Query psy14147
Match_columns 100
No_of_seqs 128 out of 1414
Neff 11.3
Searched_HMMs 46136
Date Fri Aug 16 20:41:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14147.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14147hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2.3E-28 5E-33 139.6 0.8 93 3-98 164-256 (279)
2 KOG2462|consensus 99.9 6.1E-26 1.3E-30 129.8 1.2 95 3-100 133-230 (279)
3 KOG3623|consensus 99.8 3.1E-19 6.6E-24 113.5 3.0 74 26-100 892-965 (1007)
4 KOG3576|consensus 99.7 3.4E-19 7.3E-24 98.8 1.7 92 2-94 119-221 (267)
5 KOG1074|consensus 99.7 1.4E-18 3E-23 111.6 2.0 46 3-48 356-401 (958)
6 KOG3623|consensus 99.7 3.2E-17 7E-22 104.6 4.8 97 3-100 213-324 (1007)
7 KOG3576|consensus 99.6 4E-17 8.8E-22 90.6 0.5 73 26-99 115-187 (267)
8 KOG3608|consensus 99.3 5.5E-13 1.2E-17 79.7 2.7 92 3-97 210-304 (467)
9 PHA02768 hypothetical protein; 99.3 1.4E-12 3.1E-17 58.5 2.9 41 57-99 5-45 (55)
10 PHA00733 hypothetical protein 99.3 1.1E-12 2.5E-17 69.4 2.3 83 14-98 26-112 (128)
11 PF13465 zf-H2C2_2: Zinc-finge 99.3 6.2E-12 1.3E-16 48.8 2.6 26 72-97 1-26 (26)
12 KOG3608|consensus 99.3 9.7E-12 2.1E-16 74.5 4.5 85 3-90 240-324 (467)
13 KOG1074|consensus 99.2 2E-12 4.3E-17 84.1 0.3 90 7-97 612-721 (958)
14 PLN03086 PRLI-interacting fact 99.2 1.9E-11 4.1E-16 77.7 3.1 88 3-97 456-553 (567)
15 PHA00733 hypothetical protein 99.1 1.5E-10 3.3E-15 61.4 4.8 65 14-82 60-124 (128)
16 PHA02768 hypothetical protein; 99.0 9.8E-11 2.1E-15 52.6 1.6 42 29-73 6-47 (55)
17 PF13465 zf-H2C2_2: Zinc-finge 99.0 1.3E-10 2.8E-15 45.1 0.2 24 16-39 2-25 (26)
18 PHA00616 hypothetical protein 98.8 2.2E-09 4.8E-14 46.1 1.8 33 57-89 1-33 (44)
19 PLN03086 PRLI-interacting fact 98.8 8.8E-09 1.9E-13 66.0 4.8 65 26-96 451-515 (567)
20 PHA00732 hypothetical protein 98.6 4E-08 8.6E-13 47.9 2.7 49 28-82 1-49 (79)
21 PHA00732 hypothetical protein 98.6 4.5E-08 9.9E-13 47.7 2.1 33 4-39 5-38 (79)
22 PHA00616 hypothetical protein 98.5 6E-08 1.3E-12 41.7 2.0 36 28-64 1-36 (44)
23 PF05605 zf-Di19: Drought indu 98.3 1.6E-06 3.4E-11 39.4 3.7 51 28-81 2-53 (54)
24 KOG3993|consensus 98.2 2.6E-07 5.6E-12 57.1 -0.6 69 29-98 268-369 (500)
25 KOG3993|consensus 98.1 2.1E-06 4.6E-11 53.2 2.7 79 2-81 269-380 (500)
26 PF00096 zf-C2H2: Zinc finger, 98.0 4.5E-06 9.6E-11 31.0 1.4 21 29-49 1-21 (23)
27 PF00096 zf-C2H2: Zinc finger, 98.0 4.4E-06 9.5E-11 31.1 1.4 23 58-80 1-23 (23)
28 PF13912 zf-C2H2_6: C2H2-type 97.8 1.1E-05 2.4E-10 31.1 1.4 21 28-48 1-21 (27)
29 PF13894 zf-C2H2_4: C2H2-type 97.8 1.6E-05 3.5E-10 29.5 1.9 21 29-49 1-21 (24)
30 PF13912 zf-C2H2_6: C2H2-type 97.8 1.3E-05 2.8E-10 31.0 1.4 26 57-82 1-26 (27)
31 PRK04860 hypothetical protein; 97.8 1.5E-05 3.3E-10 43.9 2.2 37 57-97 119-155 (160)
32 COG5189 SFP1 Putative transcri 97.8 7.1E-06 1.5E-10 49.4 0.6 63 26-98 347-411 (423)
33 PF13894 zf-C2H2_4: C2H2-type 97.8 2.3E-05 4.9E-10 29.1 1.8 24 58-81 1-24 (24)
34 PF12756 zf-C2H2_2: C2H2 type 97.7 3E-05 6.5E-10 39.1 2.2 71 4-80 3-73 (100)
35 COG5189 SFP1 Putative transcri 97.7 2.6E-05 5.7E-10 47.0 1.9 25 54-78 346-372 (423)
36 PF09237 GAGA: GAGA factor; I 97.6 8.2E-05 1.8E-09 32.9 2.4 32 54-85 21-52 (54)
37 smart00355 ZnF_C2H2 zinc finge 97.3 0.00032 6.8E-09 26.2 2.3 19 30-48 2-20 (26)
38 PF05605 zf-Di19: Drought indu 97.2 0.00053 1.2E-08 31.0 2.7 39 57-96 2-42 (54)
39 smart00355 ZnF_C2H2 zinc finge 97.1 0.00054 1.2E-08 25.5 1.7 24 58-81 1-24 (26)
40 PF09237 GAGA: GAGA factor; I 97.0 0.0012 2.6E-08 29.3 2.7 33 24-57 20-52 (54)
41 PF12874 zf-met: Zinc-finger o 97.0 0.00046 9.9E-09 25.9 1.1 20 29-48 1-20 (25)
42 PF12874 zf-met: Zinc-finger o 96.8 0.00082 1.8E-08 25.2 1.3 23 58-80 1-23 (25)
43 PRK04860 hypothetical protein; 96.7 0.0012 2.5E-08 36.6 2.0 38 28-70 119-156 (160)
44 PF13909 zf-H2C2_5: C2H2-type 96.3 0.0026 5.6E-08 23.6 1.3 19 29-48 1-19 (24)
45 PF12756 zf-C2H2_2: C2H2 type 96.3 0.0051 1.1E-07 30.9 2.5 23 27-49 49-71 (100)
46 PF12171 zf-C2H2_jaz: Zinc-fin 96.1 0.0019 4.1E-08 24.8 0.3 20 29-48 2-21 (27)
47 cd00350 rubredoxin_like Rubred 95.9 0.0048 1E-07 24.9 1.1 8 85-92 17-24 (33)
48 smart00451 ZnF_U1 U1-like zinc 95.3 0.015 3.3E-07 23.5 1.6 21 28-48 3-23 (35)
49 PF13913 zf-C2HC_2: zinc-finge 95.2 0.023 5E-07 21.4 1.8 18 59-77 4-21 (25)
50 KOG1146|consensus 94.9 0.027 5.9E-07 40.4 2.6 71 9-79 445-540 (1406)
51 COG4049 Uncharacterized protei 94.3 0.044 9.6E-07 24.8 1.7 29 21-49 10-38 (65)
52 PF09538 FYDLN_acid: Protein o 93.4 0.082 1.8E-06 27.5 2.1 13 57-69 26-38 (108)
53 COG2888 Predicted Zn-ribbon RN 93.2 0.053 1.1E-06 24.9 1.1 33 55-92 25-57 (61)
54 PF13719 zinc_ribbon_5: zinc-r 93.2 0.095 2.1E-06 21.7 1.8 32 59-95 4-35 (37)
55 cd00729 rubredoxin_SM Rubredox 93.0 0.056 1.2E-06 22.0 0.9 8 29-36 3-10 (34)
56 COG5048 FOG: Zn-finger [Genera 92.6 0.022 4.7E-07 35.7 -0.9 63 27-89 288-355 (467)
57 PF13717 zinc_ribbon_4: zinc-r 92.4 0.15 3.3E-06 21.0 1.8 32 59-95 4-35 (36)
58 KOG2893|consensus 92.4 0.03 6.4E-07 33.1 -0.4 42 30-76 12-53 (341)
59 TIGR02098 MJ0042_CXXC MJ0042 f 92.2 0.13 2.8E-06 21.2 1.6 11 85-95 25-35 (38)
60 TIGR00622 ssl1 transcription f 92.2 0.14 3E-06 26.8 1.9 66 27-96 14-92 (112)
61 COG1592 Rubrerythrin [Energy p 92.1 0.09 1.9E-06 29.4 1.3 10 55-64 147-156 (166)
62 PRK00464 nrdR transcriptional 91.9 0.025 5.4E-07 31.2 -1.0 11 58-68 29-39 (154)
63 PF07754 DUF1610: Domain of un 91.3 0.099 2.2E-06 19.5 0.6 10 84-93 15-24 (24)
64 PF09986 DUF2225: Uncharacteri 90.5 0.028 6.1E-07 32.7 -1.8 22 26-47 3-24 (214)
65 smart00659 RPOLCX RNA polymera 90.1 0.24 5.3E-06 21.4 1.4 10 29-38 3-12 (44)
66 TIGR00373 conserved hypothetic 90.0 0.54 1.2E-05 26.2 3.0 12 57-68 109-120 (158)
67 KOG2186|consensus 89.5 0.26 5.7E-06 29.4 1.6 52 28-83 3-54 (276)
68 PF15135 UPF0515: Uncharacteri 89.4 0.38 8.2E-06 28.7 2.2 57 26-96 110-166 (278)
69 smart00531 TFIIE Transcription 89.4 0.76 1.6E-05 25.2 3.3 13 56-68 98-110 (147)
70 COG5048 FOG: Zn-finger [Genera 89.0 0.18 4E-06 31.6 0.8 44 56-99 288-337 (467)
71 PRK09678 DNA-binding transcrip 88.9 0.084 1.8E-06 25.4 -0.6 9 30-38 3-11 (72)
72 KOG4173|consensus 88.4 0.63 1.4E-05 27.1 2.6 70 6-78 87-167 (253)
73 PRK06266 transcription initiat 88.3 0.88 1.9E-05 25.9 3.1 16 26-41 115-130 (178)
74 KOG2186|consensus 88.3 0.36 7.9E-06 28.9 1.6 43 13-58 15-57 (276)
75 KOG2893|consensus 88.1 0.08 1.7E-06 31.3 -1.1 44 6-53 16-59 (341)
76 TIGR02300 FYDLN_acid conserved 87.8 0.47 1E-05 25.4 1.7 30 29-70 10-39 (129)
77 PF14353 CpXC: CpXC protein 87.3 0.72 1.6E-05 24.5 2.3 8 31-38 4-11 (128)
78 PRK14890 putative Zn-ribbon RN 87.1 0.24 5.3E-06 22.8 0.4 34 55-93 23-56 (59)
79 PF10571 UPF0547: Uncharacteri 86.8 0.35 7.6E-06 18.4 0.7 10 87-96 16-25 (26)
80 KOG1146|consensus 86.8 0.59 1.3E-05 34.3 2.2 48 2-49 467-539 (1406)
81 smart00834 CxxC_CXXC_SSSS Puta 86.5 0.36 7.8E-06 20.1 0.7 11 86-96 6-16 (41)
82 PF13451 zf-trcl: Probable zin 85.7 0.62 1.3E-05 20.7 1.3 36 27-64 3-40 (49)
83 PHA00626 hypothetical protein 85.4 0.58 1.3E-05 21.3 1.1 15 83-97 21-35 (59)
84 PF09723 Zn-ribbon_8: Zinc rib 85.0 0.46 1E-05 20.2 0.7 11 86-96 6-16 (42)
85 COG1997 RPL43A Ribosomal prote 84.9 0.4 8.7E-06 23.9 0.5 12 85-96 53-64 (89)
86 PLN02294 cytochrome c oxidase 83.6 0.64 1.4E-05 26.2 1.0 14 83-96 139-152 (174)
87 smart00734 ZnF_Rad18 Rad18-lik 83.1 1.3 2.8E-05 16.7 1.5 19 59-78 3-21 (26)
88 PF12760 Zn_Tnp_IS1595: Transp 83.1 1.2 2.5E-05 19.3 1.6 29 56-93 17-45 (46)
89 KOG3408|consensus 82.9 0.92 2E-05 24.1 1.4 27 53-79 53-79 (129)
90 smart00154 ZnF_AN1 AN1-like Zi 82.8 0.75 1.6E-05 19.2 0.9 12 85-96 12-23 (39)
91 PF12907 zf-met2: Zinc-binding 82.6 0.65 1.4E-05 19.7 0.6 24 29-52 2-28 (40)
92 PRK03824 hypA hydrogenase nick 82.2 0.43 9.3E-06 25.9 0.0 13 57-69 70-82 (135)
93 cd00924 Cyt_c_Oxidase_Vb Cytoc 81.5 0.86 1.9E-05 23.3 1.0 17 79-96 74-90 (97)
94 COG1996 RPC10 DNA-directed RNA 81.5 0.86 1.9E-05 20.2 0.9 11 28-38 6-16 (49)
95 KOG2785|consensus 81.4 2.3 4.9E-05 27.2 2.9 51 27-78 165-241 (390)
96 TIGR02605 CxxC_CxxC_SSSS putat 81.1 0.8 1.7E-05 20.2 0.7 11 86-96 6-16 (52)
97 PF01428 zf-AN1: AN1-like Zinc 79.4 0.68 1.5E-05 19.7 0.2 12 84-95 12-23 (43)
98 PF05191 ADK_lid: Adenylate ki 79.2 0.5 1.1E-05 19.4 -0.3 8 31-38 4-11 (36)
99 PF06524 NOA36: NOA36 protein; 77.2 3 6.4E-05 25.4 2.4 72 23-95 137-219 (314)
100 PF08274 PhnA_Zn_Ribbon: PhnA 77.1 1.2 2.5E-05 17.6 0.5 12 83-94 17-28 (30)
101 COG2331 Uncharacterized protei 76.7 2 4.2E-05 20.9 1.3 32 28-67 12-43 (82)
102 PF09845 DUF2072: Zn-ribbon co 75.9 1.4 3.1E-05 23.7 0.8 15 28-42 1-15 (131)
103 PF05443 ROS_MUCR: ROS/MUCR tr 75.7 1.7 3.7E-05 23.5 1.1 25 58-85 73-97 (132)
104 PRK00398 rpoP DNA-directed RNA 75.7 1.5 3.3E-05 18.9 0.8 11 85-95 3-13 (46)
105 PF01286 XPA_N: XPA protein N- 75.7 1.5 3.3E-05 17.8 0.7 13 86-98 4-16 (34)
106 TIGR01206 lysW lysine biosynth 74.8 2 4.3E-05 19.5 1.0 10 29-38 3-12 (54)
107 PF02892 zf-BED: BED zinc fing 74.7 3.3 7.2E-05 17.5 1.7 23 26-48 14-40 (45)
108 PF04780 DUF629: Protein of un 73.5 2.8 6E-05 27.7 1.8 29 27-55 56-84 (466)
109 PF08790 zf-LYAR: LYAR-type C2 73.1 1.8 3.9E-05 16.8 0.6 11 86-96 1-11 (28)
110 COG0068 HypF Hydrogenase matur 72.7 0.61 1.3E-05 32.1 -1.3 56 30-93 125-181 (750)
111 KOG2593|consensus 72.3 6.8 0.00015 25.6 3.2 38 54-94 125-162 (436)
112 PF07282 OrfB_Zn_ribbon: Putat 72.3 3 6.5E-05 19.5 1.4 11 84-94 45-55 (69)
113 KOG4167|consensus 72.2 2 4.4E-05 29.9 1.0 23 3-25 795-817 (907)
114 COG3677 Transposase and inacti 71.6 2 4.4E-05 23.1 0.8 15 83-97 51-65 (129)
115 PF09963 DUF2197: Uncharacteri 71.5 1.5 3.2E-05 20.0 0.2 36 30-65 4-39 (56)
116 smart00614 ZnF_BED BED zinc fi 70.6 4.8 0.0001 17.6 1.8 8 71-78 37-44 (50)
117 PF04423 Rad50_zn_hook: Rad50 70.5 1.9 4.1E-05 19.3 0.4 10 87-96 22-31 (54)
118 PF01215 COX5B: Cytochrome c o 70.2 1.6 3.4E-05 23.8 0.2 17 79-96 107-123 (136)
119 PF10013 DUF2256: Uncharacteri 69.6 2.3 4.9E-05 18.2 0.5 11 87-97 10-20 (42)
120 PF12013 DUF3505: Protein of u 69.2 4.8 0.0001 20.8 1.8 25 58-82 81-109 (109)
121 PF03604 DNA_RNApol_7kD: DNA d 68.8 3.6 7.8E-05 16.4 1.0 11 86-96 1-11 (32)
122 PRK12380 hydrogenase nickel in 68.2 2.7 5.9E-05 22.0 0.8 25 57-93 70-94 (113)
123 KOG1842|consensus 67.9 4.6 9.9E-05 26.5 1.8 29 27-55 14-42 (505)
124 COG3091 SprT Zn-dependent meta 67.8 2.5 5.3E-05 23.5 0.6 35 56-95 116-150 (156)
125 PTZ00043 cytochrome c oxidase 67.6 2.9 6.4E-05 24.8 0.9 16 81-96 177-192 (268)
126 KOG2785|consensus 67.3 7.1 0.00015 25.1 2.5 23 56-78 67-89 (390)
127 PF01363 FYVE: FYVE zinc finge 66.8 3.7 7.9E-05 19.2 1.0 8 31-38 12-19 (69)
128 TIGR00100 hypA hydrogenase nic 66.7 2.5 5.4E-05 22.2 0.5 26 57-94 70-95 (115)
129 PF04959 ARS2: Arsenite-resist 66.2 4.7 0.0001 23.8 1.5 29 25-53 74-102 (214)
130 PF10276 zf-CHCC: Zinc-finger 64.6 3 6.6E-05 17.6 0.5 12 84-95 28-39 (40)
131 PF13824 zf-Mss51: Zinc-finger 63.4 6.1 0.00013 18.0 1.3 15 53-67 10-24 (55)
132 KOG4167|consensus 62.6 1.9 4.2E-05 29.9 -0.5 25 57-81 792-816 (907)
133 COG1571 Predicted DNA-binding 62.5 6 0.00013 25.8 1.6 12 57-68 367-378 (421)
134 PF02891 zf-MIZ: MIZ/SP-RING z 62.1 2.8 6E-05 18.5 0.1 8 86-93 42-49 (50)
135 PF08792 A2L_zn_ribbon: A2L zi 61.8 4.7 0.0001 16.2 0.8 11 86-96 22-32 (33)
136 KOG2807|consensus 61.7 13 0.00029 23.5 2.9 22 27-48 289-310 (378)
137 PF13878 zf-C2H2_3: zinc-finge 61.3 11 0.00023 15.9 1.8 22 59-80 15-38 (41)
138 PF10083 DUF2321: Uncharacteri 61.0 3.9 8.4E-05 22.8 0.6 16 82-97 65-80 (158)
139 COG3357 Predicted transcriptio 60.6 4.2 9.2E-05 20.5 0.6 14 84-97 57-70 (97)
140 COG4338 Uncharacterized protei 60.3 3.3 7.2E-05 18.2 0.2 16 59-74 14-29 (54)
141 smart00064 FYVE Protein presen 59.0 6.4 0.00014 18.3 1.1 11 29-39 11-21 (68)
142 PRK00564 hypA hydrogenase nick 58.9 3.9 8.5E-05 21.6 0.4 12 57-68 71-82 (117)
143 PRK14873 primosome assembly pr 58.8 7 0.00015 27.1 1.6 10 85-94 422-431 (665)
144 cd00065 FYVE FYVE domain; Zinc 58.4 8.6 0.00019 17.0 1.4 10 30-39 4-13 (57)
145 COG1198 PriA Primosomal protei 58.1 3.1 6.7E-05 29.1 -0.1 15 80-94 470-484 (730)
146 PRK00432 30S ribosomal protein 57.7 6.3 0.00014 17.5 0.9 12 84-95 36-47 (50)
147 PF02176 zf-TRAF: TRAF-type zi 56.7 6.9 0.00015 17.5 0.9 6 43-48 25-30 (60)
148 PF01155 HypA: Hydrogenase exp 56.5 3.8 8.3E-05 21.5 0.1 13 58-70 71-83 (113)
149 PF01096 TFIIS_C: Transcriptio 56.4 5.3 0.00011 16.6 0.5 10 86-95 29-38 (39)
150 COG4391 Uncharacterized protei 56.2 5 0.00011 18.7 0.4 43 50-96 17-59 (62)
151 PRK03681 hypA hydrogenase nick 54.5 4 8.6E-05 21.5 -0.0 11 57-67 70-80 (114)
152 KOG2482|consensus 54.3 7.2 0.00016 24.8 1.0 21 29-49 196-216 (423)
153 PF14369 zf-RING_3: zinc-finge 53.7 6.5 0.00014 16.0 0.5 9 87-95 23-31 (35)
154 smart00440 ZnF_C2C2 C2C2 Zinc 53.4 8 0.00017 16.2 0.8 11 86-96 29-39 (40)
155 PF04606 Ogr_Delta: Ogr/Delta- 53.3 2.2 4.7E-05 18.6 -1.0 13 84-96 24-38 (47)
156 PF01927 Mut7-C: Mut7-C RNAse 52.3 7.4 0.00016 21.3 0.8 39 58-96 92-135 (147)
157 KOG3352|consensus 52.3 7 0.00015 21.7 0.6 14 83-96 131-144 (153)
158 PF13240 zinc_ribbon_2: zinc-r 51.1 11 0.00025 13.6 1.0 7 87-93 15-21 (23)
159 PF14311 DUF4379: Domain of un 50.5 12 0.00026 16.7 1.2 10 58-67 29-38 (55)
160 PF11672 DUF3268: Protein of u 50.5 7.8 0.00017 20.1 0.6 9 28-36 2-10 (102)
161 PF08271 TF_Zn_Ribbon: TFIIB z 50.4 9 0.00019 16.1 0.7 7 87-93 2-8 (43)
162 COG1675 TFA1 Transcription ini 50.0 28 0.00061 20.0 2.8 49 8-66 93-141 (176)
163 TIGR00244 transcriptional regu 49.7 7.6 0.00016 21.5 0.5 12 86-97 29-40 (147)
164 PF08209 Sgf11: Sgf11 (transcr 49.5 8.3 0.00018 15.5 0.5 12 85-96 4-15 (33)
165 PF06220 zf-U1: U1 zinc finger 49.0 11 0.00025 15.6 0.9 13 85-97 3-15 (38)
166 PF00301 Rubredoxin: Rubredoxi 49.0 9.6 0.00021 16.7 0.7 10 86-95 2-11 (47)
167 KOG3507|consensus 48.6 9.3 0.0002 17.6 0.6 26 29-66 21-46 (62)
168 PF14787 zf-CCHC_5: GAG-polypr 48.5 9.3 0.0002 15.8 0.6 11 87-97 4-14 (36)
169 COG0675 Transposase and inacti 48.3 11 0.00024 23.2 1.2 11 84-94 321-331 (364)
170 COG4530 Uncharacterized protei 48.2 9.6 0.00021 20.0 0.7 27 59-96 11-37 (129)
171 PF10263 SprT-like: SprT-like 48.1 5 0.00011 22.0 -0.3 32 57-96 123-154 (157)
172 KOG4727|consensus 48.0 10 0.00022 21.7 0.8 20 29-48 76-95 (193)
173 PF06397 Desulfoferrod_N: Desu 47.9 9.5 0.00021 15.7 0.6 11 84-94 5-15 (36)
174 TIGR03831 YgiT_finger YgiT-typ 47.6 9.1 0.0002 16.0 0.6 10 86-95 33-42 (46)
175 COG1326 Uncharacterized archae 47.3 23 0.00051 20.7 2.2 11 57-67 30-40 (201)
176 COG5112 UFD2 U1-like Zn-finger 47.3 11 0.00023 19.7 0.8 25 54-78 52-76 (126)
177 COG1327 Predicted transcriptio 47.3 8.5 0.00019 21.5 0.5 12 86-97 29-40 (156)
178 PRK00420 hypothetical protein; 46.7 17 0.00037 19.2 1.6 9 58-66 41-49 (112)
179 KOG1280|consensus 46.3 21 0.00046 22.8 2.1 38 27-64 78-116 (381)
180 PRK01343 zinc-binding protein; 44.7 13 0.00029 17.1 0.8 11 86-96 10-20 (57)
181 PRK00762 hypA hydrogenase nick 44.1 7.8 0.00017 20.7 0.1 12 57-69 70-81 (124)
182 PF14690 zf-ISL3: zinc-finger 43.7 12 0.00027 15.8 0.7 10 85-94 2-11 (47)
183 PRK05978 hypothetical protein; 43.4 7.4 0.00016 21.6 -0.1 12 86-97 53-64 (148)
184 KOG2231|consensus 43.3 43 0.00094 23.6 3.3 19 30-48 184-202 (669)
185 KOG2231|consensus 43.2 40 0.00086 23.8 3.1 23 59-81 184-206 (669)
186 PF03966 Trm112p: Trm112p-like 42.3 11 0.00024 17.7 0.4 17 80-96 48-64 (68)
187 TIGR00627 tfb4 transcription f 42.2 20 0.00042 22.2 1.5 9 87-95 271-279 (279)
188 PF04438 zf-HIT: HIT zinc fing 42.0 15 0.00032 14.3 0.7 11 85-95 13-23 (30)
189 PF12773 DZR: Double zinc ribb 41.4 25 0.00054 15.1 1.5 9 86-94 30-38 (50)
190 COG4896 Uncharacterized protei 41.3 13 0.00029 17.3 0.6 13 53-65 27-39 (68)
191 PF05495 zf-CHY: CHY zinc fing 41.1 9.6 0.00021 18.2 0.1 31 57-95 41-71 (71)
192 PF14446 Prok-RING_1: Prokaryo 40.5 14 0.00029 16.8 0.5 10 87-96 7-16 (54)
193 PF01780 Ribosomal_L37ae: Ribo 40.2 12 0.00027 18.9 0.4 30 57-96 35-64 (90)
194 PF02591 DUF164: Putative zinc 39.6 39 0.00084 15.1 2.0 31 59-93 24-54 (56)
195 PRK04023 DNA polymerase II lar 39.5 23 0.0005 26.2 1.7 11 27-37 625-635 (1121)
196 PF07975 C1_4: TFIIH C1-like d 39.4 8.2 0.00018 17.3 -0.3 26 26-52 19-44 (51)
197 PF03811 Zn_Tnp_IS1: InsA N-te 39.3 6.1 0.00013 16.2 -0.6 16 76-91 20-35 (36)
198 KOG2907|consensus 38.9 18 0.0004 19.1 0.9 39 58-98 75-115 (116)
199 PF13248 zf-ribbon_3: zinc-rib 38.7 11 0.00024 14.0 0.1 6 88-93 19-24 (26)
200 COG5151 SSL1 RNA polymerase II 38.6 45 0.00097 21.2 2.6 22 57-78 388-409 (421)
201 PF11789 zf-Nse: Zinc-finger o 38.4 16 0.00035 16.6 0.6 30 57-90 24-53 (57)
202 PF04810 zf-Sec23_Sec24: Sec23 38.2 15 0.00032 15.3 0.5 12 54-65 21-32 (40)
203 KOG1088|consensus 38.0 19 0.00041 19.2 0.9 19 79-97 92-110 (124)
204 KOG2071|consensus 38.0 19 0.00041 24.7 1.1 28 25-53 415-442 (579)
205 COG4957 Predicted transcriptio 37.9 17 0.00038 19.9 0.8 24 59-85 78-101 (148)
206 KOG2636|consensus 37.0 21 0.00046 23.7 1.2 27 22-48 395-422 (497)
207 cd00974 DSRD Desulforedoxin (D 36.9 20 0.00043 14.2 0.7 12 84-95 3-14 (34)
208 COG1656 Uncharacterized conser 36.7 18 0.0004 20.5 0.8 37 58-96 98-141 (165)
209 PRK04351 hypothetical protein; 35.8 12 0.00025 20.8 -0.1 31 58-96 113-143 (149)
210 TIGR00595 priA primosomal prot 35.4 9.8 0.00021 25.5 -0.5 11 83-93 251-261 (505)
211 TIGR00319 desulf_FeS4 desulfof 35.4 22 0.00047 14.1 0.7 12 84-95 6-17 (34)
212 PF07295 DUF1451: Protein of u 35.2 22 0.00047 19.7 0.9 9 57-65 112-120 (146)
213 PF10537 WAC_Acf1_DNA_bd: ATP- 35.2 39 0.00085 17.5 1.8 36 28-65 3-38 (102)
214 TIGR00280 L37a ribosomal prote 34.8 20 0.00044 18.2 0.7 30 57-96 35-64 (91)
215 COG4888 Uncharacterized Zn rib 34.6 21 0.00046 18.5 0.8 12 83-94 20-31 (104)
216 COG5236 Uncharacterized conser 34.2 55 0.0012 21.2 2.6 19 31-49 223-241 (493)
217 PF02748 PyrI_C: Aspartate car 34.1 20 0.00044 16.0 0.6 15 82-96 32-46 (52)
218 PF14447 Prok-RING_4: Prokaryo 34.1 27 0.00059 15.9 1.0 10 87-96 41-50 (55)
219 COG5432 RAD18 RING-finger-cont 34.0 23 0.0005 22.2 0.9 13 52-65 55-67 (391)
220 PF11931 DUF3449: Domain of un 33.7 14 0.0003 21.6 0.0 26 23-48 96-122 (196)
221 PRK05580 primosome assembly pr 33.7 11 0.00025 26.1 -0.4 13 81-93 417-429 (679)
222 COG2093 DNA-directed RNA polym 32.8 24 0.00052 16.6 0.7 8 87-94 20-27 (64)
223 COG2879 Uncharacterized small 32.8 61 0.0013 15.3 2.0 19 38-57 22-40 (65)
224 PF10164 DUF2367: Uncharacteri 32.5 25 0.00054 18.1 0.8 12 84-95 87-98 (98)
225 KOG1409|consensus 32.3 15 0.00032 23.6 -0.0 39 58-97 283-321 (404)
226 smart00731 SprT SprT homologue 31.8 21 0.00045 19.5 0.5 33 57-96 112-144 (146)
227 PTZ00255 60S ribosomal protein 31.2 26 0.00055 17.8 0.7 30 57-96 36-65 (90)
228 KOG0782|consensus 31.1 5.9 0.00013 27.1 -1.9 27 43-70 240-266 (1004)
229 PRK08222 hydrogenase 4 subunit 30.8 18 0.00038 20.7 0.1 16 83-98 112-127 (181)
230 KOG0717|consensus 30.5 32 0.00069 23.1 1.2 21 58-78 293-313 (508)
231 PRK03976 rpl37ae 50S ribosomal 30.2 27 0.00058 17.7 0.7 30 57-96 36-65 (90)
232 TIGR00143 hypF [NiFe] hydrogen 29.8 5.6 0.00012 27.8 -2.3 9 84-92 139-147 (711)
233 KOG1994|consensus 29.7 31 0.00066 20.8 1.0 25 54-78 236-260 (268)
234 COG1885 Uncharacterized protei 29.7 27 0.00058 18.2 0.6 11 86-96 50-60 (115)
235 COG1579 Zn-ribbon protein, pos 29.6 56 0.0012 19.8 2.0 14 82-95 218-231 (239)
236 COG1545 Predicted nucleic-acid 29.5 25 0.00055 19.2 0.6 10 86-95 30-39 (140)
237 COG4306 Uncharacterized protei 29.4 26 0.00057 18.9 0.6 15 83-97 66-80 (160)
238 PF05741 zf-nanos: Nanos RNA b 29.4 19 0.00041 16.4 0.1 8 86-93 34-41 (55)
239 PF05290 Baculo_IE-1: Baculovi 29.2 32 0.0007 18.9 0.9 13 87-99 123-135 (140)
240 smart00661 RPOL9 RNA polymeras 29.2 36 0.00078 14.6 1.0 11 85-95 20-30 (52)
241 cd01410 SIRT7 SIRT7: Eukaryoti 29.1 91 0.002 18.3 2.8 12 57-68 95-106 (206)
242 COG1773 Rubredoxin [Energy pro 28.8 20 0.00044 16.3 0.1 12 28-39 3-14 (55)
243 cd04476 RPA1_DBD_C RPA1_DBD_C: 28.5 31 0.00067 19.2 0.8 12 84-95 50-61 (166)
244 PF05129 Elf1: Transcription e 28.3 27 0.00059 17.2 0.5 10 83-92 20-29 (81)
245 PF02146 SIR2: Sir2 family; I 28.0 55 0.0012 18.5 1.8 12 58-69 106-117 (178)
246 PF15269 zf-C2H2_7: Zinc-finge 27.9 38 0.00083 14.7 0.9 21 29-49 21-41 (54)
247 smart00132 LIM Zinc-binding do 27.8 30 0.00064 13.4 0.5 9 86-94 28-36 (39)
248 PRK07218 replication factor A; 27.6 36 0.00078 22.5 1.1 10 58-67 298-307 (423)
249 PF10058 DUF2296: Predicted in 27.4 34 0.00073 15.4 0.7 11 83-93 42-52 (54)
250 PLN02748 tRNA dimethylallyltra 27.3 48 0.001 22.3 1.6 24 56-79 417-441 (468)
251 PF12591 DUF3762: Protein of u 27.3 34 0.00074 16.3 0.7 11 89-99 70-80 (80)
252 PF11023 DUF2614: Protein of u 26.9 33 0.00071 18.2 0.7 13 83-95 67-79 (114)
253 KOG2857|consensus 26.8 32 0.00069 19.1 0.6 23 56-78 16-38 (157)
254 COG3364 Zn-ribbon containing p 26.4 36 0.00079 17.7 0.8 14 28-41 2-15 (112)
255 COG3024 Uncharacterized protei 26.4 32 0.00069 16.2 0.5 12 86-97 8-19 (65)
256 PF11494 Ta0938: Ta0938; Inte 26.4 25 0.00055 18.0 0.2 38 25-69 11-49 (105)
257 PF14952 zf-tcix: Putative tre 26.3 31 0.00067 14.9 0.4 8 87-94 13-20 (44)
258 PF03119 DNA_ligase_ZBD: NAD-d 26.3 31 0.00067 13.2 0.4 8 87-94 1-8 (28)
259 TIGR00686 phnA alkylphosphonat 25.8 36 0.00077 17.9 0.7 12 85-96 19-30 (109)
260 PRK08270 anaerobic ribonucleos 25.6 43 0.00093 23.5 1.2 10 85-94 639-648 (656)
261 PHA02942 putative transposase; 25.4 55 0.0012 21.3 1.6 13 83-95 340-352 (383)
262 COG0846 SIR2 NAD-dependent pro 25.0 40 0.00086 20.6 0.9 12 57-68 122-133 (250)
263 PHA02998 RNA polymerase subuni 24.9 42 0.00092 19.4 0.9 12 86-97 172-183 (195)
264 cd00730 rubredoxin Rubredoxin; 24.6 24 0.00051 15.7 -0.1 11 29-39 2-12 (50)
265 cd01413 SIR2_Af2 SIR2_Af2: Arc 24.3 79 0.0017 18.7 2.0 13 57-69 113-125 (222)
266 KOG0978|consensus 24.3 37 0.00081 24.0 0.7 13 85-97 678-690 (698)
267 PF10609 ParA: ParA/MinD ATPas 24.0 37 0.00081 16.8 0.6 10 86-95 66-75 (81)
268 PRK03922 hypothetical protein; 23.7 43 0.00094 17.7 0.8 10 87-96 51-60 (113)
269 COG1655 Uncharacterized protei 23.5 35 0.00076 20.7 0.5 12 85-96 19-30 (267)
270 COG3880 Modulator of heat shoc 23.4 17 0.00036 20.8 -0.8 30 29-69 75-104 (176)
271 KOG4118|consensus 23.3 70 0.0015 15.2 1.3 23 58-80 39-61 (74)
272 PF15227 zf-C3HC4_4: zinc fing 23.0 78 0.0017 13.2 1.8 6 86-91 37-42 (42)
273 COG1594 RPB9 DNA-directed RNA 22.5 42 0.00092 17.7 0.6 12 85-96 100-111 (113)
274 cd01675 RNR_III Class III ribo 22.2 65 0.0014 22.1 1.5 9 85-93 532-540 (555)
275 PRK10220 hypothetical protein; 22.0 53 0.0011 17.4 0.9 12 85-96 20-31 (111)
276 PRK06260 threonine synthase; V 22.0 54 0.0012 21.3 1.1 31 29-72 4-34 (397)
277 TIGR03830 CxxCG_CxxCG_HTH puta 21.6 47 0.001 17.3 0.7 11 86-96 32-42 (127)
278 PTZ00303 phosphatidylinositol 21.5 69 0.0015 23.5 1.6 11 30-40 462-472 (1374)
279 PRK14138 NAD-dependent deacety 21.4 92 0.002 18.8 1.9 13 57-69 119-131 (244)
280 COG5188 PRP9 Splicing factor 3 21.4 54 0.0012 21.3 1.0 22 57-78 238-259 (470)
281 PF05265 DUF723: Protein of un 21.2 1.1E+02 0.0024 14.3 1.7 28 58-92 33-60 (60)
282 PTZ00409 Sir2 (Silent Informat 20.9 1.4E+02 0.0029 18.5 2.6 13 57-69 137-149 (271)
283 PF11793 FANCL_C: FANCL C-term 20.9 1.2E+02 0.0025 14.4 2.0 39 58-97 21-67 (70)
284 KOG3456|consensus 20.9 46 0.001 17.5 0.5 14 84-97 103-116 (120)
285 PRK12496 hypothetical protein; 20.9 53 0.0011 18.5 0.8 12 85-96 127-138 (164)
286 PF12677 DUF3797: Domain of un 20.7 45 0.00098 14.8 0.4 9 86-94 14-22 (49)
287 TIGR00515 accD acetyl-CoA carb 20.6 51 0.0011 20.5 0.8 12 58-69 46-57 (285)
288 PF13005 zf-IS66: zinc-finger 20.4 52 0.0011 13.9 0.6 10 87-96 4-13 (47)
289 PF13901 DUF4206: Domain of un 20.4 39 0.00084 19.7 0.2 9 56-64 151-159 (202)
290 PF10367 Vps39_2: Vacuolar sor 20.4 56 0.0012 16.3 0.8 11 87-97 80-90 (109)
291 PF13408 Zn_ribbon_recom: Reco 20.2 49 0.0011 14.4 0.5 11 86-96 6-16 (58)
292 PTZ00448 hypothetical protein; 20.2 91 0.002 20.4 1.8 23 57-79 314-336 (373)
293 COG5152 Uncharacterized conser 20.1 45 0.00098 19.7 0.5 16 83-98 194-209 (259)
No 1
>KOG2462|consensus
Probab=99.94 E-value=2.3e-28 Score=139.59 Aligned_cols=93 Identities=25% Similarity=0.473 Sum_probs=86.2
Q ss_pred cchHHHHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcCC
Q psy14147 3 VRSREVMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDN 82 (100)
Q Consensus 3 ~~~~~~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 82 (100)
++.||+.+.+-.+|+.|+++|. -+.+|.+||+.|.+..-|+.|++ .|+|++||.|+.|+++|..+++|..|+++|.+
T Consensus 164 C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiR-THTGEKPF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 164 CKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIR-THTGEKPFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred CCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccc-cccCCCCccCCcccchhcchHHHHHHHHhhcC
Confidence 6778899999999999999986 46899999999999999999995 99999999999999999999999999999999
Q ss_pred CCCeecCCCccccCCC
Q psy14147 83 TPRFKCKLCPKMFTNT 98 (100)
Q Consensus 83 ~~~~~C~~C~~~f~~~ 98 (100)
.++|+|+.|+|.|+.+
T Consensus 241 ~K~~qC~~C~KsFsl~ 256 (279)
T KOG2462|consen 241 VKKHQCPRCGKSFALK 256 (279)
T ss_pred CccccCcchhhHHHHH
Confidence 9999999999999754
No 2
>KOG2462|consensus
Probab=99.91 E-value=6.1e-26 Score=129.76 Aligned_cols=95 Identities=22% Similarity=0.378 Sum_probs=87.6
Q ss_pred cchHHHHHHHHHHHHhccccccC---CCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHh
Q psy14147 3 VRSREVMEIQKDVVQSFPIILYC---VKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQR 79 (100)
Q Consensus 3 ~~~~~~~~~~~~~l~~h~~~~~~---~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 79 (100)
+.+||+++.+.++|.+|..+|.. .+.+.|..|++.|.....|..|++ +|+ .+.+|.+||+.|..++-|+.|+|+
T Consensus 133 c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHir-TH~--l~c~C~iCGKaFSRPWLLQGHiRT 209 (279)
T KOG2462|consen 133 CPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIR-THT--LPCECGICGKAFSRPWLLQGHIRT 209 (279)
T ss_pred ccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhh-ccC--CCcccccccccccchHHhhccccc
Confidence 56789999999999999999874 677999999999999999999995 665 689999999999999999999999
Q ss_pred cCCCCCeecCCCccccCCCCC
Q psy14147 80 HDNTPRFKCKLCPKMFTNTVS 100 (100)
Q Consensus 80 ~~~~~~~~C~~C~~~f~~~~s 100 (100)
|||||||.|+.|+|+|++.|+
T Consensus 210 HTGEKPF~C~hC~kAFADRSN 230 (279)
T KOG2462|consen 210 HTGEKPFSCPHCGKAFADRSN 230 (279)
T ss_pred ccCCCCccCCcccchhcchHH
Confidence 999999999999999998764
No 3
>KOG3623|consensus
Probab=99.76 E-value=3.1e-19 Score=113.55 Aligned_cols=74 Identities=38% Similarity=0.694 Sum_probs=69.6
Q ss_pred CCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcCCCCCeecCCCccccCCCCC
Q psy14147 26 VKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFTNTVS 100 (100)
Q Consensus 26 ~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~s 100 (100)
..+|.|+.|++.|.-.+.|.+|. ..|+|.+||+|.+|.++|...-.|..|.|.|.||+||+|..|+|.|+..+|
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHK-YEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGS 965 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHK-YEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGS 965 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhh-hhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccc
Confidence 46799999999999999999999 599999999999999999999999999999999999999999999997654
No 4
>KOG3576|consensus
Probab=99.75 E-value=3.4e-19 Score=98.75 Aligned_cols=92 Identities=26% Similarity=0.410 Sum_probs=84.0
Q ss_pred ccchHHHHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcC
Q psy14147 2 VVRSREVMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHD 81 (100)
Q Consensus 2 ~~~~~~~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~ 81 (100)
+++.|++.|..+..|.+|++.|...+.+-|..||+.|....+|..|++ .|+|.+||.|..|+++|.+.-.|..|++.-+
T Consensus 119 tCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~r-thtgvrpykc~~c~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 119 TCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTR-THTGVRPYKCSLCEKAFTQRCSLESHLKKVH 197 (267)
T ss_pred eeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhc-cccCccccchhhhhHHHHhhccHHHHHHHHc
Confidence 488999999999999999999999999999999999999999999995 9999999999999999999999999987433
Q ss_pred -----------CCCCeecCCCccc
Q psy14147 82 -----------NTPRFKCKLCPKM 94 (100)
Q Consensus 82 -----------~~~~~~C~~C~~~ 94 (100)
.++.|.|.+||..
T Consensus 198 gv~~~yaykerr~kl~vcedcg~t 221 (267)
T KOG3576|consen 198 GVQHQYAYKERRAKLYVCEDCGYT 221 (267)
T ss_pred CchHHHHHHHhhhheeeecccCCC
Confidence 2467899999854
No 5
>KOG1074|consensus
Probab=99.72 E-value=1.4e-18 Score=111.64 Aligned_cols=46 Identities=22% Similarity=0.290 Sum_probs=43.7
Q ss_pred cchHHHHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHH
Q psy14147 3 VRSREVMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQ 48 (100)
Q Consensus 3 ~~~~~~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~ 48 (100)
+|-|.++|-..+.|+.|.++|.+++||+|++||..|.++.+|..|.
T Consensus 356 Cr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~ 401 (958)
T KOG1074|consen 356 CRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHF 401 (958)
T ss_pred hhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeee
Confidence 6789999999999999999999999999999999999999998876
No 6
>KOG3623|consensus
Probab=99.69 E-value=3.2e-17 Score=104.57 Aligned_cols=97 Identities=20% Similarity=0.314 Sum_probs=82.0
Q ss_pred cchHHHHHHHHHHHHhcccccc--CCCceeCchhhhhccChhHHHHHHhhhcCC-------------CCCccCccccccc
Q psy14147 3 VRSREVMEIQKDVVQSFPIILY--CVKPYACEECGKAFRKKFSLTMHQRHVHLN-------------DRRYQCDLCLARF 67 (100)
Q Consensus 3 ~~~~~~~~~~~~~l~~h~~~~~--~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~-------------~~~~~c~~c~~~~ 67 (100)
+.-|+..+.....|+.|++..+ .+..|.|..|..+|.++..|..|+ ..|.. -+.|.|.+|+++|
T Consensus 213 cpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm-~~hkpg~dqa~sltqsa~lRKFKCtECgKAF 291 (1007)
T KOG3623|consen 213 CPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHM-QLHKPGGDQAISLTQSALLRKFKCTECGKAF 291 (1007)
T ss_pred chhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHH-HhhcCCCcccccccchhhhccccccccchhh
Confidence 4456777778889999986543 244589999999999999999999 57753 2458999999999
Q ss_pred cChhHHHHHHHhcCCCCCeecCCCccccCCCCC
Q psy14147 68 VTNSSLIVHKQRHDNTPRFKCKLCPKMFTNTVS 100 (100)
Q Consensus 68 ~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~s 100 (100)
...-.|..|+|.|.||+||.|+.|+|.|+..+|
T Consensus 292 KfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGS 324 (1007)
T KOG3623|consen 292 KFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGS 324 (1007)
T ss_pred hhHHHHHhhheeecCCCCcCCcccccccccCCc
Confidence 999999999999999999999999999987654
No 7
>KOG3576|consensus
Probab=99.63 E-value=4e-17 Score=90.61 Aligned_cols=73 Identities=30% Similarity=0.617 Sum_probs=67.8
Q ss_pred CCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcCCCCCeecCCCccccCCCC
Q psy14147 26 VKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFTNTV 99 (100)
Q Consensus 26 ~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~ 99 (100)
...|.|.+|++.|....-|..|++ .|...+.+.|..||++|...-+|.+|.++|+|.+||+|..|+|+|+...
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~k-ch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrc 187 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLK-CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRC 187 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhh-hccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhc
Confidence 455999999999999999999994 8998899999999999999999999999999999999999999998653
No 8
>KOG3608|consensus
Probab=99.35 E-value=5.5e-13 Score=79.72 Aligned_cols=92 Identities=24% Similarity=0.373 Sum_probs=51.3
Q ss_pred cchHHHHHHHHHHHHhccccc--cCCCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHH-h
Q psy14147 3 VRSREVMEIQKDVVQSFPIIL--YCVKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQ-R 79 (100)
Q Consensus 3 ~~~~~~~~~~~~~l~~h~~~~--~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~-~ 79 (100)
+..+|.+|..+.-|..|.+.- -...+|.|..|-+.|.+...|..|+. .|. .-|.|+.|..+...++.|..|++ .
T Consensus 210 Cp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~-rHv--n~ykCplCdmtc~~~ssL~~H~r~r 286 (467)
T KOG3608|consen 210 CPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVV-RHV--NCYKCPLCDMTCSSASSLTTHIRYR 286 (467)
T ss_pred cchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHH-Hhh--hcccccccccCCCChHHHHHHHHhh
Confidence 344444444444444443321 12334555555555555544555542 332 24667777777777777777777 3
Q ss_pred cCCCCCeecCCCccccCC
Q psy14147 80 HDNTPRFKCKLCPKMFTN 97 (100)
Q Consensus 80 ~~~~~~~~C~~C~~~f~~ 97 (100)
|...+||+|..|.+.|.+
T Consensus 287 Hs~dkpfKCd~Cd~~c~~ 304 (467)
T KOG3608|consen 287 HSKDKPFKCDECDTRCVR 304 (467)
T ss_pred hccCCCccccchhhhhcc
Confidence 556778888887776654
No 9
>PHA02768 hypothetical protein; Provisional
Probab=99.33 E-value=1.4e-12 Score=58.53 Aligned_cols=41 Identities=24% Similarity=0.598 Sum_probs=29.9
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCccccCCCC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFTNTV 99 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~ 99 (100)
.|.|+.||+.|.....|..|++.|+ +|++|..|++.|...+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s 45 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTG 45 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccc
Confidence 4677777777777777777777777 5777777777776554
No 10
>PHA00733 hypothetical protein
Probab=99.31 E-value=1.1e-12 Score=69.39 Aligned_cols=83 Identities=20% Similarity=0.244 Sum_probs=56.0
Q ss_pred HHHHhccccccCCCceeCchhhhhccChhHHHHHH--h--hhcCCCCCccCccccccccChhHHHHHHHhcCCCCCeecC
Q psy14147 14 DVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQ--R--HVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCK 89 (100)
Q Consensus 14 ~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~--~--~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~ 89 (100)
+.|.++-.....++++.|.+|.+.|.....|..+. . ..+.+..||.|..|++.|.....|..|.+.+ +.+|.|+
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~ 103 (128)
T PHA00733 26 EELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCP 103 (128)
T ss_pred HHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCC
Confidence 33444333334467788888888777666555541 0 1233467888888888888888888888865 3568888
Q ss_pred CCccccCCC
Q psy14147 90 LCPKMFTNT 98 (100)
Q Consensus 90 ~C~~~f~~~ 98 (100)
.|++.|.+.
T Consensus 104 ~CgK~F~~~ 112 (128)
T PHA00733 104 VCGKEFRNT 112 (128)
T ss_pred CCCCccCCH
Confidence 888888764
No 11
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.26 E-value=6.2e-12 Score=48.83 Aligned_cols=26 Identities=35% Similarity=0.698 Sum_probs=23.0
Q ss_pred HHHHHHHhcCCCCCeecCCCccccCC
Q psy14147 72 SLIVHKQRHDNTPRFKCKLCPKMFTN 97 (100)
Q Consensus 72 ~l~~h~~~~~~~~~~~C~~C~~~f~~ 97 (100)
+|..|++.|++++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47889999999999999999999874
No 12
>KOG3608|consensus
Probab=99.26 E-value=9.7e-12 Score=74.51 Aligned_cols=85 Identities=26% Similarity=0.399 Sum_probs=60.5
Q ss_pred cchHHHHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcCC
Q psy14147 3 VRSREVMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDN 82 (100)
Q Consensus 3 ~~~~~~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 82 (100)
+.-+-+.|.++..|..|++.|- .-|.|+.|+.+.+..++|..|++..|...+||.|..|...+...++|+.|...|.
T Consensus 240 C~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS- 316 (467)
T KOG3608|consen 240 CAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS- 316 (467)
T ss_pred HHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-
Confidence 3456778888888888887764 3477777777777777777777766777777777777777777777777776665
Q ss_pred CCCeecCC
Q psy14147 83 TPRFKCKL 90 (100)
Q Consensus 83 ~~~~~C~~ 90 (100)
+-.|.|..
T Consensus 317 ~~~y~C~h 324 (467)
T KOG3608|consen 317 KTVYQCEH 324 (467)
T ss_pred ccceecCC
Confidence 34455543
No 13
>KOG1074|consensus
Probab=99.22 E-value=2e-12 Score=84.08 Aligned_cols=90 Identities=24% Similarity=0.448 Sum_probs=70.3
Q ss_pred HHHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcCCCC----CccCc---cccccccChhHHHHHHHh
Q psy14147 7 EVMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHLNDR----RYQCD---LCLARFVTNSSLIVHKQR 79 (100)
Q Consensus 7 ~~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~----~~~c~---~c~~~~~~~~~l~~h~~~ 79 (100)
-++..=++.|+.|.++|.+++||+|.+||++|.++.+|..|+ ..|.... .+.|+ +|.+.|...-.|..|.+.
T Consensus 612 ~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~-~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQhIri 690 (958)
T KOG1074|consen 612 LRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHM-SVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQHIRI 690 (958)
T ss_pred eecccchhhhhhhhhcccCcCccccccccchhccccchhhcc-cccccCccccccccCCchhhhcccccccccccceEEe
Confidence 344455688999999999999999999999999999999999 5776543 36788 888889888889999998
Q ss_pred cCCC-CC------------eecCCCccccCC
Q psy14147 80 HDNT-PR------------FKCKLCPKMFTN 97 (100)
Q Consensus 80 ~~~~-~~------------~~C~~C~~~f~~ 97 (100)
|.+. .+ -+|..|.+.|.+
T Consensus 691 H~~~~~s~g~~a~e~~~~adq~~~~qk~~~~ 721 (958)
T KOG1074|consen 691 HLGGQISNGGTAAEGILAADQCSSCQKTFSD 721 (958)
T ss_pred ecCCCCCCCcccccccchhcccchhhhcccc
Confidence 8732 11 357777777643
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.17 E-value=1.9e-11 Score=77.73 Aligned_cols=88 Identities=15% Similarity=0.253 Sum_probs=70.4
Q ss_pred cchHHHHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccC----------hhH
Q psy14147 3 VRSREVMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVT----------NSS 72 (100)
Q Consensus 3 ~~~~~~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~----------~~~ 72 (100)
+..|+..|. ...|..|+..++ +++.|+ |+..+ ....|..|+ ..|.+.+++.|+.|+..+.. ...
T Consensus 456 C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~-~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~ 529 (567)
T PLN03086 456 CEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQ-ASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRG 529 (567)
T ss_pred CCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhh-hccCCCCceeCCCCCCccccCccccchhhhhhh
Confidence 455677775 577899998874 789999 99755 568899998 48888999999999988742 347
Q ss_pred HHHHHHhcCCCCCeecCCCccccCC
Q psy14147 73 LIVHKQRHDNTPRFKCKLCPKMFTN 97 (100)
Q Consensus 73 l~~h~~~~~~~~~~~C~~C~~~f~~ 97 (100)
|..|.... |.+++.|..||+.+..
T Consensus 530 Lt~HE~~C-G~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 530 MSEHESIC-GSRTAPCDSCGRSVML 553 (567)
T ss_pred HHHHHHhc-CCcceEccccCCeeee
Confidence 88888875 8899999999998764
No 15
>PHA00733 hypothetical protein
Probab=99.13 E-value=1.5e-10 Score=61.37 Aligned_cols=65 Identities=25% Similarity=0.433 Sum_probs=53.5
Q ss_pred HHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcCC
Q psy14147 14 DVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDN 82 (100)
Q Consensus 14 ~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 82 (100)
+.|.+|+..+ +.+||.|+.|++.|.....|..|++ .+ ..++.|..|+++|.....|..|....++
T Consensus 60 ~~l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r-~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 60 SYLYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIR-YT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HHHHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHh-cC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3455565554 4889999999999999999999984 54 3579999999999999999999886554
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.04 E-value=9.8e-11 Score=52.65 Aligned_cols=42 Identities=24% Similarity=0.461 Sum_probs=36.9
Q ss_pred eeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHH
Q psy14147 29 YACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSL 73 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l 73 (100)
|.|+.||+.|.....|..|++ .|. +++.|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r-~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLR-KHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHH-hcC--CcccCCcccceeccccee
Confidence 789999999999999999995 787 688999999999876554
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=98.95 E-value=1.3e-10 Score=45.05 Aligned_cols=24 Identities=33% Similarity=0.634 Sum_probs=13.6
Q ss_pred HHhccccccCCCceeCchhhhhcc
Q psy14147 16 VQSFPIILYCVKPYACEECGKAFR 39 (100)
Q Consensus 16 l~~h~~~~~~~~~~~c~~C~~~f~ 39 (100)
|..|+++|.+++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 455555555555555555555553
No 18
>PHA00616 hypothetical protein
Probab=98.83 E-value=2.2e-09 Score=46.12 Aligned_cols=33 Identities=21% Similarity=0.348 Sum_probs=17.6
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCK 89 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~ 89 (100)
||+|+.||+.|...+.+..|++.|++++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 345555555555555555555555555555443
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.81 E-value=8.8e-09 Score=65.96 Aligned_cols=65 Identities=23% Similarity=0.544 Sum_probs=55.0
Q ss_pred CCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 26 VKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 26 ~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
++.+.|..|++.|. ...|..|+. .+. .++.|+ |+..+ ....|..|+..|..++|+.|+.|++.|.
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~-~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMK-VFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHH-hcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccc
Confidence 35578999999996 577999995 553 689999 99755 6689999999999999999999999884
No 20
>PHA00732 hypothetical protein
Probab=98.61 E-value=4e-08 Score=47.91 Aligned_cols=49 Identities=24% Similarity=0.453 Sum_probs=37.8
Q ss_pred ceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcCC
Q psy14147 28 PYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDN 82 (100)
Q Consensus 28 ~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~ 82 (100)
||.|..|++.|.....|..|++..|. ++.|+.|++.|.. +..|.++..+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhcccCC
Confidence 57899999999999999999842354 3579999999874 6678765443
No 21
>PHA00732 hypothetical protein
Probab=98.56 E-value=4.5e-08 Score=47.71 Aligned_cols=33 Identities=12% Similarity=0.162 Sum_probs=17.9
Q ss_pred chHHHHHHHHHHHHhcccc-ccCCCceeCchhhhhcc
Q psy14147 4 RSREVMEIQKDVVQSFPII-LYCVKPYACEECGKAFR 39 (100)
Q Consensus 4 ~~~~~~~~~~~~l~~h~~~-~~~~~~~~c~~C~~~f~ 39 (100)
..++..|.....|..|++. |. ++.|+.|++.|.
T Consensus 5 ~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~ 38 (79)
T PHA00732 5 PICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR 38 (79)
T ss_pred CCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC
Confidence 4455556666666666553 32 235666666655
No 22
>PHA00616 hypothetical protein
Probab=98.54 E-value=6e-08 Score=41.72 Aligned_cols=36 Identities=25% Similarity=0.437 Sum_probs=31.2
Q ss_pred ceeCchhhhhccChhHHHHHHhhhcCCCCCccCcccc
Q psy14147 28 PYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCL 64 (100)
Q Consensus 28 ~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~ 64 (100)
||+|..||+.|.....|..|++ .|++..++.++.--
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r-~~hg~~~~~~~~~y 36 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLL-SVHKQNKLTLEYFY 36 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHH-HhcCCCccceeEEE
Confidence 6899999999999999999995 88888998886543
No 23
>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=98.30 E-value=1.6e-06 Score=39.36 Aligned_cols=51 Identities=27% Similarity=0.541 Sum_probs=39.2
Q ss_pred ceeCchhhhhccChhHHHHHHhhhcCCC-CCccCccccccccChhHHHHHHHhcC
Q psy14147 28 PYACEECGKAFRKKFSLTMHQRHVHLND-RRYQCDLCLARFVTNSSLIVHKQRHD 81 (100)
Q Consensus 28 ~~~c~~C~~~f~~~~~l~~h~~~~~~~~-~~~~c~~c~~~~~~~~~l~~h~~~~~ 81 (100)
.|.|+.|++ ..+...|..|....|..+ +.+.|++|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 488999999 566778999987677764 4688999987643 48888887654
No 24
>KOG3993|consensus
Probab=98.17 E-value=2.6e-07 Score=57.09 Aligned_cols=69 Identities=26% Similarity=0.632 Sum_probs=37.2
Q ss_pred eeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcC---------------------------
Q psy14147 29 YACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHD--------------------------- 81 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~--------------------------- 81 (100)
|.|..|...|.+.-.|..|.. ...--.-|.|++|++.|.-..+|.+|.|.|.
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC-~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRC-PRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccC-CeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 455555555555555544441 2222223455555555555555555555431
Q ss_pred ------CCCCeecCCCccccCCC
Q psy14147 82 ------NTPRFKCKLCPKMFTNT 98 (100)
Q Consensus 82 ------~~~~~~C~~C~~~f~~~ 98 (100)
.+..|.|..|+|.|..+
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRq 369 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQ 369 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHH
Confidence 12358999999999753
No 25
>KOG3993|consensus
Probab=98.13 E-value=2.1e-06 Score=53.20 Aligned_cols=79 Identities=20% Similarity=0.317 Sum_probs=63.2
Q ss_pred ccchHHHHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcCC---------------------------
Q psy14147 2 VVRSREVMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHLN--------------------------- 54 (100)
Q Consensus 2 ~~~~~~~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~--------------------------- 54 (100)
+++-|...|...-.|-+|.-..-..-.|+|..|++.|...++|..|.+. |..
T Consensus 269 iCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRW-HKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 269 ICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRW-HKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcc-cCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 3667888899999999997543344569999999999999999999862 311
Q ss_pred ------CCCccCccccccccChhHHHHHHHhcC
Q psy14147 55 ------DRRYQCDLCLARFVTNSSLIVHKQRHD 81 (100)
Q Consensus 55 ------~~~~~c~~c~~~~~~~~~l~~h~~~~~ 81 (100)
+..|.|..|++.|.....|..|+.+|.
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 124789999999999999999987765
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=97.99 E-value=4.5e-06 Score=31.04 Aligned_cols=21 Identities=48% Similarity=0.926 Sum_probs=14.0
Q ss_pred eeCchhhhhccChhHHHHHHh
Q psy14147 29 YACEECGKAFRKKFSLTMHQR 49 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~~ 49 (100)
|.|+.|++.|.....|..|++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 456677777777777766663
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.98 E-value=4.4e-06 Score=31.06 Aligned_cols=23 Identities=39% Similarity=0.833 Sum_probs=20.7
Q ss_pred ccCccccccccChhHHHHHHHhc
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQRH 80 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~~ 80 (100)
|.|+.|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 57999999999999999998864
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.84 E-value=1.1e-05 Score=31.14 Aligned_cols=21 Identities=43% Similarity=1.028 Sum_probs=14.7
Q ss_pred ceeCchhhhhccChhHHHHHH
Q psy14147 28 PYACEECGKAFRKKFSLTMHQ 48 (100)
Q Consensus 28 ~~~c~~C~~~f~~~~~l~~h~ 48 (100)
||.|..|++.|.....|..|+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHK 21 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHH
T ss_pred CCCCCccCCccCChhHHHHHh
Confidence 466777777777777777776
No 29
>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=97.84 E-value=1.6e-05 Score=29.53 Aligned_cols=21 Identities=48% Similarity=0.959 Sum_probs=12.0
Q ss_pred eeCchhhhhccChhHHHHHHh
Q psy14147 29 YACEECGKAFRKKFSLTMHQR 49 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~~ 49 (100)
|.|++|+..|.+...|..|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 456666666666666666663
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=97.81 E-value=1.3e-05 Score=30.97 Aligned_cols=26 Identities=35% Similarity=0.609 Sum_probs=22.9
Q ss_pred CccCccccccccChhHHHHHHHhcCC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDN 82 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~ 82 (100)
+|.|..|++.|.....|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 57899999999999999999987753
No 31
>PRK04860 hypothetical protein; Provisional
Probab=97.81 E-value=1.5e-05 Score=43.92 Aligned_cols=37 Identities=16% Similarity=0.535 Sum_probs=32.0
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCccccCC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFTN 97 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 97 (100)
+|.|. |+. ....+..|.++++++++|.|..|++.|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 58897 887 56678899999999999999999998864
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.78 E-value=7.1e-06 Score=49.38 Aligned_cols=63 Identities=25% Similarity=0.493 Sum_probs=36.4
Q ss_pred CCceeCch--hhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcCCCCCeecCCCccccCCC
Q psy14147 26 VKPYACEE--CGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFTNT 98 (100)
Q Consensus 26 ~~~~~c~~--C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~ 98 (100)
+|||+|++ |.+.++....|..|+..-|-..+...-+ .-..+.-.-...+||.|+.|+|.|.+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p----------~p~~~~~F~~~~KPYrCevC~KRYKNl 411 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP----------SPEKMNIFSAKDKPYRCEVCDKRYKNL 411 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCC----------CccccccccccCCceeccccchhhccC
Confidence 48899987 8888988888888874222111111111 000011112346788888888887653
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=97.77 E-value=2.3e-05 Score=29.11 Aligned_cols=24 Identities=33% Similarity=0.695 Sum_probs=19.2
Q ss_pred ccCccccccccChhHHHHHHHhcC
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQRHD 81 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~~~ 81 (100)
|.|+.|++.|.....|..|+..++
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 579999999999999999998753
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.71 E-value=3e-05 Score=39.15 Aligned_cols=71 Identities=13% Similarity=0.021 Sum_probs=21.3
Q ss_pred chHHHHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhc
Q psy14147 4 RSREVMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRH 80 (100)
Q Consensus 4 ~~~~~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~ 80 (100)
..|+..|.....|..|+...++... . ....+.....+..+.. .. -...+.|..|+..|.....|..|++.+
T Consensus 3 ~~C~~~f~~~~~l~~H~~~~H~~~~---~-~~~~l~~~~~~~~~~~-~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 3 LFCDESFSSVDDLLQHMKKKHGFDI---P-DQKYLVDPNRLLNYLR-KK-VKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccc---c-cccccccccccccccc-cc-cCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 3467778888888888754333211 1 1111222223333331 11 122689999999999999999999964
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.68 E-value=2.6e-05 Score=47.03 Aligned_cols=25 Identities=20% Similarity=0.620 Sum_probs=21.0
Q ss_pred CCCCccCcc--ccccccChhHHHHHHH
Q psy14147 54 NDRRYQCDL--CLARFVTNSSLIVHKQ 78 (100)
Q Consensus 54 ~~~~~~c~~--c~~~~~~~~~l~~h~~ 78 (100)
+++||.|++ |.+.+...-.|..|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhh
Confidence 358999977 8899998888988876
No 36
>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=97.60 E-value=8.2e-05 Score=32.90 Aligned_cols=32 Identities=16% Similarity=0.241 Sum_probs=16.4
Q ss_pred CCCCccCccccccccChhHHHHHHHhcCCCCC
Q psy14147 54 NDRRYQCDLCLARFVTNSSLIVHKQRHDNTPR 85 (100)
Q Consensus 54 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~ 85 (100)
.+.|..|++|+..+.+..+|..|+...++.+|
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 34456666666666666666666666555544
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.31 E-value=0.00032 Score=26.22 Aligned_cols=19 Identities=47% Similarity=0.943 Sum_probs=10.8
Q ss_pred eCchhhhhccChhHHHHHH
Q psy14147 30 ACEECGKAFRKKFSLTMHQ 48 (100)
Q Consensus 30 ~c~~C~~~f~~~~~l~~h~ 48 (100)
.|..|++.|.....+..|+
T Consensus 2 ~C~~C~~~f~~~~~l~~H~ 20 (26)
T smart00355 2 RCPECGKVFKSKSALKEHM 20 (26)
T ss_pred CCCCCcchhCCHHHHHHHH
Confidence 4555555555555555555
No 38
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.21 E-value=0.00053 Score=30.99 Aligned_cols=39 Identities=28% Similarity=0.665 Sum_probs=29.4
Q ss_pred CccCccccccccChhHHHHHHHh-cCC-CCCeecCCCccccC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQR-HDN-TPRFKCKLCPKMFT 96 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~-~~~-~~~~~C~~C~~~f~ 96 (100)
.|.|+.|++.| ....|..|... |.. .+.+.||.|...+.
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCEDEHRSESKNVVCPICSSRVT 42 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHhHCcCCCCCccCCCchhhhh
Confidence 47899999954 56789999774 444 35789999987654
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.06 E-value=0.00054 Score=25.55 Aligned_cols=24 Identities=33% Similarity=0.629 Sum_probs=20.8
Q ss_pred ccCccccccccChhHHHHHHHhcC
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQRHD 81 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~~~ 81 (100)
+.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 478999999999999999988664
No 40
>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=97.00 E-value=0.0012 Score=29.27 Aligned_cols=33 Identities=21% Similarity=0.435 Sum_probs=22.1
Q ss_pred cCCCceeCchhhhhccChhHHHHHHhhhcCCCCC
Q psy14147 24 YCVKPYACEECGKAFRKKFSLTMHQRHVHLNDRR 57 (100)
Q Consensus 24 ~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~ 57 (100)
..+.|..|++|+..+....+|..|+. ...+.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle-~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLE-IRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHH-HHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHH-HHhcccC
Confidence 45788999999999999999999995 5555543
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.95 E-value=0.00046 Score=25.93 Aligned_cols=20 Identities=35% Similarity=0.750 Sum_probs=10.4
Q ss_pred eeCchhhhhccChhHHHHHH
Q psy14147 29 YACEECGKAFRKKFSLTMHQ 48 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~ 48 (100)
|.|.+|+..|.+...+..|+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHL 20 (25)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCCcCCHHHHHHHH
Confidence 34555555555555555554
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.82 E-value=0.00082 Score=25.21 Aligned_cols=23 Identities=30% Similarity=0.691 Sum_probs=20.4
Q ss_pred ccCccccccccChhHHHHHHHhc
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQRH 80 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~~ 80 (100)
|.|.+|+..|.....+..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 57999999999999999998754
No 43
>PRK04860 hypothetical protein; Provisional
Probab=96.75 E-value=0.0012 Score=36.64 Aligned_cols=38 Identities=29% Similarity=0.746 Sum_probs=31.6
Q ss_pred ceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccCh
Q psy14147 28 PYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTN 70 (100)
Q Consensus 28 ~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~ 70 (100)
+|.|. |+. ...++..|.+ ++.+..+|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~r-i~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNR-VVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHH-HhcCCccEECCCCCceeEEe
Confidence 59998 987 5667889994 99999999999999887543
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.34 E-value=0.0026 Score=23.61 Aligned_cols=19 Identities=32% Similarity=0.621 Sum_probs=8.0
Q ss_pred eeCchhhhhccChhHHHHHH
Q psy14147 29 YACEECGKAFRKKFSLTMHQ 48 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~ 48 (100)
|.|..|+.... ...|..|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~ 19 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHL 19 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHH
Confidence 34555554444 44455554
No 45
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.25 E-value=0.0051 Score=30.87 Aligned_cols=23 Identities=35% Similarity=0.775 Sum_probs=20.3
Q ss_pred CceeCchhhhhccChhHHHHHHh
Q psy14147 27 KPYACEECGKAFRKKFSLTMHQR 49 (100)
Q Consensus 27 ~~~~c~~C~~~f~~~~~l~~h~~ 49 (100)
..+.|..|+..|.....|..|++
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHH
T ss_pred CCCCCCccCCCCcCHHHHHHHHc
Confidence 36999999999999999999995
No 46
>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=96.11 E-value=0.0019 Score=24.79 Aligned_cols=20 Identities=30% Similarity=0.717 Sum_probs=14.4
Q ss_pred eeCchhhhhccChhHHHHHH
Q psy14147 29 YACEECGKAFRKKFSLTMHQ 48 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~ 48 (100)
|.|..|++.|.+...+..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 56777777777777776666
No 47
>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=95.89 E-value=0.0048 Score=24.94 Aligned_cols=8 Identities=25% Similarity=0.982 Sum_probs=3.7
Q ss_pred CeecCCCc
Q psy14147 85 RFKCKLCP 92 (100)
Q Consensus 85 ~~~C~~C~ 92 (100)
++.|+.||
T Consensus 17 ~~~CP~Cg 24 (33)
T cd00350 17 PWVCPVCG 24 (33)
T ss_pred CCcCcCCC
Confidence 44444444
No 48
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.33 E-value=0.015 Score=23.45 Aligned_cols=21 Identities=24% Similarity=0.621 Sum_probs=13.2
Q ss_pred ceeCchhhhhccChhHHHHHH
Q psy14147 28 PYACEECGKAFRKKFSLTMHQ 48 (100)
Q Consensus 28 ~~~c~~C~~~f~~~~~l~~h~ 48 (100)
+|.|..|+..|.....+..|+
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~ 23 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHL 23 (35)
T ss_pred CeEccccCCccCCHHHHHHHH
Confidence 456666666666666665555
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.20 E-value=0.023 Score=21.40 Aligned_cols=18 Identities=28% Similarity=0.672 Sum_probs=8.8
Q ss_pred cCccccccccChhHHHHHH
Q psy14147 59 QCDLCLARFVTNSSLIVHK 77 (100)
Q Consensus 59 ~c~~c~~~~~~~~~l~~h~ 77 (100)
.|+.|++.| ....|..|.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 355555555 333444444
No 50
>KOG1146|consensus
Probab=94.87 E-value=0.027 Score=40.43 Aligned_cols=71 Identities=23% Similarity=0.409 Sum_probs=48.7
Q ss_pred HHHHHHHHHhcc-ccccCCCceeCchhhhhccChhHHHHHHhhhcC------------------------CCCCccCccc
Q psy14147 9 MEIQKDVVQSFP-IILYCVKPYACEECGKAFRKKFSLTMHQRHVHL------------------------NDRRYQCDLC 63 (100)
Q Consensus 9 ~~~~~~~l~~h~-~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~------------------------~~~~~~c~~c 63 (100)
.+..+..+--|. ..+...+.+.|+.|+..|+....|.-|++..|. +.++|.|..|
T Consensus 445 ~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C 524 (1406)
T KOG1146|consen 445 LLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRAC 524 (1406)
T ss_pred hhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceee
Confidence 333444444443 334455778899999999988888888864332 2456788888
Q ss_pred cccccChhHHHHHHHh
Q psy14147 64 LARFVTNSSLIVHKQR 79 (100)
Q Consensus 64 ~~~~~~~~~l~~h~~~ 79 (100)
...+.....|..|+..
T Consensus 525 ~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 525 NYSTTTNGNLSIHLQS 540 (1406)
T ss_pred eeeeecchHHHHHHHH
Confidence 8888888888888763
No 51
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.27 E-value=0.044 Score=24.79 Aligned_cols=29 Identities=21% Similarity=0.308 Sum_probs=23.4
Q ss_pred ccccCCCceeCchhhhhccChhHHHHHHh
Q psy14147 21 IILYCVKPYACEECGKAFRKKFSLTMHQR 49 (100)
Q Consensus 21 ~~~~~~~~~~c~~C~~~f~~~~~l~~h~~ 49 (100)
++..++..+.|+.|+..|....++..|.-
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 34557778899999999998888888874
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=93.41 E-value=0.082 Score=27.49 Aligned_cols=13 Identities=23% Similarity=0.488 Sum_probs=7.1
Q ss_pred CccCccccccccC
Q psy14147 57 RYQCDLCLARFVT 69 (100)
Q Consensus 57 ~~~c~~c~~~~~~ 69 (100)
|..|+.||..|..
T Consensus 26 PivCP~CG~~~~~ 38 (108)
T PF09538_consen 26 PIVCPKCGTEFPP 38 (108)
T ss_pred CccCCCCCCccCc
Confidence 4456666655543
No 53
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.25 E-value=0.053 Score=24.89 Aligned_cols=33 Identities=12% Similarity=0.356 Sum_probs=19.4
Q ss_pred CCCccCccccccccChhHHHHHHHhcCCCCCeecCCCc
Q psy14147 55 DRRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCP 92 (100)
Q Consensus 55 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 92 (100)
...|.|+.||...-.+ -.+-..-..+|.|+.||
T Consensus 25 ~v~F~CPnCGe~~I~R-----c~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 25 AVKFPCPNCGEVEIYR-----CAKCRKLGNPYRCPKCG 57 (61)
T ss_pred eeEeeCCCCCceeeeh-----hhhHHHcCCceECCCcC
Confidence 3457888888553222 11222234579999887
No 54
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.24 E-value=0.095 Score=21.69 Aligned_cols=32 Identities=22% Similarity=0.603 Sum_probs=15.4
Q ss_pred cCccccccccChhHHHHHHHhcCCCCCeecCCCcccc
Q psy14147 59 QCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMF 95 (100)
Q Consensus 59 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 95 (100)
.|+.|+..|.-... +...+.....|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcEEECCCCCcEe
Confidence 45556555544322 112233445666666555
No 55
>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=93.05 E-value=0.056 Score=21.98 Aligned_cols=8 Identities=38% Similarity=1.219 Sum_probs=4.2
Q ss_pred eeCchhhh
Q psy14147 29 YACEECGK 36 (100)
Q Consensus 29 ~~c~~C~~ 36 (100)
|.|..||.
T Consensus 3 ~~C~~CG~ 10 (34)
T cd00729 3 WVCPVCGY 10 (34)
T ss_pred EECCCCCC
Confidence 45555553
No 56
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.55 E-value=0.022 Score=35.70 Aligned_cols=63 Identities=29% Similarity=0.469 Sum_probs=46.1
Q ss_pred CceeCchhhhhccChhHHHHHHhh-hcCCC--CCccCc--cccccccChhHHHHHHHhcCCCCCeecC
Q psy14147 27 KPYACEECGKAFRKKFSLTMHQRH-VHLND--RRYQCD--LCLARFVTNSSLIVHKQRHDNTPRFKCK 89 (100)
Q Consensus 27 ~~~~c~~C~~~f~~~~~l~~h~~~-~~~~~--~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~C~ 89 (100)
.++.|..|...|.....+..|.+. .|.++ .++.|+ .|++.|.....+..|...|.+..++.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 356777788888888888888732 57777 788887 6888888877777777777776665553
No 57
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.39 E-value=0.15 Score=20.97 Aligned_cols=32 Identities=19% Similarity=0.572 Sum_probs=15.7
Q ss_pred cCccccccccChhHHHHHHHhcCCCCCeecCCCcccc
Q psy14147 59 QCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMF 95 (100)
Q Consensus 59 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 95 (100)
.|+.|+..|.-.... ........+|+.|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 455566555443221 22333445666666655
No 58
>KOG2893|consensus
Probab=92.38 E-value=0.03 Score=33.08 Aligned_cols=42 Identities=24% Similarity=0.674 Sum_probs=28.0
Q ss_pred eCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHH
Q psy14147 30 ACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVH 76 (100)
Q Consensus 30 ~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h 76 (100)
.|..|.+.|....-|+.|++ .+-|.|-+|.+.+.+-..|..|
T Consensus 12 wcwycnrefddekiliqhqk-----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK-----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhh-----hccceeeeehhhhccCCCceee
Confidence 47788888888888887774 3456788887654443334444
No 59
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=92.23 E-value=0.13 Score=21.23 Aligned_cols=11 Identities=18% Similarity=0.893 Sum_probs=6.4
Q ss_pred CeecCCCcccc
Q psy14147 85 RFKCKLCPKMF 95 (100)
Q Consensus 85 ~~~C~~C~~~f 95 (100)
...|+.|+..|
T Consensus 25 ~v~C~~C~~~~ 35 (38)
T TIGR02098 25 KVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEE
Confidence 35566666555
No 60
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.23 E-value=0.14 Score=26.77 Aligned_cols=66 Identities=21% Similarity=0.444 Sum_probs=36.0
Q ss_pred CceeCchhhhhccChhHHHHHHhhhcC-CCCCc------------cCccccccccChhHHHHHHHhcCCCCCeecCCCcc
Q psy14147 27 KPYACEECGKAFRKKFSLTMHQRHVHL-NDRRY------------QCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPK 93 (100)
Q Consensus 27 ~~~~c~~C~~~f~~~~~l~~h~~~~~~-~~~~~------------~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 93 (100)
-|..|++|+-+......|.+.. .|. .-++| .|-.|...|........ ..-.....|.|+.|..
T Consensus 14 LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~ 89 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKN 89 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhh--hccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCC
Confidence 4677888888877777776554 121 11112 26667766654321110 0012234688888887
Q ss_pred ccC
Q psy14147 94 MFT 96 (100)
Q Consensus 94 ~f~ 96 (100)
.|-
T Consensus 90 ~FC 92 (112)
T TIGR00622 90 VFC 92 (112)
T ss_pred ccc
Confidence 763
No 61
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=92.13 E-value=0.09 Score=29.44 Aligned_cols=10 Identities=20% Similarity=0.591 Sum_probs=4.7
Q ss_pred CCCccCcccc
Q psy14147 55 DRRYQCDLCL 64 (100)
Q Consensus 55 ~~~~~c~~c~ 64 (100)
+.|..||+|+
T Consensus 147 e~P~~CPiCg 156 (166)
T COG1592 147 EAPEVCPICG 156 (166)
T ss_pred CCCCcCCCCC
Confidence 3444455554
No 62
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.92 E-value=0.025 Score=31.24 Aligned_cols=11 Identities=36% Similarity=0.745 Sum_probs=5.4
Q ss_pred ccCcccccccc
Q psy14147 58 YQCDLCLARFV 68 (100)
Q Consensus 58 ~~c~~c~~~~~ 68 (100)
++|+.||++|.
T Consensus 29 ~~c~~c~~~f~ 39 (154)
T PRK00464 29 RECLACGKRFT 39 (154)
T ss_pred eeccccCCcce
Confidence 44555555443
No 63
>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=91.30 E-value=0.099 Score=19.54 Aligned_cols=10 Identities=30% Similarity=0.607 Sum_probs=6.7
Q ss_pred CCeecCCCcc
Q psy14147 84 PRFKCKLCPK 93 (100)
Q Consensus 84 ~~~~C~~C~~ 93 (100)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4577777763
No 64
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.48 E-value=0.028 Score=32.72 Aligned_cols=22 Identities=32% Similarity=0.532 Sum_probs=15.8
Q ss_pred CCceeCchhhhhccChhHHHHH
Q psy14147 26 VKPYACEECGKAFRKKFSLTMH 47 (100)
Q Consensus 26 ~~~~~c~~C~~~f~~~~~l~~h 47 (100)
.+...|++|++.|.........
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~ 24 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGK 24 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCC
Confidence 3567899999999877544333
No 65
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=90.08 E-value=0.24 Score=21.37 Aligned_cols=10 Identities=50% Similarity=1.298 Sum_probs=5.6
Q ss_pred eeCchhhhhc
Q psy14147 29 YACEECGKAF 38 (100)
Q Consensus 29 ~~c~~C~~~f 38 (100)
|.|..||..|
T Consensus 3 Y~C~~Cg~~~ 12 (44)
T smart00659 3 YICGECGREN 12 (44)
T ss_pred EECCCCCCEe
Confidence 5566666554
No 66
>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=89.95 E-value=0.54 Score=26.15 Aligned_cols=12 Identities=25% Similarity=0.478 Sum_probs=5.4
Q ss_pred CccCcccccccc
Q psy14147 57 RYQCDLCLARFV 68 (100)
Q Consensus 57 ~~~c~~c~~~~~ 68 (100)
-|.|+.|+..|+
T Consensus 109 ~Y~Cp~c~~r~t 120 (158)
T TIGR00373 109 FFICPNMCVRFT 120 (158)
T ss_pred eEECCCCCcEee
Confidence 344544444443
No 67
>KOG2186|consensus
Probab=89.50 E-value=0.26 Score=29.44 Aligned_cols=52 Identities=21% Similarity=0.395 Sum_probs=37.4
Q ss_pred ceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcCCC
Q psy14147 28 PYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDNT 83 (100)
Q Consensus 28 ~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~ 83 (100)
.|.|..||.+..-. .+..|+. ..++ .-|.|..|+..|.. .....|..--++.
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~s-rCrn-~~fSCIDC~k~F~~-~sYknH~kCITEa 54 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMS-RCRN-AYFSCIDCGKTFER-VSYKNHTKCITEA 54 (276)
T ss_pred EEehhhhhhhcccc-chHHHHH-hccC-CeeEEeeccccccc-chhhhhhhhcchH
Confidence 47899999877644 4667884 5555 57899999999987 4566676644433
No 68
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=89.39 E-value=0.38 Score=28.75 Aligned_cols=57 Identities=23% Similarity=0.562 Sum_probs=30.7
Q ss_pred CCceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 26 VKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 26 ~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
...|.|..|...+ ..+ .-.......|..|.+.|.-... .... |---|.|+.|+..|.
T Consensus 110 drqFaC~~Cd~~W--------wRr-vp~rKeVSRCr~C~~rYDPVP~---dkmw--G~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 110 DRQFACSSCDHMW--------WRR-VPQRKEVSRCRKCRKRYDPVPC---DKMW--GIAEFHCPKCRHNFR 166 (278)
T ss_pred ceeeeccccchHH--------Hhc-cCcccccccccccccccCCCcc---cccc--ceeeeecccccccch
Confidence 3679999996543 121 2222234467777766644321 1111 122378888888775
No 69
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=89.37 E-value=0.76 Score=25.21 Aligned_cols=13 Identities=23% Similarity=0.858 Sum_probs=7.5
Q ss_pred CCccCcccccccc
Q psy14147 56 RRYQCDLCLARFV 68 (100)
Q Consensus 56 ~~~~c~~c~~~~~ 68 (100)
.-|.|+.|+..|.
T Consensus 98 ~~Y~Cp~C~~~y~ 110 (147)
T smart00531 98 AYYKCPNCQSKYT 110 (147)
T ss_pred cEEECcCCCCEee
Confidence 3456666665554
No 70
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.00 E-value=0.18 Score=31.60 Aligned_cols=44 Identities=27% Similarity=0.532 Sum_probs=38.6
Q ss_pred CCccCccccccccChhHHHHHHH--hcCCC--CCeecC--CCccccCCCC
Q psy14147 56 RRYQCDLCLARFVTNSSLIVHKQ--RHDNT--PRFKCK--LCPKMFTNTV 99 (100)
Q Consensus 56 ~~~~c~~c~~~~~~~~~l~~h~~--~~~~~--~~~~C~--~C~~~f~~~~ 99 (100)
.++.|..|...|.....+..|.+ .|+++ +|+.|+ .|++.|....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~ 337 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRND 337 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccc
Confidence 35788889999999999999999 79999 999999 7999998653
No 71
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=88.91 E-value=0.084 Score=25.38 Aligned_cols=9 Identities=33% Similarity=0.689 Sum_probs=4.3
Q ss_pred eCchhhhhc
Q psy14147 30 ACEECGKAF 38 (100)
Q Consensus 30 ~c~~C~~~f 38 (100)
.|+.|+...
T Consensus 3 ~CP~Cg~~a 11 (72)
T PRK09678 3 HCPLCQHAA 11 (72)
T ss_pred cCCCCCCcc
Confidence 455555433
No 72
>KOG4173|consensus
Probab=88.44 E-value=0.63 Score=27.12 Aligned_cols=70 Identities=23% Similarity=0.240 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhc---------CCCCCccCcc--ccccccChhHHH
Q psy14147 6 REVMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVH---------LNDRRYQCDL--CLARFVTNSSLI 74 (100)
Q Consensus 6 ~~~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~---------~~~~~~~c~~--c~~~~~~~~~l~ 74 (100)
+-.+|...+....|..+.++ ..|..|.+.|++..-|..|+...| .|...|+|-+ |+-.|.....-.
T Consensus 87 c~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~Rk 163 (253)
T KOG4173|consen 87 CCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRK 163 (253)
T ss_pred hHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhh
Confidence 34556666666667654443 248888888888888877774222 2344567743 776676666555
Q ss_pred HHHH
Q psy14147 75 VHKQ 78 (100)
Q Consensus 75 ~h~~ 78 (100)
.|+-
T Consensus 164 dH~I 167 (253)
T KOG4173|consen 164 DHMI 167 (253)
T ss_pred hHHH
Confidence 5543
No 73
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=88.32 E-value=0.88 Score=25.88 Aligned_cols=16 Identities=19% Similarity=0.390 Sum_probs=9.1
Q ss_pred CCceeCchhhhhccCh
Q psy14147 26 VKPYACEECGKAFRKK 41 (100)
Q Consensus 26 ~~~~~c~~C~~~f~~~ 41 (100)
..-|.|+.|+..|+..
T Consensus 115 ~~~Y~Cp~C~~rytf~ 130 (178)
T PRK06266 115 NMFFFCPNCHIRFTFD 130 (178)
T ss_pred CCEEECCCCCcEEeHH
Confidence 3456666666655543
No 74
>KOG2186|consensus
Probab=88.26 E-value=0.36 Score=28.88 Aligned_cols=43 Identities=23% Similarity=0.455 Sum_probs=27.5
Q ss_pred HHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcCCCCCc
Q psy14147 13 KDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHLNDRRY 58 (100)
Q Consensus 13 ~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~ 58 (100)
+-.+..|+-...+ .-|.|..|++.|.. .++..|.. .-+....|
T Consensus 15 Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k-CITEaQKY 57 (276)
T KOG2186|consen 15 KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK-CITEAQKY 57 (276)
T ss_pred ccchHHHHHhccC-CeeEEeeccccccc-chhhhhhh-hcchHHHh
Confidence 3456667655444 66899999999988 55667763 44433333
No 75
>KOG2893|consensus
Probab=88.15 E-value=0.08 Score=31.34 Aligned_cols=44 Identities=18% Similarity=0.239 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcC
Q psy14147 6 REVMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHL 53 (100)
Q Consensus 6 ~~~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~ 53 (100)
|+..|..+..|.+|++. |-|+|.+|.+..-+--.|..|-.++|.
T Consensus 16 cnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 16 CNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred cccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhhh
Confidence 56678899999999864 558999999877666666666545554
No 76
>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=87.81 E-value=0.47 Score=25.40 Aligned_cols=30 Identities=23% Similarity=0.341 Sum_probs=18.0
Q ss_pred eeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccCh
Q psy14147 29 YACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTN 70 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~ 70 (100)
..|..||+.|-. .+..|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYD------------Lnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD------------LNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc------------cCCCCccCCCcCCccCcc
Confidence 567777776621 122466777787766444
No 77
>PF14353 CpXC: CpXC protein
Probab=87.28 E-value=0.72 Score=24.54 Aligned_cols=8 Identities=50% Similarity=1.543 Sum_probs=4.1
Q ss_pred Cchhhhhc
Q psy14147 31 CEECGKAF 38 (100)
Q Consensus 31 c~~C~~~f 38 (100)
|+.|+..|
T Consensus 4 CP~C~~~~ 11 (128)
T PF14353_consen 4 CPHCGHEF 11 (128)
T ss_pred CCCCCCee
Confidence 55555444
No 78
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.08 E-value=0.24 Score=22.76 Aligned_cols=34 Identities=12% Similarity=0.343 Sum_probs=19.1
Q ss_pred CCCccCccccccccChhHHHHHHHhcCCCCCeecCCCcc
Q psy14147 55 DRRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPK 93 (100)
Q Consensus 55 ~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 93 (100)
...|.|+.||...-.+- .. -..-..+|.|+.||-
T Consensus 23 ~~~F~CPnCG~~~I~RC--~~---CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRC--EK---CRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEeec--hh---HHhcCCceECCCCCC
Confidence 34678888886522221 11 112245789998883
No 79
>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=86.84 E-value=0.35 Score=18.38 Aligned_cols=10 Identities=30% Similarity=0.580 Sum_probs=6.3
Q ss_pred ecCCCccccC
Q psy14147 87 KCKLCPKMFT 96 (100)
Q Consensus 87 ~C~~C~~~f~ 96 (100)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666776664
No 80
>KOG1146|consensus
Probab=86.80 E-value=0.59 Score=34.26 Aligned_cols=48 Identities=15% Similarity=0.143 Sum_probs=40.4
Q ss_pred ccchHHHHHHHHHHHHhccccc-------------------------cCCCceeCchhhhhccChhHHHHHHh
Q psy14147 2 VVRSREVMEIQKDVVQSFPIIL-------------------------YCVKPYACEECGKAFRKKFSLTMHQR 49 (100)
Q Consensus 2 ~~~~~~~~~~~~~~l~~h~~~~-------------------------~~~~~~~c~~C~~~f~~~~~l~~h~~ 49 (100)
+++.++.+|.....|..|+|.- .+.++|.|..|..++....+|..|+.
T Consensus 467 ~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 467 KCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred cCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 4788999999999999999871 11377999999999999899988884
No 81
>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=86.48 E-value=0.36 Score=20.05 Aligned_cols=11 Identities=27% Similarity=1.008 Sum_probs=8.6
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
|.|+.||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 67888888774
No 82
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=85.66 E-value=0.62 Score=20.65 Aligned_cols=36 Identities=19% Similarity=0.425 Sum_probs=21.0
Q ss_pred CceeCchhhhhccChhHHHHHHhhhcCC--CCCccCcccc
Q psy14147 27 KPYACEECGKAFRKKFSLTMHQRHVHLN--DRRYQCDLCL 64 (100)
Q Consensus 27 ~~~~c~~C~~~f~~~~~l~~h~~~~~~~--~~~~~c~~c~ 64 (100)
+.+.|..||..|...+.-+.... . .| ..|-.|+.|.
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~fy~-e-Kgf~n~p~RC~~CR 40 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKFYA-E-KGFDNEPKRCPSCR 40 (49)
T ss_pred eeEEcccCCCeEEEehhHHHHHH-h-cCCcCCCccCHHHH
Confidence 56778888888776665444442 2 22 2355666664
No 83
>PHA00626 hypothetical protein
Probab=85.40 E-value=0.58 Score=21.29 Aligned_cols=15 Identities=13% Similarity=0.268 Sum_probs=10.9
Q ss_pred CCCeecCCCccccCC
Q psy14147 83 TPRFKCKLCPKMFTN 97 (100)
Q Consensus 83 ~~~~~C~~C~~~f~~ 97 (100)
...|.|+.||..|+.
T Consensus 21 snrYkCkdCGY~ft~ 35 (59)
T PHA00626 21 SDDYVCCDCGYNDSK 35 (59)
T ss_pred CcceEcCCCCCeech
Confidence 346888888877763
No 84
>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=84.97 E-value=0.46 Score=20.18 Aligned_cols=11 Identities=27% Similarity=1.002 Sum_probs=8.5
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 77888887774
No 85
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=84.93 E-value=0.4 Score=23.87 Aligned_cols=12 Identities=33% Similarity=0.894 Sum_probs=6.7
Q ss_pred CeecCCCccccC
Q psy14147 85 RFKCKLCPKMFT 96 (100)
Q Consensus 85 ~~~C~~C~~~f~ 96 (100)
.+.|..||..|.
T Consensus 53 IW~C~kCg~~fA 64 (89)
T COG1997 53 IWKCRKCGAKFA 64 (89)
T ss_pred eEEcCCCCCeec
Confidence 356666665553
No 86
>PLN02294 cytochrome c oxidase subunit Vb
Probab=83.58 E-value=0.64 Score=26.19 Aligned_cols=14 Identities=29% Similarity=0.923 Sum_probs=12.2
Q ss_pred CCCeecCCCccccC
Q psy14147 83 TPRFKCKLCPKMFT 96 (100)
Q Consensus 83 ~~~~~C~~C~~~f~ 96 (100)
.+|..|++||..|.
T Consensus 139 Gkp~RCpeCG~~fk 152 (174)
T PLN02294 139 GKSFECPVCTQYFE 152 (174)
T ss_pred CCceeCCCCCCEEE
Confidence 47999999999986
No 87
>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=83.15 E-value=1.3 Score=16.74 Aligned_cols=19 Identities=21% Similarity=0.567 Sum_probs=11.4
Q ss_pred cCccccccccChhHHHHHHH
Q psy14147 59 QCDLCLARFVTNSSLIVHKQ 78 (100)
Q Consensus 59 ~c~~c~~~~~~~~~l~~h~~ 78 (100)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 477777766 4455666654
No 88
>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=83.08 E-value=1.2 Score=19.28 Aligned_cols=29 Identities=28% Similarity=0.706 Sum_probs=15.7
Q ss_pred CCccCccccccccChhHHHHHHHhcCCCCCeecCCCcc
Q psy14147 56 RRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPK 93 (100)
Q Consensus 56 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 93 (100)
..+.|+.|+.. ....+ .+...|.|..|++
T Consensus 17 ~g~~CP~Cg~~--~~~~~-------~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGST--KHYRL-------KTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCe--eeEEe-------CCCCeEECCCCCC
Confidence 34668888753 11111 1145678887765
No 89
>KOG3408|consensus
Probab=82.94 E-value=0.92 Score=24.08 Aligned_cols=27 Identities=19% Similarity=0.394 Sum_probs=21.5
Q ss_pred CCCCCccCccccccccChhHHHHHHHh
Q psy14147 53 LNDRRYQCDLCLARFVTNSSLIVHKQR 79 (100)
Q Consensus 53 ~~~~~~~c~~c~~~~~~~~~l~~h~~~ 79 (100)
.|...|.|..|.+-|.....|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 455568888899989888888888774
No 90
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=82.76 E-value=0.75 Score=19.25 Aligned_cols=12 Identities=42% Similarity=1.151 Sum_probs=9.6
Q ss_pred CeecCCCccccC
Q psy14147 85 RFKCKLCPKMFT 96 (100)
Q Consensus 85 ~~~C~~C~~~f~ 96 (100)
|+.|..|++.|=
T Consensus 12 ~f~C~~C~~~FC 23 (39)
T smart00154 12 GFKCRHCGNLFC 23 (39)
T ss_pred CeECCccCCccc
Confidence 788888888773
No 91
>PF12907 zf-met2: Zinc-binding
Probab=82.60 E-value=0.65 Score=19.65 Aligned_cols=24 Identities=25% Similarity=0.531 Sum_probs=12.5
Q ss_pred eeCchhhhhccCh---hHHHHHHhhhc
Q psy14147 29 YACEECGKAFRKK---FSLTMHQRHVH 52 (100)
Q Consensus 29 ~~c~~C~~~f~~~---~~l~~h~~~~~ 52 (100)
+.|.+|..+|... ..|..|....|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKH 28 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKH 28 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccC
Confidence 3566676555433 33666654333
No 92
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=82.22 E-value=0.43 Score=25.85 Aligned_cols=13 Identities=15% Similarity=0.416 Sum_probs=7.8
Q ss_pred CccCccccccccC
Q psy14147 57 RYQCDLCLARFVT 69 (100)
Q Consensus 57 ~~~c~~c~~~~~~ 69 (100)
.+.|..|+..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 4567777765543
No 93
>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=81.52 E-value=0.86 Score=23.30 Aligned_cols=17 Identities=18% Similarity=0.477 Sum_probs=13.7
Q ss_pred hcCCCCCeecCCCccccC
Q psy14147 79 RHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 79 ~~~~~~~~~C~~C~~~f~ 96 (100)
.+.+ +|..|++||..|.
T Consensus 74 l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 74 LEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EeCC-CceeCCCCCcEEE
Confidence 4555 7999999999885
No 94
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=81.52 E-value=0.86 Score=20.20 Aligned_cols=11 Identities=36% Similarity=1.201 Sum_probs=7.1
Q ss_pred ceeCchhhhhc
Q psy14147 28 PYACEECGKAF 38 (100)
Q Consensus 28 ~~~c~~C~~~f 38 (100)
.|.|..||+.+
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 36677777665
No 95
>KOG2785|consensus
Probab=81.36 E-value=2.3 Score=27.19 Aligned_cols=51 Identities=18% Similarity=0.249 Sum_probs=38.8
Q ss_pred CceeCchhhhhccChhHHHHHHhhhcCC-----------------------CCCccCcccc---ccccChhHHHHHHH
Q psy14147 27 KPYACEECGKAFRKKFSLTMHQRHVHLN-----------------------DRRYQCDLCL---ARFVTNSSLIVHKQ 78 (100)
Q Consensus 27 ~~~~c~~C~~~f~~~~~l~~h~~~~~~~-----------------------~~~~~c~~c~---~~~~~~~~l~~h~~ 78 (100)
.|-.|..|++.+........||. .+.| ...+.|..|+ +.|.+......|+.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~-~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMF-KEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHh-hccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 45679999999998888889995 4433 2346788888 88888888888876
No 96
>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=81.07 E-value=0.8 Score=20.20 Aligned_cols=11 Identities=27% Similarity=1.026 Sum_probs=8.0
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 67888887664
No 97
>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=79.40 E-value=0.68 Score=19.73 Aligned_cols=12 Identities=58% Similarity=1.068 Sum_probs=7.8
Q ss_pred CCeecCCCcccc
Q psy14147 84 PRFKCKLCPKMF 95 (100)
Q Consensus 84 ~~~~C~~C~~~f 95 (100)
.|+.|+.|++.|
T Consensus 12 ~~~~C~~C~~~F 23 (43)
T PF01428_consen 12 LPFKCKHCGKSF 23 (43)
T ss_dssp SHEE-TTTS-EE
T ss_pred CCeECCCCCccc
Confidence 478888888877
No 98
>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=79.16 E-value=0.5 Score=19.45 Aligned_cols=8 Identities=38% Similarity=1.551 Sum_probs=3.6
Q ss_pred Cchhhhhc
Q psy14147 31 CEECGKAF 38 (100)
Q Consensus 31 c~~C~~~f 38 (100)
|..||..|
T Consensus 4 C~~Cg~~Y 11 (36)
T PF05191_consen 4 CPKCGRIY 11 (36)
T ss_dssp ETTTTEEE
T ss_pred cCCCCCcc
Confidence 44444443
No 99
>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=77.23 E-value=3 Score=25.39 Aligned_cols=72 Identities=17% Similarity=0.207 Sum_probs=39.3
Q ss_pred ccCCCceeCchhhhhccChhHHHHHHhhh-cCCCCCccCccccccccCh------hHHHHHHHh----cCCCCCeecCCC
Q psy14147 23 LYCVKPYACEECGKAFRKKFSLTMHQRHV-HLNDRRYQCDLCLARFVTN------SSLIVHKQR----HDNTPRFKCKLC 91 (100)
Q Consensus 23 ~~~~~~~~c~~C~~~f~~~~~l~~h~~~~-~~~~~~~~c~~c~~~~~~~------~~l~~h~~~----~~~~~~~~C~~C 91 (100)
.++.+.|.|..|.. |.-...-..|+... ......|.|..|++.=... ..-..|.+. ....+++.||.|
T Consensus 137 ~hGGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKC 215 (314)
T PF06524_consen 137 DHGGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKC 215 (314)
T ss_pred cCCCeEEEeecCCC-eeeccchhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCC
Confidence 34567799999975 44444444555311 1234467787777632111 111234442 234578999999
Q ss_pred cccc
Q psy14147 92 PKMF 95 (100)
Q Consensus 92 ~~~f 95 (100)
|..-
T Consensus 216 g~et 219 (314)
T PF06524_consen 216 GYET 219 (314)
T ss_pred CCcc
Confidence 8543
No 100
>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=77.14 E-value=1.2 Score=17.61 Aligned_cols=12 Identities=17% Similarity=0.365 Sum_probs=6.4
Q ss_pred CCCeecCCCccc
Q psy14147 83 TPRFKCKLCPKM 94 (100)
Q Consensus 83 ~~~~~C~~C~~~ 94 (100)
...+.|+.|+..
T Consensus 17 ~~~~vCp~C~~e 28 (30)
T PF08274_consen 17 GELLVCPECGHE 28 (30)
T ss_dssp SSSEEETTTTEE
T ss_pred CCEEeCCccccc
Confidence 344566666543
No 101
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.69 E-value=2 Score=20.93 Aligned_cols=32 Identities=34% Similarity=0.805 Sum_probs=19.8
Q ss_pred ceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccc
Q psy14147 28 PYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARF 67 (100)
Q Consensus 28 ~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~ 67 (100)
.|.|..|+..| .+..++. ...--.|+.|+..+
T Consensus 12 ~Y~c~~cg~~~----dvvq~~~----ddplt~ce~c~a~~ 43 (82)
T COG2331 12 SYECTECGNRF----DVVQAMT----DDPLTTCEECGARL 43 (82)
T ss_pred EEeecccchHH----HHHHhcc----cCccccChhhChHH
Confidence 38899999887 3444442 12223688887643
No 102
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=75.88 E-value=1.4 Score=23.74 Aligned_cols=15 Identities=33% Similarity=0.948 Sum_probs=11.4
Q ss_pred ceeCchhhhhccChh
Q psy14147 28 PYACEECGKAFRKKF 42 (100)
Q Consensus 28 ~~~c~~C~~~f~~~~ 42 (100)
|++|..||+.|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 567888888887654
No 103
>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=75.72 E-value=1.7 Score=23.53 Aligned_cols=25 Identities=28% Similarity=0.389 Sum_probs=14.9
Q ss_pred ccCccccccccChhHHHHHHHhcCCCCC
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQRHDNTPR 85 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~ 85 (100)
..|-+||+.|.. |..|++.|+|-.|
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eEEccCCcccch---HHHHHHHccCCCH
Confidence 468889998865 4789888876544
No 104
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=75.69 E-value=1.5 Score=18.86 Aligned_cols=11 Identities=27% Similarity=0.857 Sum_probs=6.7
Q ss_pred CeecCCCcccc
Q psy14147 85 RFKCKLCPKMF 95 (100)
Q Consensus 85 ~~~C~~C~~~f 95 (100)
.|.|+.||..|
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 36666666655
No 105
>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=75.67 E-value=1.5 Score=17.82 Aligned_cols=13 Identities=38% Similarity=0.754 Sum_probs=6.3
Q ss_pred eecCCCccccCCC
Q psy14147 86 FKCKLCPKMFTNT 98 (100)
Q Consensus 86 ~~C~~C~~~f~~~ 98 (100)
-.|.+|++.|..+
T Consensus 4 ~~C~eC~~~f~dS 16 (34)
T PF01286_consen 4 PKCDECGKPFMDS 16 (34)
T ss_dssp EE-TTT--EES-S
T ss_pred chHhHhCCHHHHH
Confidence 4688888888653
No 106
>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=74.79 E-value=2 Score=19.46 Aligned_cols=10 Identities=30% Similarity=1.248 Sum_probs=4.8
Q ss_pred eeCchhhhhc
Q psy14147 29 YACEECGKAF 38 (100)
Q Consensus 29 ~~c~~C~~~f 38 (100)
+.|+.|+..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 3455555443
No 107
>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=74.66 E-value=3.3 Score=17.47 Aligned_cols=23 Identities=30% Similarity=0.527 Sum_probs=10.1
Q ss_pred CCceeCchhhhhccC----hhHHHHHH
Q psy14147 26 VKPYACEECGKAFRK----KFSLTMHQ 48 (100)
Q Consensus 26 ~~~~~c~~C~~~f~~----~~~l~~h~ 48 (100)
.....|..|++.+.. .+.|..|+
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 344566666655543 24455554
No 108
>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=73.53 E-value=2.8 Score=27.66 Aligned_cols=29 Identities=24% Similarity=0.432 Sum_probs=25.1
Q ss_pred CceeCchhhhhccChhHHHHHHhhhcCCC
Q psy14147 27 KPYACEECGKAFRKKFSLTMHQRHVHLND 55 (100)
Q Consensus 27 ~~~~c~~C~~~f~~~~~l~~h~~~~~~~~ 55 (100)
+-+.|+.|.+.|.....+..|+...|.+.
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 45889999999999999999998778764
No 109
>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=73.14 E-value=1.8 Score=16.79 Aligned_cols=11 Identities=45% Similarity=0.957 Sum_probs=8.9
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
|.|..|++.|.
T Consensus 1 ~sCiDC~~~F~ 11 (28)
T PF08790_consen 1 FSCIDCSKDFD 11 (28)
T ss_dssp EEETTTTEEEE
T ss_pred CeeecCCCCcC
Confidence 46888999985
No 110
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=72.70 E-value=0.61 Score=32.06 Aligned_cols=56 Identities=18% Similarity=0.441 Sum_probs=30.5
Q ss_pred eCchhhhhccChhHHHHHHhhhcCCCCCc-cCccccccccChhHHHHHHHhcCCCCCeecCCCcc
Q psy14147 30 ACEECGKAFRKKFSLTMHQRHVHLNDRRY-QCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPK 93 (100)
Q Consensus 30 ~c~~C~~~f~~~~~l~~h~~~~~~~~~~~-~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 93 (100)
.|..||.+|+....|-. . ..++....| .|+.|.+-+..+.+-..| -+|.-|+.||=
T Consensus 125 ~CT~CGPRfTIi~alPY-D-R~nTsM~~F~lC~~C~~EY~dP~nRRfH------AQp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPY-D-RENTSMADFPLCPFCDKEYKDPLNRRFH------AQPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCC-C-cccCccccCcCCHHHHHHhcCccccccc------cccccCcccCC
Confidence 36667777765544321 1 133333333 477777766666543332 24677888874
No 111
>KOG2593|consensus
Probab=72.29 E-value=6.8 Score=25.60 Aligned_cols=38 Identities=24% Similarity=0.537 Sum_probs=24.5
Q ss_pred CCCCccCccccccccChhHHHHHHHhcCCCCCeecCCCccc
Q psy14147 54 NDRRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKM 94 (100)
Q Consensus 54 ~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 94 (100)
....|.|+.|.+.|.....+ +..-...-.|.|..|+..
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~---~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEAL---QLLDNETGEFHCENCGGE 162 (436)
T ss_pred ccccccCCccccchhhhHHH---HhhcccCceEEEecCCCc
Confidence 45578999999888664433 223333345889988754
No 112
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=72.27 E-value=3 Score=19.50 Aligned_cols=11 Identities=27% Similarity=0.507 Sum_probs=5.8
Q ss_pred CCeecCCCccc
Q psy14147 84 PRFKCKLCPKM 94 (100)
Q Consensus 84 ~~~~C~~C~~~ 94 (100)
+.|.|+.||..
T Consensus 45 r~~~C~~Cg~~ 55 (69)
T PF07282_consen 45 RVFTCPNCGFE 55 (69)
T ss_pred ceEEcCCCCCE
Confidence 34555555543
No 113
>KOG4167|consensus
Probab=72.22 E-value=2 Score=29.89 Aligned_cols=23 Identities=4% Similarity=-0.195 Sum_probs=21.4
Q ss_pred cchHHHHHHHHHHHHhccccccC
Q psy14147 3 VRSREVMEIQKDVVQSFPIILYC 25 (100)
Q Consensus 3 ~~~~~~~~~~~~~l~~h~~~~~~ 25 (100)
||.||+.|.....+..||++|.-
T Consensus 795 CreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 795 CRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred hHHHHHHHHHHhhhhHHHHHHHH
Confidence 89999999999999999999874
No 114
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=71.59 E-value=2 Score=23.12 Aligned_cols=15 Identities=47% Similarity=0.928 Sum_probs=12.0
Q ss_pred CCCeecCCCccccCC
Q psy14147 83 TPRFKCKLCPKMFTN 97 (100)
Q Consensus 83 ~~~~~C~~C~~~f~~ 97 (100)
...|.|+.|++.|..
T Consensus 51 ~qRyrC~~C~~tf~~ 65 (129)
T COG3677 51 HQRYKCKSCGSTFTV 65 (129)
T ss_pred ccccccCCcCcceee
Confidence 556889999988864
No 115
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=71.49 E-value=1.5 Score=20.05 Aligned_cols=36 Identities=22% Similarity=0.317 Sum_probs=18.0
Q ss_pred eCchhhhhccChhHHHHHHhhhcCCCCCccCccccc
Q psy14147 30 ACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLA 65 (100)
Q Consensus 30 ~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~ 65 (100)
.|-.|++.+........-.+........|.|..|..
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~ 39 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKE 39 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHH
Confidence 466777665433221111112233455678887754
No 116
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=70.62 E-value=4.8 Score=17.60 Aligned_cols=8 Identities=38% Similarity=0.339 Sum_probs=4.2
Q ss_pred hHHHHHHH
Q psy14147 71 SSLIVHKQ 78 (100)
Q Consensus 71 ~~l~~h~~ 78 (100)
+.|..|++
T Consensus 37 s~L~rHl~ 44 (50)
T smart00614 37 SNLRRHLR 44 (50)
T ss_pred HHHHHHHH
Confidence 45555555
No 117
>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=70.50 E-value=1.9 Score=19.28 Aligned_cols=10 Identities=30% Similarity=0.809 Sum_probs=3.9
Q ss_pred ecCCCccccC
Q psy14147 87 KCKLCPKMFT 96 (100)
Q Consensus 87 ~C~~C~~~f~ 96 (100)
.||.|++.|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 5666666654
No 118
>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=70.21 E-value=1.6 Score=23.81 Aligned_cols=17 Identities=24% Similarity=0.618 Sum_probs=13.3
Q ss_pred hcCCCCCeecCCCccccC
Q psy14147 79 RHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 79 ~~~~~~~~~C~~C~~~f~ 96 (100)
.+.+ +|..|++||..|.
T Consensus 107 l~~g-~~~RCpeCG~~fk 123 (136)
T PF01215_consen 107 LHKG-KPQRCPECGQVFK 123 (136)
T ss_dssp EETT-SEEEETTTEEEEE
T ss_pred EeCC-CccCCCCCCeEEE
Confidence 4444 5899999999885
No 119
>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=69.56 E-value=2.3 Score=18.19 Aligned_cols=11 Identities=36% Similarity=0.809 Sum_probs=7.5
Q ss_pred ecCCCccccCC
Q psy14147 87 KCKLCPKMFTN 97 (100)
Q Consensus 87 ~C~~C~~~f~~ 97 (100)
.|+.||+.|+.
T Consensus 10 ~C~~C~rpf~W 20 (42)
T PF10013_consen 10 ICPVCGRPFTW 20 (42)
T ss_pred cCcccCCcchH
Confidence 47777777764
No 120
>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=69.20 E-value=4.8 Score=20.76 Aligned_cols=25 Identities=16% Similarity=0.361 Sum_probs=21.4
Q ss_pred ccC----ccccccccChhHHHHHHHhcCC
Q psy14147 58 YQC----DLCLARFVTNSSLIVHKQRHDN 82 (100)
Q Consensus 58 ~~c----~~c~~~~~~~~~l~~h~~~~~~ 82 (100)
|.| ..|+........+..|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 8899999999999999987654
No 121
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=68.81 E-value=3.6 Score=16.45 Aligned_cols=11 Identities=18% Similarity=0.549 Sum_probs=5.2
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
|.|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 34555555543
No 122
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=68.20 E-value=2.7 Score=22.03 Aligned_cols=25 Identities=16% Similarity=0.284 Sum_probs=14.8
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCcc
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPK 93 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 93 (100)
.+.|..|+..|.... ..+.||.||.
T Consensus 70 ~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC------------cCccCcCCCC
Confidence 356777876554321 2345888874
No 123
>KOG1842|consensus
Probab=67.92 E-value=4.6 Score=26.53 Aligned_cols=29 Identities=17% Similarity=0.322 Sum_probs=24.8
Q ss_pred CceeCchhhhhccChhHHHHHHhhhcCCC
Q psy14147 27 KPYACEECGKAFRKKFSLTMHQRHVHLND 55 (100)
Q Consensus 27 ~~~~c~~C~~~f~~~~~l~~h~~~~~~~~ 55 (100)
+-|.|++|...|.....|..|....|.++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 45899999999999999999997667653
No 124
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=67.78 E-value=2.5 Score=23.51 Aligned_cols=35 Identities=17% Similarity=0.550 Sum_probs=22.8
Q ss_pred CCccCccccccccChhHHHHHHHhcCCCCCeecCCCcccc
Q psy14147 56 RRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMF 95 (100)
Q Consensus 56 ~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 95 (100)
-+|.|. |+..+... ..|-..-.|+ .|.|..|+...
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCceE
Confidence 357888 88765443 3454555566 89999997543
No 125
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=67.65 E-value=2.9 Score=24.83 Aligned_cols=16 Identities=19% Similarity=0.627 Sum_probs=12.8
Q ss_pred CCCCCeecCCCccccC
Q psy14147 81 DNTPRFKCKLCPKMFT 96 (100)
Q Consensus 81 ~~~~~~~C~~C~~~f~ 96 (100)
+..++..|++||..|.
T Consensus 177 rEGkpqRCpECGqVFK 192 (268)
T PTZ00043 177 REGFLYRCGECDQIFM 192 (268)
T ss_pred cCCCCccCCCCCcEEE
Confidence 3456899999999885
No 126
>KOG2785|consensus
Probab=67.29 E-value=7.1 Score=25.10 Aligned_cols=23 Identities=17% Similarity=0.340 Sum_probs=12.8
Q ss_pred CCccCccccccccChhHHHHHHH
Q psy14147 56 RRYQCDLCLARFVTNSSLIVHKQ 78 (100)
Q Consensus 56 ~~~~c~~c~~~~~~~~~l~~h~~ 78 (100)
.++.|.+|.+.|........|+.
T Consensus 67 ~~~~c~~c~k~~~s~~a~~~hl~ 89 (390)
T KOG2785|consen 67 SVVYCEACNKSFASPKAHENHLK 89 (390)
T ss_pred cceehHHhhccccChhhHHHHHH
Confidence 34556666666665555555544
No 127
>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=66.75 E-value=3.7 Score=19.17 Aligned_cols=8 Identities=63% Similarity=1.443 Sum_probs=2.0
Q ss_pred Cchhhhhc
Q psy14147 31 CEECGKAF 38 (100)
Q Consensus 31 c~~C~~~f 38 (100)
|..|++.|
T Consensus 12 C~~C~~~F 19 (69)
T PF01363_consen 12 CMICGKKF 19 (69)
T ss_dssp -TTT--B-
T ss_pred CcCcCCcC
Confidence 44455544
No 128
>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=66.67 E-value=2.5 Score=22.24 Aligned_cols=26 Identities=15% Similarity=0.598 Sum_probs=15.7
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCccc
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKM 94 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~ 94 (100)
...|..|+..|..... .+.||.||..
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------LYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecCCc------------CccCcCCcCC
Confidence 3567788766644321 3568888753
No 129
>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=66.19 E-value=4.7 Score=23.80 Aligned_cols=29 Identities=24% Similarity=0.371 Sum_probs=21.0
Q ss_pred CCCceeCchhhhhccChhHHHHHHhhhcC
Q psy14147 25 CVKPYACEECGKAFRKKFSLTMHQRHVHL 53 (100)
Q Consensus 25 ~~~~~~c~~C~~~f~~~~~l~~h~~~~~~ 53 (100)
.+..|.|..|++.|.-..-+..|+...|.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 45569999999999999888899864443
No 130
>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=64.65 E-value=3 Score=17.61 Aligned_cols=12 Identities=17% Similarity=0.562 Sum_probs=8.1
Q ss_pred CCeecCCCcccc
Q psy14147 84 PRFKCKLCPKMF 95 (100)
Q Consensus 84 ~~~~C~~C~~~f 95 (100)
.+-.|+.||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 356777777766
No 131
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=63.39 E-value=6.1 Score=18.01 Aligned_cols=15 Identities=13% Similarity=0.288 Sum_probs=10.1
Q ss_pred CCCCCccCccccccc
Q psy14147 53 LNDRRYQCDLCLARF 67 (100)
Q Consensus 53 ~~~~~~~c~~c~~~~ 67 (100)
.+...|.|+.||-..
T Consensus 10 ~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 10 PAHVNFECPDCGIPT 24 (55)
T ss_pred ccccCCcCCCCCCcC
Confidence 345578888888654
No 132
>KOG4167|consensus
Probab=62.64 E-value=1.9 Score=29.95 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=21.9
Q ss_pred CccCccccccccChhHHHHHHHhcC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHD 81 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~ 81 (100)
.|-|.+|++.|.....++.|+++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4789999999999999999998875
No 133
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=62.52 E-value=6 Score=25.81 Aligned_cols=12 Identities=25% Similarity=0.656 Sum_probs=5.7
Q ss_pred CccCcccccccc
Q psy14147 57 RYQCDLCLARFV 68 (100)
Q Consensus 57 ~~~c~~c~~~~~ 68 (100)
.|.|+.|+..+.
T Consensus 367 g~rC~kCg~~~~ 378 (421)
T COG1571 367 GFRCKKCGTRAR 378 (421)
T ss_pred CcccccccccCC
Confidence 445555554443
No 134
>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=62.13 E-value=2.8 Score=18.55 Aligned_cols=8 Identities=50% Similarity=1.427 Sum_probs=3.1
Q ss_pred eecCCCcc
Q psy14147 86 FKCKLCPK 93 (100)
Q Consensus 86 ~~C~~C~~ 93 (100)
|.|+.|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 77777765
No 135
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=61.80 E-value=4.7 Score=16.19 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=7.1
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
+.|..||..|.
T Consensus 22 ~~C~~Cg~~~~ 32 (33)
T PF08792_consen 22 EVCIFCGSSFP 32 (33)
T ss_pred EEcccCCcEee
Confidence 56777776654
No 136
>KOG2807|consensus
Probab=61.69 E-value=13 Score=23.53 Aligned_cols=22 Identities=18% Similarity=0.315 Sum_probs=14.3
Q ss_pred CceeCchhhhhccChhHHHHHH
Q psy14147 27 KPYACEECGKAFRKKFSLTMHQ 48 (100)
Q Consensus 27 ~~~~c~~C~~~f~~~~~l~~h~ 48 (100)
-|-.|++|+-+......|.+..
T Consensus 289 LP~eCpiC~ltLVss~hLARSy 310 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSY 310 (378)
T ss_pred CCccCCccceeEecchHHHHHH
Confidence 3466777777776666665544
No 137
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=61.32 E-value=11 Score=15.92 Aligned_cols=22 Identities=23% Similarity=0.448 Sum_probs=9.5
Q ss_pred cCccccccccC--hhHHHHHHHhc
Q psy14147 59 QCDLCLARFVT--NSSLIVHKQRH 80 (100)
Q Consensus 59 ~c~~c~~~~~~--~~~l~~h~~~~ 80 (100)
.|+.|+..|.. +.+-..|.+.|
T Consensus 15 ~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 15 TCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCCCCEECCCCHHHHHHHHHHH
Confidence 45555544322 33344444433
No 138
>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=60.96 E-value=3.9 Score=22.82 Aligned_cols=16 Identities=19% Similarity=0.301 Sum_probs=13.5
Q ss_pred CCCCeecCCCccccCC
Q psy14147 82 NTPRFKCKLCPKMFTN 97 (100)
Q Consensus 82 ~~~~~~C~~C~~~f~~ 97 (100)
-+.|..|..||+.|.+
T Consensus 65 ~~~PsYC~~CGkpyPW 80 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPW 80 (158)
T ss_pred CCCChhHHhCCCCCch
Confidence 3478899999999986
No 139
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=60.57 E-value=4.2 Score=20.53 Aligned_cols=14 Identities=29% Similarity=0.591 Sum_probs=10.0
Q ss_pred CCeecCCCccccCC
Q psy14147 84 PRFKCKLCPKMFTN 97 (100)
Q Consensus 84 ~~~~C~~C~~~f~~ 97 (100)
+|-.|..||-.|.+
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 56678888877765
No 140
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.31 E-value=3.3 Score=18.23 Aligned_cols=16 Identities=19% Similarity=0.430 Sum_probs=11.9
Q ss_pred cCccccccccChhHHH
Q psy14147 59 QCDLCLARFVTNSSLI 74 (100)
Q Consensus 59 ~c~~c~~~~~~~~~l~ 74 (100)
.|++|++.|.....+.
T Consensus 14 ICpvCqRPFsWRkKW~ 29 (54)
T COG4338 14 ICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhcCchHHHHHHH
Confidence 6899999887765443
No 141
>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 PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=58.93 E-value=3.9 Score=21.60 Aligned_cols=12 Identities=25% Similarity=0.611 Sum_probs=7.3
Q ss_pred CccCcccccccc
Q psy14147 57 RYQCDLCLARFV 68 (100)
Q Consensus 57 ~~~c~~c~~~~~ 68 (100)
.+.|..|+..|.
T Consensus 71 ~~~C~~Cg~~~~ 82 (117)
T PRK00564 71 ELECKDCSHVFK 82 (117)
T ss_pred EEEhhhCCCccc
Confidence 356777775553
No 143
>PRK14873 primosome assembly protein PriA; Provisional
Probab=58.80 E-value=7 Score=27.13 Aligned_cols=10 Identities=20% Similarity=0.723 Sum_probs=6.8
Q ss_pred CeecCCCccc
Q psy14147 85 RFKCKLCPKM 94 (100)
Q Consensus 85 ~~~C~~C~~~ 94 (100)
|+.|+.||..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 5678888753
No 144
>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=58.39 E-value=8.6 Score=17.03 Aligned_cols=10 Identities=50% Similarity=1.272 Sum_probs=5.8
Q ss_pred eCchhhhhcc
Q psy14147 30 ACEECGKAFR 39 (100)
Q Consensus 30 ~c~~C~~~f~ 39 (100)
.|..|++.|.
T Consensus 4 ~C~~C~~~F~ 13 (57)
T cd00065 4 SCMGCGKPFT 13 (57)
T ss_pred cCcccCcccc
Confidence 3566666654
No 145
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=58.07 E-value=3.1 Score=29.09 Aligned_cols=15 Identities=13% Similarity=0.220 Sum_probs=10.2
Q ss_pred cCCCCCeecCCCccc
Q psy14147 80 HDNTPRFKCKLCPKM 94 (100)
Q Consensus 80 ~~~~~~~~C~~C~~~ 94 (100)
+....|..|+.||..
T Consensus 470 ~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 470 YQEPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCCCC
Confidence 344567888888754
No 146
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=57.66 E-value=6.3 Score=17.48 Aligned_cols=12 Identities=25% Similarity=0.551 Sum_probs=7.4
Q ss_pred CCeecCCCcccc
Q psy14147 84 PRFKCKLCPKMF 95 (100)
Q Consensus 84 ~~~~C~~C~~~f 95 (100)
..+.|..||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 356677777544
No 147
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=56.69 E-value=6.9 Score=17.55 Aligned_cols=6 Identities=33% Similarity=0.313 Sum_probs=3.2
Q ss_pred HHHHHH
Q psy14147 43 SLTMHQ 48 (100)
Q Consensus 43 ~l~~h~ 48 (100)
.|..|.
T Consensus 25 ~l~~H~ 30 (60)
T PF02176_consen 25 ELDDHL 30 (60)
T ss_dssp CHHHHH
T ss_pred HHHHHH
Confidence 455555
No 148
>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=56.55 E-value=3.8 Score=21.45 Aligned_cols=13 Identities=23% Similarity=0.529 Sum_probs=7.7
Q ss_pred ccCccccccccCh
Q psy14147 58 YQCDLCLARFVTN 70 (100)
Q Consensus 58 ~~c~~c~~~~~~~ 70 (100)
+.|..|+..|...
T Consensus 71 ~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 71 ARCRDCGHEFEPD 83 (113)
T ss_dssp EEETTTS-EEECH
T ss_pred EECCCCCCEEecC
Confidence 5677777766543
No 149
>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=56.40 E-value=5.3 Score=16.60 Aligned_cols=10 Identities=20% Similarity=0.717 Sum_probs=6.5
Q ss_pred eecCCCcccc
Q psy14147 86 FKCKLCPKMF 95 (100)
Q Consensus 86 ~~C~~C~~~f 95 (100)
|.|..||..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 5677777655
No 150
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.21 E-value=5 Score=18.67 Aligned_cols=43 Identities=9% Similarity=0.189 Sum_probs=24.3
Q ss_pred hhcCCCCCccCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 50 HVHLNDRRYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 50 ~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
..+.+..++.|+.-+..+..+.-+.. . ..+.--.|+.|+..|.
T Consensus 17 ~I~~~~~~l~C~g~~~p~~HPrV~L~---m-g~~gev~CPYC~t~y~ 59 (62)
T COG4391 17 TIEIGDLPLMCPGPEPPNDHPRVFLD---M-GDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEEeCCeeEEcCCCCCCCCCCEEEEE---c-CCCCcEecCccccEEE
Confidence 45667778888755444433322111 1 2233457999998886
No 151
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=54.55 E-value=4 Score=21.46 Aligned_cols=11 Identities=18% Similarity=0.549 Sum_probs=6.9
Q ss_pred CccCccccccc
Q psy14147 57 RYQCDLCLARF 67 (100)
Q Consensus 57 ~~~c~~c~~~~ 67 (100)
.+.|..|+..|
T Consensus 70 ~~~C~~Cg~~~ 80 (114)
T PRK03681 70 ECWCETCQQYV 80 (114)
T ss_pred EEEcccCCCee
Confidence 35677777544
No 152
>KOG2482|consensus
Probab=54.35 E-value=7.2 Score=24.83 Aligned_cols=21 Identities=43% Similarity=0.700 Sum_probs=19.9
Q ss_pred eeCchhhhhccChhHHHHHHh
Q psy14147 29 YACEECGKAFRKKFSLTMHQR 49 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~~ 49 (100)
+.|-.|.+.|..+..|..||+
T Consensus 196 ~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred heeeeeccccCCcHHHHHHHH
Confidence 789999999999999999996
No 153
>PF14369 zf-RING_3: zinc-finger
Probab=53.71 E-value=6.5 Score=15.97 Aligned_cols=9 Identities=33% Similarity=0.781 Sum_probs=5.4
Q ss_pred ecCCCcccc
Q psy14147 87 KCKLCPKMF 95 (100)
Q Consensus 87 ~C~~C~~~f 95 (100)
.|+.|+..|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 366666655
No 154
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=53.42 E-value=8 Score=16.17 Aligned_cols=11 Identities=18% Similarity=0.760 Sum_probs=7.9
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
|.|..|+..|.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 67877877664
No 155
>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=53.31 E-value=2.2 Score=18.55 Aligned_cols=13 Identities=23% Similarity=0.567 Sum_probs=7.2
Q ss_pred CCeecCC--CccccC
Q psy14147 84 PRFKCKL--CPKMFT 96 (100)
Q Consensus 84 ~~~~C~~--C~~~f~ 96 (100)
.-+.|.. ||..|.
T Consensus 24 ~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 24 LYCQCTNPECGHTFV 38 (47)
T ss_pred EEEEECCCcCCCEEE
Confidence 3455644 766664
No 156
>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=52.31 E-value=7.4 Score=21.34 Aligned_cols=39 Identities=18% Similarity=0.347 Sum_probs=21.9
Q ss_pred ccCccccccccChhHHHHHHHh-----cCCCCCeecCCCccccC
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQR-----HDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~-----~~~~~~~~C~~C~~~f~ 96 (100)
-.|..|+..+.....-...... ...+.-+.|+.||+.|.
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW 135 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYW 135 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEec
Confidence 4789998765443211110011 11234678999999985
No 157
>KOG3352|consensus
Probab=52.28 E-value=7 Score=21.73 Aligned_cols=14 Identities=21% Similarity=0.567 Sum_probs=11.0
Q ss_pred CCCeecCCCccccC
Q psy14147 83 TPRFKCKLCPKMFT 96 (100)
Q Consensus 83 ~~~~~C~~C~~~f~ 96 (100)
.+...|++||..|.
T Consensus 131 ge~~rc~eCG~~fk 144 (153)
T KOG3352|consen 131 GETQRCPECGHYFK 144 (153)
T ss_pred CCcccCCcccceEE
Confidence 45667999998885
No 158
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=51.08 E-value=11 Score=13.63 Aligned_cols=7 Identities=29% Similarity=0.695 Sum_probs=3.5
Q ss_pred ecCCCcc
Q psy14147 87 KCKLCPK 93 (100)
Q Consensus 87 ~C~~C~~ 93 (100)
.|+.||.
T Consensus 15 fC~~CG~ 21 (23)
T PF13240_consen 15 FCPNCGT 21 (23)
T ss_pred chhhhCC
Confidence 4555554
No 159
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=50.54 E-value=12 Score=16.66 Aligned_cols=10 Identities=20% Similarity=0.820 Sum_probs=5.1
Q ss_pred ccCccccccc
Q psy14147 58 YQCDLCLARF 67 (100)
Q Consensus 58 ~~c~~c~~~~ 67 (100)
+.|+.|+..+
T Consensus 29 W~C~~Cgh~w 38 (55)
T PF14311_consen 29 WKCPKCGHEW 38 (55)
T ss_pred EECCCCCCee
Confidence 4555555444
No 160
>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=50.47 E-value=7.8 Score=20.07 Aligned_cols=9 Identities=44% Similarity=1.161 Sum_probs=4.7
Q ss_pred ceeCchhhh
Q psy14147 28 PYACEECGK 36 (100)
Q Consensus 28 ~~~c~~C~~ 36 (100)
|-.|+.||.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 445555554
No 161
>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=50.37 E-value=9 Score=16.14 Aligned_cols=7 Identities=43% Similarity=1.004 Sum_probs=3.7
Q ss_pred ecCCCcc
Q psy14147 87 KCKLCPK 93 (100)
Q Consensus 87 ~C~~C~~ 93 (100)
.|+.||.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 4555554
No 162
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=50.04 E-value=28 Score=20.01 Aligned_cols=49 Identities=12% Similarity=0.154 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhccccccCCCceeCchhhhhccChhHHHHHHhhhcCCCCCccCcccccc
Q psy14147 8 VMEIQKDVVQSFPIILYCVKPYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLAR 66 (100)
Q Consensus 8 ~~~~~~~~l~~h~~~~~~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 66 (100)
.+......|+.-...-....-|.|+.|...++... -+ ..+ |.|+.||..
T Consensus 93 ~~~~~le~Lk~~le~~~~~~~y~C~~~~~r~sfde----A~---~~~---F~Cp~Cg~~ 141 (176)
T COG1675 93 KKRKILEKLKRKLEKETENNYYVCPNCHVKYSFDE----AM---ELG---FTCPKCGED 141 (176)
T ss_pred HHHHHHHHHHHHHHhhccCCceeCCCCCCcccHHH----HH---HhC---CCCCCCCch
Confidence 33444444444444444555677877765554322 11 222 678887754
No 163
>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=49.75 E-value=7.6 Score=21.53 Aligned_cols=12 Identities=33% Similarity=0.681 Sum_probs=8.0
Q ss_pred eecCCCccccCC
Q psy14147 86 FKCKLCPKMFTN 97 (100)
Q Consensus 86 ~~C~~C~~~f~~ 97 (100)
-.|..||+.|++
T Consensus 29 ReC~~C~~RFTT 40 (147)
T TIGR00244 29 RECLECHERFTT 40 (147)
T ss_pred ccCCccCCccce
Confidence 457777777764
No 164
>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=49.54 E-value=8.3 Score=15.54 Aligned_cols=12 Identities=17% Similarity=0.509 Sum_probs=7.1
Q ss_pred CeecCCCccccC
Q psy14147 85 RFKCKLCPKMFT 96 (100)
Q Consensus 85 ~~~C~~C~~~f~ 96 (100)
-+.|+.|++...
T Consensus 4 ~~~C~nC~R~v~ 15 (33)
T PF08209_consen 4 YVECPNCGRPVA 15 (33)
T ss_dssp EEE-TTTSSEEE
T ss_pred eEECCCCcCCcc
Confidence 367888876543
No 165
>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=49.04 E-value=11 Score=15.55 Aligned_cols=13 Identities=38% Similarity=1.007 Sum_probs=4.7
Q ss_pred CeecCCCccccCC
Q psy14147 85 RFKCKLCPKMFTN 97 (100)
Q Consensus 85 ~~~C~~C~~~f~~ 97 (100)
.|-|+.|...|++
T Consensus 3 ryyCdyC~~~~~~ 15 (38)
T PF06220_consen 3 RYYCDYCKKYLTH 15 (38)
T ss_dssp S-B-TTT--B-S-
T ss_pred CeecccccceecC
Confidence 3667888777743
No 166
>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=48.96 E-value=9.6 Score=16.70 Aligned_cols=10 Identities=20% Similarity=1.125 Sum_probs=5.6
Q ss_pred eecCCCcccc
Q psy14147 86 FKCKLCPKMF 95 (100)
Q Consensus 86 ~~C~~C~~~f 95 (100)
|.|..||..|
T Consensus 2 y~C~~CgyvY 11 (47)
T PF00301_consen 2 YQCPVCGYVY 11 (47)
T ss_dssp EEETTTSBEE
T ss_pred cCCCCCCEEE
Confidence 4566666444
No 167
>KOG3507|consensus
Probab=48.58 E-value=9.3 Score=17.64 Aligned_cols=26 Identities=27% Similarity=0.639 Sum_probs=14.9
Q ss_pred eeCchhhhhccChhHHHHHHhhhcCCCCCccCcccccc
Q psy14147 29 YACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLAR 66 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~ 66 (100)
|.|..|+..- .....-++.|..||..
T Consensus 21 YiCgdC~~en------------~lk~~D~irCReCG~R 46 (62)
T KOG3507|consen 21 YICGDCGQEN------------TLKRGDVIRCRECGYR 46 (62)
T ss_pred EEeccccccc------------cccCCCcEehhhcchH
Confidence 7777777432 1122335678778754
No 168
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=48.53 E-value=9.3 Score=15.75 Aligned_cols=11 Identities=36% Similarity=0.585 Sum_probs=6.8
Q ss_pred ecCCCccccCC
Q psy14147 87 KCKLCPKMFTN 97 (100)
Q Consensus 87 ~C~~C~~~f~~ 97 (100)
.|+.|++.|-+
T Consensus 4 ~CprC~kg~Hw 14 (36)
T PF14787_consen 4 LCPRCGKGFHW 14 (36)
T ss_dssp C-TTTSSSCS-
T ss_pred cCcccCCCcch
Confidence 57888887744
No 169
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=48.29 E-value=11 Score=23.17 Aligned_cols=11 Identities=36% Similarity=0.727 Sum_probs=6.4
Q ss_pred CCeecCCCccc
Q psy14147 84 PRFKCKLCPKM 94 (100)
Q Consensus 84 ~~~~C~~C~~~ 94 (100)
+.|.|+.||..
T Consensus 321 r~~~C~~cg~~ 331 (364)
T COG0675 321 RLFKCPRCGFV 331 (364)
T ss_pred eeEECCCCCCe
Confidence 44666666654
No 170
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.19 E-value=9.6 Score=20.03 Aligned_cols=27 Identities=15% Similarity=0.057 Sum_probs=18.2
Q ss_pred cCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 59 QCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 59 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
.|+.|++.|.. | ...|..|+.||+.|.
T Consensus 11 idPetg~KFYD---L--------NrdPiVsPytG~s~P 37 (129)
T COG4530 11 IDPETGKKFYD---L--------NRDPIVSPYTGKSYP 37 (129)
T ss_pred cCccccchhhc---c--------CCCccccCcccccch
Confidence 57777776633 2 235788888888885
No 171
>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=48.06 E-value=5 Score=21.97 Aligned_cols=32 Identities=22% Similarity=0.679 Sum_probs=18.9
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
.|.|..|+..+.. +.+. ....|.|+.|+..|.
T Consensus 123 ~~~C~~C~~~~~r------~~~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRRS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeee------eccc--chhhEECCCCCCEEE
Confidence 3678778765522 2222 223388999987664
No 172
>KOG4727|consensus
Probab=48.04 E-value=10 Score=21.66 Aligned_cols=20 Identities=20% Similarity=0.566 Sum_probs=18.6
Q ss_pred eeCchhhhhccChhHHHHHH
Q psy14147 29 YACEECGKAFRKKFSLTMHQ 48 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~ 48 (100)
|-|++|+-.+..+.++..|+
T Consensus 76 yyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 76 YYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred eeeeecceeehhhHHHHHHh
Confidence 88999999999999998887
No 173
>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=47.92 E-value=9.5 Score=15.73 Aligned_cols=11 Identities=27% Similarity=0.866 Sum_probs=5.9
Q ss_pred CCeecCCCccc
Q psy14147 84 PRFKCKLCPKM 94 (100)
Q Consensus 84 ~~~~C~~C~~~ 94 (100)
+.|+|..||..
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 45889998854
No 174
>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=47.62 E-value=9.1 Score=15.98 Aligned_cols=10 Identities=20% Similarity=0.793 Sum_probs=5.5
Q ss_pred eecCCCcccc
Q psy14147 86 FKCKLCPKMF 95 (100)
Q Consensus 86 ~~C~~C~~~f 95 (100)
+.|+.||..+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 4566666554
No 175
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=47.34 E-value=23 Score=20.69 Aligned_cols=11 Identities=18% Similarity=0.461 Sum_probs=5.7
Q ss_pred CccCccccccc
Q psy14147 57 RYQCDLCLARF 67 (100)
Q Consensus 57 ~~~c~~c~~~~ 67 (100)
...|..||.-+
T Consensus 30 lvrC~eCG~V~ 40 (201)
T COG1326 30 LVRCEECGTVH 40 (201)
T ss_pred EEEccCCCcEe
Confidence 34566665443
No 176
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=47.32 E-value=11 Score=19.74 Aligned_cols=25 Identities=28% Similarity=0.478 Sum_probs=17.1
Q ss_pred CCCCccCccccccccChhHHHHHHH
Q psy14147 54 NDRRYQCDLCLARFVTNSSLIVHKQ 78 (100)
Q Consensus 54 ~~~~~~c~~c~~~~~~~~~l~~h~~ 78 (100)
|...+-|..|.+-|.....|..|.+
T Consensus 52 GlGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhc
Confidence 3344667778887777777777765
No 177
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=47.29 E-value=8.5 Score=21.46 Aligned_cols=12 Identities=33% Similarity=0.667 Sum_probs=8.5
Q ss_pred eecCCCccccCC
Q psy14147 86 FKCKLCPKMFTN 97 (100)
Q Consensus 86 ~~C~~C~~~f~~ 97 (100)
-.|+.||+.|++
T Consensus 29 ReC~~C~~RFTT 40 (156)
T COG1327 29 RECLECGERFTT 40 (156)
T ss_pred hcccccccccch
Confidence 457778777765
No 178
>PRK00420 hypothetical protein; Validated
Probab=46.75 E-value=17 Score=19.19 Aligned_cols=9 Identities=11% Similarity=0.073 Sum_probs=4.7
Q ss_pred ccCcccccc
Q psy14147 58 YQCDLCLAR 66 (100)
Q Consensus 58 ~~c~~c~~~ 66 (100)
..|+.|+..
T Consensus 41 ~~Cp~Cg~~ 49 (112)
T PRK00420 41 VVCPVHGKV 49 (112)
T ss_pred eECCCCCCe
Confidence 355555553
No 179
>KOG1280|consensus
Probab=46.29 E-value=21 Score=22.84 Aligned_cols=38 Identities=21% Similarity=0.422 Sum_probs=22.3
Q ss_pred CceeCchhhhhccChhHHHHHHhhhcCCCCC-ccCcccc
Q psy14147 27 KPYACEECGKAFRKKFSLTMHQRHVHLNDRR-YQCDLCL 64 (100)
Q Consensus 27 ~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~-~~c~~c~ 64 (100)
..|.|+.|+..-.+...+..|....|....+ ..|++|+
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 3477777877666677777777444433221 2455554
No 180
>PRK01343 zinc-binding protein; Provisional
Probab=44.72 E-value=13 Score=17.05 Aligned_cols=11 Identities=36% Similarity=0.446 Sum_probs=6.3
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
..|+.|++.+.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 34666666554
No 181
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.06 E-value=7.8 Score=20.71 Aligned_cols=12 Identities=25% Similarity=0.379 Sum_probs=7.1
Q ss_pred CccCccccccccC
Q psy14147 57 RYQCDLCLARFVT 69 (100)
Q Consensus 57 ~~~c~~c~~~~~~ 69 (100)
.+.| .|+..|..
T Consensus 70 ~~~C-~Cg~~~~~ 81 (124)
T PRK00762 70 EIEC-ECGYEGVV 81 (124)
T ss_pred eEEe-eCcCcccc
Confidence 3567 77765543
No 182
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=43.72 E-value=12 Score=15.77 Aligned_cols=10 Identities=20% Similarity=0.487 Sum_probs=6.9
Q ss_pred CeecCCCccc
Q psy14147 85 RFKCKLCPKM 94 (100)
Q Consensus 85 ~~~C~~C~~~ 94 (100)
|..|+.||..
T Consensus 2 ~~~Cp~Cg~~ 11 (47)
T PF14690_consen 2 PPRCPHCGSP 11 (47)
T ss_pred CccCCCcCCC
Confidence 5678888743
No 183
>PRK05978 hypothetical protein; Provisional
Probab=43.45 E-value=7.4 Score=21.60 Aligned_cols=12 Identities=33% Similarity=0.689 Sum_probs=8.0
Q ss_pred eecCCCccccCC
Q psy14147 86 FKCKLCPKMFTN 97 (100)
Q Consensus 86 ~~C~~C~~~f~~ 97 (100)
-.|+.||..|..
T Consensus 53 ~~C~~CG~~~~~ 64 (148)
T PRK05978 53 DHCAACGEDFTH 64 (148)
T ss_pred CCccccCCcccc
Confidence 357788777653
No 184
>KOG2231|consensus
Probab=43.34 E-value=43 Score=23.59 Aligned_cols=19 Identities=26% Similarity=0.433 Sum_probs=10.7
Q ss_pred eCchhhhhccChhHHHHHH
Q psy14147 30 ACEECGKAFRKKFSLTMHQ 48 (100)
Q Consensus 30 ~c~~C~~~f~~~~~l~~h~ 48 (100)
.|..|...|.....|..|+
T Consensus 184 ~C~~C~~~fld~~el~rH~ 202 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHL 202 (669)
T ss_pred cchhhhhhhccHHHHHHhh
Confidence 3555555555555555555
No 185
>KOG2231|consensus
Probab=43.15 E-value=40 Score=23.77 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=14.9
Q ss_pred cCccccccccChhHHHHHHHhcC
Q psy14147 59 QCDLCLARFVTNSSLIVHKQRHD 81 (100)
Q Consensus 59 ~c~~c~~~~~~~~~l~~h~~~~~ 81 (100)
.|..|...|.....|..|++.++
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce
Confidence 56667777766667777666443
No 186
>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=42.27 E-value=11 Score=17.68 Aligned_cols=17 Identities=12% Similarity=0.333 Sum_probs=12.0
Q ss_pred cCCCCCeecCCCccccC
Q psy14147 80 HDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 80 ~~~~~~~~C~~C~~~f~ 96 (100)
+-.+....|+.|+..|.
T Consensus 48 ~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 48 EIVEGELICPECGREYP 64 (68)
T ss_dssp ETTTTEEEETTTTEEEE
T ss_pred cccCCEEEcCCCCCEEe
Confidence 34455678888888875
No 187
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.16 E-value=20 Score=22.22 Aligned_cols=9 Identities=44% Similarity=1.058 Sum_probs=5.4
Q ss_pred ecCCCcccc
Q psy14147 87 KCKLCPKMF 95 (100)
Q Consensus 87 ~C~~C~~~f 95 (100)
.|+.||..|
T Consensus 271 ~C~~Cgt~f 279 (279)
T TIGR00627 271 ICKTCKTAF 279 (279)
T ss_pred CCCCCCCCC
Confidence 566666554
No 188
>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=41.96 E-value=15 Score=14.35 Aligned_cols=11 Identities=18% Similarity=0.972 Sum_probs=4.6
Q ss_pred CeecCCCcccc
Q psy14147 85 RFKCKLCPKMF 95 (100)
Q Consensus 85 ~~~C~~C~~~f 95 (100)
.|.|+.|+..+
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 46666666543
No 189
>PF12773 DZR: Double zinc ribbon
Probab=41.41 E-value=25 Score=15.10 Aligned_cols=9 Identities=22% Similarity=0.371 Sum_probs=4.7
Q ss_pred eecCCCccc
Q psy14147 86 FKCKLCPKM 94 (100)
Q Consensus 86 ~~C~~C~~~ 94 (100)
..|+.||..
T Consensus 30 ~~C~~Cg~~ 38 (50)
T PF12773_consen 30 KICPNCGAE 38 (50)
T ss_pred CCCcCCcCC
Confidence 445555544
No 190
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.25 E-value=13 Score=17.29 Aligned_cols=13 Identities=31% Similarity=0.524 Sum_probs=7.3
Q ss_pred CCCCCccCccccc
Q psy14147 53 LNDRRYQCDLCLA 65 (100)
Q Consensus 53 ~~~~~~~c~~c~~ 65 (100)
..-..|.|++|..
T Consensus 27 ~PIrtymC~eC~~ 39 (68)
T COG4896 27 KPIRTYMCPECEH 39 (68)
T ss_pred CCceeEechhhHh
Confidence 3344566776654
No 191
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=41.06 E-value=9.6 Score=18.17 Aligned_cols=31 Identities=19% Similarity=0.475 Sum_probs=15.9
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCcccc
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMF 95 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f 95 (100)
...|..|+..+..... ..+ ..+.|+.|+..|
T Consensus 41 ~v~Cg~C~~~~~~~~~-------~c~-~~~~C~~C~~~~ 71 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEY-------SCG-ADYFCPICGLYF 71 (71)
T ss_dssp EEEETTT--EEES-SB-------TT---SEEETTTTEEE
T ss_pred CeECCCCCCccChhhh-------hcC-CCccCcCcCCCC
Confidence 5567777765544332 111 468898888654
No 192
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=40.48 E-value=14 Score=16.82 Aligned_cols=10 Identities=50% Similarity=1.155 Sum_probs=6.4
Q ss_pred ecCCCccccC
Q psy14147 87 KCKLCPKMFT 96 (100)
Q Consensus 87 ~C~~C~~~f~ 96 (100)
.|+.||+.|.
T Consensus 7 ~C~~Cg~~~~ 16 (54)
T PF14446_consen 7 KCPVCGKKFK 16 (54)
T ss_pred cChhhCCccc
Confidence 5666766664
No 193
>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=40.23 E-value=12 Score=18.91 Aligned_cols=30 Identities=33% Similarity=0.732 Sum_probs=17.8
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
.|.|+.|++.-.. +...| .|.|..|++.|.
T Consensus 35 ky~Cp~Cgk~~vk--------R~a~G--IW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVK--------RVATG--IWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEE--------EEETT--EEEETTTTEEEE
T ss_pred CCcCCCCCCceeE--------EeeeE--EeecCCCCCEEe
Confidence 5778888764311 12233 478888887774
No 194
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=39.56 E-value=39 Score=15.07 Aligned_cols=31 Identities=13% Similarity=0.320 Sum_probs=17.1
Q ss_pred cCccccccccChhHHHHHHHhcCCCCCeecCCCcc
Q psy14147 59 QCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPK 93 (100)
Q Consensus 59 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~ 93 (100)
.|..|+...+.. .... ...++....|+.||+
T Consensus 24 ~C~gC~~~l~~~--~~~~--i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQ--ELNE--IRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHH--HHHH--HHcCCCeEECcCCCc
Confidence 566666544222 2222 233456778999986
No 195
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.53 E-value=23 Score=26.20 Aligned_cols=11 Identities=36% Similarity=0.857 Sum_probs=6.8
Q ss_pred CceeCchhhhh
Q psy14147 27 KPYACEECGKA 37 (100)
Q Consensus 27 ~~~~c~~C~~~ 37 (100)
....|+.||..
T Consensus 625 g~RfCpsCG~~ 635 (1121)
T PRK04023 625 GRRKCPSCGKE 635 (1121)
T ss_pred cCccCCCCCCc
Confidence 33567777754
No 196
>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=39.40 E-value=8.2 Score=17.28 Aligned_cols=26 Identities=23% Similarity=0.618 Sum_probs=14.3
Q ss_pred CCceeCchhhhhccChhHHHHHHhhhc
Q psy14147 26 VKPYACEECGKAFRKKFSLTMHQRHVH 52 (100)
Q Consensus 26 ~~~~~c~~C~~~f~~~~~l~~h~~~~~ 52 (100)
...|.|+.|.+.|-..-++-.|. ..|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE-~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHE-TLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTT-TS-
T ss_pred CCeEECCCCCCccccCcChhhhc-ccc
Confidence 35699999999998887776676 344
No 197
>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=39.31 E-value=6.1 Score=16.24 Aligned_cols=16 Identities=25% Similarity=0.738 Sum_probs=8.2
Q ss_pred HHHhcCCCCCeecCCC
Q psy14147 76 HKQRHDNTPRFKCKLC 91 (100)
Q Consensus 76 h~~~~~~~~~~~C~~C 91 (100)
|=+...|...|.|..|
T Consensus 20 ~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 20 NGKSPSGHQRYRCKDC 35 (36)
T ss_pred CCCCCCCCEeEecCcC
Confidence 3334445555666655
No 198
>KOG2907|consensus
Probab=38.93 E-value=18 Score=19.11 Aligned_cols=39 Identities=18% Similarity=0.408 Sum_probs=20.7
Q ss_pred ccCccccccccChhHHHHHHHhcC-CC-CCeecCCCccccCCC
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQRHD-NT-PRFKCKLCPKMFTNT 98 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~~~-~~-~~~~C~~C~~~f~~~ 98 (100)
..|+.||..=..-.. ..+|+.. |+ .-|.|+.|+..|+..
T Consensus 75 ~kCpkCghe~m~Y~T--~QlRSADEGQTVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHT--LQLRSADEGQTVFYTCPKCKYKFTEN 115 (116)
T ss_pred ccCcccCCchhhhhh--hhcccccCCceEEEEcCccceeeecc
Confidence 468888753111111 1122322 22 238899999988754
No 199
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=38.71 E-value=11 Score=14.00 Aligned_cols=6 Identities=33% Similarity=0.966 Sum_probs=2.8
Q ss_pred cCCCcc
Q psy14147 88 CKLCPK 93 (100)
Q Consensus 88 C~~C~~ 93 (100)
|+.||.
T Consensus 19 C~~CG~ 24 (26)
T PF13248_consen 19 CPNCGA 24 (26)
T ss_pred ChhhCC
Confidence 444443
No 200
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=38.61 E-value=45 Score=21.22 Aligned_cols=22 Identities=36% Similarity=1.031 Sum_probs=11.1
Q ss_pred CccCccccccccChhHHHHHHH
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQ 78 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~ 78 (100)
.|.|+.|...|..--+.-.|..
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHET 409 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHH
Confidence 4555555555555444444443
No 201
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=38.36 E-value=16 Score=16.62 Aligned_cols=30 Identities=10% Similarity=0.207 Sum_probs=12.0
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKL 90 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~ 90 (100)
|.....|+..|..... ..++ .......|+.
T Consensus 24 PV~s~~C~H~fek~aI-~~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 24 PVKSKKCGHTFEKEAI-LQYI---QRNGSKRCPV 53 (57)
T ss_dssp EEEESSS--EEEHHHH-HHHC---TTTS-EE-SC
T ss_pred CcCcCCCCCeecHHHH-HHHH---HhcCCCCCCC
Confidence 3444456666654433 2333 2334566665
No 202
>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=38.19 E-value=15 Score=15.27 Aligned_cols=12 Identities=17% Similarity=0.794 Sum_probs=5.6
Q ss_pred CCCCccCccccc
Q psy14147 54 NDRRYQCDLCLA 65 (100)
Q Consensus 54 ~~~~~~c~~c~~ 65 (100)
+.+.|.|..|+.
T Consensus 21 ~~~~w~C~~C~~ 32 (40)
T PF04810_consen 21 GGKTWICNFCGT 32 (40)
T ss_dssp TTTEEEETTT--
T ss_pred CCCEEECcCCCC
Confidence 344566666654
No 203
>KOG1088|consensus
Probab=38.01 E-value=19 Score=19.20 Aligned_cols=19 Identities=11% Similarity=0.106 Sum_probs=14.0
Q ss_pred hcCCCCCeecCCCccccCC
Q psy14147 79 RHDNTPRFKCKLCPKMFTN 97 (100)
Q Consensus 79 ~~~~~~~~~C~~C~~~f~~ 97 (100)
.+-.+....|++||..|.-
T Consensus 92 ~~v~EG~l~CpetG~vfpI 110 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFPI 110 (124)
T ss_pred hhhccceEecCCCCcEeec
Confidence 3444566899999999964
No 204
>KOG2071|consensus
Probab=38.01 E-value=19 Score=24.67 Aligned_cols=28 Identities=25% Similarity=0.477 Sum_probs=22.3
Q ss_pred CCCceeCchhhhhccChhHHHHHHhhhcC
Q psy14147 25 CVKPYACEECGKAFRKKFSLTMHQRHVHL 53 (100)
Q Consensus 25 ~~~~~~c~~C~~~f~~~~~l~~h~~~~~~ 53 (100)
...|..|..||.+|........||. .|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md-~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMD-IHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhh-hhh
Confidence 3567899999999999988877773 553
No 205
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=37.91 E-value=17 Score=19.89 Aligned_cols=24 Identities=21% Similarity=0.133 Sum_probs=16.1
Q ss_pred cCccccccccChhHHHHHHHhcCCCCC
Q psy14147 59 QCDLCLARFVTNSSLIVHKQRHDNTPR 85 (100)
Q Consensus 59 ~c~~c~~~~~~~~~l~~h~~~~~~~~~ 85 (100)
.|-++|+.|.+ |.+|+.+|.+--|
T Consensus 78 icLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 78 ICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEeccCcchHH---HHHHHhcccCCCH
Confidence 56777777643 7778887766444
No 206
>KOG2636|consensus
Probab=37.01 E-value=21 Score=23.69 Aligned_cols=27 Identities=22% Similarity=0.455 Sum_probs=18.3
Q ss_pred cccCCCceeCchhh-hhccChhHHHHHH
Q psy14147 22 ILYCVKPYACEECG-KAFRKKFSLTMHQ 48 (100)
Q Consensus 22 ~~~~~~~~~c~~C~-~~f~~~~~l~~h~ 48 (100)
.|.-...|.|.+|| .++.-...+..|.
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHh
Confidence 34545668899998 5666666666665
No 207
>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=36.87 E-value=20 Score=14.20 Aligned_cols=12 Identities=25% Similarity=0.960 Sum_probs=8.4
Q ss_pred CCeecCCCcccc
Q psy14147 84 PRFKCKLCPKMF 95 (100)
Q Consensus 84 ~~~~C~~C~~~f 95 (100)
+-|+|..||...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 358888887543
No 208
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=36.74 E-value=18 Score=20.49 Aligned_cols=37 Identities=19% Similarity=0.372 Sum_probs=20.7
Q ss_pred ccCccccccccChhHHHH-------HHHhcCCCCCeecCCCccccC
Q psy14147 58 YQCDLCLARFVTNSSLIV-------HKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~-------h~~~~~~~~~~~C~~C~~~f~ 96 (100)
-.|++|+......+.=.. +... .+.-+.|+.||+.|.
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~--~~~f~~C~~CgkiYW 141 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRN--YEEFYRCPKCGKIYW 141 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhc--ccceeECCCCccccc
Confidence 369999875433221111 1111 123467999999885
No 209
>PRK04351 hypothetical protein; Provisional
Probab=35.82 E-value=12 Score=20.81 Aligned_cols=31 Identities=29% Similarity=0.821 Sum_probs=18.5
Q ss_pred ccCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
|.|..|+..+... +.+ ....|.|..|+..+.
T Consensus 113 Y~C~~Cg~~~~r~-------Rr~-n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 113 YECQSCGQQYLRK-------RRI-NTKRYRCGKCRGKLK 143 (149)
T ss_pred EECCCCCCEeeee-------eec-CCCcEEeCCCCcEee
Confidence 6787787554321 112 235688888886653
No 210
>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=35.40 E-value=9.8 Score=25.47 Aligned_cols=11 Identities=18% Similarity=0.386 Sum_probs=6.4
Q ss_pred CCCeecCCCcc
Q psy14147 83 TPRFKCKLCPK 93 (100)
Q Consensus 83 ~~~~~C~~C~~ 93 (100)
..|..|+.||.
T Consensus 251 ~~~~~Cp~C~s 261 (505)
T TIGR00595 251 PIPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCCC
Confidence 34556666654
No 211
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=35.40 E-value=22 Score=14.06 Aligned_cols=12 Identities=25% Similarity=0.941 Sum_probs=8.7
Q ss_pred CCeecCCCcccc
Q psy14147 84 PRFKCKLCPKMF 95 (100)
Q Consensus 84 ~~~~C~~C~~~f 95 (100)
+-|+|..||...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 468898888544
No 212
>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=35.18 E-value=22 Score=19.75 Aligned_cols=9 Identities=22% Similarity=0.586 Sum_probs=4.5
Q ss_pred CccCccccc
Q psy14147 57 RYQCDLCLA 65 (100)
Q Consensus 57 ~~~c~~c~~ 65 (100)
.+.|..||.
T Consensus 112 ~l~C~~Cg~ 120 (146)
T PF07295_consen 112 TLVCENCGH 120 (146)
T ss_pred eEecccCCC
Confidence 345555554
No 213
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=35.17 E-value=39 Score=17.49 Aligned_cols=36 Identities=17% Similarity=0.227 Sum_probs=22.7
Q ss_pred ceeCchhhhhccChhHHHHHHhhhcCCCCCccCccccc
Q psy14147 28 PYACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLA 65 (100)
Q Consensus 28 ~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~ 65 (100)
.|.|+.-+..|.+...+...+. .-..+.|.|...|+
T Consensus 3 Vf~i~~T~EiF~dYe~Y~~R~~--~y~~~vwtC~~TGk 38 (102)
T PF10537_consen 3 VFYIPFTGEIFRDYEEYLKRMI--LYNQRVWTCEITGK 38 (102)
T ss_pred eEEeCCCCcccCCHHHHHHHHH--HHhCCeeEEecCCC
Confidence 4666666777777777666653 23345677776665
No 214
>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=34.81 E-value=20 Score=18.19 Aligned_cols=30 Identities=27% Similarity=0.698 Sum_probs=18.3
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
.|.|+.|++.-.. +.. .-.+.|..|++.|.
T Consensus 35 ~y~CpfCgk~~vk--------R~a--~GIW~C~~C~~~~A 64 (91)
T TIGR00280 35 KYVCPFCGKKTVK--------RGS--TGIWTCRKCGAKFA 64 (91)
T ss_pred CccCCCCCCCceE--------EEe--eEEEEcCCCCCEEe
Confidence 5778888754211 112 23588888888774
No 215
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=34.61 E-value=21 Score=18.47 Aligned_cols=12 Identities=25% Similarity=0.656 Sum_probs=7.4
Q ss_pred CCCeecCCCccc
Q psy14147 83 TPRFKCKLCPKM 94 (100)
Q Consensus 83 ~~~~~C~~C~~~ 94 (100)
.+.|.|+.||..
T Consensus 20 ~k~FtCp~Cghe 31 (104)
T COG4888 20 PKTFTCPRCGHE 31 (104)
T ss_pred CceEecCccCCe
Confidence 455677777654
No 216
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=34.22 E-value=55 Score=21.20 Aligned_cols=19 Identities=32% Similarity=0.410 Sum_probs=10.5
Q ss_pred CchhhhhccChhHHHHHHh
Q psy14147 31 CEECGKAFRKKFSLTMHQR 49 (100)
Q Consensus 31 c~~C~~~f~~~~~l~~h~~ 49 (100)
|..|...|-....|..|++
T Consensus 223 C~FC~~~FYdDDEL~~HcR 241 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCR 241 (493)
T ss_pred hhhccceecChHHHHHHHH
Confidence 5555555555555555554
No 217
>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=34.12 E-value=20 Score=16.04 Aligned_cols=15 Identities=20% Similarity=0.835 Sum_probs=8.4
Q ss_pred CCCCeecCCCccccC
Q psy14147 82 NTPRFKCKLCPKMFT 96 (100)
Q Consensus 82 ~~~~~~C~~C~~~f~ 96 (100)
+...|.|.+|++.+.
T Consensus 32 ~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 32 EPIKLRCHYCERIIT 46 (52)
T ss_dssp TTCEEEETTT--EEE
T ss_pred CCCEEEeeCCCCEec
Confidence 445577888877654
No 218
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=34.10 E-value=27 Score=15.92 Aligned_cols=10 Identities=30% Similarity=0.876 Sum_probs=5.7
Q ss_pred ecCCCccccC
Q psy14147 87 KCKLCPKMFT 96 (100)
Q Consensus 87 ~C~~C~~~f~ 96 (100)
-|+.|++.|.
T Consensus 41 gCPfC~~~~~ 50 (55)
T PF14447_consen 41 GCPFCGTPFE 50 (55)
T ss_pred CCCCCCCccc
Confidence 3566666554
No 219
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=34.02 E-value=23 Score=22.19 Aligned_cols=13 Identities=31% Similarity=0.777 Sum_probs=5.8
Q ss_pred cCCCCCccCccccc
Q psy14147 52 HLNDRRYQCDLCLA 65 (100)
Q Consensus 52 ~~~~~~~~c~~c~~ 65 (100)
|.+..| .|++|..
T Consensus 55 hL~~qp-~CP~Cr~ 67 (391)
T COG5432 55 HLGTQP-FCPVCRE 67 (391)
T ss_pred HhcCCC-CCccccc
Confidence 334434 2555544
No 220
>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=33.72 E-value=14 Score=21.61 Aligned_cols=26 Identities=23% Similarity=0.471 Sum_probs=0.0
Q ss_pred ccCCCceeCchhhhh-ccChhHHHHHH
Q psy14147 23 LYCVKPYACEECGKA-FRKKFSLTMHQ 48 (100)
Q Consensus 23 ~~~~~~~~c~~C~~~-f~~~~~l~~h~ 48 (100)
|.-...|.|.+||.. |.-...+..|-
T Consensus 96 hGL~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 96 HGLGVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ---------------------------
T ss_pred hCCCCeeeeEeCCCcceecHHHHHHhc
Confidence 444556899999963 43445555555
No 221
>PRK05580 primosome assembly protein PriA; Validated
Probab=33.70 E-value=11 Score=26.15 Aligned_cols=13 Identities=15% Similarity=0.330 Sum_probs=7.6
Q ss_pred CCCCCeecCCCcc
Q psy14147 81 DNTPRFKCKLCPK 93 (100)
Q Consensus 81 ~~~~~~~C~~C~~ 93 (100)
+...|..|+.||.
T Consensus 417 ~~~~~~~Cp~Cg~ 429 (679)
T PRK05580 417 QEPIPKACPECGS 429 (679)
T ss_pred CCCCCCCCCCCcC
Confidence 3344666777764
No 222
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=32.82 E-value=24 Score=16.56 Aligned_cols=8 Identities=25% Similarity=0.833 Sum_probs=4.2
Q ss_pred ecCCCccc
Q psy14147 87 KCKLCPKM 94 (100)
Q Consensus 87 ~C~~C~~~ 94 (100)
.||.||..
T Consensus 20 ~CP~Cgs~ 27 (64)
T COG2093 20 ICPVCGST 27 (64)
T ss_pred cCCCCCCc
Confidence 35555544
No 223
>COG2879 Uncharacterized small protein [Function unknown]
Probab=32.78 E-value=61 Score=15.27 Aligned_cols=19 Identities=21% Similarity=0.191 Sum_probs=12.1
Q ss_pred ccChhHHHHHHhhhcCCCCC
Q psy14147 38 FRKKFSLTMHQRHVHLNDRR 57 (100)
Q Consensus 38 f~~~~~l~~h~~~~~~~~~~ 57 (100)
.++..++..||+..|+ .+|
T Consensus 22 vpdYdnYVehmr~~hP-d~p 40 (65)
T COG2879 22 VPDYDNYVEHMRKKHP-DKP 40 (65)
T ss_pred CCcHHHHHHHHHHhCc-CCC
Confidence 3556778899975454 444
No 224
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=32.54 E-value=25 Score=18.10 Aligned_cols=12 Identities=25% Similarity=0.653 Sum_probs=9.1
Q ss_pred CCeecCCCcccc
Q psy14147 84 PRFKCKLCPKMF 95 (100)
Q Consensus 84 ~~~~C~~C~~~f 95 (100)
+..+|..||..|
T Consensus 87 r~~rC~nCG~~f 98 (98)
T PF10164_consen 87 RERRCSNCGATF 98 (98)
T ss_pred CccccCCCCccC
Confidence 446789998876
No 225
>KOG1409|consensus
Probab=32.29 E-value=15 Score=23.60 Aligned_cols=39 Identities=18% Similarity=0.369 Sum_probs=23.0
Q ss_pred ccCccccccccChhHHHHHHHhcCCCCCeecCCCccccCC
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFTN 97 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~ 97 (100)
..|+.|...|.... ...+.+.-.|-+...|+.||+.+..
T Consensus 283 ~~cQ~c~qpffwn~-~~m~~~k~~glr~h~crkcg~avc~ 321 (404)
T KOG1409|consen 283 DSCQKCNQPFFWNF-RQMWDRKQLGLRQHHCRKCGKAVCG 321 (404)
T ss_pred chhhhhCchHHHHH-HHHHhhhhhhhhhhhhhhhhhhcCc
Confidence 35777877664432 2234444455666778887776643
No 226
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=31.78 E-value=21 Score=19.54 Aligned_cols=33 Identities=24% Similarity=0.707 Sum_probs=17.9
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
.|.|..|+..+. .+.+ +..-..|.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~------~~rr-~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 112 PYRCTGCGQRYL------RVRR-SNNVSRYRCGKCGGKLI 144 (146)
T ss_pred EEECCCCCCCCc------eEcc-ccCcceEEcCCCCCEEE
Confidence 467777775542 1222 12224578888876653
No 227
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=31.17 E-value=26 Score=17.80 Aligned_cols=30 Identities=27% Similarity=0.646 Sum_probs=18.8
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
.|.|+.|++.-.. + .+.-.+.|..|++.|.
T Consensus 36 ~y~CpfCgk~~vk--------R--~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 36 KYFCPFCGKHAVK--------R--QAVGIWRCKGCKKTVA 65 (90)
T ss_pred CccCCCCCCCcee--------e--eeeEEEEcCCCCCEEe
Confidence 6788888754211 1 1224688888888775
No 228
>KOG0782|consensus
Probab=31.07 E-value=5.9 Score=27.12 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=13.1
Q ss_pred HHHHHHhhhcCCCCCccCccccccccCh
Q psy14147 43 SLTMHQRHVHLNDRRYQCDLCLARFVTN 70 (100)
Q Consensus 43 ~l~~h~~~~~~~~~~~~c~~c~~~~~~~ 70 (100)
.+..|- .+|....--.|..|++.|.+.
T Consensus 240 ~fvrHH-WVHrrRqeGkC~~CgKgFQQK 266 (1004)
T KOG0782|consen 240 GFVRHH-WVHRRRQEGKCNTCGKGFQQK 266 (1004)
T ss_pred cchHHh-HhhHhhhccccchhhhhhhhh
Confidence 444444 344433333566666665443
No 229
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=30.77 E-value=18 Score=20.71 Aligned_cols=16 Identities=19% Similarity=0.459 Sum_probs=12.8
Q ss_pred CCCeecCCCccccCCC
Q psy14147 83 TPRFKCKLCPKMFTNT 98 (100)
Q Consensus 83 ~~~~~C~~C~~~f~~~ 98 (100)
.....|..||+.|...
T Consensus 112 ~~~~~C~~Cg~~f~~~ 127 (181)
T PRK08222 112 FHLQRCSRCERPFAPQ 127 (181)
T ss_pred cccCcCcccCCccCcH
Confidence 3577899999999753
No 230
>KOG0717|consensus
Probab=30.47 E-value=32 Score=23.10 Aligned_cols=21 Identities=24% Similarity=0.512 Sum_probs=18.4
Q ss_pred ccCccccccccChhHHHHHHH
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQ 78 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~ 78 (100)
+.|.+|.+.|.+...+..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 789999999999988888865
No 231
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=30.22 E-value=27 Score=17.73 Aligned_cols=30 Identities=23% Similarity=0.518 Sum_probs=18.1
Q ss_pred CccCccccccccChhHHHHHHHhcCCCCCeecCCCccccC
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCPKMFT 96 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~ 96 (100)
.|.|+.|++.-.. +.. .-.+.|..|++.|.
T Consensus 36 ~y~CpfCgk~~vk--------R~a--~GIW~C~~C~~~~A 65 (90)
T PRK03976 36 KHVCPVCGRPKVK--------RVG--TGIWECRKCGAKFA 65 (90)
T ss_pred CccCCCCCCCceE--------EEE--EEEEEcCCCCCEEe
Confidence 5778888654211 112 23588888888774
No 232
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=29.83 E-value=5.6 Score=27.81 Aligned_cols=9 Identities=22% Similarity=0.670 Sum_probs=5.8
Q ss_pred CCeecCCCc
Q psy14147 84 PRFKCKLCP 92 (100)
Q Consensus 84 ~~~~C~~C~ 92 (100)
.+..|+.||
T Consensus 139 ~~~~C~~Cg 147 (711)
T TIGR00143 139 QPIACPRCG 147 (711)
T ss_pred CCccCCCCC
Confidence 355677776
No 233
>KOG1994|consensus
Probab=29.75 E-value=31 Score=20.81 Aligned_cols=25 Identities=20% Similarity=0.471 Sum_probs=20.6
Q ss_pred CCCCccCccccccccChhHHHHHHH
Q psy14147 54 NDRRYQCDLCLARFVTNSSLIVHKQ 78 (100)
Q Consensus 54 ~~~~~~c~~c~~~~~~~~~l~~h~~ 78 (100)
....|-|-.||..|....+|..|-.
T Consensus 236 R~eh~YC~fCG~~y~~~edl~ehCP 260 (268)
T KOG1994|consen 236 RSEHYYCFFCGIKYKDEEDLYEHCP 260 (268)
T ss_pred hccceEEEEeccccCCHHHHHHhCC
Confidence 3456889999999999999988743
No 234
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.70 E-value=27 Score=18.24 Aligned_cols=11 Identities=27% Similarity=0.676 Sum_probs=7.8
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
..||.||..|.
T Consensus 50 t~CP~Cg~~~e 60 (115)
T COG1885 50 TSCPKCGEPFE 60 (115)
T ss_pred ccCCCCCCccc
Confidence 46888887664
No 235
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=29.62 E-value=56 Score=19.84 Aligned_cols=14 Identities=14% Similarity=0.541 Sum_probs=8.9
Q ss_pred CCCCeecCCCcccc
Q psy14147 82 NTPRFKCKLCPKMF 95 (100)
Q Consensus 82 ~~~~~~C~~C~~~f 95 (100)
+..+-.||+||.-.
T Consensus 218 ~d~iv~CP~CgRIL 231 (239)
T COG1579 218 KDEIVFCPYCGRIL 231 (239)
T ss_pred CCCCccCCccchHH
Confidence 45556688887643
No 236
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=29.50 E-value=25 Score=19.22 Aligned_cols=10 Identities=40% Similarity=1.095 Sum_probs=7.4
Q ss_pred eecCCCcccc
Q psy14147 86 FKCKLCPKMF 95 (100)
Q Consensus 86 ~~C~~C~~~f 95 (100)
-+|+.||..|
T Consensus 30 ~kC~~CG~v~ 39 (140)
T COG1545 30 TKCKKCGRVY 39 (140)
T ss_pred EEcCCCCeEE
Confidence 4688888766
No 237
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.43 E-value=26 Score=18.94 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=11.7
Q ss_pred CCCeecCCCccccCC
Q psy14147 83 TPRFKCKLCPKMFTN 97 (100)
Q Consensus 83 ~~~~~C~~C~~~f~~ 97 (100)
+-|-.|..||+.|.+
T Consensus 66 e~psfchncgs~fpw 80 (160)
T COG4306 66 EPPSFCHNCGSRFPW 80 (160)
T ss_pred CCcchhhcCCCCCCc
Confidence 345679999999976
No 238
>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=29.42 E-value=19 Score=16.42 Aligned_cols=8 Identities=25% Similarity=1.107 Sum_probs=2.1
Q ss_pred eecCCCcc
Q psy14147 86 FKCKLCPK 93 (100)
Q Consensus 86 ~~C~~C~~ 93 (100)
|.|+.||.
T Consensus 34 y~Cp~CgA 41 (55)
T PF05741_consen 34 YVCPICGA 41 (55)
T ss_dssp ---TTT--
T ss_pred CcCCCCcC
Confidence 56666664
No 239
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=29.22 E-value=32 Score=18.86 Aligned_cols=13 Identities=23% Similarity=0.746 Sum_probs=11.0
Q ss_pred ecCCCccccCCCC
Q psy14147 87 KCKLCPKMFTNTV 99 (100)
Q Consensus 87 ~C~~C~~~f~~~~ 99 (100)
.||.|..+|.+.+
T Consensus 123 vCPvCkTSFKss~ 135 (140)
T PF05290_consen 123 VCPVCKTSFKSSS 135 (140)
T ss_pred CCCcccccccccc
Confidence 6999999998754
No 240
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=29.20 E-value=36 Score=14.64 Aligned_cols=11 Identities=36% Similarity=0.727 Sum_probs=6.4
Q ss_pred CeecCCCcccc
Q psy14147 85 RFKCKLCPKMF 95 (100)
Q Consensus 85 ~~~C~~C~~~f 95 (100)
.+.|+.||..+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 45666666544
No 241
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=29.12 E-value=91 Score=18.27 Aligned_cols=12 Identities=25% Similarity=0.545 Sum_probs=6.5
Q ss_pred CccCcccccccc
Q psy14147 57 RYQCDLCLARFV 68 (100)
Q Consensus 57 ~~~c~~c~~~~~ 68 (100)
...|..|+..+.
T Consensus 95 ~~~C~~C~~~~~ 106 (206)
T cd01410 95 IEVCKSCGPEYV 106 (206)
T ss_pred cccCCCCCCccc
Confidence 345666665443
No 242
>COG1773 Rubredoxin [Energy production and conversion]
Probab=28.80 E-value=20 Score=16.34 Aligned_cols=12 Identities=25% Similarity=0.924 Sum_probs=7.7
Q ss_pred ceeCchhhhhcc
Q psy14147 28 PYACEECGKAFR 39 (100)
Q Consensus 28 ~~~c~~C~~~f~ 39 (100)
.|+|..||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 467777776553
No 243
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=28.51 E-value=31 Score=19.18 Aligned_cols=12 Identities=25% Similarity=0.808 Sum_probs=7.6
Q ss_pred CCeecCCCcccc
Q psy14147 84 PRFKCKLCPKMF 95 (100)
Q Consensus 84 ~~~~C~~C~~~f 95 (100)
..|.|..|++.+
T Consensus 50 ~~~~C~~C~~~~ 61 (166)
T cd04476 50 GTYRCEKCNKSV 61 (166)
T ss_pred CcEECCCCCCcC
Confidence 456777777654
No 244
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=28.29 E-value=27 Score=17.20 Aligned_cols=10 Identities=30% Similarity=0.949 Sum_probs=3.5
Q ss_pred CCCeecCCCc
Q psy14147 83 TPRFKCKLCP 92 (100)
Q Consensus 83 ~~~~~C~~C~ 92 (100)
.+.|.|+.|+
T Consensus 20 ~~~F~CPfC~ 29 (81)
T PF05129_consen 20 PKVFDCPFCN 29 (81)
T ss_dssp SS----TTT-
T ss_pred CceEcCCcCC
Confidence 3568888887
No 245
>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=28.00 E-value=55 Score=18.45 Aligned_cols=12 Identities=17% Similarity=0.570 Sum_probs=6.9
Q ss_pred ccCccccccccC
Q psy14147 58 YQCDLCLARFVT 69 (100)
Q Consensus 58 ~~c~~c~~~~~~ 69 (100)
..|..|++.+..
T Consensus 106 ~~C~~C~~~~~~ 117 (178)
T PF02146_consen 106 LRCSKCGKEYDR 117 (178)
T ss_dssp EEETTTSBEEEG
T ss_pred eeecCCCccccc
Confidence 456666665543
No 246
>PF15269 zf-C2H2_7: Zinc-finger
Probab=27.93 E-value=38 Score=14.72 Aligned_cols=21 Identities=29% Similarity=0.510 Sum_probs=15.2
Q ss_pred eeCchhhhhccChhHHHHHHh
Q psy14147 29 YACEECGKAFRKKFSLTMHQR 49 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~~ 49 (100)
|+|-+|..+-..++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 678888777767777777774
No 247
>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=27.76 E-value=30 Score=13.39 Aligned_cols=9 Identities=56% Similarity=1.124 Sum_probs=3.8
Q ss_pred eecCCCccc
Q psy14147 86 FKCKLCPKM 94 (100)
Q Consensus 86 ~~C~~C~~~ 94 (100)
|.|..|++.
T Consensus 28 f~C~~C~~~ 36 (39)
T smart00132 28 FKCSKCGKP 36 (39)
T ss_pred CCCcccCCc
Confidence 344444443
No 248
>PRK07218 replication factor A; Provisional
Probab=27.58 E-value=36 Score=22.51 Aligned_cols=10 Identities=20% Similarity=0.411 Sum_probs=7.1
Q ss_pred ccCccccccc
Q psy14147 58 YQCDLCLARF 67 (100)
Q Consensus 58 ~~c~~c~~~~ 67 (100)
..||.|++..
T Consensus 298 ~rCP~C~r~v 307 (423)
T PRK07218 298 ERCPECGRVI 307 (423)
T ss_pred ecCcCccccc
Confidence 4688887765
No 249
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=27.37 E-value=34 Score=15.45 Aligned_cols=11 Identities=18% Similarity=0.818 Sum_probs=7.8
Q ss_pred CCCeecCCCcc
Q psy14147 83 TPRFKCKLCPK 93 (100)
Q Consensus 83 ~~~~~C~~C~~ 93 (100)
+-.|.|+.||.
T Consensus 42 ~i~y~C~~Cg~ 52 (54)
T PF10058_consen 42 EIQYRCPYCGA 52 (54)
T ss_pred ceEEEcCCCCC
Confidence 34588888874
No 250
>PLN02748 tRNA dimethylallyltransferase
Probab=27.35 E-value=48 Score=22.28 Aligned_cols=24 Identities=25% Similarity=0.418 Sum_probs=19.4
Q ss_pred CCccCccccc-cccChhHHHHHHHh
Q psy14147 56 RRYQCDLCLA-RFVTNSSLIVHKQR 79 (100)
Q Consensus 56 ~~~~c~~c~~-~~~~~~~l~~h~~~ 79 (100)
..|.|..|+. .+.....+..|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4568999997 78888888888874
No 251
>PF12591 DUF3762: Protein of unknown function (DUF3762); InterPro: IPR022239 This domain family is found in viruses, and is approximately 80 amino acids in length. The family is found in association with PF05533 from PFAM.
Probab=27.28 E-value=34 Score=16.34 Aligned_cols=11 Identities=18% Similarity=0.628 Sum_probs=7.6
Q ss_pred CCCccccCCCC
Q psy14147 89 KLCPKMFTNTV 99 (100)
Q Consensus 89 ~~C~~~f~~~~ 99 (100)
..||..|.+.|
T Consensus 70 rkcgrvfps~s 80 (80)
T PF12591_consen 70 RKCGRVFPSGS 80 (80)
T ss_pred ccccccCCCCC
Confidence 45888887653
No 252
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=26.91 E-value=33 Score=18.21 Aligned_cols=13 Identities=23% Similarity=0.498 Sum_probs=7.5
Q ss_pred CCCeecCCCcccc
Q psy14147 83 TPRFKCKLCPKMF 95 (100)
Q Consensus 83 ~~~~~C~~C~~~f 95 (100)
.....||.|++..
T Consensus 67 av~V~CP~C~K~T 79 (114)
T PF11023_consen 67 AVQVECPNCGKQT 79 (114)
T ss_pred ceeeECCCCCChH
Confidence 3445677776543
No 253
>KOG2857|consensus
Probab=26.76 E-value=32 Score=19.09 Aligned_cols=23 Identities=22% Similarity=0.629 Sum_probs=19.0
Q ss_pred CCccCccccccccChhHHHHHHH
Q psy14147 56 RRYQCDLCLARFVTNSSLIVHKQ 78 (100)
Q Consensus 56 ~~~~c~~c~~~~~~~~~l~~h~~ 78 (100)
..|.|+.|...+.+...+..|..
T Consensus 16 ~KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 16 IKYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hhccCCCCCCccccchhhhhccC
Confidence 36889999998888888888865
No 254
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=26.43 E-value=36 Score=17.72 Aligned_cols=14 Identities=36% Similarity=1.011 Sum_probs=11.1
Q ss_pred ceeCchhhhhccCh
Q psy14147 28 PYACEECGKAFRKK 41 (100)
Q Consensus 28 ~~~c~~C~~~f~~~ 41 (100)
|++|..||..|..-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 57788899888764
No 255
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.40 E-value=32 Score=16.25 Aligned_cols=12 Identities=25% Similarity=0.454 Sum_probs=7.8
Q ss_pred eecCCCccccCC
Q psy14147 86 FKCKLCPKMFTN 97 (100)
Q Consensus 86 ~~C~~C~~~f~~ 97 (100)
-.|+.||+.-.+
T Consensus 8 v~CP~Cgkpv~w 19 (65)
T COG3024 8 VPCPTCGKPVVW 19 (65)
T ss_pred ccCCCCCCcccc
Confidence 358888876543
No 256
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=26.39 E-value=25 Score=18.05 Aligned_cols=38 Identities=24% Similarity=0.503 Sum_probs=13.6
Q ss_pred CCCceeCchhhhhccChhHHHHHHhhhcCCCCC-ccCccccccccC
Q psy14147 25 CVKPYACEECGKAFRKKFSLTMHQRHVHLNDRR-YQCDLCLARFVT 69 (100)
Q Consensus 25 ~~~~~~c~~C~~~f~~~~~l~~h~~~~~~~~~~-~~c~~c~~~~~~ 69 (100)
+.|.-.|..|+.++... ++ .-.+++- |-|..|.+-|..
T Consensus 11 g~ke~~CalCG~tWg~~-----y~--Ev~G~rLfFCCd~ca~EF~n 49 (105)
T PF11494_consen 11 GTKEMGCALCGATWGDY-----YE--EVDGERLFFCCDDCAKEFKN 49 (105)
T ss_dssp -SGGGS-SS---S---S-----S---B-TT--BSSS--SSSS-TTS
T ss_pred ccccccccccCCcHHHH-----HH--hhcCCEEEEEcHHHHHHHHH
Confidence 44566788888887633 22 2334443 556778777655
No 257
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=26.33 E-value=31 Score=14.93 Aligned_cols=8 Identities=38% Similarity=0.908 Sum_probs=5.2
Q ss_pred ecCCCccc
Q psy14147 87 KCKLCPKM 94 (100)
Q Consensus 87 ~C~~C~~~ 94 (100)
+|+.||..
T Consensus 13 kCp~CGt~ 20 (44)
T PF14952_consen 13 KCPKCGTY 20 (44)
T ss_pred cCCcCcCc
Confidence 57777743
No 258
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=26.26 E-value=31 Score=13.15 Aligned_cols=8 Identities=25% Similarity=0.891 Sum_probs=3.2
Q ss_pred ecCCCccc
Q psy14147 87 KCKLCPKM 94 (100)
Q Consensus 87 ~C~~C~~~ 94 (100)
.|+.||..
T Consensus 1 ~CP~C~s~ 8 (28)
T PF03119_consen 1 TCPVCGSK 8 (28)
T ss_dssp B-TTT--B
T ss_pred CcCCCCCE
Confidence 37778754
No 259
>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=25.84 E-value=36 Score=17.93 Aligned_cols=12 Identities=17% Similarity=0.539 Sum_probs=8.0
Q ss_pred CeecCCCccccC
Q psy14147 85 RFKCKLCPKMFT 96 (100)
Q Consensus 85 ~~~C~~C~~~f~ 96 (100)
.|.|++|+..+.
T Consensus 19 ~~iCpeC~~EW~ 30 (109)
T TIGR00686 19 QLICPSCLYEWN 30 (109)
T ss_pred eeECcccccccc
Confidence 477777776664
No 260
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.63 E-value=43 Score=23.53 Aligned_cols=10 Identities=20% Similarity=0.378 Sum_probs=7.8
Q ss_pred CeecCCCccc
Q psy14147 85 RFKCKLCPKM 94 (100)
Q Consensus 85 ~~~C~~C~~~ 94 (100)
-+.||.||..
T Consensus 639 ~~~CP~CG~~ 648 (656)
T PRK08270 639 HEFCPKCGEE 648 (656)
T ss_pred CCCCcCCcCc
Confidence 4789999854
No 261
>PHA02942 putative transposase; Provisional
Probab=25.43 E-value=55 Score=21.30 Aligned_cols=13 Identities=23% Similarity=0.414 Sum_probs=9.6
Q ss_pred CCCeecCCCcccc
Q psy14147 83 TPRFKCKLCPKMF 95 (100)
Q Consensus 83 ~~~~~C~~C~~~f 95 (100)
.+.|.|+.||...
T Consensus 340 ~r~f~C~~CG~~~ 352 (383)
T PHA02942 340 HRYFHCPSCGYEN 352 (383)
T ss_pred CCEEECCCCCCEe
Confidence 4578999998653
No 262
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=25.00 E-value=40 Score=20.56 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=6.8
Q ss_pred CccCcccccccc
Q psy14147 57 RYQCDLCLARFV 68 (100)
Q Consensus 57 ~~~c~~c~~~~~ 68 (100)
.+.|..|+..+.
T Consensus 122 ~~~C~~C~~~~~ 133 (250)
T COG0846 122 RVRCSKCGNQYY 133 (250)
T ss_pred eeEeCCCcCccc
Confidence 455666665543
No 263
>PHA02998 RNA polymerase subunit; Provisional
Probab=24.94 E-value=42 Score=19.44 Aligned_cols=12 Identities=33% Similarity=0.797 Sum_probs=10.1
Q ss_pred eecCCCccccCC
Q psy14147 86 FKCKLCPKMFTN 97 (100)
Q Consensus 86 ~~C~~C~~~f~~ 97 (100)
|.|..||..|.-
T Consensus 172 YkC~~CG~~wkp 183 (195)
T PHA02998 172 HACRDCKKHFKP 183 (195)
T ss_pred EEcCCCCCccCC
Confidence 799999998863
No 264
>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=24.57 E-value=24 Score=15.68 Aligned_cols=11 Identities=36% Similarity=1.120 Sum_probs=7.0
Q ss_pred eeCchhhhhcc
Q psy14147 29 YACEECGKAFR 39 (100)
Q Consensus 29 ~~c~~C~~~f~ 39 (100)
|+|..||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 56777776554
No 265
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=24.30 E-value=79 Score=18.70 Aligned_cols=13 Identities=15% Similarity=0.342 Sum_probs=7.6
Q ss_pred CccCccccccccC
Q psy14147 57 RYQCDLCLARFVT 69 (100)
Q Consensus 57 ~~~c~~c~~~~~~ 69 (100)
...|..|+..+..
T Consensus 113 ~~~C~~C~~~~~~ 125 (222)
T cd01413 113 TAYCVNCGSKYDL 125 (222)
T ss_pred cceECCCCCCcch
Confidence 3467777765543
No 266
>KOG0978|consensus
Probab=24.29 E-value=37 Score=24.02 Aligned_cols=13 Identities=31% Similarity=0.651 Sum_probs=10.5
Q ss_pred CeecCCCccccCC
Q psy14147 85 RFKCKLCPKMFTN 97 (100)
Q Consensus 85 ~~~C~~C~~~f~~ 97 (100)
--+||.|+.+|..
T Consensus 678 qRKCP~Cn~aFga 690 (698)
T KOG0978|consen 678 QRKCPKCNAAFGA 690 (698)
T ss_pred cCCCCCCCCCCCc
Confidence 3579999999974
No 267
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=24.02 E-value=37 Score=16.81 Aligned_cols=10 Identities=30% Similarity=0.823 Sum_probs=4.8
Q ss_pred eecCCCcccc
Q psy14147 86 FKCKLCPKMF 95 (100)
Q Consensus 86 ~~C~~C~~~f 95 (100)
|.|+.|++..
T Consensus 66 ~~Cp~Cg~~~ 75 (81)
T PF10609_consen 66 FVCPHCGERI 75 (81)
T ss_dssp EE-TTT--EE
T ss_pred cCCCCCCCee
Confidence 6788887654
No 268
>PRK03922 hypothetical protein; Provisional
Probab=23.72 E-value=43 Score=17.67 Aligned_cols=10 Identities=30% Similarity=0.746 Sum_probs=6.6
Q ss_pred ecCCCccccC
Q psy14147 87 KCKLCPKMFT 96 (100)
Q Consensus 87 ~C~~C~~~f~ 96 (100)
.||.||..|.
T Consensus 51 ~cP~cge~~~ 60 (113)
T PRK03922 51 ICPKCGEPFD 60 (113)
T ss_pred cCCCCCCcCC
Confidence 4777776664
No 269
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.53 E-value=35 Score=20.66 Aligned_cols=12 Identities=25% Similarity=0.863 Sum_probs=7.3
Q ss_pred CeecCCCccccC
Q psy14147 85 RFKCKLCPKMFT 96 (100)
Q Consensus 85 ~~~C~~C~~~f~ 96 (100)
.+.||+|+-.|.
T Consensus 19 ~ieCPvC~tkFk 30 (267)
T COG1655 19 TIECPVCNTKFK 30 (267)
T ss_pred eeccCcccchhh
Confidence 456666666654
No 270
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=23.44 E-value=17 Score=20.76 Aligned_cols=30 Identities=23% Similarity=0.747 Sum_probs=18.5
Q ss_pred eeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccC
Q psy14147 29 YACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVT 69 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~ 69 (100)
-.|..|+.+|... .+. ..|.|..|.++|..
T Consensus 75 l~C~~C~~Tfk~f---------~~~--g~fGCaeCY~tf~~ 104 (176)
T COG3880 75 LGCHNCGMTFKEF---------IQS--GLFGCAECYKTFES 104 (176)
T ss_pred hcCccccccHHHH---------HHh--cccchHHHHHHHHH
Confidence 5677788776421 122 25678888887754
No 271
>KOG4118|consensus
Probab=23.27 E-value=70 Score=15.19 Aligned_cols=23 Identities=13% Similarity=0.475 Sum_probs=12.2
Q ss_pred ccCccccccccChhHHHHHHHhc
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQRH 80 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~~ 80 (100)
+.|.+|-.....+..+..|...-
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~k 61 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENK 61 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhc
Confidence 34555555555555555555543
No 272
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=22.98 E-value=78 Score=13.18 Aligned_cols=6 Identities=50% Similarity=1.481 Sum_probs=1.8
Q ss_pred eecCCC
Q psy14147 86 FKCKLC 91 (100)
Q Consensus 86 ~~C~~C 91 (100)
+.|+.|
T Consensus 37 ~~CP~C 42 (42)
T PF15227_consen 37 FSCPEC 42 (42)
T ss_dssp ---SSS
T ss_pred CCCcCC
Confidence 667665
No 273
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=22.45 E-value=42 Score=17.69 Aligned_cols=12 Identities=25% Similarity=0.667 Sum_probs=10.0
Q ss_pred CeecCCCccccC
Q psy14147 85 RFKCKLCPKMFT 96 (100)
Q Consensus 85 ~~~C~~C~~~f~ 96 (100)
-|.|..||..|.
T Consensus 100 Fy~C~~Cg~~wr 111 (113)
T COG1594 100 FYKCTRCGYRWR 111 (113)
T ss_pred EEEecccCCEee
Confidence 389999998875
No 274
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=22.18 E-value=65 Score=22.15 Aligned_cols=9 Identities=44% Similarity=1.036 Sum_probs=6.6
Q ss_pred CeecCCCcc
Q psy14147 85 RFKCKLCPK 93 (100)
Q Consensus 85 ~~~C~~C~~ 93 (100)
-+.||.||.
T Consensus 532 ~~~CP~CGs 540 (555)
T cd01675 532 GFKCPKCGS 540 (555)
T ss_pred CCCCcCCCC
Confidence 377888884
No 275
>PRK10220 hypothetical protein; Provisional
Probab=22.00 E-value=53 Score=17.36 Aligned_cols=12 Identities=17% Similarity=0.664 Sum_probs=8.3
Q ss_pred CeecCCCccccC
Q psy14147 85 RFKCKLCPKMFT 96 (100)
Q Consensus 85 ~~~C~~C~~~f~ 96 (100)
.|.|++|+..+.
T Consensus 20 ~~vCpeC~hEW~ 31 (111)
T PRK10220 20 MYICPECAHEWN 31 (111)
T ss_pred eEECCcccCcCC
Confidence 477777776664
No 276
>PRK06260 threonine synthase; Validated
Probab=21.99 E-value=54 Score=21.26 Aligned_cols=31 Identities=26% Similarity=0.570 Sum_probs=19.8
Q ss_pred eeCchhhhhccChhHHHHHHhhhcCCCCCccCccccccccChhH
Q psy14147 29 YACEECGKAFRKKFSLTMHQRHVHLNDRRYQCDLCLARFVTNSS 72 (100)
Q Consensus 29 ~~c~~C~~~f~~~~~l~~h~~~~~~~~~~~~c~~c~~~~~~~~~ 72 (100)
+.|..|+..+. .....+.|+.|+..+....+
T Consensus 4 ~~C~~cg~~~~-------------~~~~~~~Cp~cg~~l~~~y~ 34 (397)
T PRK06260 4 LKCIECGKEYD-------------PDEIIYTCPECGGLLEVIYD 34 (397)
T ss_pred EEECCCCCCCC-------------CCCccccCCCCCCeEEEEec
Confidence 67888887652 12335779889866554444
No 277
>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=21.64 E-value=47 Score=17.32 Aligned_cols=11 Identities=18% Similarity=0.637 Sum_probs=7.1
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
+.|+.||..+.
T Consensus 32 ~~C~~CGe~~~ 42 (127)
T TIGR03830 32 WYCPACGEELL 42 (127)
T ss_pred eECCCCCCEEE
Confidence 56777776654
No 278
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=21.52 E-value=69 Score=23.46 Aligned_cols=11 Identities=45% Similarity=1.216 Sum_probs=6.7
Q ss_pred eCchhhhhccC
Q psy14147 30 ACEECGKAFRK 40 (100)
Q Consensus 30 ~c~~C~~~f~~ 40 (100)
.|..|++.|..
T Consensus 462 tC~~C~kkFfS 472 (1374)
T PTZ00303 462 SCPSCGRAFIS 472 (1374)
T ss_pred cccCcCCcccc
Confidence 46666666643
No 279
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=21.42 E-value=92 Score=18.80 Aligned_cols=13 Identities=31% Similarity=0.754 Sum_probs=7.7
Q ss_pred CccCccccccccC
Q psy14147 57 RYQCDLCLARFVT 69 (100)
Q Consensus 57 ~~~c~~c~~~~~~ 69 (100)
...|..|+..+..
T Consensus 119 ~~~C~~C~~~~~~ 131 (244)
T PRK14138 119 EYYCVRCGKRYTV 131 (244)
T ss_pred eeEECCCCCcccH
Confidence 3457777766543
No 280
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=21.37 E-value=54 Score=21.28 Aligned_cols=22 Identities=18% Similarity=0.348 Sum_probs=18.9
Q ss_pred CccCccccccccChhHHHHHHH
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQ 78 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~ 78 (100)
.+-|..|++.|....-+..|+.
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHh
Confidence 4679999999999888988876
No 281
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=21.19 E-value=1.1e+02 Score=14.29 Aligned_cols=28 Identities=11% Similarity=0.202 Sum_probs=12.7
Q ss_pred ccCccccccccChhHHHHHHHhcCCCCCeecCCCc
Q psy14147 58 YQCDLCLARFVTNSSLIVHKQRHDNTPRFKCKLCP 92 (100)
Q Consensus 58 ~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~C~ 92 (100)
..|+.-|...... ++...++..| ||.||
T Consensus 33 I~CP~HG~~~~s~--~~~~~~sk~G-----CP~Cg 60 (60)
T PF05265_consen 33 IRCPKHGNFTCST--FNSFIKSKHG-----CPECG 60 (60)
T ss_pred EECCCCCcEEecc--HHhhhhhccC-----CCCCC
Confidence 3566555443332 2333333332 77765
No 282
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=20.93 E-value=1.4e+02 Score=18.54 Aligned_cols=13 Identities=15% Similarity=0.350 Sum_probs=8.1
Q ss_pred CccCccccccccC
Q psy14147 57 RYQCDLCLARFVT 69 (100)
Q Consensus 57 ~~~c~~c~~~~~~ 69 (100)
...|..|+..+..
T Consensus 137 ~~~C~~C~~~~~~ 149 (271)
T PTZ00409 137 EARCCTCRKTIQL 149 (271)
T ss_pred cceeCCCCCCccc
Confidence 3567777766543
No 283
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=20.93 E-value=1.2e+02 Score=14.37 Aligned_cols=39 Identities=18% Similarity=0.346 Sum_probs=14.9
Q ss_pred ccCc--cccccccChhHHHHHHHhcCCCC-Ce-----ecCCCccccCC
Q psy14147 58 YQCD--LCLARFVTNSSLIVHKQRHDNTP-RF-----KCKLCPKMFTN 97 (100)
Q Consensus 58 ~~c~--~c~~~~~~~~~l~~h~~~~~~~~-~~-----~C~~C~~~f~~ 97 (100)
..|+ .|+..|... -|..+++...+.+ .| .||.|.+..+.
T Consensus 21 ~~C~n~~C~~~fH~~-CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 21 VVCPNPSCGKKFHLL-CLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp B--S-TT----B-SG-GGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred eEcCCcccCCHHHHH-HHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 3564 688777554 4445544322221 12 68999876553
No 284
>KOG3456|consensus
Probab=20.92 E-value=46 Score=17.49 Aligned_cols=14 Identities=21% Similarity=0.465 Sum_probs=10.9
Q ss_pred CCeecCCCccccCC
Q psy14147 84 PRFKCKLCPKMFTN 97 (100)
Q Consensus 84 ~~~~C~~C~~~f~~ 97 (100)
.+..|.+||-.|.+
T Consensus 103 ~~~~CgYCGlrf~~ 116 (120)
T KOG3456|consen 103 GPHICGYCGLRFVQ 116 (120)
T ss_pred CCcccccchhhhhh
Confidence 45789999988863
No 285
>PRK12496 hypothetical protein; Provisional
Probab=20.90 E-value=53 Score=18.55 Aligned_cols=12 Identities=42% Similarity=0.775 Sum_probs=9.4
Q ss_pred CeecCCCccccC
Q psy14147 85 RFKCKLCPKMFT 96 (100)
Q Consensus 85 ~~~C~~C~~~f~ 96 (100)
.|.|.-|++.|.
T Consensus 127 ~~~C~gC~~~~~ 138 (164)
T PRK12496 127 RKVCKGCKKKYP 138 (164)
T ss_pred eEECCCCCcccc
Confidence 367888998885
No 286
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=20.73 E-value=45 Score=14.79 Aligned_cols=9 Identities=33% Similarity=0.700 Sum_probs=5.9
Q ss_pred eecCCCccc
Q psy14147 86 FKCKLCPKM 94 (100)
Q Consensus 86 ~~C~~C~~~ 94 (100)
-.||.||-.
T Consensus 14 ~~Cp~CGN~ 22 (49)
T PF12677_consen 14 CKCPKCGND 22 (49)
T ss_pred ccCcccCCc
Confidence 368888744
No 287
>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=20.60 E-value=51 Score=20.54 Aligned_cols=12 Identities=17% Similarity=0.302 Sum_probs=8.3
Q ss_pred ccCccccccccC
Q psy14147 58 YQCDLCLARFVT 69 (100)
Q Consensus 58 ~~c~~c~~~~~~ 69 (100)
+.|+.|+..|.-
T Consensus 46 ~vc~~c~~h~rl 57 (285)
T TIGR00515 46 EVCPKCDHHMRM 57 (285)
T ss_pred CCCCCCCCcCcC
Confidence 468888876643
No 288
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=20.42 E-value=52 Score=13.85 Aligned_cols=10 Identities=20% Similarity=0.514 Sum_probs=6.0
Q ss_pred ecCCCccccC
Q psy14147 87 KCKLCPKMFT 96 (100)
Q Consensus 87 ~C~~C~~~f~ 96 (100)
.|+.||..+.
T Consensus 4 ~C~~Cg~~l~ 13 (47)
T PF13005_consen 4 ACPDCGGELK 13 (47)
T ss_pred cCCCCCceee
Confidence 4666766554
No 289
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=20.41 E-value=39 Score=19.74 Aligned_cols=9 Identities=22% Similarity=1.125 Sum_probs=5.1
Q ss_pred CCccCcccc
Q psy14147 56 RRYQCDLCL 64 (100)
Q Consensus 56 ~~~~c~~c~ 64 (100)
+.|.|..|+
T Consensus 151 kGfiCe~C~ 159 (202)
T PF13901_consen 151 KGFICEICN 159 (202)
T ss_pred CCCCCccCC
Confidence 455666664
No 290
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=20.39 E-value=56 Score=16.35 Aligned_cols=11 Identities=45% Similarity=0.969 Sum_probs=8.3
Q ss_pred ecCCCccccCC
Q psy14147 87 KCKLCPKMFTN 97 (100)
Q Consensus 87 ~C~~C~~~f~~ 97 (100)
.|..|++.+.+
T Consensus 80 ~C~vC~k~l~~ 90 (109)
T PF10367_consen 80 KCSVCGKPLGN 90 (109)
T ss_pred CccCcCCcCCC
Confidence 48888887764
No 291
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=20.21 E-value=49 Score=14.44 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=7.2
Q ss_pred eecCCCccccC
Q psy14147 86 FKCKLCPKMFT 96 (100)
Q Consensus 86 ~~C~~C~~~f~ 96 (100)
..|..||..+.
T Consensus 6 l~C~~CG~~m~ 16 (58)
T PF13408_consen 6 LRCGHCGSKMT 16 (58)
T ss_pred EEcccCCcEeE
Confidence 45777776654
No 292
>PTZ00448 hypothetical protein; Provisional
Probab=20.15 E-value=91 Score=20.37 Aligned_cols=23 Identities=13% Similarity=0.369 Sum_probs=17.4
Q ss_pred CccCccccccccChhHHHHHHHh
Q psy14147 57 RYQCDLCLARFVTNSSLIVHKQR 79 (100)
Q Consensus 57 ~~~c~~c~~~~~~~~~l~~h~~~ 79 (100)
.|.|..|+-.|........|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57799999888777666677663
No 293
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=20.06 E-value=45 Score=19.70 Aligned_cols=16 Identities=25% Similarity=0.663 Sum_probs=12.6
Q ss_pred CCCeecCCCccccCCC
Q psy14147 83 TPRFKCKLCPKMFTNT 98 (100)
Q Consensus 83 ~~~~~C~~C~~~f~~~ 98 (100)
.-||.|..|.+.|.+.
T Consensus 194 ~IPF~C~iCKkdy~sp 209 (259)
T COG5152 194 KIPFLCGICKKDYESP 209 (259)
T ss_pred CCceeehhchhhccch
Confidence 3589999998888654
Done!