (103)
+-|.|..||..|.....+ .. .....|+.||.
T Consensus 4 Yey~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 347888888777543211 11 34456888875
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=92.01 E-value=0.22 Score=21.94 Aligned_cols=26 Identities=19% Similarity=0.581 Sum_probs=14.0
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCcc
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFK 49 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~ 49 (103)
|.|..||..|... ...+..|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 5666666655321 2344566666643
No 72
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=91.93 E-value=0.22 Score=22.01 Aligned_cols=10 Identities=30% Similarity=0.640 Sum_probs=6.0
Q ss_pred eeeCCCCCcc
Q psy7454 13 YVCFACKFYT 22 (103)
Q Consensus 13 ~~C~~C~~~f 22 (103)
|.|+.||..|
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 5666666554
No 73
>KOG2893|consensus
Probab=91.70 E-value=0.059 Score=32.51 Aligned_cols=47 Identities=23% Similarity=0.484 Sum_probs=36.3
Q ss_pred eCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcC
Q psy7454 15 CFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHT 65 (103)
Q Consensus 15 C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~ 65 (103)
|=.|++.|..+..|..|++. +-|.|-+|.+.+.+-..|..|.+.+|-
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhhh
Confidence 66799999988888888653 557899998888887777777666653
No 74
>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=91.24 E-value=0.17 Score=28.64 Aligned_cols=35 Identities=14% Similarity=0.287 Sum_probs=22.0
Q ss_pred cCCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccc
Q psy7454 35 HLGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKA 79 (103)
Q Consensus 35 h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f 79 (103)
.....-|.|+.|+..|.....+. ..|.|+.||...
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAML 138 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEe
Confidence 34455678888887776644431 247888888643
No 75
>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=90.76 E-value=0.12 Score=22.03 Aligned_cols=30 Identities=23% Similarity=0.312 Sum_probs=16.1
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCc
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEF 48 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~ 48 (103)
-|.|+.||..|...... .. .....|+.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI------SD-DPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEec------CC-CCCCCCCCCCC
Confidence 46777777766432221 11 33446777775
No 76
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=90.61 E-value=0.31 Score=22.87 Aligned_cols=33 Identities=21% Similarity=0.474 Sum_probs=18.9
Q ss_pred CCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCc
Q psy7454 39 KPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDY 77 (103)
Q Consensus 39 ~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~ 77 (103)
-.|.|+.||........- --....+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~~------CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEK------CRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeechh------HHhcCCceECCCCCC
Confidence 447888888763332211 111246788888884
No 77
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.42 E-value=0.18 Score=29.20 Aligned_cols=33 Identities=15% Similarity=0.433 Sum_probs=19.8
Q ss_pred CCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccc
Q psy7454 37 GEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKA 79 (103)
Q Consensus 37 ~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f 79 (103)
...-|.|+.|+..|.....+ +..|.|+.||...
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~----------~~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAM----------EYGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCCCcEEeHHHHh----------hcCCcCCCCCCCC
Confidence 34557777777766554332 1247777777543
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.38 E-value=0.72 Score=25.79 Aligned_cols=39 Identities=13% Similarity=0.335 Sum_probs=24.8
Q ss_pred CCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 37 GEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 37 ~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
...-|.|+.|+..|.....+. .... ...|.|+.||....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~----~~d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQ----LLDM-DGTFTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHH----hcCC-CCcEECCCCCCEEE
Confidence 445689999998887644321 1122 33489999997543
No 79
>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=89.75 E-value=0.21 Score=21.70 Aligned_cols=30 Identities=20% Similarity=0.453 Sum_probs=16.8
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCc
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEF 48 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~ 48 (103)
-|.|..||..|..... ... ..+..|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~------~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQS------ISE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEE------cCC-CCCCcCCCCCC
Confidence 4777777777643221 111 34456777775
No 80
>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=89.71 E-value=0.24 Score=20.80 Aligned_cols=9 Identities=22% Similarity=0.556 Sum_probs=5.0
Q ss_pred eeCCCCCcc
Q psy7454 14 VCFACKFYT 22 (103)
Q Consensus 14 ~C~~C~~~f 22 (103)
.|+.||..|
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 455565554
No 81
>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=89.36 E-value=0.21 Score=27.48 Aligned_cols=28 Identities=25% Similarity=0.267 Sum_probs=17.3
Q ss_pred CCCeeCCCCCccccCcHHHHHHHHhhCCCCC
Q psy7454 67 QKPYPCRYCDYKARETQALKVHTKRYHPKMY 97 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~~~~l~~H~~~~~~~~~ 97 (103)
+....|.+||+.|.. |++|++.|+|-.|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 334689999998886 5899999987654
No 82
>PHA00626 hypothetical protein
Probab=89.17 E-value=0.37 Score=22.34 Aligned_cols=15 Identities=13% Similarity=0.567 Sum_probs=9.3
Q ss_pred CCCeecCCCCccccC
Q psy7454 38 EKPFTCNMCEFKCRD 52 (103)
Q Consensus 38 ~~~~~c~~C~~~~~~ 52 (103)
...|.|..||..|..
T Consensus 21 snrYkCkdCGY~ft~ 35 (59)
T PHA00626 21 SDDYVCCDCGYNDSK 35 (59)
T ss_pred CcceEcCCCCCeech
Confidence 455677777765544
No 83
>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=88.90 E-value=0.48 Score=24.98 Aligned_cols=26 Identities=27% Similarity=0.668 Sum_probs=23.5
Q ss_pred CeeC----CCCCccccCcHHHHHHHHhhCC
Q psy7454 69 PYPC----RYCDYKARETQALKVHTKRYHP 94 (103)
Q Consensus 69 ~~~c----~~C~~~f~~~~~l~~H~~~~~~ 94 (103)
.|.| ..|+....+...+..|.+.+||
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3889 9999999999999999998875
No 84
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=88.53 E-value=0.72 Score=29.61 Aligned_cols=75 Identities=28% Similarity=0.599 Sum_probs=51.4
Q ss_pred eeCCCCCcccCchhHHHHHhhcCCCCCeecCCCC----ccccCchHHHHHHHHhcCCCCCeeCCC--CC----ccccCcH
Q psy7454 14 VCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCE----FKCRDNRTLKAHHINIHTGQKPYPCRY--CD----YKARETQ 83 (103)
Q Consensus 14 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~----~~~~~~~~l~~h~~~~h~~~~~~~c~~--C~----~~f~~~~ 83 (103)
.|..|...|.+...|..|++... ++-+.|+.-+ +-|+.-..|..| ...-.|.|.+ |- .+|....
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~H-----F~~~hy~ct~qtc~~~k~~vf~~~~ 295 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAH-----FRNAHYCCTFQTCRVGKCYVFPYHT 295 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHH-----hhcCceEEEEEEEecCcEEEeccHH
Confidence 59999999999999999988743 6666666544 234444555554 3333455542 22 4789999
Q ss_pred HHHHHHHhhCC
Q psy7454 84 ALKVHTKRYHP 94 (103)
Q Consensus 84 ~l~~H~~~~~~ 94 (103)
.|..|+...++
T Consensus 296 el~~h~~~~h~ 306 (493)
T COG5236 296 ELLEHLTRFHK 306 (493)
T ss_pred HHHHHHHHHhh
Confidence 99999887654
No 85
>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=87.89 E-value=0.58 Score=20.31 Aligned_cols=23 Identities=39% Similarity=0.642 Sum_probs=11.4
Q ss_pred CCeeCCCCCccccC----cHHHHHHHH
Q psy7454 68 KPYPCRYCDYKARE----TQALKVHTK 90 (103)
Q Consensus 68 ~~~~c~~C~~~f~~----~~~l~~H~~ 90 (103)
....|..|++.+.. .+.|..|++
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 34566666665554 356666664
No 86
>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=87.31 E-value=0.15 Score=20.23 Aligned_cols=9 Identities=22% Similarity=0.567 Sum_probs=4.4
Q ss_pred ecCCCCccc
Q psy7454 42 TCNMCEFKC 50 (103)
Q Consensus 42 ~c~~C~~~~ 50 (103)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344555544
No 87
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.76 E-value=0.67 Score=24.60 Aligned_cols=26 Identities=12% Similarity=0.064 Sum_probs=16.9
Q ss_pred eeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccc
Q psy7454 14 VCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKC 50 (103)
Q Consensus 14 ~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~ 50 (103)
.|+.||+.|+. ....|.+|+.||+.|
T Consensus 11 idPetg~KFYD-----------LNrdPiVsPytG~s~ 36 (129)
T COG4530 11 IDPETGKKFYD-----------LNRDPIVSPYTGKSY 36 (129)
T ss_pred cCccccchhhc-----------cCCCccccCcccccc
Confidence 56777776653 234666777777777
No 88
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=86.27 E-value=0.72 Score=20.85 Aligned_cols=11 Identities=27% Similarity=0.618 Sum_probs=6.2
Q ss_pred ceeeCCCCCcc
Q psy7454 12 KYVCFACKFYT 22 (103)
Q Consensus 12 ~~~C~~C~~~f 22 (103)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 45566665554
No 89
>PF14353 CpXC: CpXC protein
Probab=86.07 E-value=0.11 Score=28.20 Aligned_cols=47 Identities=21% Similarity=0.157 Sum_probs=25.2
Q ss_pred eeeCCCCCcccCchhHHHH--------HhhcC-CCCCeecCCCCccccCchHHHHH
Q psy7454 13 YVCFACKFYTYNTGNIKRH--------LGMHL-GEKPFTCNMCEFKCRDNRTLKAH 59 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h--------~~~h~-~~~~~~c~~C~~~~~~~~~l~~h 59 (103)
.+|+.|+..|......... .++-. .--.+.|+.||..+.....+..|
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEE
Confidence 4688998877542110000 01111 12347899999877666555443
No 90
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=85.90 E-value=0.19 Score=28.44 Aligned_cols=15 Identities=13% Similarity=0.239 Sum_probs=10.3
Q ss_pred eecCCCCccccCchH
Q psy7454 41 FTCNMCEFKCRDNRT 55 (103)
Q Consensus 41 ~~c~~C~~~~~~~~~ 55 (103)
+.|+.||..|.....
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 678888877766543
No 91
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=85.61 E-value=1.3 Score=19.86 Aligned_cols=21 Identities=29% Similarity=0.705 Sum_probs=11.9
Q ss_pred eeCCCCCccccCc-----HHHHHHHH
Q psy7454 70 YPCRYCDYKARET-----QALKVHTK 90 (103)
Q Consensus 70 ~~c~~C~~~f~~~-----~~l~~H~~ 90 (103)
-.|..|++.+... +.|.+|+.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 3566666555443 46666666
No 92
>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=85.15 E-value=1.1 Score=17.25 Aligned_cols=19 Identities=16% Similarity=0.396 Sum_probs=11.2
Q ss_pred eCCCCCccccCcHHHHHHHH
Q psy7454 71 PCRYCDYKARETQALKVHTK 90 (103)
Q Consensus 71 ~c~~C~~~f~~~~~l~~H~~ 90 (103)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 466676665 4455566654
No 93
>KOG2593|consensus
Probab=84.59 E-value=0.91 Score=29.88 Aligned_cols=33 Identities=21% Similarity=0.435 Sum_probs=14.1
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCC
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCE 47 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~ 47 (103)
.|.|+.|++.|.. |.+-+..-.....|.|..|+
T Consensus 128 ~Y~Cp~C~kkyt~---Lea~~L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 128 GYVCPNCQKKYTS---LEALQLLDNETGEFHCENCG 160 (436)
T ss_pred cccCCccccchhh---hHHHHhhcccCceEEEecCC
Confidence 4555555554432 33333333333344555554
No 94
>KOG4173|consensus
Probab=83.66 E-value=0.32 Score=28.83 Aligned_cols=78 Identities=26% Similarity=0.463 Sum_probs=49.7
Q ss_pred eeeCC--CCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcC---------CCCCeeCC--CCCccc
Q psy7454 13 YVCFA--CKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHT---------GQKPYPCR--YCDYKA 79 (103)
Q Consensus 13 ~~C~~--C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~---------~~~~~~c~--~C~~~f 79 (103)
+.|++ |-..|..-..+..|..+-.+ -.|+.|.+.|.+...|..|+...|. |.--|.|. .|+..|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 55666 44555555555555433222 2589999999888888777443332 33347775 488889
Q ss_pred cCcHHHHHHHHhhC
Q psy7454 80 RETQALKVHTKRYH 93 (103)
Q Consensus 80 ~~~~~l~~H~~~~~ 93 (103)
.+...-+.|+-..+
T Consensus 157 kT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhHHHHhc
Confidence 88888888876543
No 95
>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=83.43 E-value=1.9 Score=17.60 Aligned_cols=10 Identities=30% Similarity=0.753 Sum_probs=4.8
Q ss_pred eeeCCCCCcc
Q psy7454 13 YVCFACKFYT 22 (103)
Q Consensus 13 ~~C~~C~~~f 22 (103)
|.|..||..+
T Consensus 1 Y~C~~Cg~~~ 10 (32)
T PF03604_consen 1 YICGECGAEV 10 (32)
T ss_dssp EBESSSSSSE
T ss_pred CCCCcCCCee
Confidence 3455555443
No 96
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=83.33 E-value=0.77 Score=25.34 Aligned_cols=25 Identities=20% Similarity=0.001 Sum_probs=19.0
Q ss_pred eeCCCCCccccCcHHHHHHHHhhCCCCC
Q psy7454 70 YPCRYCDYKARETQALKVHTKRYHPKMY 97 (103)
Q Consensus 70 ~~c~~C~~~f~~~~~l~~H~~~~~~~~~ 97 (103)
..|.++|+.|.+ |++|+.+|++-.|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 478888888764 7888888876554
No 97
>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=82.62 E-value=1.2 Score=19.33 Aligned_cols=12 Identities=17% Similarity=0.562 Sum_probs=6.1
Q ss_pred CCCeecCCCCcc
Q psy7454 38 EKPFTCNMCEFK 49 (103)
Q Consensus 38 ~~~~~c~~C~~~ 49 (103)
...+.|..||..
T Consensus 17 ~g~~vC~~CG~V 28 (43)
T PF08271_consen 17 RGELVCPNCGLV 28 (43)
T ss_dssp TTEEEETTT-BB
T ss_pred CCeEECCCCCCE
Confidence 344566666644
No 98
>KOG2893|consensus
Probab=82.58 E-value=0.29 Score=29.65 Aligned_cols=41 Identities=27% Similarity=0.557 Sum_probs=31.9
Q ss_pred cCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHH
Q psy7454 43 CNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALKVH 88 (103)
Q Consensus 43 c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H 88 (103)
|=+|...|.....|.+| + ..+.|+|-+|-+..-+--.|..|
T Consensus 13 cwycnrefddekiliqh-q----kakhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQH-Q----KAKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhh-h----hhccceeeeehhhhccCCCceee
Confidence 66799999999988887 4 45678999998876666666665
No 99
>KOG4173|consensus
Probab=82.34 E-value=0.69 Score=27.47 Aligned_cols=50 Identities=18% Similarity=0.440 Sum_probs=35.8
Q ss_pred CCeecCC--CCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHHHHhh
Q psy7454 39 KPFTCNM--CEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALKVHTKRY 92 (103)
Q Consensus 39 ~~~~c~~--C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H~~~~ 92 (103)
..+.|++ |...+........|....|.. .|.+|.++|++.-.|..|+.--
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~----sCs~C~r~~Pt~hLLd~HI~E~ 129 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGN----SCSFCKRAFPTGHLLDAHILEW 129 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccc----hhHHHHHhCCchhhhhHHHHHH
Confidence 3466765 666777766666654344443 7999999999999999997653
No 100
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=81.94 E-value=1.3 Score=19.08 Aligned_cols=24 Identities=21% Similarity=0.253 Sum_probs=16.7
Q ss_pred eeeCCCCCcccC--chhHHHHHhhcC
Q psy7454 13 YVCFACKFYTYN--TGNIKRHLGMHL 36 (103)
Q Consensus 13 ~~C~~C~~~f~~--~~~l~~h~~~h~ 36 (103)
-+|+.||..|.. ...-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 579999988765 345566766653
No 101
>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=81.83 E-value=0.94 Score=18.22 Aligned_cols=9 Identities=22% Similarity=0.748 Sum_probs=4.6
Q ss_pred CCeecCCCC
Q psy7454 39 KPFTCNMCE 47 (103)
Q Consensus 39 ~~~~c~~C~ 47 (103)
..++|+.|+
T Consensus 18 ~~~vCp~C~ 26 (30)
T PF08274_consen 18 ELLVCPECG 26 (30)
T ss_dssp SSEEETTTT
T ss_pred CEEeCCccc
Confidence 345555554
No 102
>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=81.80 E-value=0.83 Score=17.38 Aligned_cols=9 Identities=33% Similarity=1.017 Sum_probs=7.3
Q ss_pred ceeeCCCCC
Q psy7454 12 KYVCFACKF 20 (103)
Q Consensus 12 ~~~C~~C~~ 20 (103)
.|.|+.||.
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 689999984
No 103
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=80.49 E-value=1.5 Score=20.15 Aligned_cols=34 Identities=18% Similarity=0.372 Sum_probs=15.9
Q ss_pred CceeeCC--CCCcccCchhHHHHHhhcCCCCCeecCC
Q psy7454 11 YKYVCFA--CKFYTYNTGNIKRHLGMHLGEKPFTCNM 45 (103)
Q Consensus 11 ~~~~C~~--C~~~f~~~~~l~~h~~~h~~~~~~~c~~ 45 (103)
.+..|+. |...+ .+..|..|....-..++..|..
T Consensus 8 ~~v~C~~~cc~~~i-~r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 8 RPVPCPNGCCNEMI-PRKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp SEEE-TT--S-BEE-ECCCHHHHHHTTSTTSEEE-SS
T ss_pred CEeeCCCCCcccce-eHHHHHHHHHccCCCCcEECCC
Confidence 3455655 33323 3445666665444455556666
No 104
>KOG1280|consensus
Probab=80.41 E-value=2.3 Score=27.34 Aligned_cols=37 Identities=16% Similarity=0.489 Sum_probs=23.1
Q ss_pred CceeeCCCCCcccCchhHHHHHh-hcCCC-CCeecCCCC
Q psy7454 11 YKYVCFACKFYTYNTGNIKRHLG-MHLGE-KPFTCNMCE 47 (103)
Q Consensus 11 ~~~~C~~C~~~f~~~~~l~~h~~-~h~~~-~~~~c~~C~ 47 (103)
..|.|+.|+..-.....|..|.. .|... -..+|++|+
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 36888888877777777777754 34322 223566664
No 105
>KOG4167|consensus
Probab=80.30 E-value=0.33 Score=34.03 Aligned_cols=27 Identities=15% Similarity=0.284 Sum_probs=23.2
Q ss_pred CCceeeCCCCCcccCchhHHHHHhhcC
Q psy7454 10 RYKYVCFACKFYTYNTGNIKRHLGMHL 36 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~~~l~~h~~~h~ 36 (103)
...|.|..|++.|....++.+||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 346999999999988888999999885
No 106
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=80.13 E-value=1.6 Score=19.73 Aligned_cols=13 Identities=15% Similarity=0.181 Sum_probs=6.8
Q ss_pred ceeeCCCCCcccC
Q psy7454 12 KYVCFACKFYTYN 24 (103)
Q Consensus 12 ~~~C~~C~~~f~~ 24 (103)
.+.|..||..|..
T Consensus 4 ~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 4 TLTCKDCGAEFVF 16 (49)
T ss_pred eEEcccCCCeEEE
Confidence 4555555555543
No 107
>KOG1146|consensus
Probab=79.58 E-value=0.21 Score=37.02 Aligned_cols=75 Identities=17% Similarity=0.219 Sum_probs=49.2
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhc-----------------CCCCCeeCCCC
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIH-----------------TGQKPYPCRYC 75 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h-----------------~~~~~~~c~~C 75 (103)
+.|..|+..+.....+. + -....+|.|..|...|...+.|..| .+.- ..-.+| |..|
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~---l~~~~~~~~~~~~~~~~~~~~l~~~-~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c 1334 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-T---LDVTHRYLCRQCKMAFDGEAPLTAH-QRKFCFAGRGSGGSMPPPLRVPDCTYH-CLAC 1334 (1406)
T ss_pred chhhhccccccCcccee-e---cccchhHHHHHHHhhhcchhHHHHH-HHHHHhccCccccCCCCcccCcccccc-chHH
Confidence 66777776665544333 2 1234567777777777777777776 3221 112345 8999
Q ss_pred CccccCcHHHHHHHHhhC
Q psy7454 76 DYKARETQALKVHTKRYH 93 (103)
Q Consensus 76 ~~~f~~~~~l~~H~~~~~ 93 (103)
...|.....|..|++...
T Consensus 1335 ~~~~~~~~alqihm~~~~ 1352 (1406)
T KOG1146|consen 1335 EVLLSGREALQIHMRSSA 1352 (1406)
T ss_pred HhhcchhHHHHHHHHHhh
Confidence 999999999999988744
No 108
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.49 E-value=0.4 Score=28.91 Aligned_cols=25 Identities=8% Similarity=0.114 Sum_probs=17.0
Q ss_pred CCceeeCCCCCcccCchhHHHHHhh
Q psy7454 10 RYKYVCFACKFYTYNTGNIKRHLGM 34 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~~~l~~h~~~ 34 (103)
++...||+|+..|..+..+..-.++
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRi 41 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRI 41 (267)
T ss_pred hceeccCcccchhhhhheeccceeE
Confidence 3457899999988766555444444
No 109
>KOG2785|consensus
Probab=79.31 E-value=2.3 Score=27.65 Aligned_cols=80 Identities=11% Similarity=0.186 Sum_probs=45.9
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCCCCCe---e---cCCCCccccCchHHHHH--HHHhcCCCCCeeCCCCCccccCcH
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLGEKPF---T---CNMCEFKCRDNRTLKAH--HINIHTGQKPYPCRYCDYKARETQ 83 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~---~---c~~C~~~~~~~~~l~~h--~~~~h~~~~~~~c~~C~~~f~~~~ 83 (103)
.|+|..|...|........|.++....-.. + .++-...|........- -...-....++.|..|.+.|....
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~ 82 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPK 82 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChh
Confidence 489999999999887778888763211110 1 12221222211110000 000122345788999999999998
Q ss_pred HHHHHHHh
Q psy7454 84 ALKVHTKR 91 (103)
Q Consensus 84 ~l~~H~~~ 91 (103)
....|+..
T Consensus 83 a~~~hl~S 90 (390)
T KOG2785|consen 83 AHENHLKS 90 (390)
T ss_pred hHHHHHHH
Confidence 88888765
No 110
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=79.23 E-value=1.1 Score=22.80 Aligned_cols=32 Identities=22% Similarity=0.474 Sum_probs=20.2
Q ss_pred CCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 38 EKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 38 ~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
...|.|+.|++.- + .+.- ...|.|..||..|.
T Consensus 33 ~~~~~Cp~C~~~~-----V----kR~a--~GIW~C~kCg~~fA 64 (89)
T COG1997 33 RAKHVCPFCGRTT-----V----KRIA--TGIWKCRKCGAKFA 64 (89)
T ss_pred hcCCcCCCCCCcc-----e----eeec--cCeEEcCCCCCeec
Confidence 3557899998531 1 2222 33688999988775
No 111
>KOG3408|consensus
Probab=78.96 E-value=1.3 Score=23.96 Aligned_cols=26 Identities=19% Similarity=0.453 Sum_probs=21.5
Q ss_pred CCCceeeCCCCCcccCchhHHHHHhh
Q psy7454 9 YRYKYVCFACKFYTYNTGNIKRHLGM 34 (103)
Q Consensus 9 ~~~~~~C~~C~~~f~~~~~l~~h~~~ 34 (103)
|-..|-|-.|.+.|.+...|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 34468899999999999999999765
No 112
>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=78.67 E-value=1.1 Score=17.33 Aligned_cols=11 Identities=18% Similarity=0.386 Sum_probs=7.6
Q ss_pred eeeCCCCCccc
Q psy7454 13 YVCFACKFYTY 23 (103)
Q Consensus 13 ~~C~~C~~~f~ 23 (103)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 35788887764
No 113
>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=77.82 E-value=2.5 Score=22.28 Aligned_cols=24 Identities=21% Similarity=0.538 Sum_probs=17.9
Q ss_pred ceee----CCCCCcccCchhHHHHHhhc
Q psy7454 12 KYVC----FACKFYTYNTGNIKRHLGMH 35 (103)
Q Consensus 12 ~~~C----~~C~~~f~~~~~l~~h~~~h 35 (103)
.|.| ..|+..+.+...+..|.+.+
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKE 107 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHh
Confidence 4778 78888777777788887654
No 114
>PF15269 zf-C2H2_7: Zinc-finger
Probab=77.75 E-value=4.6 Score=17.84 Aligned_cols=23 Identities=30% Similarity=0.748 Sum_probs=14.5
Q ss_pred ceeeCCCCCcccCchhHHHHHhh
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGM 34 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~ 34 (103)
.|.|-+|......++.|-.||+.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 36677776666666666666653
No 115
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=77.62 E-value=2 Score=24.28 Aligned_cols=33 Identities=24% Similarity=0.674 Sum_probs=15.5
Q ss_pred CCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCc
Q psy7454 39 KPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDY 77 (103)
Q Consensus 39 ~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~ 77 (103)
-+|.|. |+..+... .+| ...-.|+ .|.|..|+.
T Consensus 116 ~~Y~C~-C~q~~l~~---RRh-n~~~~g~-~YrC~~C~g 148 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRH-NTVRRGE-VYRCGKCGG 148 (156)
T ss_pred eeEEee-cCCccchh---hhc-ccccccc-eEEeccCCc
Confidence 456666 66554332 222 1222233 566666654
No 116
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=77.15 E-value=2 Score=30.53 Aligned_cols=34 Identities=18% Similarity=0.513 Sum_probs=15.6
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCC
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCE 47 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~ 47 (103)
..|..||..+.-+.- ..-+..|.......|-.||
T Consensus 436 l~C~~Cg~v~~Cp~C-d~~lt~H~~~~~L~CH~Cg 469 (730)
T COG1198 436 LLCRDCGYIAECPNC-DSPLTLHKATGQLRCHYCG 469 (730)
T ss_pred eecccCCCcccCCCC-CcceEEecCCCeeEeCCCC
Confidence 346666655543211 0012334444555666665
No 117
>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=77.00 E-value=2 Score=26.55 Aligned_cols=81 Identities=22% Similarity=0.454 Sum_probs=41.4
Q ss_pred CCCceeeCCCCCcccCchhHHHHHhhc--CCCCCeecCCCCccccCc------hHHHHHHHHh----cCCCCCeeCCCCC
Q psy7454 9 YRYKYVCFACKFYTYNTGNIKRHLGMH--LGEKPFTCNMCEFKCRDN------RTLKAHHINI----HTGQKPYPCRYCD 76 (103)
Q Consensus 9 ~~~~~~C~~C~~~f~~~~~l~~h~~~h--~~~~~~~c~~C~~~~~~~------~~l~~h~~~~----h~~~~~~~c~~C~ 76 (103)
|.+.|.|..|+...-....|. |+.+- .....|.|..|.+.-..+ ..-..| .+. ....+++.|+.||
T Consensus 139 GGrif~CsfC~~flCEDDQFE-HQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddH-vrrKg~ky~k~k~~PCPKCg 216 (314)
T PF06524_consen 139 GGRIFKCSFCDNFLCEDDQFE-HQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDH-VRRKGFKYEKGKPIPCPKCG 216 (314)
T ss_pred CCeEEEeecCCCeeeccchhh-hhhhhhhhhcccccccccccccchhhhheeeeehhhh-hhhcccccccCCCCCCCCCC
Confidence 456899999974433333343 55432 234456666665321111 001122 111 2234688999999
Q ss_pred ccccCcHHHHHHHHh
Q psy7454 77 YKARETQALKVHTKR 91 (103)
Q Consensus 77 ~~f~~~~~l~~H~~~ 91 (103)
........|..-.++
T Consensus 217 ~et~eTkdLSmStR~ 231 (314)
T PF06524_consen 217 YETQETKDLSMSTRS 231 (314)
T ss_pred Ccccccccceeeeec
Confidence 776666555443333
No 118
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.95 E-value=1.5 Score=24.20 Aligned_cols=13 Identities=15% Similarity=0.023 Sum_probs=7.5
Q ss_pred ceeeCCCCCcccC
Q psy7454 12 KYVCFACKFYTYN 24 (103)
Q Consensus 12 ~~~C~~C~~~f~~ 24 (103)
.+.|..||..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 3566666655543
No 119
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=76.18 E-value=2.3 Score=25.50 Aligned_cols=26 Identities=19% Similarity=0.487 Sum_probs=14.6
Q ss_pred CCeecCCCCccccCchHHHHHHHHhc
Q psy7454 39 KPFTCNMCEFKCRDNRTLKAHHINIH 64 (103)
Q Consensus 39 ~~~~c~~C~~~~~~~~~l~~h~~~~h 64 (103)
..|.|..|++.|.....+..|+...|
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CEECCCCCCcccCChHHHHHHHhhcC
Confidence 34667777777777777777644334
No 120
>KOG2593|consensus
Probab=76.01 E-value=3.8 Score=27.20 Aligned_cols=38 Identities=16% Similarity=0.400 Sum_probs=26.9
Q ss_pred CCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCc
Q psy7454 36 LGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDY 77 (103)
Q Consensus 36 ~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~ 77 (103)
+...-|.|+.|.+.|.....++ ......--|.|..|+-
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~----L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ----LLDNETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHH----hhcccCceEEEecCCC
Confidence 4566799999999998766543 3333344689999984
No 121
>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=75.43 E-value=2.9 Score=19.34 Aligned_cols=10 Identities=20% Similarity=0.514 Sum_probs=6.1
Q ss_pred eeeCCCCCcc
Q psy7454 13 YVCFACKFYT 22 (103)
Q Consensus 13 ~~C~~C~~~f 22 (103)
+.|+.||..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 4666666554
No 122
>KOG4167|consensus
Probab=74.51 E-value=0.68 Score=32.57 Aligned_cols=25 Identities=24% Similarity=0.462 Sum_probs=22.6
Q ss_pred CeeCCCCCccccCcHHHHHHHHhhC
Q psy7454 69 PYPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 69 ~~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
.|.|..|+++|.-..++..||++|-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999999999999999884
No 123
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=74.14 E-value=1.4 Score=21.62 Aligned_cols=42 Identities=12% Similarity=0.214 Sum_probs=20.2
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecC--CCCccccCchHH
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCN--MCEFKCRDNRTL 56 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~--~C~~~~~~~~~l 56 (103)
+.|+.||..-.-..+-... ....+.-+.|. .||..|.....+
T Consensus 2 m~CP~Cg~~a~irtSr~~s--~~~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYIT--DTTKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcC--hhhheeeeecCCCCCCCEEEEEEEE
Confidence 4677777543221111111 11334456676 777777665443
No 124
>KOG2785|consensus
Probab=73.58 E-value=5.8 Score=25.93 Aligned_cols=50 Identities=18% Similarity=0.424 Sum_probs=33.5
Q ss_pred eecCCCCccccCchHHHHHHHHhcCC-----------------------CCCeeCCCCC---ccccCcHHHHHHHHh
Q psy7454 41 FTCNMCEFKCRDNRTLKAHHINIHTG-----------------------QKPYPCRYCD---YKARETQALKVHTKR 91 (103)
Q Consensus 41 ~~c~~C~~~~~~~~~l~~h~~~~h~~-----------------------~~~~~c~~C~---~~f~~~~~l~~H~~~ 91 (103)
-.|..|+..+.....-..| |..+.+ .+.+.|..|. +.|.+......||..
T Consensus 167 t~CLfC~~~~k~~e~~~~H-M~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKH-MFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cceeecCCCcccHHHHHHH-HhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 3566666666666555555 433322 2447888888 889988899999875
No 125
>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=73.05 E-value=1.9 Score=25.84 Aligned_cols=29 Identities=17% Similarity=0.458 Sum_probs=22.3
Q ss_pred CCCeeCCCCCccccCcHHHHHHHHhhCCC
Q psy7454 67 QKPYPCRYCDYKARETQALKVHTKRYHPK 95 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~~~~l~~H~~~~~~~ 95 (103)
+..|.|..|++.|.-.-....|+..-|.|
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 45699999999999999999999876644
No 126
>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=72.47 E-value=0.91 Score=23.30 Aligned_cols=31 Identities=26% Similarity=0.652 Sum_probs=19.0
Q ss_pred CCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 39 KPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 39 ~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
..|.|+.||+.- + .+.-.+ .|.|..|++.|.
T Consensus 34 ~ky~Cp~Cgk~~-----v----kR~a~G--IW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTS-----V----KRVATG--IWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSE-----E----EEEETT--EEEETTTTEEEE
T ss_pred CCCcCCCCCCce-----e----EEeeeE--EeecCCCCCEEe
Confidence 567888888643 1 122333 488888887664
No 127
>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=71.92 E-value=1.5 Score=19.06 Aligned_cols=14 Identities=14% Similarity=0.245 Sum_probs=10.9
Q ss_pred eCCCCCccccCcHH
Q psy7454 71 PCRYCDYKARETQA 84 (103)
Q Consensus 71 ~c~~C~~~f~~~~~ 84 (103)
.|.+||+.|.+..-
T Consensus 10 ~C~~C~rpf~WRKK 23 (42)
T PF10013_consen 10 ICPVCGRPFTWRKK 23 (42)
T ss_pred cCcccCCcchHHHH
Confidence 68899998887643
No 128
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=71.42 E-value=1.1 Score=23.45 Aligned_cols=37 Identities=14% Similarity=0.357 Sum_probs=18.2
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccC
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRD 52 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~ 52 (103)
.|.|+.||..-.....+. .-.......|..||..|..
T Consensus 22 ~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVK----KTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred eEecCccCCeeeeEEEEE----ecCceeEEEcccCcceEEE
Confidence 477888875433222211 1112233567777765543
No 129
>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=71.39 E-value=3.1 Score=22.31 Aligned_cols=10 Identities=20% Similarity=0.331 Sum_probs=4.7
Q ss_pred eeeCCCCCcc
Q psy7454 13 YVCFACKFYT 22 (103)
Q Consensus 13 ~~C~~C~~~f 22 (103)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (115)
T TIGR00100 71 CECEDCSEEV 80 (115)
T ss_pred EEcccCCCEE
Confidence 4455555443
No 130
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=71.13 E-value=1.9 Score=22.15 Aligned_cols=32 Identities=13% Similarity=0.412 Sum_probs=20.3
Q ss_pred CCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 38 EKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 38 ~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
...|.|+.|++.- + .+.-. -.|.|..|++.|.
T Consensus 34 ~a~y~CpfCgk~~-----v----kR~a~--GIW~C~~C~~~~A 65 (90)
T PTZ00255 34 HAKYFCPFCGKHA-----V----KRQAV--GIWRCKGCKKTVA 65 (90)
T ss_pred hCCccCCCCCCCc-----e----eeeee--EEEEcCCCCCEEe
Confidence 4568899998531 1 12222 3688999988765
No 131
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=70.28 E-value=0.93 Score=19.44 Aligned_cols=8 Identities=25% Similarity=1.094 Sum_probs=3.9
Q ss_pred eecCCCCc
Q psy7454 41 FTCNMCEF 48 (103)
Q Consensus 41 ~~c~~C~~ 48 (103)
|.|..|+.
T Consensus 29 y~C~~C~~ 36 (40)
T smart00440 29 YVCTKCGH 36 (40)
T ss_pred EEeCCCCC
Confidence 44555543
No 132
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=69.12 E-value=4.1 Score=21.80 Aligned_cols=10 Identities=20% Similarity=0.597 Sum_probs=4.4
Q ss_pred eeeCCCCCcc
Q psy7454 13 YVCFACKFYT 22 (103)
Q Consensus 13 ~~C~~C~~~f 22 (103)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 3444444333
No 133
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.45 E-value=2.9 Score=20.74 Aligned_cols=33 Identities=21% Similarity=0.514 Sum_probs=19.0
Q ss_pred CCceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCcc
Q psy7454 10 RYKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFK 49 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~ 49 (103)
-+.|.|..|+..| .+..+++- .-.-.|+.|+..
T Consensus 10 tY~Y~c~~cg~~~----dvvq~~~d---dplt~ce~c~a~ 42 (82)
T COG2331 10 TYSYECTECGNRF----DVVQAMTD---DPLTTCEECGAR 42 (82)
T ss_pred ceEEeecccchHH----HHHHhccc---CccccChhhChH
Confidence 4568899998665 33333322 222368888753
No 134
>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=68.41 E-value=1.9 Score=22.16 Aligned_cols=32 Identities=28% Similarity=0.598 Sum_probs=19.8
Q ss_pred CCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 38 EKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 38 ~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
...|.|+.|++.- + .+.-.+ .|.|..|++.|.
T Consensus 33 ~a~y~CpfCgk~~-----v----kR~a~G--IW~C~~C~~~~A 64 (91)
T TIGR00280 33 KAKYVCPFCGKKT-----V----KRGSTG--IWTCRKCGAKFA 64 (91)
T ss_pred hcCccCCCCCCCc-----e----EEEeeE--EEEcCCCCCEEe
Confidence 3568899998531 1 222223 688888887765
No 135
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=68.39 E-value=3.3 Score=17.64 Aligned_cols=13 Identities=15% Similarity=0.381 Sum_probs=9.9
Q ss_pred ceeeCCCCCcccC
Q psy7454 12 KYVCFACKFYTYN 24 (103)
Q Consensus 12 ~~~C~~C~~~f~~ 24 (103)
++.|..|+..|=.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 6888888877754
No 136
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=68.07 E-value=3.5 Score=21.22 Aligned_cols=14 Identities=43% Similarity=1.099 Sum_probs=8.9
Q ss_pred CCeecCCCCccccC
Q psy7454 39 KPFTCNMCEFKCRD 52 (103)
Q Consensus 39 ~~~~c~~C~~~~~~ 52 (103)
+|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 45567777766644
No 137
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.74 E-value=2 Score=20.36 Aligned_cols=45 Identities=22% Similarity=0.432 Sum_probs=27.5
Q ss_pred HHhhcCCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 31 HLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 31 h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
|..++.+..++.|+.-+..+..+..+.. + .. +.-..|++|+..|+
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~L~--m-g~--~gev~CPYC~t~y~ 59 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVFLD--M-GD--EGEVVCPYCSTRYR 59 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEEEE--c-CC--CCcEecCccccEEE
Confidence 4556667778888776666555544432 2 12 22347888888775
No 138
>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=67.69 E-value=4 Score=22.99 Aligned_cols=8 Identities=25% Similarity=0.949 Sum_probs=5.2
Q ss_pred eecCCCCc
Q psy7454 41 FTCNMCEF 48 (103)
Q Consensus 41 ~~c~~C~~ 48 (103)
|.|..||.
T Consensus 113 l~C~~Cg~ 120 (146)
T PF07295_consen 113 LVCENCGH 120 (146)
T ss_pred EecccCCC
Confidence 66666664
No 139
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=67.22 E-value=4.9 Score=18.18 Aligned_cols=10 Identities=30% Similarity=0.999 Sum_probs=5.9
Q ss_pred CeeCCCCCcc
Q psy7454 69 PYPCRYCDYK 78 (103)
Q Consensus 69 ~~~c~~C~~~ 78 (103)
.+.|..||..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 4566666653
No 140
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=66.49 E-value=4.8 Score=17.14 Aligned_cols=18 Identities=22% Similarity=0.183 Sum_probs=9.5
Q ss_pred CeecCCCCccccCchHHH
Q psy7454 40 PFTCNMCEFKCRDNRTLK 57 (103)
Q Consensus 40 ~~~c~~C~~~~~~~~~l~ 57 (103)
...|..|+..+.....|.
T Consensus 19 id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEECCCCCeEEccHHHHH
Confidence 345666665555554443
No 141
>KOG2482|consensus
Probab=66.07 E-value=4 Score=26.36 Aligned_cols=23 Identities=30% Similarity=0.694 Sum_probs=21.1
Q ss_pred CeeCCCCCccccCcHHHHHHHHh
Q psy7454 69 PYPCRYCDYKARETQALKVHTKR 91 (103)
Q Consensus 69 ~~~c~~C~~~f~~~~~l~~H~~~ 91 (103)
.+.|..|.+.|+....|..||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 36899999999999999999985
No 142
>COG1773 Rubredoxin [Energy production and conversion]
Probab=65.83 E-value=3.6 Score=19.09 Aligned_cols=13 Identities=23% Similarity=0.697 Sum_probs=9.5
Q ss_pred CeeCCCCCccccC
Q psy7454 69 PYPCRYCDYKARE 81 (103)
Q Consensus 69 ~~~c~~C~~~f~~ 81 (103)
.|+|..||.+|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 5778888877764
No 143
>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=64.91 E-value=3.1 Score=18.92 Aligned_cols=11 Identities=18% Similarity=0.226 Sum_probs=5.8
Q ss_pred eeCCCCCcccC
Q psy7454 14 VCFACKFYTYN 24 (103)
Q Consensus 14 ~C~~C~~~f~~ 24 (103)
.||+|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 89999988865
No 144
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.15 E-value=5.8 Score=18.81 Aligned_cols=40 Identities=15% Similarity=0.336 Sum_probs=23.6
Q ss_pred eeCCCCCc-ccCchhHHHHHhhcCCCCCeecCCCCccccCc
Q psy7454 14 VCFACKFY-TYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDN 53 (103)
Q Consensus 14 ~C~~C~~~-f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~ 53 (103)
.|..|++. +.....+..-+........|-|+.|......+
T Consensus 4 kCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva~k 44 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVAIK 44 (68)
T ss_pred eEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhchh
Confidence 56677654 55555555444334456678888887655443
No 145
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=63.63 E-value=2.6 Score=21.65 Aligned_cols=32 Identities=25% Similarity=0.534 Sum_probs=19.8
Q ss_pred CCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 38 EKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 38 ~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
...|.|+.|++.- + .+.-.+ .|.|..|++.|.
T Consensus 34 ~a~y~CpfCgk~~-----v----kR~a~G--IW~C~~C~~~~A 65 (90)
T PRK03976 34 RAKHVCPVCGRPK-----V----KRVGTG--IWECRKCGAKFA 65 (90)
T ss_pred hcCccCCCCCCCc-----e----EEEEEE--EEEcCCCCCEEe
Confidence 3568899997431 1 222223 688888887765
No 146
>KOG2807|consensus
Probab=63.14 E-value=11 Score=24.27 Aligned_cols=26 Identities=15% Similarity=0.235 Sum_probs=21.7
Q ss_pred CCeeCCCCCccccCcHHHHHHHHhhC
Q psy7454 68 KPYPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 68 ~~~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
..|.|..|...|-...+.-.|...|.
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhhc
Confidence 35888999999999888888888875
No 147
>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=62.85 E-value=7.5 Score=18.48 Aligned_cols=15 Identities=13% Similarity=0.702 Sum_probs=9.4
Q ss_pred CCCeeCCCCCccccC
Q psy7454 67 QKPYPCRYCDYKARE 81 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~ 81 (103)
.+.|.|+.||.....
T Consensus 44 ~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 44 GRVFTCPNCGFEMDR 58 (69)
T ss_pred cceEEcCCCCCEECc
Confidence 445677777765443
No 148
>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=62.33 E-value=4.1 Score=17.61 Aligned_cols=14 Identities=14% Similarity=0.232 Sum_probs=8.2
Q ss_pred CceeeCCCCCcccC
Q psy7454 11 YKYVCFACKFYTYN 24 (103)
Q Consensus 11 ~~~~C~~C~~~f~~ 24 (103)
-++.|+.|+..|=.
T Consensus 12 ~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 12 LPFKCKHCGKSFCL 25 (43)
T ss_dssp SHEE-TTTS-EE-T
T ss_pred CCeECCCCCcccCc
Confidence 46888888887754
No 149
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=62.30 E-value=6.5 Score=20.74 Aligned_cols=13 Identities=15% Similarity=0.181 Sum_probs=8.5
Q ss_pred ceeeCCCCCcccC
Q psy7454 12 KYVCFACKFYTYN 24 (103)
Q Consensus 12 ~~~C~~C~~~f~~ 24 (103)
|+.|..||..|..
T Consensus 2 pH~CtrCG~vf~~ 14 (112)
T COG3364 2 PHQCTRCGEVFDD 14 (112)
T ss_pred Cceeccccccccc
Confidence 4567777777655
No 150
>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=62.02 E-value=5.2 Score=21.37 Aligned_cols=11 Identities=18% Similarity=0.199 Sum_probs=6.2
Q ss_pred eeeCCCCCccc
Q psy7454 13 YVCFACKFYTY 23 (103)
Q Consensus 13 ~~C~~C~~~f~ 23 (103)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 55666666654
No 151
>KOG1280|consensus
Probab=61.84 E-value=9 Score=24.85 Aligned_cols=25 Identities=28% Similarity=0.587 Sum_probs=12.4
Q ss_pred eecCCCCccccCchHHHHHHHHhcC
Q psy7454 41 FTCNMCEFKCRDNRTLKAHHINIHT 65 (103)
Q Consensus 41 ~~c~~C~~~~~~~~~l~~h~~~~h~ 65 (103)
|.|++|+..-.....|..|....|.
T Consensus 80 ftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 80 FTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred ccCCcccccccchhHHHHHhhhcCc
Confidence 4555555555555555555333333
No 152
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.34 E-value=5.6 Score=21.41 Aligned_cols=10 Identities=20% Similarity=0.474 Sum_probs=4.6
Q ss_pred eeeCCCCCcc
Q psy7454 13 YVCFACKFYT 22 (103)
Q Consensus 13 ~~C~~C~~~f 22 (103)
..|..||..|
T Consensus 72 ~~C~~Cg~~~ 81 (117)
T PRK00564 72 LECKDCSHVF 81 (117)
T ss_pred EEhhhCCCcc
Confidence 4455554333
No 153
>PRK04351 hypothetical protein; Provisional
Probab=61.22 E-value=7.9 Score=21.87 Aligned_cols=33 Identities=21% Similarity=0.442 Sum_probs=18.9
Q ss_pred CeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccC
Q psy7454 40 PFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARE 81 (103)
Q Consensus 40 ~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~ 81 (103)
.|.|..||..+... +.+ +...|.|..|+..+..
T Consensus 112 ~Y~C~~Cg~~~~r~--------Rr~-n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRK--------RRI-NTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeee--------eec-CCCcEEeCCCCcEeee
Confidence 37787787654321 112 2356788888765543
No 154
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.99 E-value=6.9 Score=26.64 Aligned_cols=13 Identities=31% Similarity=0.761 Sum_probs=6.2
Q ss_pred cCCCCCeecCCCC
Q psy7454 35 HLGEKPFTCNMCE 47 (103)
Q Consensus 35 h~~~~~~~c~~C~ 47 (103)
|.......|..||
T Consensus 235 h~~~~~l~Ch~Cg 247 (505)
T TIGR00595 235 HKKEGKLRCHYCG 247 (505)
T ss_pred ecCCCeEEcCCCc
Confidence 3334444555555
No 155
>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=59.92 E-value=3.8 Score=17.18 Aligned_cols=14 Identities=21% Similarity=0.657 Sum_probs=6.4
Q ss_pred hhcCCCCCeecCCC
Q psy7454 33 GMHLGEKPFTCNMC 46 (103)
Q Consensus 33 ~~h~~~~~~~c~~C 46 (103)
....|...|.|..|
T Consensus 22 ~~~~G~qryrC~~C 35 (36)
T PF03811_consen 22 KSPSGHQRYRCKDC 35 (36)
T ss_pred CCCCCCEeEecCcC
Confidence 33344444555544
No 156
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=59.67 E-value=8 Score=17.97 Aligned_cols=11 Identities=27% Similarity=0.727 Sum_probs=5.7
Q ss_pred CCCeecCCCCc
Q psy7454 38 EKPFTCNMCEF 48 (103)
Q Consensus 38 ~~~~~c~~C~~ 48 (103)
...|.|+.||-
T Consensus 12 ~v~~~Cp~cGi 22 (55)
T PF13824_consen 12 HVNFECPDCGI 22 (55)
T ss_pred ccCCcCCCCCC
Confidence 34455555553
No 157
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=59.62 E-value=5 Score=25.61 Aligned_cols=49 Identities=14% Similarity=0.242 Sum_probs=31.6
Q ss_pred ecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHHHHHHHHhhC
Q psy7454 42 TCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 42 ~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
.|-.|...|..+..-.- ...+....|.|..|...|-...+.-.|...|.
T Consensus 364 ~Cf~CQ~~fp~~~~~~~---~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 364 HCFVCQGPFPKPPVSPF---DESTSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceeccCCCCCCCCCcc---cccccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 36666655555432111 11223456999999999999988888888774
No 158
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=59.42 E-value=2.9 Score=17.82 Aligned_cols=12 Identities=33% Similarity=0.933 Sum_probs=5.1
Q ss_pred CCCeeCCCCCcc
Q psy7454 67 QKPYPCRYCDYK 78 (103)
Q Consensus 67 ~~~~~c~~C~~~ 78 (103)
.+.|.|..|+..
T Consensus 22 ~~~w~C~~C~~~ 33 (40)
T PF04810_consen 22 GKTWICNFCGTK 33 (40)
T ss_dssp TTEEEETTT--E
T ss_pred CCEEECcCCCCc
Confidence 344555555543
No 159
>PRK14873 primosome assembly protein PriA; Provisional
Probab=58.95 E-value=14 Score=26.28 Aligned_cols=13 Identities=15% Similarity=0.335 Sum_probs=7.8
Q ss_pred cCCCCCeecCCCC
Q psy7454 35 HLGEKPFTCNMCE 47 (103)
Q Consensus 35 h~~~~~~~c~~C~ 47 (103)
|...+...|..||
T Consensus 405 h~~~~~l~Ch~CG 417 (665)
T PRK14873 405 PSAGGTPRCRWCG 417 (665)
T ss_pred ecCCCeeECCCCc
Confidence 4444556677776
No 160
>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=58.82 E-value=9.7 Score=25.77 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=22.0
Q ss_pred CCeeCCCCCccccCcHHHHHHHHhhC
Q psy7454 68 KPYPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 68 ~~~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
+-|.|+.|.+.|.....+..|+-.-|
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhh
Confidence 35789999999999999999988644
No 161
>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=57.97 E-value=2.2 Score=19.48 Aligned_cols=24 Identities=17% Similarity=0.265 Sum_probs=8.2
Q ss_pred CeeCCCCCccccCcHHHHHHHHhh
Q psy7454 69 PYPCRYCDYKARETQALKVHTKRY 92 (103)
Q Consensus 69 ~~~c~~C~~~f~~~~~l~~H~~~~ 92 (103)
.|.|+.|...|-..-++-.|..+|
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-
T ss_pred eEECCCCCCccccCcChhhhcccc
Confidence 355555555554444444444333
No 162
>PLN02294 cytochrome c oxidase subunit Vb
Probab=57.81 E-value=6.7 Score=22.72 Aligned_cols=15 Identities=20% Similarity=0.439 Sum_probs=12.4
Q ss_pred CCCeeCCCCCccccC
Q psy7454 67 QKPYPCRYCDYKARE 81 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~ 81 (103)
.++..|++||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 468899999998874
No 163
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=55.95 E-value=15 Score=22.77 Aligned_cols=11 Identities=18% Similarity=0.797 Sum_probs=7.6
Q ss_pred CCceeeCCCCC
Q psy7454 10 RYKYVCFACKF 20 (103)
Q Consensus 10 ~~~~~C~~C~~ 20 (103)
.+.|.|..|+.
T Consensus 110 drqFaC~~Cd~ 120 (278)
T PF15135_consen 110 DRQFACSSCDH 120 (278)
T ss_pred ceeeeccccch
Confidence 35688888853
No 164
>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=55.61 E-value=8.3 Score=20.15 Aligned_cols=18 Identities=28% Similarity=0.558 Sum_probs=13.6
Q ss_pred HhcCCCCCeeCCCCCcccc
Q psy7454 62 NIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 62 ~~h~~~~~~~c~~C~~~f~ 80 (103)
..+.+ ++..|..||..|.
T Consensus 73 ~l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 73 WLEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EEeCC-CceeCCCCCcEEE
Confidence 33444 6899999998886
No 165
>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=55.27 E-value=6.3 Score=17.86 Aligned_cols=12 Identities=42% Similarity=1.029 Sum_probs=9.2
Q ss_pred eeCCCCCccccC
Q psy7454 70 YPCRYCDYKARE 81 (103)
Q Consensus 70 ~~c~~C~~~f~~ 81 (103)
|+|..||.++.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 678888887764
No 166
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=55.00 E-value=15 Score=16.69 Aligned_cols=9 Identities=33% Similarity=1.158 Sum_probs=5.9
Q ss_pred CeeCCCCCc
Q psy7454 69 PYPCRYCDY 77 (103)
Q Consensus 69 ~~~c~~C~~ 77 (103)
.|.|..||.
T Consensus 37 R~~CGkCgy 45 (51)
T COG1998 37 RWACGKCGY 45 (51)
T ss_pred eeEeccccc
Confidence 466777765
No 167
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=54.86 E-value=6.8 Score=21.01 Aligned_cols=7 Identities=29% Similarity=0.900 Sum_probs=3.2
Q ss_pred ecCCCCc
Q psy7454 42 TCNMCEF 48 (103)
Q Consensus 42 ~c~~C~~ 48 (103)
.|..|+.
T Consensus 72 ~C~~Cg~ 78 (114)
T PRK03681 72 WCETCQQ 78 (114)
T ss_pred EcccCCC
Confidence 4444443
No 168
>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=54.06 E-value=6.8 Score=21.86 Aligned_cols=32 Identities=22% Similarity=0.515 Sum_probs=16.5
Q ss_pred CeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 40 PFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 40 ~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
.|.|..|+..+.... +. ....|.|..|+..+.
T Consensus 123 ~~~C~~C~~~~~r~~-------~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRHR-------RS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeeec-------cc--chhhEECCCCCCEEE
Confidence 466777775542221 11 222367777775543
No 169
>KOG0227|consensus
Probab=53.86 E-value=7.6 Score=22.97 Aligned_cols=28 Identities=21% Similarity=0.365 Sum_probs=21.4
Q ss_pred CCCCCCCCCceeeCCCCCcccCchhHHHHH
Q psy7454 3 MPRPNAYRYKYVCFACKFYTYNTGNIKRHL 32 (103)
Q Consensus 3 ~~~~h~~~~~~~C~~C~~~f~~~~~l~~h~ 32 (103)
+|+.|.|. |.|..|......+.++.+|.
T Consensus 46 ~mkNh~G~--yeCkLClT~H~ne~Syl~Ht 73 (222)
T KOG0227|consen 46 FMKNHLGK--YECKLCLTLHNNEGSYLAHT 73 (222)
T ss_pred hhhccCcc--eeehhhhhhhcchhhhhhhh
Confidence 45677776 99999988777777777663
No 170
>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=53.51 E-value=7 Score=16.85 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=6.3
Q ss_pred CeeCCCCCccc
Q psy7454 69 PYPCRYCDYKA 79 (103)
Q Consensus 69 ~~~c~~C~~~f 79 (103)
+-.|++||..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 34666666554
No 171
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=53.46 E-value=12 Score=21.93 Aligned_cols=32 Identities=19% Similarity=0.566 Sum_probs=16.8
Q ss_pred CCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCc
Q psy7454 36 LGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDY 77 (103)
Q Consensus 36 ~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~ 77 (103)
....-|.|+.|...+...... ..+ |.|+.||.
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~-------~~~---F~Cp~Cg~ 140 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAM-------ELG---FTCPKCGE 140 (176)
T ss_pred ccCCceeCCCCCCcccHHHHH-------HhC---CCCCCCCc
Confidence 344557776666554432221 122 67777775
No 172
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=53.36 E-value=6.1 Score=16.61 Aligned_cols=15 Identities=13% Similarity=0.184 Sum_probs=9.0
Q ss_pred eCCCCCccccCcHHH
Q psy7454 71 PCRYCDYKARETQAL 85 (103)
Q Consensus 71 ~c~~C~~~f~~~~~l 85 (103)
.|..|++.|.+.++-
T Consensus 4 ~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 4 LCPRCGKGFHWASEC 18 (36)
T ss_dssp C-TTTSSSCS-TTT-
T ss_pred cCcccCCCcchhhhh
Confidence 577888888776654
No 173
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=53.03 E-value=2.7 Score=29.69 Aligned_cols=29 Identities=24% Similarity=0.644 Sum_probs=17.1
Q ss_pred ecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCc
Q psy7454 42 TCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDY 77 (103)
Q Consensus 42 ~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~ 77 (103)
-|+.|.+-|..+.. ++.|.. |..|+.||-
T Consensus 153 lC~~C~~EY~dP~n-----RRfHAQ--p~aCp~CGP 181 (750)
T COG0068 153 LCPFCDKEYKDPLN-----RRFHAQ--PIACPKCGP 181 (750)
T ss_pred CCHHHHHHhcCccc-----cccccc--cccCcccCC
Confidence 47777665555432 344543 567888885
No 174
>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=53.03 E-value=4.5 Score=24.36 Aligned_cols=32 Identities=9% Similarity=-0.091 Sum_probs=0.0
Q ss_pred CeeCCCCCccccCcHHHHHHHHhhCCCCCcccc
Q psy7454 69 PYPCRYCDYKARETQALKVHTKRYHPKMYDVEY 101 (103)
Q Consensus 69 ~~~c~~C~~~f~~~~~l~~H~~~~~~~~~~~~~ 101 (103)
-..|+.||...+ .+.|..|+++...+..|++.
T Consensus 168 ~~~cPitGe~IP-~~e~~eHmRi~LlDP~wkEq 199 (229)
T PF12230_consen 168 MIICPITGEMIP-ADEMDEHMRIELLDPRWKEQ 199 (229)
T ss_dssp ---------------------------------
T ss_pred cccccccccccc-cccccccccccccccccccc
Confidence 357888887654 45677888887777777654
No 175
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.70 E-value=2.8 Score=18.82 Aligned_cols=13 Identities=15% Similarity=0.294 Sum_probs=10.4
Q ss_pred eCCCCCccccCcH
Q psy7454 71 PCRYCDYKARETQ 83 (103)
Q Consensus 71 ~c~~C~~~f~~~~ 83 (103)
+|++|++.|.+..
T Consensus 14 ICpvCqRPFsWRk 26 (54)
T COG4338 14 ICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhcCchHHHH
Confidence 6889999888754
No 176
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=52.56 E-value=6 Score=17.34 Aligned_cols=11 Identities=27% Similarity=0.833 Sum_probs=6.5
Q ss_pred CCCeeCCCCCc
Q psy7454 67 QKPYPCRYCDY 77 (103)
Q Consensus 67 ~~~~~c~~C~~ 77 (103)
...|.|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 34567766653
No 177
>KOG2907|consensus
Probab=52.20 E-value=9.8 Score=20.46 Aligned_cols=13 Identities=46% Similarity=0.940 Sum_probs=9.0
Q ss_pred CeeCCCCCccccC
Q psy7454 69 PYPCRYCDYKARE 81 (103)
Q Consensus 69 ~~~c~~C~~~f~~ 81 (103)
-|.|+.|+..|..
T Consensus 102 FYTC~kC~~k~~e 114 (116)
T KOG2907|consen 102 FYTCPKCKYKFTE 114 (116)
T ss_pred EEEcCccceeeec
Confidence 4678888776653
No 178
>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=52.19 E-value=7.9 Score=17.29 Aligned_cols=13 Identities=31% Similarity=0.812 Sum_probs=9.2
Q ss_pred eeCCCCCccccCc
Q psy7454 70 YPCRYCDYKARET 82 (103)
Q Consensus 70 ~~c~~C~~~f~~~ 82 (103)
|.|..||.++...
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 6788888776643
No 179
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=51.81 E-value=16 Score=16.57 Aligned_cols=12 Identities=17% Similarity=0.725 Sum_probs=6.2
Q ss_pred eecCCCCccccC
Q psy7454 41 FTCNMCEFKCRD 52 (103)
Q Consensus 41 ~~c~~C~~~~~~ 52 (103)
..|..||..+..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 456666554433
No 180
>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=51.56 E-value=13 Score=19.67 Aligned_cols=12 Identities=17% Similarity=0.204 Sum_probs=7.8
Q ss_pred ceeeCCCCCccc
Q psy7454 12 KYVCFACKFYTY 23 (103)
Q Consensus 12 ~~~C~~C~~~f~ 23 (103)
|-.|+.||....
T Consensus 2 p~~CpYCg~~~~ 13 (102)
T PF11672_consen 2 PIICPYCGGPAE 13 (102)
T ss_pred CcccCCCCCeeE
Confidence 557888875543
No 181
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=51.16 E-value=19 Score=16.41 Aligned_cols=32 Identities=22% Similarity=0.482 Sum_probs=17.4
Q ss_pred ecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcc
Q psy7454 42 TCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYK 78 (103)
Q Consensus 42 ~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~ 78 (103)
.|..|......... . ....++....|+.||+.
T Consensus 24 ~C~gC~~~l~~~~~--~---~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 24 TCSGCHMELPPQEL--N---EIRKGDEIVFCPNCGRI 55 (56)
T ss_pred ccCCCCEEcCHHHH--H---HHHcCCCeEECcCCCcc
Confidence 67777655433221 1 22233456678888863
No 182
>KOG0696|consensus
Probab=50.68 E-value=4 Score=27.48 Aligned_cols=41 Identities=17% Similarity=0.284 Sum_probs=20.7
Q ss_pred CCceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCchHHHHH
Q psy7454 10 RYKYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAH 59 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h 59 (103)
+..|.|++|. +..|.+.|. --.|.|+.-++++.+...-..|
T Consensus 71 KQGfQCqvC~--------fvvHkrChe-fVtF~CPGadkg~dtDdpr~kH 111 (683)
T KOG0696|consen 71 KQGFQCQVCC--------FVVHKRCHE-FVTFSCPGADKGPDTDDPRSKH 111 (683)
T ss_pred cCceeeeEEe--------ehhhhhhcc-eEEEECCCCCCCCCCCCccccc
Confidence 3446666663 455666653 2345565555555544443333
No 183
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.59 E-value=5.5 Score=21.84 Aligned_cols=18 Identities=22% Similarity=0.350 Sum_probs=11.6
Q ss_pred CCCCeeCCCCCccccCcH
Q psy7454 66 GQKPYPCRYCDYKARETQ 83 (103)
Q Consensus 66 ~~~~~~c~~C~~~f~~~~ 83 (103)
-+.|--|..||..|+|.-
T Consensus 65 ye~psfchncgs~fpwte 82 (160)
T COG4306 65 YEPPSFCHNCGSRFPWTE 82 (160)
T ss_pred CCCcchhhcCCCCCCcHH
Confidence 345556777777777653
No 184
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=50.37 E-value=14 Score=20.55 Aligned_cols=33 Identities=21% Similarity=0.434 Sum_probs=17.6
Q ss_pred CeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 40 PFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 40 ~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
.|.|..|+..+.. + . .+..-..|.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~~------~-r-r~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYLR------V-R-RSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCce------E-c-cccCcceEEcCCCCCEEE
Confidence 5677777755431 1 1 122224577777776543
No 185
>KOG0717|consensus
Probab=49.88 E-value=12 Score=25.40 Aligned_cols=21 Identities=19% Similarity=0.377 Sum_probs=18.5
Q ss_pred eeeCCCCCcccCchhHHHHHh
Q psy7454 13 YVCFACKFYTYNTGNIKRHLG 33 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~ 33 (103)
+-|.+|+++|.+.-.+..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 789999999999988888864
No 186
>KOG3507|consensus
Probab=49.66 E-value=14 Score=17.39 Aligned_cols=9 Identities=44% Similarity=1.091 Sum_probs=4.3
Q ss_pred CeeCCCCCc
Q psy7454 69 PYPCRYCDY 77 (103)
Q Consensus 69 ~~~c~~C~~ 77 (103)
.+.|..||.
T Consensus 37 ~irCReCG~ 45 (62)
T KOG3507|consen 37 VIRCRECGY 45 (62)
T ss_pred cEehhhcch
Confidence 344555553
No 187
>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=49.57 E-value=9.7 Score=16.00 Aligned_cols=12 Identities=25% Similarity=0.376 Sum_probs=6.6
Q ss_pred CceeeCCCCCcc
Q psy7454 11 YKYVCFACKFYT 22 (103)
Q Consensus 11 ~~~~C~~C~~~f 22 (103)
+.|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 468899998654
No 188
>KOG2482|consensus
Probab=49.52 E-value=11 Score=24.43 Aligned_cols=23 Identities=17% Similarity=0.475 Sum_probs=20.7
Q ss_pred ceeeCCCCCcccCchhHHHHHhh
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGM 34 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~ 34 (103)
.+.|-.|.+.|..+..|..||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999974
No 189
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=49.50 E-value=13 Score=24.89 Aligned_cols=13 Identities=31% Similarity=0.902 Sum_probs=7.0
Q ss_pred CeecCCCCccccC
Q psy7454 40 PFTCNMCEFKCRD 52 (103)
Q Consensus 40 ~~~c~~C~~~~~~ 52 (103)
-|.|..||..+..
T Consensus 367 g~rC~kCg~~~~~ 379 (421)
T COG1571 367 GFRCKKCGTRARE 379 (421)
T ss_pred CcccccccccCCc
Confidence 5556666554443
No 190
>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=48.61 E-value=14 Score=17.45 Aligned_cols=12 Identities=17% Similarity=0.243 Sum_probs=4.8
Q ss_pred ceeeCCCCCccc
Q psy7454 12 KYVCFACKFYTY 23 (103)
Q Consensus 12 ~~~C~~C~~~f~ 23 (103)
.-.|..|++.|.
T Consensus 9 ~~~C~~C~~~F~ 20 (69)
T PF01363_consen 9 ASNCMICGKKFS 20 (69)
T ss_dssp -SB-TTT--B-B
T ss_pred CCcCcCcCCcCC
Confidence 356777887774
No 191
>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=48.57 E-value=14 Score=25.04 Aligned_cols=26 Identities=15% Similarity=0.294 Sum_probs=21.5
Q ss_pred ceeeCCCCCcccCchhHHHHHh-hcCC
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLG-MHLG 37 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~-~h~~ 37 (103)
-+.|+.|++.|.....+..|+. .|.+
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 4789999999999999999975 4543
No 192
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=48.16 E-value=9.9 Score=21.04 Aligned_cols=14 Identities=14% Similarity=0.166 Sum_probs=10.5
Q ss_pred ceeeCCCCCcccCc
Q psy7454 12 KYVCFACKFYTYNT 25 (103)
Q Consensus 12 ~~~C~~C~~~f~~~ 25 (103)
|+.|..||+.|..-
T Consensus 1 PH~Ct~Cg~~f~dg 14 (131)
T PF09845_consen 1 PHQCTKCGRVFEDG 14 (131)
T ss_pred CcccCcCCCCcCCC
Confidence 56788888888753
No 193
>PTZ00448 hypothetical protein; Provisional
Probab=48.15 E-value=13 Score=24.41 Aligned_cols=24 Identities=17% Similarity=0.419 Sum_probs=18.7
Q ss_pred ceeeCCCCCcccCchhHHHHHhhc
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMH 35 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h 35 (103)
.|.|..|+..|.+......|.++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 477999998887777777787764
No 194
>PHA02998 RNA polymerase subunit; Provisional
Probab=48.12 E-value=5.6 Score=23.22 Aligned_cols=11 Identities=27% Similarity=0.679 Sum_probs=6.6
Q ss_pred eeCCCCCcccc
Q psy7454 70 YPCRYCDYKAR 80 (103)
Q Consensus 70 ~~c~~C~~~f~ 80 (103)
|.|..||..|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 56666665554
No 195
>KOG2231|consensus
Probab=48.06 E-value=48 Score=23.80 Aligned_cols=17 Identities=29% Similarity=0.694 Sum_probs=7.9
Q ss_pred cCCCCccccCchHHHHH
Q psy7454 43 CNMCEFKCRDNRTLKAH 59 (103)
Q Consensus 43 c~~C~~~~~~~~~l~~h 59 (103)
|..|...|.....|..|
T Consensus 185 C~~C~~~fld~~el~rH 201 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRH 201 (669)
T ss_pred chhhhhhhccHHHHHHh
Confidence 44444444444444443
No 196
>PRK05580 primosome assembly protein PriA; Validated
Probab=47.64 E-value=24 Score=25.11 Aligned_cols=8 Identities=25% Similarity=0.945 Sum_probs=3.7
Q ss_pred eeCCCCCc
Q psy7454 14 VCFACKFY 21 (103)
Q Consensus 14 ~C~~C~~~ 21 (103)
.|..||..
T Consensus 383 ~C~~Cg~~ 390 (679)
T PRK05580 383 LCRDCGWV 390 (679)
T ss_pred EhhhCcCc
Confidence 35555443
No 197
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=47.31 E-value=35 Score=20.37 Aligned_cols=13 Identities=15% Similarity=0.309 Sum_probs=8.5
Q ss_pred CCeecCCCCcccc
Q psy7454 39 KPFTCNMCEFKCR 51 (103)
Q Consensus 39 ~~~~c~~C~~~~~ 51 (103)
-.+.|..||..+.
T Consensus 29 ~lvrC~eCG~V~~ 41 (201)
T COG1326 29 PLVRCEECGTVHP 41 (201)
T ss_pred eEEEccCCCcEee
Confidence 4567888876553
No 198
>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=46.82 E-value=17 Score=19.44 Aligned_cols=13 Identities=15% Similarity=0.636 Sum_probs=7.7
Q ss_pred CCeecCCCCcccc
Q psy7454 39 KPFTCNMCEFKCR 51 (103)
Q Consensus 39 ~~~~c~~C~~~~~ 51 (103)
..+.|+.|+.-+.
T Consensus 18 ~~~iCpeC~~EW~ 30 (109)
T TIGR00686 18 TQLICPSCLYEWN 30 (109)
T ss_pred CeeECcccccccc
Confidence 3467777765443
No 199
>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=46.42 E-value=11 Score=15.58 Aligned_cols=12 Identities=17% Similarity=0.168 Sum_probs=5.4
Q ss_pred eeeCCCCCcccC
Q psy7454 13 YVCFACKFYTYN 24 (103)
Q Consensus 13 ~~C~~C~~~f~~ 24 (103)
-.|..|++.|..
T Consensus 4 ~~C~eC~~~f~d 15 (34)
T PF01286_consen 4 PKCDECGKPFMD 15 (34)
T ss_dssp EE-TTT--EES-
T ss_pred chHhHhCCHHHH
Confidence 367777777754
No 200
>KOG2071|consensus
Probab=44.99 E-value=19 Score=25.17 Aligned_cols=27 Identities=15% Similarity=0.431 Sum_probs=22.4
Q ss_pred CCCeeCCCCCccccCcHHHHHHHHhhC
Q psy7454 67 QKPYPCRYCDYKARETQALKVHTKRYH 93 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~~~~l~~H~~~~~ 93 (103)
..|-.|..||..|........|+..|-
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 456789999999999988888877764
No 201
>PRK00420 hypothetical protein; Validated
Probab=44.96 E-value=25 Score=18.94 Aligned_cols=7 Identities=14% Similarity=0.211 Sum_probs=3.3
Q ss_pred eCCCCCc
Q psy7454 71 PCRYCDY 77 (103)
Q Consensus 71 ~c~~C~~ 77 (103)
.|+.||.
T Consensus 42 ~Cp~Cg~ 48 (112)
T PRK00420 42 VCPVHGK 48 (112)
T ss_pred ECCCCCC
Confidence 4444444
No 202
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=44.88 E-value=9.1 Score=17.02 Aligned_cols=10 Identities=20% Similarity=0.524 Sum_probs=4.6
Q ss_pred ceeeCCCCCc
Q psy7454 12 KYVCFACKFY 21 (103)
Q Consensus 12 ~~~C~~C~~~ 21 (103)
+-.|.+|++.
T Consensus 11 ~~~C~~C~~~ 20 (53)
T PF00130_consen 11 PTYCDVCGKF 20 (53)
T ss_dssp TEB-TTSSSB
T ss_pred CCCCcccCcc
Confidence 4455555544
No 203
>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=44.52 E-value=11 Score=18.02 Aligned_cols=14 Identities=14% Similarity=0.190 Sum_probs=9.4
Q ss_pred CCceeeCCCCCccc
Q psy7454 10 RYKYVCFACKFYTY 23 (103)
Q Consensus 10 ~~~~~C~~C~~~f~ 23 (103)
+....|+.|++.|.
T Consensus 51 eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 51 EGELICPECGREYP 64 (68)
T ss_dssp TTEEEETTTTEEEE
T ss_pred CCEEEcCCCCCEEe
Confidence 44577777777664
No 204
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=44.33 E-value=23 Score=16.56 Aligned_cols=11 Identities=18% Similarity=0.697 Sum_probs=5.7
Q ss_pred CCCeecCCCCc
Q psy7454 38 EKPFTCNMCEF 48 (103)
Q Consensus 38 ~~~~~c~~C~~ 48 (103)
...|.|+.|..
T Consensus 29 i~tYmC~eC~~ 39 (56)
T PF09963_consen 29 IHTYMCDECKE 39 (56)
T ss_pred CcceeChhHHH
Confidence 44455665543
No 205
>KOG0717|consensus
Probab=43.93 E-value=16 Score=24.85 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=19.0
Q ss_pred eeCCCCCccccCcHHHHHHHHh
Q psy7454 70 YPCRYCDYKARETQALKVHTKR 91 (103)
Q Consensus 70 ~~c~~C~~~f~~~~~l~~H~~~ 91 (103)
+-|.+|.+.|.+...+.+|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6799999999999999998654
No 206
>KOG3183|consensus
Probab=43.69 E-value=19 Score=22.19 Aligned_cols=41 Identities=15% Similarity=0.335 Sum_probs=24.2
Q ss_pred ceeeCCCCCcccCc-hhHHHHH---hhcCCCCCeecCCCCccccC
Q psy7454 12 KYVCFACKFYTYNT-GNIKRHL---GMHLGEKPFTCNMCEFKCRD 52 (103)
Q Consensus 12 ~~~C~~C~~~f~~~-~~l~~h~---~~h~~~~~~~c~~C~~~~~~ 52 (103)
||.|+.|+..|-.. ..+..|- .....+.--+|+.|.+....
T Consensus 23 Pf~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~~ 67 (250)
T KOG3183|consen 23 PFKCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVPT 67 (250)
T ss_pred ceeeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCCCC
Confidence 79999999887654 3344442 12233444467777655443
No 207
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=43.51 E-value=20 Score=16.86 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=7.6
Q ss_pred CCCCCeeCCCCCc
Q psy7454 65 TGQKPYPCRYCDY 77 (103)
Q Consensus 65 ~~~~~~~c~~C~~ 77 (103)
.|++.-.|+.|..
T Consensus 40 ~GE~VArCPSCSL 52 (67)
T COG5216 40 NGEVVARCPSCSL 52 (67)
T ss_pred CCceEEEcCCceE
Confidence 4555566666654
No 208
>KOG0782|consensus
Probab=43.33 E-value=2.9 Score=28.96 Aligned_cols=51 Identities=18% Similarity=0.335 Sum_probs=30.4
Q ss_pred hhHHHHHhhcCCCCCeecCCCCccccCchHHHHHHHHhcCCCC-CeeCCCCCccccCcH
Q psy7454 26 GNIKRHLGMHLGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQK-PYPCRYCDYKARETQ 83 (103)
Q Consensus 26 ~~l~~h~~~h~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~-~~~c~~C~~~f~~~~ 83 (103)
..|.+|.=+|.....-.|..||++|..+-.+ |..+. ...|.+|...|....
T Consensus 239 ~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~F-------hsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 239 SGFVRHHWVHRRRQEGKCNTCGKGFQQKFFF-------HSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccchHHhHhhHhhhccccchhhhhhhhheee-------ccccEEEEEehHHHHHhhcch
Confidence 4566665566554445788888887554333 33332 457888877766543
No 209
>KOG1940|consensus
Probab=43.30 E-value=24 Score=22.28 Aligned_cols=8 Identities=38% Similarity=1.211 Sum_probs=4.5
Q ss_pred eecCCCCc
Q psy7454 41 FTCNMCEF 48 (103)
Q Consensus 41 ~~c~~C~~ 48 (103)
|.|++|.+
T Consensus 197 y~CP~C~~ 204 (276)
T KOG1940|consen 197 YTCPICSK 204 (276)
T ss_pred CCCCcccc
Confidence 55555554
No 210
>COG2879 Uncharacterized small protein [Function unknown]
Probab=41.20 E-value=37 Score=16.27 Aligned_cols=19 Identities=16% Similarity=0.300 Sum_probs=14.3
Q ss_pred CcHHHHHHHHhhCCCCCcc
Q psy7454 81 ETQALKVHTKRYHPKMYDV 99 (103)
Q Consensus 81 ~~~~l~~H~~~~~~~~~~~ 99 (103)
.-.++..|++.+++++|..
T Consensus 24 dYdnYVehmr~~hPd~p~m 42 (65)
T COG2879 24 DYDNYVEHMRKKHPDKPPM 42 (65)
T ss_pred cHHHHHHHHHHhCcCCCcc
Confidence 3456778999988888864
No 211
>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=41.13 E-value=31 Score=14.16 Aligned_cols=20 Identities=20% Similarity=0.240 Sum_probs=10.1
Q ss_pred ceeeCCCCCcccCchhHHHHH
Q psy7454 12 KYVCFACKFYTYNTGNIKRHL 32 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~ 32 (103)
.+.|+.|++.+.. .-+..|.
T Consensus 4 ~~~C~nC~R~v~a-~RfA~HL 23 (33)
T PF08209_consen 4 YVECPNCGRPVAA-SRFAPHL 23 (33)
T ss_dssp EEE-TTTSSEEEG-GGHHHHH
T ss_pred eEECCCCcCCcch-hhhHHHH
Confidence 3567777766543 3344453
No 212
>KOG1088|consensus
Probab=40.23 E-value=16 Score=19.88 Aligned_cols=19 Identities=11% Similarity=-0.036 Sum_probs=11.7
Q ss_pred CCCCCceeeCCCCCcccCc
Q psy7454 7 NAYRYKYVCFACKFYTYNT 25 (103)
Q Consensus 7 h~~~~~~~C~~C~~~f~~~ 25 (103)
+-.+....|+.||+.|.-+
T Consensus 93 ~v~EG~l~CpetG~vfpI~ 111 (124)
T KOG1088|consen 93 DVIEGELVCPETGRVFPIS 111 (124)
T ss_pred hhccceEecCCCCcEeecc
Confidence 3344557777777777543
No 213
>PF12773 DZR: Double zinc ribbon
Probab=40.21 E-value=17 Score=15.91 Aligned_cols=8 Identities=25% Similarity=0.538 Sum_probs=3.8
Q ss_pred eecCCCCc
Q psy7454 41 FTCNMCEF 48 (103)
Q Consensus 41 ~~c~~C~~ 48 (103)
..|+.|+.
T Consensus 30 ~~C~~Cg~ 37 (50)
T PF12773_consen 30 KICPNCGA 37 (50)
T ss_pred CCCcCCcC
Confidence 34555543
No 214
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=40.05 E-value=18 Score=14.79 Aligned_cols=12 Identities=25% Similarity=0.257 Sum_probs=8.6
Q ss_pred ceeeCCCCCccc
Q psy7454 12 KYVCFACKFYTY 23 (103)
Q Consensus 12 ~~~C~~C~~~f~ 23 (103)
.+.|..||..|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 467888887663
No 215
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=40.04 E-value=7.8 Score=23.04 Aligned_cols=35 Identities=26% Similarity=0.505 Sum_probs=18.1
Q ss_pred eeeCCCCCcccCchhHHHHHhh----cCCC---CCeecCCCCccccCc
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGM----HLGE---KPFTCNMCEFKCRDN 53 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~----h~~~---~~~~c~~C~~~~~~~ 53 (103)
..||+||..+ ..|+.. +.|+ ....|..||..+...
T Consensus 15 ~~CPvCg~~l------~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV 56 (201)
T COG1779 15 IDCPVCGGTL------KAHMYLYDIPYFGEVLISTGVCERCGYRSTDV 56 (201)
T ss_pred ecCCccccee------eEEEeeecCCccceEEEEEEEccccCCcccce
Confidence 5688887533 223222 2332 234677777655443
No 216
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=39.98 E-value=10 Score=20.38 Aligned_cols=16 Identities=25% Similarity=0.432 Sum_probs=11.5
Q ss_pred CCceeeCCCCCcccCc
Q psy7454 10 RYKYVCFACKFYTYNT 25 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~ 25 (103)
...+.|+.||......
T Consensus 20 ~~~l~C~kCgye~~~~ 35 (113)
T COG1594 20 GGKLVCRKCGYEEEAS 35 (113)
T ss_pred CcEEECCCCCcchhcc
Confidence 3468899999776544
No 217
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.98 E-value=15 Score=20.19 Aligned_cols=16 Identities=19% Similarity=0.341 Sum_probs=12.5
Q ss_pred CCceeeCCCCCcccCc
Q psy7454 10 RYKYVCFACKFYTYNT 25 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~ 25 (103)
...|.|+.|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4468999999988753
No 218
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.86 E-value=18 Score=18.99 Aligned_cols=8 Identities=25% Similarity=0.775 Sum_probs=5.3
Q ss_pred ceeeCCCC
Q psy7454 12 KYVCFACK 19 (103)
Q Consensus 12 ~~~C~~C~ 19 (103)
.|.|+.|+
T Consensus 21 ~f~CP~Cg 28 (99)
T PRK14892 21 IFECPRCG 28 (99)
T ss_pred EeECCCCC
Confidence 46677776
No 219
>KOG4727|consensus
Probab=39.81 E-value=24 Score=20.60 Aligned_cols=22 Identities=23% Similarity=0.412 Sum_probs=18.0
Q ss_pred CceeeCCCCCcccCchhHHHHH
Q psy7454 11 YKYVCFACKFYTYNTGNIKRHL 32 (103)
Q Consensus 11 ~~~~C~~C~~~f~~~~~l~~h~ 32 (103)
..|-|.+|+..|...-++..|+
T Consensus 74 ~GyyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 74 GGYYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred CceeeeecceeehhhHHHHHHh
Confidence 3588999999998888887775
No 220
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=39.67 E-value=27 Score=16.19 Aligned_cols=32 Identities=19% Similarity=0.363 Sum_probs=16.1
Q ss_pred CCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCC
Q psy7454 38 EKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRY 74 (103)
Q Consensus 38 ~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~ 74 (103)
+.|+....|+..|...+.+.. + .......|++
T Consensus 22 ~~PV~s~~C~H~fek~aI~~~--i---~~~~~~~CPv 53 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEAILQY--I---QRNGSKRCPV 53 (57)
T ss_dssp SSEEEESSS--EEEHHHHHHH--C---TTTS-EE-SC
T ss_pred hCCcCcCCCCCeecHHHHHHH--H---HhcCCCCCCC
Confidence 456667788887776654422 2 2344567776
No 221
>KOG2636|consensus
Probab=39.63 E-value=26 Score=23.76 Aligned_cols=27 Identities=15% Similarity=0.586 Sum_probs=19.7
Q ss_pred hhcCCCCCeecCCCC-ccccCchHHHHH
Q psy7454 33 GMHLGEKPFTCNMCE-FKCRDNRTLKAH 59 (103)
Q Consensus 33 ~~h~~~~~~~c~~C~-~~~~~~~~l~~h 59 (103)
+.|.-...|.|.+|| +.+.-+..+.+|
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHH
Confidence 456666778888888 677777777776
No 222
>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=39.25 E-value=34 Score=15.71 Aligned_cols=10 Identities=40% Similarity=1.079 Sum_probs=5.5
Q ss_pred CCeeCCCCCc
Q psy7454 68 KPYPCRYCDY 77 (103)
Q Consensus 68 ~~~~c~~C~~ 77 (103)
..|.|..||.
T Consensus 43 i~y~C~~Cg~ 52 (54)
T PF10058_consen 43 IQYRCPYCGA 52 (54)
T ss_pred eEEEcCCCCC
Confidence 3456666653
No 223
>KOG1842|consensus
Probab=39.24 E-value=19 Score=24.36 Aligned_cols=29 Identities=21% Similarity=0.362 Sum_probs=17.9
Q ss_pred CCeecCCCCccccCchHHHHHHHHhcCCC
Q psy7454 39 KPFTCNMCEFKCRDNRTLKAHHINIHTGQ 67 (103)
Q Consensus 39 ~~~~c~~C~~~~~~~~~l~~h~~~~h~~~ 67 (103)
+.|.|++|...|..-..|..|....|.++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 34667777777777777766644445444
No 224
>PRK05978 hypothetical protein; Provisional
Probab=39.15 E-value=12 Score=21.25 Aligned_cols=11 Identities=18% Similarity=0.452 Sum_probs=6.5
Q ss_pred eCCCCCccccC
Q psy7454 71 PCRYCDYKARE 81 (103)
Q Consensus 71 ~c~~C~~~f~~ 81 (103)
.|+.||..|..
T Consensus 54 ~C~~CG~~~~~ 64 (148)
T PRK05978 54 HCAACGEDFTH 64 (148)
T ss_pred CccccCCcccc
Confidence 56666665543
No 225
>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=39.09 E-value=17 Score=20.33 Aligned_cols=44 Identities=16% Similarity=0.194 Sum_probs=23.1
Q ss_pred eecCCCCccccCchHHHHH-HH---HhcCCCCCeeCCCCCccccCcHH
Q psy7454 41 FTCNMCEFKCRDNRTLKAH-HI---NIHTGQKPYPCRYCDYKARETQA 84 (103)
Q Consensus 41 ~~c~~C~~~~~~~~~l~~h-~~---~~h~~~~~~~c~~C~~~f~~~~~ 84 (103)
-.|..|+..+...+.-..- .. .....+.-+.|+.||+.|=.-+.
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH 139 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSH 139 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEeccccc
Confidence 5799998755443221000 00 00112346899999998744333
No 226
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=38.53 E-value=17 Score=22.19 Aligned_cols=15 Identities=27% Similarity=0.306 Sum_probs=12.6
Q ss_pred CCCeeCCCCCccccC
Q psy7454 67 QKPYPCRYCDYKARE 81 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~ 81 (103)
.++..|..||..|.-
T Consensus 179 GkpqRCpECGqVFKL 193 (268)
T PTZ00043 179 GFLYRCGECDQIFML 193 (268)
T ss_pred CCCccCCCCCcEEEE
Confidence 468899999998875
No 227
>PRK12722 transcriptional activator FlhC; Provisional
Probab=38.48 E-value=27 Score=20.68 Aligned_cols=9 Identities=22% Similarity=0.870 Sum_probs=5.7
Q ss_pred CeeCCCCCc
Q psy7454 69 PYPCRYCDY 77 (103)
Q Consensus 69 ~~~c~~C~~ 77 (103)
.|.|+.|..
T Consensus 154 ~f~CplC~~ 162 (187)
T PRK12722 154 SFVCGLCQP 162 (187)
T ss_pred CCcCCCCCC
Confidence 566776654
No 228
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=38.35 E-value=23 Score=19.04 Aligned_cols=17 Identities=18% Similarity=0.075 Sum_probs=11.0
Q ss_pred CCCcccC-chhHHHHHhh
Q psy7454 18 CKFYTYN-TGNIKRHLGM 34 (103)
Q Consensus 18 C~~~f~~-~~~l~~h~~~ 34 (103)
||..|.. ..+.+.|-.+
T Consensus 29 CGh~f~d~r~NwK~~alv 46 (112)
T PF08882_consen 29 CGHEFCDARENWKLGALV 46 (112)
T ss_pred CCCeecChhcChhhCcEE
Confidence 9988876 3556655443
No 229
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=37.60 E-value=20 Score=24.29 Aligned_cols=14 Identities=14% Similarity=0.650 Sum_probs=6.7
Q ss_pred CCeecCCCCccccC
Q psy7454 39 KPFTCNMCEFKCRD 52 (103)
Q Consensus 39 ~~~~c~~C~~~~~~ 52 (103)
..|.|..||..|..
T Consensus 424 ~~~~c~~c~~~yd~ 437 (479)
T PRK05452 424 PRMQCSVCQWIYDP 437 (479)
T ss_pred CeEEECCCCeEECC
Confidence 34555555544443
No 230
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=37.40 E-value=29 Score=20.49 Aligned_cols=27 Identities=22% Similarity=0.472 Sum_probs=20.1
Q ss_pred CCCCCCCCceeeCCCCCcccCchhHHHHH
Q psy7454 4 PRPNAYRYKYVCFACKFYTYNTGNIKRHL 32 (103)
Q Consensus 4 ~~~h~~~~~~~C~~C~~~f~~~~~l~~h~ 32 (103)
++.|.|. |.|..|.....++.++..|.
T Consensus 47 ~knh~Gk--~vC~LC~T~H~~e~Sy~~H~ 73 (222)
T COG5246 47 SKNHTGK--YVCLLCKTKHLTEMSYVKHR 73 (222)
T ss_pred hhcCCCc--EEeeeeccccccHHHHHHhh
Confidence 4556666 89999988877777777664
No 231
>PRK12860 transcriptional activator FlhC; Provisional
Probab=37.19 E-value=27 Score=20.69 Aligned_cols=11 Identities=27% Similarity=0.347 Sum_probs=6.3
Q ss_pred eecCCCCcccc
Q psy7454 41 FTCNMCEFKCR 51 (103)
Q Consensus 41 ~~c~~C~~~~~ 51 (103)
..|..||..|.
T Consensus 135 ~~C~~Cgg~fv 145 (189)
T PRK12860 135 ARCCRCGGKFV 145 (189)
T ss_pred ccCCCCCCCee
Confidence 35666665553
No 232
>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=37.00 E-value=22 Score=14.15 Aligned_cols=11 Identities=36% Similarity=0.621 Sum_probs=5.1
Q ss_pred ceeeCCCCCcc
Q psy7454 12 KYVCFACKFYT 22 (103)
Q Consensus 12 ~~~C~~C~~~f 22 (103)
.|.|+.|+..+
T Consensus 13 kY~Cp~C~~~~ 23 (30)
T PF04438_consen 13 KYRCPRCGARY 23 (30)
T ss_dssp SEE-TTT--EE
T ss_pred EEECCCcCCce
Confidence 47777776543
No 233
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.86 E-value=26 Score=19.10 Aligned_cols=6 Identities=33% Similarity=1.143 Sum_probs=3.4
Q ss_pred eCCCCC
Q psy7454 71 PCRYCD 76 (103)
Q Consensus 71 ~c~~C~ 76 (103)
.|+.||
T Consensus 94 ~CP~Cg 99 (124)
T PRK00762 94 ECPVCG 99 (124)
T ss_pred cCcCCC
Confidence 455555
No 234
>PRK10220 hypothetical protein; Provisional
Probab=36.73 E-value=37 Score=18.25 Aligned_cols=13 Identities=23% Similarity=0.700 Sum_probs=7.5
Q ss_pred CeecCCCCccccC
Q psy7454 40 PFTCNMCEFKCRD 52 (103)
Q Consensus 40 ~~~c~~C~~~~~~ 52 (103)
.+.|+.|+.-+..
T Consensus 20 ~~vCpeC~hEW~~ 32 (111)
T PRK10220 20 MYICPECAHEWND 32 (111)
T ss_pred eEECCcccCcCCc
Confidence 4667777654433
No 235
>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=35.76 E-value=13 Score=17.41 Aligned_cols=16 Identities=19% Similarity=0.478 Sum_probs=10.3
Q ss_pred CCCeeCCCCCccccCc
Q psy7454 67 QKPYPCRYCDYKARET 82 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~~ 82 (103)
...|.|..||..+-..
T Consensus 9 ~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGR 24 (63)
T ss_dssp SSEEEETTTS-EEETT
T ss_pred CceEEeCCCCcccccC
Confidence 4567788888766654
No 236
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=35.68 E-value=30 Score=21.66 Aligned_cols=15 Identities=13% Similarity=0.622 Sum_probs=8.4
Q ss_pred CCeeCCCCCccccCc
Q psy7454 68 KPYPCRYCDYKARET 82 (103)
Q Consensus 68 ~~~~c~~C~~~f~~~ 82 (103)
+.|.|+.||..+...
T Consensus 321 r~~~C~~cg~~~~rD 335 (364)
T COG0675 321 RLFKCPRCGFVHDRD 335 (364)
T ss_pred eeEECCCCCCeehhh
Confidence 346677776554433
No 237
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=35.61 E-value=25 Score=14.50 Aligned_cols=12 Identities=42% Similarity=0.830 Sum_probs=7.8
Q ss_pred CceeeCCCCCcc
Q psy7454 11 YKYVCFACKFYT 22 (103)
Q Consensus 11 ~~~~C~~C~~~f 22 (103)
..+.|+.||...
T Consensus 21 ~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 21 ERLVCPACGFIH 32 (34)
T ss_dssp -EEEETTTTEEE
T ss_pred cceECCCCCCEE
Confidence 357788887654
No 238
>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=35.61 E-value=19 Score=15.23 Aligned_cols=12 Identities=25% Similarity=0.418 Sum_probs=8.6
Q ss_pred eeeCCCCCcccC
Q psy7454 13 YVCFACKFYTYN 24 (103)
Q Consensus 13 ~~C~~C~~~f~~ 24 (103)
+.|+.||..+.+
T Consensus 33 ~~C~~CGE~~~~ 44 (46)
T TIGR03831 33 LVCPQCGEEYLD 44 (46)
T ss_pred cccccCCCEeeC
Confidence 568888877643
No 239
>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=35.49 E-value=25 Score=14.18 Aligned_cols=11 Identities=27% Similarity=0.540 Sum_probs=7.5
Q ss_pred ceeeCCCCCcc
Q psy7454 12 KYVCFACKFYT 22 (103)
Q Consensus 12 ~~~C~~C~~~f 22 (103)
.|+|..||...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 57777777554
No 240
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=35.25 E-value=24 Score=14.18 Aligned_cols=12 Identities=25% Similarity=0.473 Sum_probs=8.7
Q ss_pred CceeeCCCCCcc
Q psy7454 11 YKYVCFACKFYT 22 (103)
Q Consensus 11 ~~~~C~~C~~~f 22 (103)
+.|+|..||...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 368888888655
No 241
>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=35.07 E-value=37 Score=15.18 Aligned_cols=10 Identities=20% Similarity=0.418 Sum_probs=6.2
Q ss_pred eeCCCCCccc
Q psy7454 14 VCFACKFYTY 23 (103)
Q Consensus 14 ~C~~C~~~f~ 23 (103)
.|..|++.|.
T Consensus 4 ~C~~C~~~F~ 13 (57)
T cd00065 4 SCMGCGKPFT 13 (57)
T ss_pred cCcccCcccc
Confidence 4666766664
No 242
>KOG2923|consensus
Probab=34.81 E-value=31 Score=16.57 Aligned_cols=10 Identities=20% Similarity=0.600 Sum_probs=4.1
Q ss_pred CCCeeCCCCC
Q psy7454 67 QKPYPCRYCD 76 (103)
Q Consensus 67 ~~~~~c~~C~ 76 (103)
+....|+.|.
T Consensus 42 e~Va~CpsCS 51 (67)
T KOG2923|consen 42 EDVARCPSCS 51 (67)
T ss_pred CeeecCCCce
Confidence 3333444443
No 243
>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=34.63 E-value=16 Score=20.45 Aligned_cols=18 Identities=33% Similarity=0.693 Sum_probs=13.3
Q ss_pred hcCCCCCeeCCCCCccccC
Q psy7454 63 IHTGQKPYPCRYCDYKARE 81 (103)
Q Consensus 63 ~h~~~~~~~c~~C~~~f~~ 81 (103)
.+.+ ++..|..||..|.-
T Consensus 107 l~~g-~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 107 LHKG-KPQRCPECGQVFKL 124 (136)
T ss_dssp EETT-SEEEETTTEEEEEE
T ss_pred EeCC-CccCCCCCCeEEEE
Confidence 3444 58899999988863
No 244
>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 PF15616 TerY-C: TerY-C metal binding domain
Probab=34.17 E-value=15 Score=20.43 Aligned_cols=13 Identities=23% Similarity=0.815 Sum_probs=8.7
Q ss_pred CCCCeeCCCCCcc
Q psy7454 66 GQKPYPCRYCDYK 78 (103)
Q Consensus 66 ~~~~~~c~~C~~~ 78 (103)
++.-..|++|+..
T Consensus 102 g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 102 GEGEVTCPWCGNE 114 (131)
T ss_pred CCCCEECCCCCCe
Confidence 3445688888864
No 246
>KOG4118|consensus
Probab=33.78 E-value=23 Score=17.10 Aligned_cols=29 Identities=24% Similarity=0.394 Sum_probs=14.7
Q ss_pred eeCCCCCccccCcHHHHHHHHhhCCCCCc
Q psy7454 70 YPCRYCDYKARETQALKVHTKRYHPKMYD 98 (103)
Q Consensus 70 ~~c~~C~~~f~~~~~l~~H~~~~~~~~~~ 98 (103)
+.|.+|.-.-.....+..|.-.-++..|+
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk~~~ 67 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPKEPL 67 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCCCCC
Confidence 45555555555555555555554444443
No 247
>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=33.67 E-value=14 Score=16.25 Aligned_cols=6 Identities=17% Similarity=0.290 Sum_probs=2.9
Q ss_pred CCcccc
Q psy7454 75 CDYKAR 80 (103)
Q Consensus 75 C~~~f~ 80 (103)
||..|.
T Consensus 33 Cg~tfv 38 (47)
T PF04606_consen 33 CGHTFV 38 (47)
T ss_pred CCCEEE
Confidence 555443
No 248
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=32.49 E-value=65 Score=20.58 Aligned_cols=24 Identities=33% Similarity=0.573 Sum_probs=16.9
Q ss_pred CCCeeCCCCCccccCcHHHHHHHH
Q psy7454 67 QKPYPCRYCDYKARETQALKVHTK 90 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~~~~l~~H~~ 90 (103)
..-|.|..|-+-|.....+.+|+.
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHH
Confidence 445777777777777777777766
No 249
>KOG1994|consensus
Probab=32.35 E-value=25 Score=21.51 Aligned_cols=25 Identities=24% Similarity=0.546 Sum_probs=20.5
Q ss_pred CCCCeeCCCCCccccCcHHHHHHHH
Q psy7454 66 GQKPYPCRYCDYKARETQALKVHTK 90 (103)
Q Consensus 66 ~~~~~~c~~C~~~f~~~~~l~~H~~ 90 (103)
....|-|.+||-.|.....|..|=.
T Consensus 236 R~eh~YC~fCG~~y~~~edl~ehCP 260 (268)
T KOG1994|consen 236 RSEHYYCFFCGIKYKDEEDLYEHCP 260 (268)
T ss_pred hccceEEEEeccccCCHHHHHHhCC
Confidence 4567899999999999999887743
No 250
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=31.76 E-value=18 Score=17.51 Aligned_cols=34 Identities=18% Similarity=0.431 Sum_probs=15.5
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCc
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEF 48 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~ 48 (103)
.|+|..|+..-.. .+..+ .-+.|.--..|+.|..
T Consensus 4 ~FTC~~C~~Rs~~--~~sk~-aY~~GvViv~C~gC~~ 37 (66)
T PF05180_consen 4 TFTCNKCGTRSAK--MFSKQ-AYHKGVVIVQCPGCKN 37 (66)
T ss_dssp EEEETTTTEEEEE--EEEHH-HHHTSEEEEE-TTS--
T ss_pred EEEcCCCCCccce--eeCHH-HHhCCeEEEECCCCcc
Confidence 3778888633221 11111 3334555566777764
No 251
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.60 E-value=45 Score=21.07 Aligned_cols=25 Identities=20% Similarity=0.448 Sum_probs=16.1
Q ss_pred CeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccc
Q psy7454 40 PFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKA 79 (103)
Q Consensus 40 ~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f 79 (103)
.|.|+.|...|... |-.|..||-.|
T Consensus 255 GyvCs~Clsi~C~~---------------p~~C~~Cgt~f 279 (279)
T TIGR00627 255 GFVCSVCLSVLCQY---------------TPICKTCKTAF 279 (279)
T ss_pred eEECCCccCCcCCC---------------CCCCCCCCCCC
Confidence 38888887665431 12788887654
No 252
>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=31.49 E-value=21 Score=16.56 Aligned_cols=10 Identities=50% Similarity=0.916 Sum_probs=3.0
Q ss_pred ceeeCCCCCc
Q psy7454 12 KYVCFACKFY 21 (103)
Q Consensus 12 ~~~C~~C~~~ 21 (103)
.|.|+.||.+
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 4788888755
No 253
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=30.94 E-value=28 Score=15.89 Aligned_cols=15 Identities=20% Similarity=0.547 Sum_probs=8.5
Q ss_pred CCCCeeCCCCCcccc
Q psy7454 66 GQKPYPCRYCDYKAR 80 (103)
Q Consensus 66 ~~~~~~c~~C~~~f~ 80 (103)
....+.|.+|++.+.
T Consensus 32 ~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 32 EPIKLRCHYCERIIT 46 (52)
T ss_dssp TTCEEEETTT--EEE
T ss_pred CCCEEEeeCCCCEec
Confidence 445677888877654
No 254
>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=30.92 E-value=8.8 Score=15.38 Aligned_cols=6 Identities=33% Similarity=1.209 Sum_probs=2.3
Q ss_pred ecCCCC
Q psy7454 42 TCNMCE 47 (103)
Q Consensus 42 ~c~~C~ 47 (103)
.|..|+
T Consensus 29 ~C~~C~ 34 (39)
T smart00132 29 KCSKCG 34 (39)
T ss_pred CCcccC
Confidence 333333
No 255
>KOG0978|consensus
Probab=30.49 E-value=24 Score=25.33 Aligned_cols=13 Identities=15% Similarity=0.439 Sum_probs=7.9
Q ss_pred eCCCCCccccCcH
Q psy7454 71 PCRYCDYKARETQ 83 (103)
Q Consensus 71 ~c~~C~~~f~~~~ 83 (103)
+||.|+..|....
T Consensus 680 KCP~Cn~aFganD 692 (698)
T KOG0978|consen 680 KCPKCNAAFGAND 692 (698)
T ss_pred CCCCCCCCCCccc
Confidence 5666666665443
No 256
>PF14369 zf-RING_3: zinc-finger
Probab=30.38 E-value=24 Score=14.56 Aligned_cols=10 Identities=20% Similarity=0.228 Sum_probs=8.2
Q ss_pred eeCCCCCccc
Q psy7454 14 VCFACKFYTY 23 (103)
Q Consensus 14 ~C~~C~~~f~ 23 (103)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999998875
No 257
>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=30.20 E-value=7.2 Score=17.57 Aligned_cols=14 Identities=29% Similarity=0.631 Sum_probs=8.1
Q ss_pred CCeecCCCCccccC
Q psy7454 39 KPFTCNMCEFKCRD 52 (103)
Q Consensus 39 ~~~~c~~C~~~~~~ 52 (103)
.-|.|..|+..+..
T Consensus 25 ~Cf~C~~C~~~l~~ 38 (58)
T PF00412_consen 25 ECFKCSKCGKPLND 38 (58)
T ss_dssp TTSBETTTTCBTTT
T ss_pred cccccCCCCCccCC
Confidence 44566777655443
No 258
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=29.86 E-value=40 Score=19.18 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=5.4
Q ss_pred CCeecCCCCc
Q psy7454 39 KPFTCNMCEF 48 (103)
Q Consensus 39 ~~~~c~~C~~ 48 (103)
....|++||.
T Consensus 31 glv~CP~Cgs 40 (148)
T PF06676_consen 31 GLVSCPVCGS 40 (148)
T ss_pred CCccCCCCCC
Confidence 3445666654
No 259
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=29.82 E-value=22 Score=23.36 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=18.4
Q ss_pred ceeeCCCCCcccCchhHHHHHh
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLG 33 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~ 33 (103)
.+-|+.|++.|.....+..|..
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHh
Confidence 4679999999999888888863
No 260
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=29.80 E-value=40 Score=14.23 Aligned_cols=10 Identities=20% Similarity=0.520 Sum_probs=4.9
Q ss_pred ceeeCCCCCc
Q psy7454 12 KYVCFACKFY 21 (103)
Q Consensus 12 ~~~C~~C~~~ 21 (103)
+..|..|+..
T Consensus 11 ~~~C~~C~~~ 20 (49)
T smart00109 11 PTKCCVCRKS 20 (49)
T ss_pred CCCccccccc
Confidence 3445555543
No 261
>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=29.41 E-value=28 Score=14.67 Aligned_cols=9 Identities=22% Similarity=0.958 Sum_probs=4.5
Q ss_pred eecCCCCcc
Q psy7454 41 FTCNMCEFK 49 (103)
Q Consensus 41 ~~c~~C~~~ 49 (103)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 455555543
No 262
>KOG2272|consensus
Probab=29.20 E-value=66 Score=20.21 Aligned_cols=19 Identities=16% Similarity=0.312 Sum_probs=12.2
Q ss_pred cCCCCCeeCCCCCccccCc
Q psy7454 64 HTGQKPYPCRYCDYKARET 82 (103)
Q Consensus 64 h~~~~~~~c~~C~~~f~~~ 82 (103)
|..-..|.|..|.+.|.-.
T Consensus 216 hWHveHFvCa~CekPFlGH 234 (332)
T KOG2272|consen 216 HWHVEHFVCAKCEKPFLGH 234 (332)
T ss_pred ccchhheeehhcCCcccch
Confidence 4444567788888777643
No 263
>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=29.09 E-value=20 Score=20.51 Aligned_cols=21 Identities=19% Similarity=0.204 Sum_probs=16.5
Q ss_pred CCCCeeCCCCCccccCcHHHH
Q psy7454 66 GQKPYPCRYCDYKARETQALK 86 (103)
Q Consensus 66 ~~~~~~c~~C~~~f~~~~~l~ 86 (103)
-+.|.-|..||+.|+|.....
T Consensus 65 ~~~PsYC~~CGkpyPWt~~~L 85 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPWTENAL 85 (158)
T ss_pred CCCChhHHhCCCCCchHHHHH
Confidence 356788999999999876543
No 264
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=29.06 E-value=33 Score=15.08 Aligned_cols=13 Identities=23% Similarity=0.664 Sum_probs=10.2
Q ss_pred ceeeCCCCCcccC
Q psy7454 12 KYVCFACKFYTYN 24 (103)
Q Consensus 12 ~~~C~~C~~~f~~ 24 (103)
.+.|+.||..+..
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 6889999976654
No 265
>PHA02942 putative transposase; Provisional
Probab=29.06 E-value=39 Score=22.31 Aligned_cols=16 Identities=19% Similarity=0.706 Sum_probs=11.3
Q ss_pred CCCeeCCCCCccccCc
Q psy7454 67 QKPYPCRYCDYKARET 82 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~~ 82 (103)
.+.|.|..||......
T Consensus 340 ~r~f~C~~CG~~~drD 355 (383)
T PHA02942 340 HRYFHCPSCGYENDRD 355 (383)
T ss_pred CCEEECCCCCCEeCcH
Confidence 4568999999765543
No 266
>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=28.55 E-value=39 Score=17.43 Aligned_cols=18 Identities=17% Similarity=0.370 Sum_probs=12.8
Q ss_pred ceeeCCCCCcccCchhHH
Q psy7454 12 KYVCFACKFYTYNTGNIK 29 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~ 29 (103)
...|+.||..+.....+.
T Consensus 35 a~~C~~CGe~y~~dev~~ 52 (89)
T TIGR03829 35 SISCSHCGMEYQDDTTVK 52 (89)
T ss_pred cccccCCCcEeecHHHHH
Confidence 367899998887755543
No 267
>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=27.93 E-value=42 Score=15.00 Aligned_cols=9 Identities=22% Similarity=0.903 Sum_probs=3.4
Q ss_pred CeeCCCCCc
Q psy7454 69 PYPCRYCDY 77 (103)
Q Consensus 69 ~~~c~~C~~ 77 (103)
.|.|+.|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 388888864
No 268
>PRK11032 hypothetical protein; Provisional
Probab=27.66 E-value=48 Score=19.13 Aligned_cols=8 Identities=25% Similarity=1.032 Sum_probs=4.3
Q ss_pred eecCCCCc
Q psy7454 41 FTCNMCEF 48 (103)
Q Consensus 41 ~~c~~C~~ 48 (103)
..|..||.
T Consensus 125 LvC~~Cg~ 132 (160)
T PRK11032 125 LVCEKCHH 132 (160)
T ss_pred EEecCCCC
Confidence 45555553
No 269
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=27.65 E-value=30 Score=15.84 Aligned_cols=10 Identities=30% Similarity=0.870 Sum_probs=6.7
Q ss_pred eCCCCCcccc
Q psy7454 71 PCRYCDYKAR 80 (103)
Q Consensus 71 ~c~~C~~~f~ 80 (103)
.|++||..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 5777876554
No 270
>PLN02748 tRNA dimethylallyltransferase
Probab=27.30 E-value=48 Score=22.67 Aligned_cols=23 Identities=26% Similarity=0.387 Sum_probs=14.8
Q ss_pred ceeeCCCCC-cccCchhHHHHHhh
Q psy7454 12 KYVCFACKF-YTYNTGNIKRHLGM 34 (103)
Q Consensus 12 ~~~C~~C~~-~f~~~~~l~~h~~~ 34 (103)
.|.|.+|+. .+.-......|.+.
T Consensus 418 ~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 418 QYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred cccccCCCCcccCCHHHHHHHhcc
Confidence 467777776 56666666666543
No 271
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=27.11 E-value=15 Score=19.13 Aligned_cols=37 Identities=24% Similarity=0.441 Sum_probs=18.9
Q ss_pred eecCCCCccccCchHHHHHHHHh--cCCCCCeeCCCCCcccc
Q psy7454 41 FTCNMCEFKCRDNRTLKAHHINI--HTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 41 ~~c~~C~~~~~~~~~l~~h~~~~--h~~~~~~~c~~C~~~f~ 80 (103)
..|+.||..-..-..++ .++ -....-|.|..|+..+.
T Consensus 63 ~~Cp~Cg~~~a~f~~~Q---~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 63 VECPKCGHKEAYYWLLQ---TRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred CCCCCCCCCeeEEEEec---cCCCCCCcEEEEEeCCCCCeeE
Confidence 57888885432222221 111 11223588988987543
No 272
>PRK01343 zinc-binding protein; Provisional
Probab=26.40 E-value=62 Score=15.18 Aligned_cols=11 Identities=18% Similarity=0.295 Sum_probs=7.7
Q ss_pred ceeeCCCCCcc
Q psy7454 12 KYVCFACKFYT 22 (103)
Q Consensus 12 ~~~C~~C~~~f 22 (103)
...|+.|++.+
T Consensus 9 ~~~CP~C~k~~ 19 (57)
T PRK01343 9 TRPCPECGKPS 19 (57)
T ss_pred CCcCCCCCCcC
Confidence 45688888765
No 273
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=26.24 E-value=31 Score=19.57 Aligned_cols=13 Identities=15% Similarity=0.294 Sum_probs=10.1
Q ss_pred eeCCCCCccccCc
Q psy7454 70 YPCRYCDYKARET 82 (103)
Q Consensus 70 ~~c~~C~~~f~~~ 82 (103)
-.|..||+.|++-
T Consensus 29 ReC~~C~~RFTTy 41 (147)
T TIGR00244 29 RECLECHERFTTF 41 (147)
T ss_pred ccCCccCCcccee
Confidence 4788899888754
No 274
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=25.50 E-value=36 Score=14.56 Aligned_cols=8 Identities=25% Similarity=0.484 Sum_probs=4.6
Q ss_pred ceeeCCCC
Q psy7454 12 KYVCFACK 19 (103)
Q Consensus 12 ~~~C~~C~ 19 (103)
+..|+.||
T Consensus 2 ~~~Cp~Cg 9 (47)
T PF14690_consen 2 PPRCPHCG 9 (47)
T ss_pred CccCCCcC
Confidence 34566666
No 275
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=25.34 E-value=27 Score=22.25 Aligned_cols=13 Identities=15% Similarity=0.595 Sum_probs=7.5
Q ss_pred eecCCCCccccCc
Q psy7454 41 FTCNMCEFKCRDN 53 (103)
Q Consensus 41 ~~c~~C~~~~~~~ 53 (103)
++|+.|+.-+...
T Consensus 58 ~vcp~c~~h~rlt 70 (296)
T CHL00174 58 NICEQCGYHLKMS 70 (296)
T ss_pred CCCCCCCCCcCCC
Confidence 4666666655443
No 276
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=24.90 E-value=37 Score=15.57 Aligned_cols=10 Identities=20% Similarity=0.162 Sum_probs=5.3
Q ss_pred ceeeCCCCCc
Q psy7454 12 KYVCFACKFY 21 (103)
Q Consensus 12 ~~~C~~C~~~ 21 (103)
..+||.||..
T Consensus 3 LkPCPFCG~~ 12 (61)
T PF14354_consen 3 LKPCPFCGSA 12 (61)
T ss_pred CcCCCCCCCc
Confidence 3456666533
No 277
>KOG3214|consensus
Probab=24.82 E-value=22 Score=18.73 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=6.3
Q ss_pred eecCCCCccccC
Q psy7454 41 FTCNMCEFKCRD 52 (103)
Q Consensus 41 ~~c~~C~~~~~~ 52 (103)
..|.+|+..|..
T Consensus 48 ~sC~iC~esFqt 59 (109)
T KOG3214|consen 48 ASCRICEESFQT 59 (109)
T ss_pred eeeeehhhhhcc
Confidence 345555555544
No 278
>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=24.82 E-value=1.3e+02 Score=17.20 Aligned_cols=11 Identities=18% Similarity=0.624 Sum_probs=5.4
Q ss_pred eecCCCCcccc
Q psy7454 41 FTCNMCEFKCR 51 (103)
Q Consensus 41 ~~c~~C~~~~~ 51 (103)
..|..|+..+.
T Consensus 106 ~~C~~C~~~~~ 116 (178)
T PF02146_consen 106 LRCSKCGKEYD 116 (178)
T ss_dssp EEETTTSBEEE
T ss_pred eeecCCCcccc
Confidence 34555555444
No 279
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=24.59 E-value=36 Score=18.19 Aligned_cols=24 Identities=17% Similarity=0.292 Sum_probs=18.6
Q ss_pred CCceeeCCCCCcccCchhHHHHHh
Q psy7454 10 RYKYVCFACKFYTYNTGNIKRHLG 33 (103)
Q Consensus 10 ~~~~~C~~C~~~f~~~~~l~~h~~ 33 (103)
-..+-|-.|.+.|.+...|..|.+
T Consensus 53 lGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 53 LGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CceeeeehhHHHHHHHHHHHHHhc
Confidence 335778889999988888888864
No 280
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=24.42 E-value=42 Score=19.47 Aligned_cols=45 Identities=11% Similarity=0.208 Sum_probs=23.8
Q ss_pred eecCCCCccccCchHHHHHHHHh-----cCCCCCeeCCCCCccccCcHHHH
Q psy7454 41 FTCNMCEFKCRDNRTLKAHHINI-----HTGQKPYPCRYCDYKARETQALK 86 (103)
Q Consensus 41 ~~c~~C~~~~~~~~~l~~h~~~~-----h~~~~~~~c~~C~~~f~~~~~l~ 86 (103)
-.|+.|+......+.=.-- .+. -..+.-+.|..||+.|=--+...
T Consensus 98 ~RCp~CN~~L~~vs~eev~-~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~ 147 (165)
T COG1656 98 SRCPECNGELEKVSREEVK-EKVPEKVYRNYEEFYRCPKCGKIYWKGSHWR 147 (165)
T ss_pred ccCcccCCEeccCcHHHHh-hccchhhhhcccceeECCCCcccccCchHHH
Confidence 4699998655443321100 000 11234578999999875444443
No 281
>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=24.36 E-value=38 Score=15.88 Aligned_cols=12 Identities=17% Similarity=0.052 Sum_probs=5.4
Q ss_pred eeeCCCCCcccC
Q psy7454 13 YVCFACKFYTYN 24 (103)
Q Consensus 13 ~~C~~C~~~f~~ 24 (103)
..|+.|++.+..
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 468888876543
No 282
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=24.18 E-value=41 Score=15.53 Aligned_cols=23 Identities=17% Similarity=0.364 Sum_probs=14.5
Q ss_pred CCCCCeeCCCCCccccCcHHHHH
Q psy7454 65 TGQKPYPCRYCDYKARETQALKV 87 (103)
Q Consensus 65 ~~~~~~~c~~C~~~f~~~~~l~~ 87 (103)
.+.+.+-|-+||-.|.....|..
T Consensus 23 LR~~~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 23 LREEHNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred HHhhCceeeeeCCccCCHHHHHh
Confidence 34445567777777777666643
No 283
>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=24.15 E-value=30 Score=21.87 Aligned_cols=13 Identities=23% Similarity=0.590 Sum_probs=7.7
Q ss_pred eecCCCCccccCc
Q psy7454 41 FTCNMCEFKCRDN 53 (103)
Q Consensus 41 ~~c~~C~~~~~~~ 53 (103)
++|+.|+.-+...
T Consensus 46 ~vc~~c~~h~rl~ 58 (285)
T TIGR00515 46 EVCPKCDHHMRMD 58 (285)
T ss_pred CCCCCCCCcCcCC
Confidence 4677777655543
No 284
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=23.85 E-value=27 Score=22.30 Aligned_cols=10 Identities=20% Similarity=0.584 Sum_probs=6.5
Q ss_pred eeCCCCCccc
Q psy7454 70 YPCRYCDYKA 79 (103)
Q Consensus 70 ~~c~~C~~~f 79 (103)
|.|..||..+
T Consensus 287 ~~C~~Cg~~w 296 (299)
T TIGR01385 287 VTCEECGNRW 296 (299)
T ss_pred EEcCCCCCee
Confidence 5777777544
No 285
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=23.52 E-value=48 Score=16.18 Aligned_cols=26 Identities=31% Similarity=0.757 Sum_probs=12.6
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccc
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKC 50 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~ 50 (103)
|.| .||+.... ..+.+.-.| .||+..
T Consensus 4 frC-~Cgr~lya----------~e~~kTkkC-~CG~~l 29 (68)
T PF09082_consen 4 FRC-DCGRYLYA----------KEGAKTKKC-VCGKTL 29 (68)
T ss_dssp EEE-TTS--EEE----------ETT-SEEEE-TTTEEE
T ss_pred EEe-cCCCEEEe----------cCCcceeEe-cCCCee
Confidence 567 47755432 233444567 777654
No 286
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=23.35 E-value=75 Score=21.70 Aligned_cols=25 Identities=28% Similarity=0.574 Sum_probs=21.5
Q ss_pred CCCeeCCCCCccccCcHHHHHHHHh
Q psy7454 67 QKPYPCRYCDYKARETQALKVHTKR 91 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~~~~l~~H~~~ 91 (103)
...|.|..|-+-|.....|.+|+..
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhc
Confidence 4568999999999999999999874
No 287
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=22.98 E-value=32 Score=21.84 Aligned_cols=32 Identities=19% Similarity=0.404 Sum_probs=16.9
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccccCc
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKCRDN 53 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~~~~ 53 (103)
.+|+.|+.....+. |. +..++|+.|+.-+...
T Consensus 28 ~~c~~c~~~~~~~~-l~--------~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 28 TKCPSCGQVLYRKE-LE--------ANLNVCPKCGHHMRIS 59 (292)
T ss_pred eECCCccchhhHHH-HH--------hcCCCCCCCCCCeeCC
Confidence 45777765442211 11 1234677887766544
No 288
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.73 E-value=52 Score=21.19 Aligned_cols=11 Identities=18% Similarity=0.443 Sum_probs=8.0
Q ss_pred CceeeCCCCCc
Q psy7454 11 YKYVCFACKFY 21 (103)
Q Consensus 11 ~~~~C~~C~~~ 21 (103)
....|++||..
T Consensus 186 ~~~~CPvCGs~ 196 (309)
T PRK03564 186 QRQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCCc
Confidence 34679999854
No 289
>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=22.41 E-value=36 Score=16.34 Aligned_cols=9 Identities=33% Similarity=0.667 Sum_probs=5.9
Q ss_pred eeeCCCCCc
Q psy7454 13 YVCFACKFY 21 (103)
Q Consensus 13 ~~C~~C~~~ 21 (103)
|.|+.||..
T Consensus 1 y~C~KCg~~ 9 (64)
T PF09855_consen 1 YKCPKCGNE 9 (64)
T ss_pred CCCCCCCCc
Confidence 567777753
No 290
>KOG3277|consensus
Probab=22.28 E-value=56 Score=18.81 Aligned_cols=33 Identities=21% Similarity=0.477 Sum_probs=14.7
Q ss_pred ceeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCC
Q psy7454 12 KYVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCE 47 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~ 47 (103)
.|+|.+|+..-. ..+.. +..+.|.--..|+.|.
T Consensus 79 ~yTCkvCntRs~--ktisk-~AY~~GvVivqC~gC~ 111 (165)
T KOG3277|consen 79 AYTCKVCNTRST--KTISK-QAYEKGVVIVQCPGCK 111 (165)
T ss_pred EEEeeccCCccc--cccCh-hhhhCceEEEECCCCc
Confidence 366777763321 11111 1333444445566664
No 291
>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=22.25 E-value=49 Score=12.89 Aligned_cols=8 Identities=38% Similarity=0.737 Sum_probs=4.1
Q ss_pred eCCCCCcc
Q psy7454 71 PCRYCDYK 78 (103)
Q Consensus 71 ~c~~C~~~ 78 (103)
.|..|++.
T Consensus 2 ~C~~C~~~ 9 (30)
T PF03107_consen 2 WCDVCRRK 9 (30)
T ss_pred CCCCCCCC
Confidence 45555543
No 292
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=22.03 E-value=61 Score=18.91 Aligned_cols=18 Identities=11% Similarity=0.104 Sum_probs=12.1
Q ss_pred ceeeCCCCCcccCchhHH
Q psy7454 12 KYVCFACKFYTYNTGNIK 29 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~ 29 (103)
...|..||+.|.....+.
T Consensus 114 ~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 114 LQRCSRCERPFAPQKTVA 131 (181)
T ss_pred cCcCcccCCccCcHhHHH
Confidence 566888888887654443
No 293
>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=21.88 E-value=88 Score=16.59 Aligned_cols=18 Identities=22% Similarity=0.340 Sum_probs=13.8
Q ss_pred ceeeCCCCCcccCchhHH
Q psy7454 12 KYVCFACKFYTYNTGNIK 29 (103)
Q Consensus 12 ~~~C~~C~~~f~~~~~l~ 29 (103)
.+.|+.||..+.......
T Consensus 31 ~~~C~~CGe~~~~~e~~~ 48 (127)
T TIGR03830 31 GWYCPACGEELLDPEESK 48 (127)
T ss_pred eeECCCCCCEEEcHHHHH
Confidence 478999999888765544
No 294
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=21.81 E-value=25 Score=16.27 Aligned_cols=26 Identities=19% Similarity=0.408 Sum_probs=17.5
Q ss_pred eeeCCCCCcccCchhHHHHHhhcCCCCCeecCCCCccc
Q psy7454 13 YVCFACKFYTYNTGNIKRHLGMHLGEKPFTCNMCEFKC 50 (103)
Q Consensus 13 ~~C~~C~~~f~~~~~l~~h~~~h~~~~~~~c~~C~~~~ 50 (103)
-.|+.||..|.. +.-...|+.|+..+
T Consensus 6 ~~C~~Cg~~~~~------------~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 6 CKCPVCGKKFKD------------GDDIVVCPECGAPY 31 (54)
T ss_pred ccChhhCCcccC------------CCCEEECCCCCCcc
Confidence 478889877743 23445788888654
No 295
>KOG3352|consensus
Probab=21.70 E-value=48 Score=18.92 Aligned_cols=13 Identities=15% Similarity=0.368 Sum_probs=10.2
Q ss_pred CCeeCCCCCcccc
Q psy7454 68 KPYPCRYCDYKAR 80 (103)
Q Consensus 68 ~~~~c~~C~~~f~ 80 (103)
+...|.+||..|.
T Consensus 132 e~~rc~eCG~~fk 144 (153)
T KOG3352|consen 132 ETQRCPECGHYFK 144 (153)
T ss_pred CcccCCcccceEE
Confidence 4567999998876
No 296
>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=21.70 E-value=86 Score=13.15 Aligned_cols=10 Identities=20% Similarity=0.750 Sum_probs=2.3
Q ss_pred eecCCCCccc
Q psy7454 41 FTCNMCEFKC 50 (103)
Q Consensus 41 ~~c~~C~~~~ 50 (103)
|-|+.|...+
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 3445554433
No 297
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=21.67 E-value=49 Score=14.35 Aligned_cols=10 Identities=20% Similarity=0.597 Sum_probs=4.4
Q ss_pred eeCCCCCccc
Q psy7454 70 YPCRYCDYKA 79 (103)
Q Consensus 70 ~~c~~C~~~f 79 (103)
|.|..|+.++
T Consensus 12 ~~CL~C~~~~ 21 (50)
T smart00290 12 WLCLTCGQVG 21 (50)
T ss_pred EEecCCCCcc
Confidence 4444444433
No 298
>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=21.56 E-value=31 Score=20.60 Aligned_cols=23 Identities=22% Similarity=0.560 Sum_probs=0.0
Q ss_pred CceeeCCCCCccc-CchhHHHHHh
Q psy7454 11 YKYVCFACKFYTY-NTGNIKRHLG 33 (103)
Q Consensus 11 ~~~~C~~C~~~f~-~~~~l~~h~~ 33 (103)
..|.|.+||.... -+..+..|..
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp ------------------------
T ss_pred CeeeeEeCCCcceecHHHHHHhcC
Confidence 3599999996544 4677777754
No 299
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=21.52 E-value=92 Score=19.98 Aligned_cols=24 Identities=13% Similarity=0.076 Sum_probs=17.0
Q ss_pred CCCCceeeCCCCCcccCchhHHHH
Q psy7454 8 AYRYKYVCFACKFYTYNTGNIKRH 31 (103)
Q Consensus 8 ~~~~~~~C~~C~~~f~~~~~l~~h 31 (103)
++....+|..||..|.-...+.+|
T Consensus 271 T~~~~ik~n~c~~~~~~e~~~~~H 294 (306)
T COG5539 271 TASPSIKCNICGTGFVGEKDYYAH 294 (306)
T ss_pred cCCceEEeeccccccchhhHHHHH
Confidence 344457788888888776666666
No 300
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=21.43 E-value=42 Score=19.63 Aligned_cols=12 Identities=17% Similarity=0.312 Sum_probs=4.9
Q ss_pred eecCCCCccccC
Q psy7454 41 FTCNMCEFKCRD 52 (103)
Q Consensus 41 ~~c~~C~~~~~~ 52 (103)
-.|..|+..|..
T Consensus 135 ~~C~~C~~~fv~ 146 (175)
T PF05280_consen 135 APCRRCGGHFVT 146 (175)
T ss_dssp EE-TTT--EEEE
T ss_pred cCCCCCCCCeEC
Confidence 356666655543
No 301
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=21.35 E-value=43 Score=19.18 Aligned_cols=13 Identities=15% Similarity=0.286 Sum_probs=9.9
Q ss_pred eeCCCCCccccCc
Q psy7454 70 YPCRYCDYKARET 82 (103)
Q Consensus 70 ~~c~~C~~~f~~~ 82 (103)
-.|..||..|++-
T Consensus 29 ReC~~C~~RFTTf 41 (156)
T COG1327 29 RECLECGERFTTF 41 (156)
T ss_pred hcccccccccchh
Confidence 4788899888753
No 302
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=21.10 E-value=49 Score=14.76 Aligned_cols=9 Identities=22% Similarity=0.268 Sum_probs=4.4
Q ss_pred eCCCCCccc
Q psy7454 15 CFACKFYTY 23 (103)
Q Consensus 15 C~~C~~~f~ 23 (103)
|+.||..|.
T Consensus 1 CP~Cg~~f~ 9 (50)
T PF14375_consen 1 CPRCGAPFE 9 (50)
T ss_pred CCCCCCcCC
Confidence 445555443
No 303
>KOG3014|consensus
Probab=21.09 E-value=84 Score=19.66 Aligned_cols=23 Identities=22% Similarity=0.229 Sum_probs=13.0
Q ss_pred eeCCCCCcccCc--hhHHHHHhhcC
Q psy7454 14 VCFACKFYTYNT--GNIKRHLGMHL 36 (103)
Q Consensus 14 ~C~~C~~~f~~~--~~l~~h~~~h~ 36 (103)
.|..||..+... ..-..|.+.|.
T Consensus 39 ~C~~Cgm~Yt~~s~EDe~~H~~fH~ 63 (257)
T KOG3014|consen 39 KCKECGMKYTVTSPEDEALHEKFHN 63 (257)
T ss_pred ehhhcCceecCCCHHHHHHHHHHHH
Confidence 577777665542 33455666554
No 304
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.92 E-value=1e+02 Score=21.54 Aligned_cols=25 Identities=24% Similarity=0.210 Sum_probs=21.7
Q ss_pred CCCeeCCCCCccccCcHHHHHHHHh
Q psy7454 67 QKPYPCRYCDYKARETQALKVHTKR 91 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~~~~l~~H~~~ 91 (103)
...|.|..|-+-|.....|.+|+..
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhc
Confidence 4568999999999999999999874
No 305
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=20.81 E-value=85 Score=20.48 Aligned_cols=45 Identities=18% Similarity=0.353 Sum_probs=27.5
Q ss_pred CCCCCeecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCccccCcHH
Q psy7454 36 LGEKPFTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKARETQA 84 (103)
Q Consensus 36 ~~~~~~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~~~~~ 84 (103)
+.+.|-.-..||-.....+ |. +.+..|...|+|++|.......+.
T Consensus 347 t~ENpP~ml~CgHVIskea-l~---~LS~nG~~~FKCPYCP~~~~~~~~ 391 (396)
T COG5109 347 TDENPPVMLECGHVISKEA-LS---VLSQNGVLSFKCPYCPEMSKYENI 391 (396)
T ss_pred cccCCCeeeeccceeeHHH-HH---HHhhcCcEEeeCCCCCcchhhhhh
Confidence 3455545566886654443 32 345667778999999865544433
No 306
>PRK06260 threonine synthase; Validated
Probab=20.68 E-value=1.1e+02 Score=20.22 Aligned_cols=10 Identities=20% Similarity=0.444 Sum_probs=5.6
Q ss_pred eeeCCCCCcc
Q psy7454 13 YVCFACKFYT 22 (103)
Q Consensus 13 ~~C~~C~~~f 22 (103)
+.|..||..|
T Consensus 4 ~~C~~cg~~~ 13 (397)
T PRK06260 4 LKCIECGKEY 13 (397)
T ss_pred EEECCCCCCC
Confidence 4566666554
No 307
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.59 E-value=49 Score=17.62 Aligned_cols=13 Identities=15% Similarity=0.102 Sum_probs=9.1
Q ss_pred ceeeCCCCCcccC
Q psy7454 12 KYVCFACKFYTYN 24 (103)
Q Consensus 12 ~~~C~~C~~~f~~ 24 (103)
...||.||..|..
T Consensus 49 ~t~CP~Cg~~~e~ 61 (115)
T COG1885 49 STSCPKCGEPFES 61 (115)
T ss_pred cccCCCCCCccce
Confidence 4678888876643
No 308
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=20.58 E-value=1.1e+02 Score=19.02 Aligned_cols=35 Identities=17% Similarity=0.346 Sum_probs=19.5
Q ss_pred eecCCCCccccCchHHHHHHHHhcCCCCCeeCCCCCcccc
Q psy7454 41 FTCNMCEFKCRDNRTLKAHHINIHTGQKPYPCRYCDYKAR 80 (103)
Q Consensus 41 ~~c~~C~~~~~~~~~l~~h~~~~h~~~~~~~c~~C~~~f~ 80 (103)
-.|..|...... ....- ++. +...-.|+.||+.-.
T Consensus 198 ~~C~GC~m~l~~--~~~~~-V~~--~d~iv~CP~CgRILy 232 (239)
T COG1579 198 RVCGGCHMKLPS--QTLSK-VRK--KDEIVFCPYCGRILY 232 (239)
T ss_pred CcccCCeeeecH--HHHHH-Hhc--CCCCccCCccchHHH
Confidence 357777654433 33332 333 444557999997543
No 309
>PLN03239 histone acetyltransferase; Provisional
Probab=20.24 E-value=79 Score=20.82 Aligned_cols=25 Identities=12% Similarity=0.110 Sum_probs=21.8
Q ss_pred CCCeeCCCCCccccCcHHHHHHHHh
Q psy7454 67 QKPYPCRYCDYKARETQALKVHTKR 91 (103)
Q Consensus 67 ~~~~~c~~C~~~f~~~~~l~~H~~~ 91 (103)
...|.|..|-+-|.....|.+|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 4679999999999999999999764
No 310
>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=20.15 E-value=48 Score=23.13 Aligned_cols=12 Identities=17% Similarity=0.105 Sum_probs=7.2
Q ss_pred eeeCCCCCcccC
Q psy7454 13 YVCFACKFYTYN 24 (103)
Q Consensus 13 ~~C~~C~~~f~~ 24 (103)
.+|+.||..+..
T Consensus 201 vpCPhCg~~~~l 212 (557)
T PF05876_consen 201 VPCPHCGEEQVL 212 (557)
T ss_pred ccCCCCCCCccc
Confidence 457777765543
Done!