Query psy7447
Match_columns 114
No_of_seqs 118 out of 1427
Neff 10.3
Searched_HMMs 46136
Date Fri Aug 16 18:32:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7447.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7447hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 2.8E-22 6E-27 127.6 2.4 91 10-105 175-265 (279)
2 KOG2462|consensus 99.8 5.7E-20 1.2E-24 117.2 1.9 96 6-106 140-238 (279)
3 KOG3623|consensus 99.6 7.6E-16 1.7E-20 109.1 2.7 81 21-103 890-970 (1007)
4 KOG3623|consensus 99.5 3.1E-15 6.8E-20 106.0 0.9 93 12-105 226-331 (1007)
5 KOG1074|consensus 99.4 2.4E-14 5.1E-19 102.7 1.0 49 56-105 607-655 (958)
6 KOG3576|consensus 99.3 8.8E-14 1.9E-18 85.8 -0.7 76 21-98 113-188 (267)
7 KOG3576|consensus 99.3 2.8E-13 6E-18 83.7 -0.9 81 12-95 133-224 (267)
8 KOG3608|consensus 99.1 1.9E-11 4.2E-16 81.1 -0.4 98 7-105 190-314 (467)
9 KOG1074|consensus 99.1 2.3E-11 5E-16 87.8 -0.1 69 9-78 618-692 (958)
10 KOG3608|consensus 99.0 1.9E-10 4.2E-15 76.4 2.1 89 6-96 273-365 (467)
11 PHA02768 hypothetical protein; 98.9 8.8E-10 1.9E-14 54.8 2.6 39 54-95 5-43 (55)
12 PF13465 zf-H2C2_2: Zinc-finge 98.9 1.7E-09 3.8E-14 46.2 2.1 25 69-94 1-25 (26)
13 PHA00733 hypothetical protein 98.9 1.1E-09 2.4E-14 64.2 1.8 74 21-98 36-114 (128)
14 PHA00733 hypothetical protein 98.8 4.4E-09 9.6E-14 61.8 3.9 63 12-79 62-124 (128)
15 PHA02768 hypothetical protein; 98.8 1.8E-09 3.9E-14 53.7 1.9 42 26-70 6-47 (55)
16 PLN03086 PRLI-interacting fact 98.7 1.3E-08 2.8E-13 72.2 2.8 66 24-94 477-552 (567)
17 PF13465 zf-H2C2_2: Zinc-finge 98.6 6E-08 1.3E-12 41.3 2.5 25 40-65 1-25 (26)
18 PHA00616 hypothetical protein 98.5 3.7E-08 7.9E-13 46.8 1.4 33 54-87 1-33 (44)
19 PLN03086 PRLI-interacting fact 98.5 3.1E-07 6.8E-12 65.4 5.2 67 21-94 449-515 (567)
20 PHA00616 hypothetical protein 98.5 1E-07 2.2E-12 45.3 1.7 33 25-58 1-33 (44)
21 PHA00732 hypothetical protein 98.3 6.8E-07 1.5E-11 48.2 2.7 45 25-76 1-46 (79)
22 PHA00732 hypothetical protein 98.1 1.9E-06 4.2E-11 46.4 2.1 40 54-96 1-40 (79)
23 PF00096 zf-C2H2: Zinc finger, 97.9 9.6E-06 2.1E-10 33.2 1.8 22 26-47 1-22 (23)
24 PF05605 zf-Di19: Drought indu 97.8 4.4E-05 9.5E-10 38.2 4.1 52 25-79 2-54 (54)
25 PF00096 zf-C2H2: Zinc finger, 97.8 1.9E-05 4.1E-10 32.3 2.1 23 55-77 1-23 (23)
26 PF13894 zf-C2H2_4: C2H2-type 97.5 0.00013 2.9E-09 29.7 2.3 22 56-77 2-23 (24)
27 PF13912 zf-C2H2_6: C2H2-type 97.5 6.5E-05 1.4E-09 31.9 1.3 23 26-48 2-24 (27)
28 PF13912 zf-C2H2_6: C2H2-type 97.4 7.3E-05 1.6E-09 31.7 1.2 26 54-79 1-26 (27)
29 KOG3993|consensus 97.4 9.3E-05 2E-09 51.0 1.8 56 24-79 294-381 (500)
30 PF13894 zf-C2H2_4: C2H2-type 97.4 0.00019 4.1E-09 29.2 2.0 23 26-48 1-23 (24)
31 COG5189 SFP1 Putative transcri 97.3 8.3E-05 1.8E-09 49.5 0.8 66 23-99 347-414 (423)
32 PF09237 GAGA: GAGA factor; I 97.3 0.00037 8E-09 34.0 2.7 31 52-82 22-52 (54)
33 PRK04860 hypothetical protein; 97.3 0.0003 6.5E-09 42.9 2.9 38 54-96 119-156 (160)
34 PF09237 GAGA: GAGA factor; I 97.2 0.00084 1.8E-08 32.8 3.5 44 10-54 9-52 (54)
35 PF12756 zf-C2H2_2: C2H2 type 97.1 0.00069 1.5E-08 37.6 2.9 25 54-78 50-74 (100)
36 smart00355 ZnF_C2H2 zinc finge 96.8 0.0015 3.1E-08 26.8 2.3 20 56-75 2-21 (26)
37 smart00355 ZnF_C2H2 zinc finge 96.8 0.0012 2.6E-08 27.1 2.0 24 26-49 1-24 (26)
38 PRK04860 hypothetical protein; 96.7 0.002 4.2E-08 39.4 2.9 39 24-67 118-156 (160)
39 COG5189 SFP1 Putative transcri 96.7 0.0013 2.7E-08 44.1 2.0 25 52-76 347-373 (423)
40 PF05605 zf-Di19: Drought indu 96.4 0.0058 1.2E-07 30.4 3.1 39 54-93 2-41 (54)
41 PF12874 zf-met: Zinc-finger o 96.3 0.0029 6.3E-08 26.1 1.4 21 26-46 1-21 (25)
42 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0053 1.2E-07 25.1 2.0 23 55-78 1-23 (24)
43 PF12874 zf-met: Zinc-finger o 95.8 0.0062 1.4E-07 25.0 1.3 23 55-77 1-23 (25)
44 KOG3993|consensus 94.9 0.0048 1E-07 42.9 -0.8 52 25-77 267-318 (500)
45 PF12171 zf-C2H2_jaz: Zinc-fin 94.1 0.013 2.7E-07 24.7 -0.2 21 26-46 2-22 (27)
46 PF13913 zf-C2HC_2: zinc-finge 94.1 0.056 1.2E-06 22.4 1.8 18 56-74 4-21 (25)
47 cd00350 rubredoxin_like Rubred 94.1 0.051 1.1E-06 24.1 1.8 24 55-91 2-25 (33)
48 COG5048 FOG: Zn-finger [Genera 92.6 0.025 5.5E-07 38.9 -0.6 63 24-88 288-356 (467)
49 smart00451 ZnF_U1 U1-like zinc 92.3 0.12 2.5E-06 22.9 1.6 22 25-46 3-24 (35)
50 KOG1146|consensus 91.3 0.17 3.6E-06 40.3 2.3 64 11-75 451-539 (1406)
51 PF12756 zf-C2H2_2: C2H2 type 90.0 0.28 6.1E-06 26.8 2.0 26 25-50 50-75 (100)
52 PF13719 zinc_ribbon_5: zinc-r 89.1 0.39 8.4E-06 21.8 1.8 10 84-93 26-35 (37)
53 PF05290 Baculo_IE-1: Baculovi 88.4 0.9 2E-05 26.9 3.3 60 21-97 76-135 (140)
54 cd00729 rubredoxin_SM Rubredox 88.3 0.45 9.8E-06 21.2 1.7 8 84-91 19-26 (34)
55 COG1592 Rubrerythrin [Energy p 88.1 0.33 7.1E-06 29.9 1.5 26 52-91 132-157 (166)
56 PF09538 FYDLN_acid: Protein o 87.8 0.47 1E-05 27.2 1.9 13 54-66 26-38 (108)
57 PF09986 DUF2225: Uncharacteri 87.8 0.076 1.6E-06 34.1 -1.5 13 84-96 49-61 (214)
58 KOG4317|consensus 86.7 0.23 5E-06 33.6 0.2 30 84-113 20-49 (383)
59 TIGR00373 conserved hypothetic 85.6 1.2 2.7E-05 27.2 3.0 33 52-94 107-139 (158)
60 KOG2186|consensus 85.3 0.61 1.3E-05 30.7 1.6 50 26-79 4-53 (276)
61 KOG2893|consensus 84.3 0.27 5.8E-06 32.1 -0.3 45 23-73 9-53 (341)
62 PF13717 zinc_ribbon_4: zinc-r 83.9 1.1 2.3E-05 20.3 1.7 10 84-93 26-35 (36)
63 TIGR00622 ssl1 transcription f 82.4 4.3 9.3E-05 23.4 4.1 71 24-97 14-95 (112)
64 COG1997 RPL43A Ribosomal prote 82.2 0.38 8.2E-06 26.3 -0.2 31 53-94 34-64 (89)
65 KOG2186|consensus 82.1 0.79 1.7E-05 30.2 1.2 39 54-95 3-41 (276)
66 COG4049 Uncharacterized protei 81.6 1.1 2.5E-05 22.3 1.4 31 20-50 12-42 (65)
67 PRK06266 transcription initiat 81.0 2 4.4E-05 26.8 2.7 33 52-94 115-147 (178)
68 TIGR02098 MJ0042_CXXC MJ0042 f 80.9 1.3 2.8E-05 19.9 1.4 10 84-93 26-35 (38)
69 smart00659 RPOLCX RNA polymera 80.7 1.7 3.6E-05 20.6 1.8 11 84-94 20-30 (44)
70 smart00531 TFIIE Transcription 80.1 3.9 8.5E-05 24.6 3.7 38 52-94 97-134 (147)
71 PRK00398 rpoP DNA-directed RNA 79.6 1.2 2.7E-05 21.1 1.2 11 84-94 22-32 (46)
72 COG0068 HypF Hydrogenase matur 78.4 0.27 5.8E-06 36.8 -2.0 62 27-96 125-186 (750)
73 smart00834 CxxC_CXXC_SSSS Puta 77.9 0.89 1.9E-05 20.7 0.3 12 55-66 6-17 (41)
74 PF05443 ROS_MUCR: ROS/MUCR tr 77.0 1.6 3.4E-05 26.0 1.3 26 54-82 72-97 (132)
75 TIGR02300 FYDLN_acid conserved 76.8 2.1 4.6E-05 25.2 1.7 30 26-67 10-39 (129)
76 TIGR02605 CxxC_CxxC_SSSS putat 75.9 1.1 2.4E-05 21.8 0.4 12 55-66 6-17 (52)
77 COG2888 Predicted Zn-ribbon RN 75.9 2.3 5E-05 21.6 1.5 34 52-91 25-58 (61)
78 COG1996 RPC10 DNA-directed RNA 74.4 2.1 4.6E-05 20.8 1.1 11 25-35 6-16 (49)
79 PF03604 DNA_RNApol_7kD: DNA d 74.4 2.4 5.1E-05 18.7 1.2 11 84-94 18-28 (32)
80 PF09845 DUF2072: Zn-ribbon co 74.1 6 0.00013 23.5 3.2 15 25-39 1-15 (131)
81 PF12013 DUF3505: Protein of u 73.9 3.5 7.6E-05 23.3 2.2 26 54-79 80-109 (109)
82 COG5048 FOG: Zn-finger [Genera 73.6 1.7 3.7E-05 29.9 1.0 45 53-98 288-338 (467)
83 PF14353 CpXC: CpXC protein 73.1 4.1 8.8E-05 23.8 2.4 10 27-36 3-12 (128)
84 PF10571 UPF0547: Uncharacteri 72.4 2.1 4.5E-05 17.9 0.7 11 84-94 15-25 (26)
85 smart00734 ZnF_Rad18 Rad18-lik 72.2 4.6 9.9E-05 16.7 1.8 19 56-75 3-21 (26)
86 PF04959 ARS2: Arsenite-resist 70.5 3 6.6E-05 26.9 1.5 29 22-50 74-102 (214)
87 KOG2231|consensus 69.1 1.2 2.6E-05 33.4 -0.6 30 56-90 184-213 (669)
88 PRK14890 putative Zn-ribbon RN 68.9 5.4 0.00012 20.2 1.9 32 53-91 24-56 (59)
89 PF04959 ARS2: Arsenite-resist 67.9 1.9 4.2E-05 27.8 0.2 29 52-80 75-103 (214)
90 KOG2593|consensus 66.3 6.6 0.00014 28.0 2.5 39 52-94 126-164 (436)
91 TIGR00595 priA primosomal prot 64.5 3.5 7.7E-05 30.0 1.1 15 84-98 254-268 (505)
92 COG1198 PriA Primosomal protei 63.2 2.1 4.6E-05 32.6 -0.3 23 83-107 475-497 (730)
93 COG5236 Uncharacterized conser 60.9 11 0.00025 26.3 2.9 43 6-49 198-244 (493)
94 KOG2893|consensus 60.4 4.4 9.5E-05 26.7 0.8 42 52-99 9-50 (341)
95 KOG2785|consensus 60.3 17 0.00037 25.6 3.6 55 25-79 166-245 (390)
96 PF09963 DUF2197: Uncharacteri 60.3 3.7 7.9E-05 20.6 0.4 10 27-36 4-13 (56)
97 PF07754 DUF1610: Domain of un 60.0 4.3 9.4E-05 16.6 0.5 7 84-90 17-23 (24)
98 PRK00464 nrdR transcriptional 59.9 1.9 4.1E-05 26.4 -0.8 11 26-36 29-39 (154)
99 PF02892 zf-BED: BED zinc fing 59.7 8.4 0.00018 17.8 1.6 13 24-36 15-27 (45)
100 KOG1146|consensus 58.7 0.87 1.9E-05 36.5 -2.9 74 29-104 440-539 (1406)
101 PF09723 Zn-ribbon_8: Zinc rib 56.8 4.5 9.8E-05 18.8 0.4 18 84-101 6-23 (42)
102 COG3357 Predicted transcriptio 56.5 9.3 0.0002 21.2 1.5 14 53-66 57-70 (97)
103 TIGR03831 YgiT_finger YgiT-typ 56.2 5.9 0.00013 18.3 0.7 14 82-95 31-44 (46)
104 smart00154 ZnF_AN1 AN1-like Zi 54.6 6.1 0.00013 18.1 0.6 14 84-97 13-26 (39)
105 PHA00626 hypothetical protein 54.4 6.3 0.00014 19.8 0.6 14 83-96 23-36 (59)
106 PRK00432 30S ribosomal protein 54.2 8.1 0.00017 18.8 1.0 10 84-93 38-47 (50)
107 PRK03824 hypA hydrogenase nick 53.8 5.9 0.00013 23.6 0.6 15 53-67 69-83 (135)
108 KOG4167|consensus 53.7 3.9 8.5E-05 31.2 -0.2 28 23-50 790-817 (907)
109 smart00614 ZnF_BED BED zinc fi 53.6 19 0.00041 17.2 2.3 8 68-75 37-44 (50)
110 COG4957 Predicted transcriptio 53.4 8.3 0.00018 23.1 1.1 24 56-82 78-101 (148)
111 COG3364 Zn-ribbon containing p 53.1 10 0.00023 21.5 1.4 15 25-39 2-16 (112)
112 PF10263 SprT-like: SprT-like 53.0 4.2 9.2E-05 24.4 -0.1 33 54-95 123-155 (157)
113 PF02176 zf-TRAF: TRAF-type zi 51.4 8.9 0.00019 18.9 1.0 20 39-59 24-43 (60)
114 PF06524 NOA36: NOA36 protein; 51.0 24 0.00051 23.7 3.0 72 20-94 137-220 (314)
115 COG3091 SprT Zn-dependent meta 49.1 7.5 0.00016 23.7 0.5 36 53-94 116-151 (156)
116 PRK14873 primosome assembly pr 49.0 19 0.00042 27.4 2.7 55 27-100 385-439 (665)
117 TIGR00100 hypA hydrogenase nic 48.4 12 0.00025 21.6 1.2 27 54-93 70-96 (115)
118 PRK05580 primosome assembly pr 48.2 8.5 0.00018 29.2 0.8 13 84-96 422-434 (679)
119 PRK12380 hydrogenase nickel in 48.1 9.2 0.0002 22.0 0.8 26 54-92 70-95 (113)
120 PF13878 zf-C2H2_3: zinc-finge 48.1 25 0.00054 16.2 2.1 22 56-77 15-38 (41)
121 PF10276 zf-CHCC: Zinc-finger 47.7 6.7 0.00015 18.2 0.1 10 84-93 30-39 (40)
122 KOG2231|consensus 47.5 22 0.00048 27.1 2.7 48 26-78 183-236 (669)
123 PRK03681 hypA hydrogenase nick 46.9 8.8 0.00019 22.1 0.6 28 54-93 70-97 (114)
124 KOG3507|consensus 46.9 13 0.00028 18.8 1.1 27 25-63 20-46 (62)
125 smart00440 ZnF_C2C2 C2C2 Zinc 46.6 2 4.3E-05 19.8 -1.8 8 84-91 29-36 (40)
126 PF01428 zf-AN1: AN1-like Zinc 46.6 6.4 0.00014 18.3 -0.0 15 83-97 13-27 (43)
127 KOG3362|consensus 45.5 8.1 0.00018 23.3 0.3 20 84-103 130-149 (156)
128 PF05191 ADK_lid: Adenylate ki 45.4 24 0.00051 15.9 1.8 10 84-93 22-31 (36)
129 PF01363 FYVE: FYVE zinc finge 45.3 11 0.00025 19.2 0.8 11 84-94 26-36 (69)
130 KOG2482|consensus 44.0 15 0.00032 25.7 1.3 24 25-48 195-218 (423)
131 cd00924 Cyt_c_Oxidase_Vb Cytoc 43.1 12 0.00025 21.1 0.6 14 24-37 78-91 (97)
132 PRK00564 hypA hydrogenase nick 41.8 19 0.00041 20.8 1.4 29 54-94 71-99 (117)
133 KOG4167|consensus 41.7 5.4 0.00012 30.5 -1.0 26 54-79 792-817 (907)
134 PF01155 HypA: Hydrogenase exp 41.7 7.3 0.00016 22.4 -0.3 28 54-94 70-97 (113)
135 PLN02294 cytochrome c oxidase 41.6 13 0.00028 23.2 0.7 15 23-37 139-153 (174)
136 COG1655 Uncharacterized protei 41.6 3.6 7.8E-05 26.9 -1.7 10 84-93 63-72 (267)
137 KOG3408|consensus 40.6 23 0.00051 20.8 1.6 26 21-46 53-78 (129)
138 PF15269 zf-C2H2_7: Zinc-finge 40.4 23 0.00049 16.9 1.3 21 55-75 21-41 (54)
139 COG3677 Transposase and inacti 40.3 18 0.00038 21.4 1.2 17 84-100 54-70 (129)
140 PF13451 zf-trcl: Probable zin 39.9 11 0.00024 18.3 0.2 15 84-98 5-19 (49)
141 PF04423 Rad50_zn_hook: Rad50 39.5 11 0.00024 18.4 0.2 11 85-95 22-32 (54)
142 COG1998 RPS31 Ribosomal protei 38.8 13 0.00029 18.1 0.4 9 84-92 38-46 (51)
143 PRK09678 DNA-binding transcrip 38.7 12 0.00025 19.9 0.2 8 27-34 3-10 (72)
144 PF10013 DUF2256: Uncharacteri 38.6 16 0.00035 17.2 0.6 11 84-94 9-19 (42)
145 COG1571 Predicted DNA-binding 38.5 24 0.00052 25.3 1.7 13 54-66 367-379 (421)
146 PF14311 DUF4379: Domain of un 37.5 36 0.00078 16.6 1.9 12 55-66 29-40 (55)
147 smart00064 FYVE Protein presen 36.4 30 0.00064 17.5 1.5 10 27-36 12-21 (68)
148 COG1675 TFA1 Transcription ini 35.9 63 0.0014 20.3 3.1 33 52-94 111-143 (176)
149 TIGR03829 YokU_near_AblA uncha 35.9 19 0.00041 19.9 0.8 17 80-96 32-48 (89)
150 COG1773 Rubredoxin [Energy pro 35.9 20 0.00043 17.9 0.8 13 54-66 3-15 (55)
151 cd00065 FYVE FYVE domain; Zinc 35.8 36 0.00078 16.4 1.8 9 28-36 5-13 (57)
152 PRK12496 hypothetical protein; 35.0 29 0.00064 21.4 1.6 12 25-36 127-138 (164)
153 PF04216 FdhE: Protein involve 34.8 4 8.7E-05 27.4 -2.4 9 26-34 173-181 (290)
154 PF06397 Desulfoferrod_N: Desu 34.8 15 0.00032 16.6 0.2 13 84-96 7-19 (36)
155 smart00731 SprT SprT homologue 34.0 25 0.00054 21.0 1.2 10 84-93 134-143 (146)
156 PF07282 OrfB_Zn_ribbon: Putat 34.0 33 0.00071 17.4 1.5 15 52-66 44-58 (69)
157 COG4391 Uncharacterized protei 33.3 19 0.00041 18.4 0.4 11 84-94 49-59 (62)
158 KOG2071|consensus 33.3 31 0.00067 25.8 1.7 28 52-79 416-443 (579)
159 TIGR00143 hypF [NiFe] hydrogen 33.0 2.3 5E-05 32.3 -4.1 60 27-94 92-151 (711)
160 PF10537 WAC_Acf1_DNA_bd: ATP- 32.8 78 0.0017 17.9 2.9 38 24-63 2-39 (102)
161 TIGR00515 accD acetyl-CoA carb 32.6 26 0.00057 23.7 1.2 32 26-67 27-58 (285)
162 PRK04351 hypothetical protein; 32.5 19 0.00042 21.9 0.5 34 54-96 112-145 (149)
163 KOG2636|consensus 32.3 37 0.0008 24.7 1.8 27 20-46 396-423 (497)
164 PF02591 DUF164: Putative zinc 32.1 59 0.0013 15.9 2.2 13 78-91 42-54 (56)
165 PF06220 zf-U1: U1 zinc finger 32.0 24 0.00052 16.0 0.7 11 84-94 4-14 (38)
166 PF14255 Cys_rich_CPXG: Cystei 31.7 26 0.00055 17.3 0.8 13 84-96 1-13 (52)
167 COG4888 Uncharacterized Zn rib 31.2 7.9 0.00017 21.9 -1.2 15 22-36 19-33 (104)
168 PF08274 PhnA_Zn_Ribbon: PhnA 30.6 28 0.00061 15.0 0.7 8 54-61 19-26 (30)
169 PF14369 zf-RING_3: zinc-finge 30.1 27 0.00059 15.5 0.7 10 85-94 23-32 (35)
170 COG4306 Uncharacterized protei 29.9 18 0.0004 21.3 0.1 14 53-66 67-80 (160)
171 PRK05452 anaerobic nitric oxid 29.5 15 0.00031 26.8 -0.4 15 52-66 423-437 (479)
172 PF11672 DUF3268: Protein of u 29.4 21 0.00045 20.3 0.2 11 24-34 1-11 (102)
173 cd00730 rubredoxin Rubredoxin; 29.2 30 0.00065 16.8 0.8 15 84-98 2-16 (50)
174 COG2331 Uncharacterized protei 28.9 19 0.00041 19.3 0.0 32 54-93 12-43 (82)
175 PRK04023 DNA polymerase II lar 28.6 59 0.0013 26.3 2.5 10 25-34 626-635 (1121)
176 PRK11823 DNA repair protein Ra 28.4 54 0.0012 23.7 2.2 13 23-35 5-17 (446)
177 PF00301 Rubredoxin: Rubredoxi 28.4 26 0.00056 16.8 0.5 15 84-98 2-16 (47)
178 TIGR00416 sms DNA repair prote 28.3 54 0.0012 23.8 2.2 23 24-61 6-28 (454)
179 PF13824 zf-Mss51: Zinc-finger 28.0 61 0.0013 16.2 1.7 14 52-65 12-25 (55)
180 KOG4173|consensus 27.6 41 0.0009 21.8 1.4 68 25-96 79-159 (253)
181 PRK00762 hypA hydrogenase nick 27.6 25 0.00053 20.6 0.4 34 54-94 70-103 (124)
182 PF04438 zf-HIT: HIT zinc fing 27.4 20 0.00044 15.3 -0.0 13 84-96 14-26 (30)
183 PHA02998 RNA polymerase subuni 27.1 12 0.00026 23.5 -1.0 11 84-94 172-182 (195)
184 CHL00174 accD acetyl-CoA carbo 26.5 35 0.00076 23.3 1.0 14 54-67 57-70 (296)
185 TIGR00686 phnA alkylphosphonat 26.3 42 0.00092 19.3 1.1 13 54-66 19-31 (109)
186 cd00974 DSRD Desulforedoxin (D 26.3 36 0.00077 14.8 0.7 15 84-98 5-19 (34)
187 PF07295 DUF1451: Protein of u 26.2 52 0.0011 20.0 1.6 8 85-92 132-139 (146)
188 PRK05978 hypothetical protein; 26.1 42 0.00091 20.5 1.2 13 84-96 53-65 (148)
189 KOG1842|consensus 26.1 39 0.00084 24.6 1.1 27 24-50 14-40 (505)
190 PRK14714 DNA polymerase II lar 26.0 62 0.0013 26.9 2.3 11 84-94 710-720 (1337)
191 TIGR00319 desulf_FeS4 desulfof 25.8 36 0.00077 14.8 0.7 14 84-97 8-21 (34)
192 KOG1280|consensus 25.5 75 0.0016 22.4 2.4 26 54-79 79-104 (381)
193 COG1594 RPB9 DNA-directed RNA 25.2 16 0.00034 21.1 -0.7 11 84-94 101-111 (113)
194 PF01927 Mut7-C: Mut7-C RNAse 24.5 70 0.0015 19.2 2.0 47 26-72 92-142 (147)
195 PF14787 zf-CCHC_5: GAG-polypr 24.0 41 0.00088 15.2 0.6 13 84-96 3-15 (36)
196 PF09855 DUF2082: Nucleic-acid 24.0 43 0.00093 17.2 0.8 9 84-92 1-9 (64)
197 PF01780 Ribosomal_L37ae: Ribo 23.8 27 0.00059 19.4 0.0 31 53-94 34-64 (90)
198 PF07503 zf-HYPF: HypF finger; 23.7 11 0.00024 16.9 -1.2 6 56-61 23-28 (35)
199 PF03811 Zn_Tnp_IS1: InsA N-te 23.3 83 0.0018 14.1 1.6 14 46-60 22-35 (36)
200 TIGR01562 FdhE formate dehydro 23.0 96 0.0021 21.4 2.5 10 25-34 184-193 (305)
201 PRK05654 acetyl-CoA carboxylas 22.5 47 0.001 22.6 1.0 31 27-67 29-59 (292)
202 PF01215 COX5B: Cytochrome c o 22.4 32 0.00069 20.7 0.2 16 23-38 110-125 (136)
203 COG5151 SSL1 RNA polymerase II 22.3 75 0.0016 22.1 1.9 12 84-95 389-400 (421)
204 PF08209 Sgf11: Sgf11 (transcr 22.0 37 0.00081 15.0 0.3 11 84-94 5-15 (33)
205 PF10071 DUF2310: Zn-ribbon-co 22.0 44 0.00095 22.4 0.8 27 56-90 222-248 (258)
206 PF07975 C1_4: TFIIH C1-like d 21.9 41 0.00088 16.5 0.5 15 84-98 22-36 (51)
207 PF01286 XPA_N: XPA protein N- 21.6 38 0.00082 15.1 0.3 13 84-96 4-16 (34)
208 PTZ00043 cytochrome c oxidase 21.3 43 0.00093 22.1 0.6 17 22-38 178-194 (268)
209 TIGR01385 TFSII transcription 21.3 18 0.0004 24.6 -1.1 10 84-93 287-296 (299)
210 PF08792 A2L_zn_ribbon: A2L zi 21.2 41 0.00088 14.8 0.3 10 84-93 22-31 (33)
211 COG0675 Transposase and inacti 21.0 1E+02 0.0022 20.6 2.4 16 52-67 320-335 (364)
212 smart00661 RPOL9 RNA polymeras 21.0 44 0.00094 15.8 0.5 12 84-95 21-32 (52)
213 cd01121 Sms Sms (bacterial rad 20.6 70 0.0015 22.6 1.6 10 24-33 13-22 (372)
214 PF02891 zf-MIZ: MIZ/SP-RING z 20.5 53 0.0011 15.8 0.7 8 84-91 42-49 (50)
215 TIGR00280 L37a ribosomal prote 20.4 44 0.00095 18.6 0.4 31 53-94 34-64 (91)
216 PF02748 PyrI_C: Aspartate car 20.2 40 0.00086 16.5 0.2 16 21-36 31-46 (52)
No 1
>KOG2462|consensus
Probab=99.85 E-value=2.8e-22 Score=127.61 Aligned_cols=91 Identities=20% Similarity=0.302 Sum_probs=79.8
Q ss_pred cCCCCccccCCCCCCceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCC
Q psy7447 10 FNLPPHTLFNPLLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQ 89 (114)
Q Consensus 10 ~~l~~h~~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C 89 (114)
-.|+.|+++ |+ -+..|.+||+.|..++-|+.|+++|+| +|||.|..|+++|...++|+.|+++|.+.|+ |.|..|
T Consensus 175 pALkMHirT-H~--l~c~C~iCGKaFSRPWLLQGHiRTHTG-EKPF~C~hC~kAFADRSNLRAHmQTHS~~K~-~qC~~C 249 (279)
T KOG2462|consen 175 PALKMHIRT-HT--LPCECGICGKAFSRPWLLQGHIRTHTG-EKPFSCPHCGKAFADRSNLRAHMQTHSDVKK-HQCPRC 249 (279)
T ss_pred HHHhhHhhc-cC--CCcccccccccccchHHhhcccccccC-CCCccCCcccchhcchHHHHHHHHhhcCCcc-ccCcch
Confidence 356788888 75 688999999999999999999999999 9999999999999999999999999999998 999999
Q ss_pred CcccccccccCCCccc
Q psy7447 90 GPEMLSIKHQGPETLS 105 (114)
Q Consensus 90 ~~~f~~~~~~~~~~~~ 105 (114)
++.|.-.+=...|..+
T Consensus 250 ~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 250 GKSFALKSYLNKHSES 265 (279)
T ss_pred hhHHHHHHHHHHhhhh
Confidence 9999855444444433
No 2
>KOG2462|consensus
Probab=99.78 E-value=5.7e-20 Score=117.16 Aligned_cols=96 Identities=19% Similarity=0.213 Sum_probs=82.8
Q ss_pred ccCccCCCCccccCC---CCCCceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCC
Q psy7447 6 RFSEFNLPPHTLFNP---LLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPE 82 (114)
Q Consensus 6 ~~~~~~l~~h~~~~h---~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p 82 (114)
..+.++|..|.-+ | ...+.+.|.+|++.+..-..|..|+++|+. +++|.+||+.|.+..-|+.|+|+||||||
T Consensus 140 ysT~snLsrHkQ~-H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l---~c~C~iCGKaFSRPWLLQGHiRTHTGEKP 215 (279)
T KOG2462|consen 140 YSTSSNLSRHKQT-HRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL---PCECGICGKAFSRPWLLQGHIRTHTGEKP 215 (279)
T ss_pred cccccccchhhcc-cccccccccccCCCCCceeeehHHHhhHhhccCC---CcccccccccccchHHhhcccccccCCCC
Confidence 3456677777655 4 335778999999999999999999999954 78999999999999999999999999999
Q ss_pred cccccCCCcccccccccCCCcccc
Q psy7447 83 MLSVKHQGPEMLSIKHQGPETLSI 106 (114)
Q Consensus 83 ~~~C~~C~~~f~~~~~~~~~~~~~ 106 (114)
|.|..|++.|++.++..+|+..+
T Consensus 216 -F~C~hC~kAFADRSNLRAHmQTH 238 (279)
T KOG2462|consen 216 -FSCPHCGKAFADRSNLRAHMQTH 238 (279)
T ss_pred -ccCCcccchhcchHHHHHHHHhh
Confidence 99999999999998877776654
No 3
>KOG3623|consensus
Probab=99.58 E-value=7.6e-16 Score=109.08 Aligned_cols=81 Identities=23% Similarity=0.354 Sum_probs=73.3
Q ss_pred CCCCceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccccccccC
Q psy7447 21 LLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSIKHQG 100 (114)
Q Consensus 21 ~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~~~~~ 100 (114)
+.+..|.|..|.+.|...++|.+|.-.|+| .+||+|.+|.++|..+.+|..|+|+|.|+|| |.|++|++.|.-...+.
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsG-qRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP-fQCdKClKRFSHSGSYS 967 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSG-QRPYQCIICKKAFKHKHHLTEHKRLHSGEKP-FQCDKCLKRFSHSGSYS 967 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcC-CCCcccchhhHhhhhhhhhhhhhhhccCCCc-chhhhhhhhcccccchH
Confidence 456789999999999999999999999999 9999999999999999999999999999999 99999999998654444
Q ss_pred CCc
Q psy7447 101 PET 103 (114)
Q Consensus 101 ~~~ 103 (114)
.|+
T Consensus 968 QHM 970 (1007)
T KOG3623|consen 968 QHM 970 (1007)
T ss_pred hhh
Confidence 443
No 4
>KOG3623|consensus
Probab=99.51 E-value=3.1e-15 Score=106.04 Aligned_cols=93 Identities=19% Similarity=0.290 Sum_probs=79.0
Q ss_pred CCCccccCC-CCCCceecCcchhhcCCchHHHHHHHHhcCC------------CCCeeCCCCCcccCCchHHHHHHHHhc
Q psy7447 12 LPPHTLFNP-LLQFRYTCDSCGKVYKLKRSLYRHRTLECGK------------EPRYQCPHCPYRGKQKVHLKTHVAIKH 78 (114)
Q Consensus 12 l~~h~~~~h-~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~------------~k~~~C~~c~~~~~~~~~l~~h~~~~~ 78 (114)
|+.|++..| ..+..|.|..|..+|.....|.+|+..|... .+.|.|.+|+++|..+.+|..|+|+|.
T Consensus 226 lkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHS 305 (1007)
T KOG3623|consen 226 LKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHS 305 (1007)
T ss_pred HHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeec
Confidence 466776655 3456789999999999999999999998532 467899999999999999999999999
Q ss_pred CCCCcccccCCCcccccccccCCCccc
Q psy7447 79 QGPEMLSVKHQGPEMLSIKHQGPETLS 105 (114)
Q Consensus 79 ~~~p~~~C~~C~~~f~~~~~~~~~~~~ 105 (114)
|+|| |.|+.|++.|.-...+..|+.+
T Consensus 306 GEKP-feCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 306 GEKP-FECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred CCCC-cCCcccccccccCCcccccccc
Confidence 9999 9999999999876556666654
No 5
>KOG1074|consensus
Probab=99.43 E-value=2.4e-14 Score=102.74 Aligned_cols=49 Identities=14% Similarity=0.083 Sum_probs=26.2
Q ss_pred eCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccccccccCCCccc
Q psy7447 56 QCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSIKHQGPETLS 105 (114)
Q Consensus 56 ~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~~~~~~~~~~ 105 (114)
+|.+|.+...-.++|+.|.|+|+||+| |+|.+||+.|..+-+...|+.-
T Consensus 607 qCiiC~rVlSC~saLqmHyrtHtGERP-FkCKiCgRAFtTkGNLkaH~~v 655 (958)
T KOG1074|consen 607 QCIICLRVLSCPSALQMHYRTHTGERP-FKCKICGRAFTTKGNLKAHMSV 655 (958)
T ss_pred ceeeeeecccchhhhhhhhhcccCcCc-cccccccchhccccchhhcccc
Confidence 455555555555555555555555555 5555555555554444444433
No 6
>KOG3576|consensus
Probab=99.34 E-value=8.8e-14 Score=85.84 Aligned_cols=76 Identities=22% Similarity=0.274 Sum_probs=64.7
Q ss_pred CCCCceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccccccc
Q psy7447 21 LLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSIKH 98 (114)
Q Consensus 21 ~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~~~ 98 (114)
+..-.+.|.+|++.|....-|.+|++-|.. .+.+.|..||+.|...-.|.+|.++|+|-+| |+|..|++.|+..-.
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~-vkr~lct~cgkgfndtfdlkrh~rthtgvrp-ykc~~c~kaftqrcs 188 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSD-VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP-YKCSLCEKAFTQRCS 188 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccH-HHHHHHhhccCcccchhhhhhhhccccCccc-cchhhhhHHHHhhcc
Confidence 334567899999999888888899998888 8888999999999998899999999999888 999999998886543
No 7
>KOG3576|consensus
Probab=99.29 E-value=2.8e-13 Score=83.67 Aligned_cols=81 Identities=23% Similarity=0.275 Sum_probs=72.1
Q ss_pred CCCccccCCCCCCceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCC-----------
Q psy7447 12 LPPHTLFNPLLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQG----------- 80 (114)
Q Consensus 12 l~~h~~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~----------- 80 (114)
|..|++. |..-|.+.|.-||+.|.....|.+|+++|+| .+||.|..|+++|.+...|..|.+..+|.
T Consensus 133 lnrh~kc-h~~vkr~lct~cgkgfndtfdlkrh~rthtg-vrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~ 210 (267)
T KOG3576|consen 133 LNRHLKC-HSDVKRHLCTFCGKGFNDTFDLKRHTRTHTG-VRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRA 210 (267)
T ss_pred HHHHhhh-ccHHHHHHHhhccCcccchhhhhhhhccccC-ccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhh
Confidence 4678888 9889999999999999999999999999999 99999999999999999999999887773
Q ss_pred CCcccccCCCccccc
Q psy7447 81 PEMLSVKHQGPEMLS 95 (114)
Q Consensus 81 ~p~~~C~~C~~~f~~ 95 (114)
+- |.|..||..-..
T Consensus 211 kl-~vcedcg~t~~~ 224 (267)
T KOG3576|consen 211 KL-YVCEDCGYTSER 224 (267)
T ss_pred he-eeecccCCCCCC
Confidence 34 899999975443
No 8
>KOG3608|consensus
Probab=99.06 E-value=1.9e-11 Score=81.07 Aligned_cols=98 Identities=16% Similarity=0.308 Sum_probs=71.4
Q ss_pred cCccCCCCccccCCCCCCceecCcchhhcCCchHHHHHHHHhcCC---------------------------CCCeeCCC
Q psy7447 7 FSEFNLPPHTLFNPLLQFRYTCDSCGKVYKLKRSLYRHRTLECGK---------------------------EPRYQCPH 59 (114)
Q Consensus 7 ~~~~~l~~h~~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~---------------------------~k~~~C~~ 59 (114)
-++..|+.|+++ |+++|...|..||..|.....|..|.+..+.- ..-|.|+.
T Consensus 190 ~~k~~LreH~r~-Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCpl 268 (467)
T KOG3608|consen 190 GNKYRLREHIRT-HSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPL 268 (467)
T ss_pred ccHHHHHHHHHh-cCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccc
Confidence 456778889998 99988777777777776666666665543211 34567888
Q ss_pred CCcccCCchHHHHHHHHhcCCCCcccccCCCcccccccccCCCccc
Q psy7447 60 CPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSIKHQGPETLS 105 (114)
Q Consensus 60 c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~~~~~~~~~~ 105 (114)
|.......+.|..|++.-+...+||+|+.|+..+........|...
T Consensus 269 Cdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~ 314 (467)
T KOG3608|consen 269 CDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQV 314 (467)
T ss_pred cccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHh
Confidence 8888888999999999776655559999999998877765555443
No 9
>KOG1074|consensus
Probab=99.06 E-value=2.3e-11 Score=87.80 Aligned_cols=69 Identities=23% Similarity=0.430 Sum_probs=45.1
Q ss_pred ccCCCCccccCCCCCCceecCcchhhcCCchHHHHHHHHhcCC---CCCeeCC---CCCcccCCchHHHHHHHHhc
Q psy7447 9 EFNLPPHTLFNPLLQFRYTCDSCGKVYKLKRSLYRHRTLECGK---EPRYQCP---HCPYRGKQKVHLKTHVAIKH 78 (114)
Q Consensus 9 ~~~l~~h~~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~---~k~~~C~---~c~~~~~~~~~l~~h~~~~~ 78 (114)
+++|+.|+++ |+|++||+|.+||+.|..+.+|+.|+..|... ...+.|+ +|-+.|...-.+..|+++|.
T Consensus 618 ~saLqmHyrt-HtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 618 PSALQMHYRT-HTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQHIRIHL 692 (958)
T ss_pred hhhhhhhhhc-ccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccccceEEeec
Confidence 3556677777 77777777777777777777777776666541 1234566 66666776666777777665
No 10
>KOG3608|consensus
Probab=98.99 E-value=1.9e-10 Score=76.42 Aligned_cols=89 Identities=19% Similarity=0.323 Sum_probs=76.9
Q ss_pred ccCccCCCCccccCCCCCCceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCC--CCcccCCchHHHHHHHHhc-CCCC
Q psy7447 6 RFSEFNLPPHTLFNPLLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPH--CPYRGKQKVHLKTHVAIKH-QGPE 82 (114)
Q Consensus 6 ~~~~~~l~~h~~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~--c~~~~~~~~~l~~h~~~~~-~~~p 82 (114)
+...++|..|++..|+..|||+|..|.+.+...+.|.+|...|+ +..|.|.- |..++.+...+..|.+-++ |..|
T Consensus 273 c~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS--~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np 350 (467)
T KOG3608|consen 273 CSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS--KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNP 350 (467)
T ss_pred CCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc--ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCC
Confidence 45678899999999999999999999999999999999999887 56789976 9999999999999988776 5443
Q ss_pred -cccccCCCcccccc
Q psy7447 83 -MLSVKHQGPEMLSI 96 (114)
Q Consensus 83 -~~~C~~C~~~f~~~ 96 (114)
+|.|-.|++-|.+=
T Consensus 351 ~~Y~CH~Cdr~ft~G 365 (467)
T KOG3608|consen 351 ILYACHCCDRFFTSG 365 (467)
T ss_pred Cceeeecchhhhccc
Confidence 49999999988754
No 11
>PHA02768 hypothetical protein; Provisional
Probab=98.93 E-value=8.8e-10 Score=54.77 Aligned_cols=39 Identities=21% Similarity=0.343 Sum_probs=31.0
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCccccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLS 95 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~ 95 (114)
.|+|+.||+.|...++|..|+++|+ ++ +.|..|++.|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~C~k~f~~ 43 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TN-LKLSNCKRISLR 43 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Cc-ccCCcccceecc
Confidence 4678888888888888888888887 45 888888887763
No 12
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.86 E-value=1.7e-09 Score=46.15 Aligned_cols=25 Identities=12% Similarity=0.163 Sum_probs=19.5
Q ss_pred HHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 69 HLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 69 ~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
+|..|+++|+|++| |.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~-~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP-YKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSS-EEESSSSEEES
T ss_pred CHHHHhhhcCCCCC-CCCCCCcCeeC
Confidence 46778888888887 88888888775
No 13
>PHA00733 hypothetical protein
Probab=98.86 E-value=1.1e-09 Score=64.24 Aligned_cols=74 Identities=18% Similarity=0.118 Sum_probs=54.7
Q ss_pred CCCCceecCcchhhcCCchHHHHH--H---HHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCccccc
Q psy7447 21 LLQFRYTCDSCGKVYKLKRSLYRH--R---TLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLS 95 (114)
Q Consensus 21 ~~~k~~~C~~C~~~f~~~~~l~~h--~---~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~ 95 (114)
+.++++.|.+|...|..+..|..+ . ..+.+ .++|.|..|++.|.....|..|++.+ +.+ |.|..|++.|..
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~-~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~-~~C~~CgK~F~~ 111 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKA-VSPYVCPLCLMPFSSSVSLKQHIRYT--EHS-KVCPVCGKEFRN 111 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCC-CCCccCCCCCCcCCCHHHHHHHHhcC--CcC-ccCCCCCCccCC
Confidence 346788899988887766555444 1 12234 67899999999999999999998875 345 899999999886
Q ss_pred ccc
Q psy7447 96 IKH 98 (114)
Q Consensus 96 ~~~ 98 (114)
...
T Consensus 112 ~~s 114 (128)
T PHA00733 112 TDS 114 (128)
T ss_pred HHH
Confidence 544
No 14
>PHA00733 hypothetical protein
Probab=98.84 E-value=4.4e-09 Score=61.75 Aligned_cols=63 Identities=24% Similarity=0.258 Sum_probs=52.5
Q ss_pred CCCccccCCCCCCceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcC
Q psy7447 12 LPPHTLFNPLLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQ 79 (114)
Q Consensus 12 l~~h~~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~ 79 (114)
|..|+.. .+.+||.|..|++.|.....|..|++.+ ..++.|..|++.|.....|..|+...++
T Consensus 62 l~~~~~~--~~~kPy~C~~Cgk~Fss~s~L~~H~r~h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 62 LYKLLTS--KAVSPYVCPLCLMPFSSSVSLKQHIRYT---EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HHhhccc--CCCCCccCCCCCCcCCCHHHHHHHHhcC---CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3444333 3579999999999999999999999876 3468999999999999999999887765
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.84 E-value=1.8e-09 Score=53.68 Aligned_cols=42 Identities=19% Similarity=0.461 Sum_probs=37.6
Q ss_pred eecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHH
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHL 70 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l 70 (114)
|.|..||+.|...+.|..|++.|. +++.|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~---k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN---TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC---CcccCCcccceeccccee
Confidence 689999999999999999999995 578899999999877655
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.68 E-value=1.3e-08 Score=72.24 Aligned_cols=66 Identities=18% Similarity=0.318 Sum_probs=30.3
Q ss_pred CceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCC----------chHHHHHHHHhcCCCCcccccCCCccc
Q psy7447 24 FRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQ----------KVHLKTHVAIKHQGPEMLSVKHQGPEM 93 (114)
Q Consensus 24 k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~----------~~~l~~h~~~~~~~~p~~~C~~C~~~f 93 (114)
+++.|. |+..+ ....|..|+..|.. .+++.|..|+..+.. ...|..|.... |.++ +.|..||+.+
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp-~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt-~~C~~Cgk~V 551 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCP-LRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRT-APCDSCGRSV 551 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCC-CCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcc-eEccccCCee
Confidence 444554 55332 33445555555544 455555555544421 12444444442 4444 5555555444
Q ss_pred c
Q psy7447 94 L 94 (114)
Q Consensus 94 ~ 94 (114)
+
T Consensus 552 r 552 (567)
T PLN03086 552 M 552 (567)
T ss_pred e
Confidence 4
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=98.58 E-value=6e-08 Score=41.32 Aligned_cols=25 Identities=36% Similarity=0.639 Sum_probs=18.0
Q ss_pred HHHHHHHHhcCCCCCeeCCCCCcccC
Q psy7447 40 SLYRHRTLECGKEPRYQCPHCPYRGK 65 (114)
Q Consensus 40 ~l~~h~~~h~~~~k~~~C~~c~~~~~ 65 (114)
+|..|++.|++ ++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~-~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTG-EKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSS-SSSEEESSSSEEES
T ss_pred CHHHHhhhcCC-CCCCCCCCCcCeeC
Confidence 35677777777 77777777777664
No 18
>PHA00616 hypothetical protein
Probab=98.54 E-value=3.7e-08 Score=46.77 Aligned_cols=33 Identities=24% Similarity=0.415 Sum_probs=19.8
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCccccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVK 87 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~ 87 (114)
||+|..||+.|...+.+..|++.++|+++ +.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~-~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK-LTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc-ccee
Confidence 35566666666666666666666666655 5554
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.47 E-value=3.1e-07 Score=65.37 Aligned_cols=67 Identities=18% Similarity=0.354 Sum_probs=56.6
Q ss_pred CCCCceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 21 LLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 21 ~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
..++++.|..|++.|. ...+..|+..++ +++.|+ |+..+ ....|..|+..+.+.++ +.|.+|+..|.
T Consensus 449 el~~H~~C~~Cgk~f~-~s~LekH~~~~H---kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp-i~C~fC~~~v~ 515 (567)
T PLN03086 449 EAKNHVHCEKCGQAFQ-QGEMEKHMKVFH---EPLQCP-CGVVL-EKEQMVQHQASTCPLRL-ITCRFCGDMVQ 515 (567)
T ss_pred ccccCccCCCCCCccc-hHHHHHHHHhcC---CCccCC-CCCCc-chhHHHhhhhccCCCCc-eeCCCCCCccc
Confidence 3456789999999996 577999999873 578999 99765 55889999999999988 99999999883
No 20
>PHA00616 hypothetical protein
Probab=98.46 E-value=1e-07 Score=45.27 Aligned_cols=33 Identities=18% Similarity=0.449 Sum_probs=30.8
Q ss_pred ceecCcchhhcCCchHHHHHHHHhcCCCCCeeCC
Q psy7447 25 RYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCP 58 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~ 58 (114)
||+|..||+.|...+.|..|++.|++ ++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg-~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK-QNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC-CCcccee
Confidence 68999999999999999999999999 8988875
No 21
>PHA00732 hypothetical protein
Probab=98.29 E-value=6.8e-07 Score=48.17 Aligned_cols=45 Identities=22% Similarity=0.388 Sum_probs=30.0
Q ss_pred ceecCcchhhcCCchHHHHHHHH-hcCCCCCeeCCCCCcccCCchHHHHHHHH
Q psy7447 25 RYTCDSCGKVYKLKRSLYRHRTL-ECGKEPRYQCPHCPYRGKQKVHLKTHVAI 76 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~~l~~h~~~-h~~~~k~~~C~~c~~~~~~~~~l~~h~~~ 76 (114)
||.|..|++.|.....|..|++. |.+ +.|+.|++.|.+ +..|...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~----~~C~~CgKsF~~---l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL----TKCPVCNKSYRR---LNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC----CccCCCCCEeCC---hhhhhcc
Confidence 46777787777777777777763 433 367777777763 5556543
No 22
>PHA00732 hypothetical protein
Probab=98.11 E-value=1.9e-06 Score=46.40 Aligned_cols=40 Identities=18% Similarity=0.329 Sum_probs=33.8
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSI 96 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~ 96 (114)
||.|..|++.|.....|..|++.++. + +.|+.||+.|..+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~-~~C~~CgKsF~~l 40 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--L-TKCPVCNKSYRRL 40 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--C-CccCCCCCEeCCh
Confidence 57899999999999999999985332 3 7899999999865
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.89 E-value=9.6e-06 Score=33.21 Aligned_cols=22 Identities=41% Similarity=0.798 Sum_probs=10.9
Q ss_pred eecCcchhhcCCchHHHHHHHH
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRTL 47 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~~ 47 (114)
|.|..|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 3455555555555555555443
No 24
>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=97.85 E-value=4.4e-05 Score=38.15 Aligned_cols=52 Identities=29% Similarity=0.491 Sum_probs=37.1
Q ss_pred ceecCcchhhcCCchHHHHHHH-HhcCCCCCeeCCCCCcccCCchHHHHHHHHhcC
Q psy7447 25 RYTCDSCGKVYKLKRSLYRHRT-LECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQ 79 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~~l~~h~~-~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~ 79 (114)
.|.|+.|++. .....|..|.. .|....+.+.|++|...+. .+|..|+...++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 4789999994 44677888855 4554245789999987544 478888887654
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.81 E-value=1.9e-05 Score=32.30 Aligned_cols=23 Identities=35% Similarity=0.645 Sum_probs=20.9
Q ss_pred eeCCCCCcccCCchHHHHHHHHh
Q psy7447 55 YQCPHCPYRGKQKVHLKTHVAIK 77 (114)
Q Consensus 55 ~~C~~c~~~~~~~~~l~~h~~~~ 77 (114)
|.|+.|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 67999999999999999999874
No 26
>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=97.48 E-value=0.00013 Score=29.67 Aligned_cols=22 Identities=32% Similarity=0.625 Sum_probs=9.7
Q ss_pred eCCCCCcccCCchHHHHHHHHh
Q psy7447 56 QCPHCPYRGKQKVHLKTHVAIK 77 (114)
Q Consensus 56 ~C~~c~~~~~~~~~l~~h~~~~ 77 (114)
.|+.|+..|.....|..|+..+
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHhh
Confidence 4444555555555555554443
No 27
>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=97.47 E-value=6.5e-05 Score=31.91 Aligned_cols=23 Identities=30% Similarity=0.782 Sum_probs=12.1
Q ss_pred eecCcchhhcCCchHHHHHHHHh
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRTLE 48 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~~h 48 (114)
|.|..|++.|.....|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 45555555555555555555443
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=97.44 E-value=7.3e-05 Score=31.75 Aligned_cols=26 Identities=15% Similarity=0.308 Sum_probs=22.6
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcC
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQ 79 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~ 79 (114)
+++|..|++.|.....|..|++.|.+
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 57899999999999999999987653
No 29
>KOG3993|consensus
Probab=97.38 E-value=9.3e-05 Score=50.97 Aligned_cols=56 Identities=21% Similarity=0.501 Sum_probs=41.8
Q ss_pred CceecCcchhhcCCchHHHHHHHHhcCC-------C-------------------------CCeeCCCCCcccCCchHHH
Q psy7447 24 FRYTCDSCGKVYKLKRSLYRHRTLECGK-------E-------------------------PRYQCPHCPYRGKQKVHLK 71 (114)
Q Consensus 24 k~~~C~~C~~~f~~~~~l~~h~~~h~~~-------~-------------------------k~~~C~~c~~~~~~~~~l~ 71 (114)
--|+|.+|+|.|+-..+|..|.+=|.-. . -.|.|..|++.|.++..|+
T Consensus 294 vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLr 373 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLR 373 (500)
T ss_pred eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHH
Confidence 4578999999999999998888766211 1 1367888888888888888
Q ss_pred HHHHHhcC
Q psy7447 72 THVAIKHQ 79 (114)
Q Consensus 72 ~h~~~~~~ 79 (114)
.|+-+|+.
T Consensus 374 KHqlthq~ 381 (500)
T KOG3993|consen 374 KHQLTHQR 381 (500)
T ss_pred HhHHhhhc
Confidence 88777754
No 30
>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=97.36 E-value=0.00019 Score=29.22 Aligned_cols=23 Identities=30% Similarity=0.728 Sum_probs=19.2
Q ss_pred eecCcchhhcCCchHHHHHHHHh
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRTLE 48 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~~h 48 (114)
|.|..|+..|.....|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 68999999999999999999875
No 31
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.29 E-value=8.3e-05 Score=49.55 Aligned_cols=66 Identities=14% Similarity=0.145 Sum_probs=36.5
Q ss_pred CCceecCc--chhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCccccccccc
Q psy7447 23 QFRYTCDS--CGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSIKHQ 99 (114)
Q Consensus 23 ~k~~~C~~--C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~~~~ 99 (114)
+|||.|++ |.+.++..-.|..|+..-.-..+..+-+ .. . .+.-.....|| |.|.+|++.+-.+.|.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p-------~p--~-~~~~F~~~~KP-YrCevC~KRYKNlNGL 414 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP-------SP--E-KMNIFSAKDKP-YRCEVCDKRYKNLNGL 414 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCC-------Cc--c-ccccccccCCc-eeccccchhhccCccc
Confidence 48899875 8888888888888866322101111111 00 0 00011223455 8888888887777663
No 32
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.27 E-value=0.00037 Score=33.99 Aligned_cols=31 Identities=29% Similarity=0.488 Sum_probs=17.8
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcCCCC
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPE 82 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p 82 (114)
+.|..|++|+..+.+.-+|.+|+.+.++.+|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 5566777777777777777777777766655
No 33
>PRK04860 hypothetical protein; Provisional
Probab=97.26 E-value=0.0003 Score=42.91 Aligned_cols=38 Identities=13% Similarity=0.392 Sum_probs=31.7
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSI 96 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~ 96 (114)
+|.|. |+. ....+.+|.++++++++ |.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~-YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAV-YRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCcc-EECCCCCceeEEe
Confidence 58887 876 55667899999999998 9999999988754
No 34
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.20 E-value=0.00084 Score=32.77 Aligned_cols=44 Identities=20% Similarity=0.215 Sum_probs=26.1
Q ss_pred cCCCCccccCCCCCCceecCcchhhcCCchHHHHHHHHhcCCCCC
Q psy7447 10 FNLPPHTLFNPLLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPR 54 (114)
Q Consensus 10 ~~l~~h~~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~ 54 (114)
.....+.+..+..+.|-.|.+|+..+....+|.+|+..+.+ .+|
T Consensus 9 ~~~~~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~-~k~ 52 (54)
T PF09237_consen 9 KPSTKKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHF-KKP 52 (54)
T ss_dssp SS-----CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTT-TS-
T ss_pred chhhhHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhc-ccC
Confidence 33344555544556889999999999999999999988776 554
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.06 E-value=0.00069 Score=37.56 Aligned_cols=25 Identities=28% Similarity=0.655 Sum_probs=20.1
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKH 78 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~ 78 (114)
.+.|..|+..|.+...|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 5889999999999899999988654
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.84 E-value=0.0015 Score=26.81 Aligned_cols=20 Identities=40% Similarity=0.675 Sum_probs=9.7
Q ss_pred eCCCCCcccCCchHHHHHHH
Q psy7447 56 QCPHCPYRGKQKVHLKTHVA 75 (114)
Q Consensus 56 ~C~~c~~~~~~~~~l~~h~~ 75 (114)
.|..|++.|.....+..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 34445555555444544444
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.82 E-value=0.0012 Score=27.10 Aligned_cols=24 Identities=42% Similarity=0.818 Sum_probs=21.2
Q ss_pred eecCcchhhcCCchHHHHHHHHhc
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRTLEC 49 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~~h~ 49 (114)
|.|..|++.|.....+..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998664
No 38
>PRK04860 hypothetical protein; Provisional
Probab=96.70 E-value=0.002 Score=39.40 Aligned_cols=39 Identities=31% Similarity=0.644 Sum_probs=33.3
Q ss_pred CceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCc
Q psy7447 24 FRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQK 67 (114)
Q Consensus 24 k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~ 67 (114)
-+|.|. |+. ....+..|.+++.+ .++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g-~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRG-EAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcC-CccEECCCCCceeEEe
Confidence 479998 987 56778999999999 9999999999887654
No 39
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.65 E-value=0.0013 Score=44.12 Aligned_cols=25 Identities=32% Similarity=0.568 Sum_probs=21.3
Q ss_pred CCCeeCCC--CCcccCCchHHHHHHHH
Q psy7447 52 EPRYQCPH--CPYRGKQKVHLKTHVAI 76 (114)
Q Consensus 52 ~k~~~C~~--c~~~~~~~~~l~~h~~~ 76 (114)
+|||.|++ |.+.+.+...|+.|+..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lh 373 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLH 373 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhc
Confidence 68999986 88999999999988653
No 40
>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=96.42 E-value=0.0058 Score=30.39 Aligned_cols=39 Identities=15% Similarity=0.308 Sum_probs=29.5
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCC-CcccccCCCccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGP-EMLSVKHQGPEM 93 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~-p~~~C~~C~~~f 93 (114)
.|.|+.|++. .....|..|....+... ..+.|+.|...+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~ 41 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRV 41 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhh
Confidence 4789999994 55678999988776543 349999998743
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.28 E-value=0.0029 Score=26.09 Aligned_cols=21 Identities=33% Similarity=0.727 Sum_probs=11.8
Q ss_pred eecCcchhhcCCchHHHHHHH
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRT 46 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~ 46 (114)
|.|..|+..|.....+..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 345555555555555555554
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.21 E-value=0.0053 Score=25.07 Aligned_cols=23 Identities=48% Similarity=1.084 Sum_probs=11.9
Q ss_pred eeCCCCCcccCCchHHHHHHHHhc
Q psy7447 55 YQCPHCPYRGKQKVHLKTHVAIKH 78 (114)
Q Consensus 55 ~~C~~c~~~~~~~~~l~~h~~~~~ 78 (114)
|.|..|+.... ...|..|++.++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 34566665555 556666665544
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.81 E-value=0.0062 Score=25.04 Aligned_cols=23 Identities=22% Similarity=0.428 Sum_probs=19.2
Q ss_pred eeCCCCCcccCCchHHHHHHHHh
Q psy7447 55 YQCPHCPYRGKQKVHLKTHVAIK 77 (114)
Q Consensus 55 ~~C~~c~~~~~~~~~l~~h~~~~ 77 (114)
|.|.+|+..|.+...+..|++.+
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 57899999999999998887643
No 44
>KOG3993|consensus
Probab=94.90 E-value=0.0048 Score=42.89 Aligned_cols=52 Identities=25% Similarity=0.461 Sum_probs=43.8
Q ss_pred ceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHh
Q psy7447 25 RYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIK 77 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~ 77 (114)
-|.|..|...|.....|.+|.-...- ...|.|++|++.|+-..+|..|.|=|
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV-~vEYrCPEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIV-HVEYRCPECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeE-EeeecCCcccccccCchhhhhhhccc
Confidence 37899999888888888888765555 56799999999999999999998755
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.08 E-value=0.013 Score=24.73 Aligned_cols=21 Identities=29% Similarity=0.743 Sum_probs=12.7
Q ss_pred eecCcchhhcCCchHHHHHHH
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRT 46 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~ 46 (114)
|.|..|++.|.....+..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 456666666666666655544
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.07 E-value=0.056 Score=22.41 Aligned_cols=18 Identities=28% Similarity=0.547 Sum_probs=8.0
Q ss_pred eCCCCCcccCCchHHHHHH
Q psy7447 56 QCPHCPYRGKQKVHLKTHV 74 (114)
Q Consensus 56 ~C~~c~~~~~~~~~l~~h~ 74 (114)
.|+.||+.| ....|..|.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 345555555 223344443
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=94.06 E-value=0.051 Score=24.11 Aligned_cols=24 Identities=25% Similarity=0.466 Sum_probs=14.5
Q ss_pred eeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCc
Q psy7447 55 YQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGP 91 (114)
Q Consensus 55 ~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~ 91 (114)
|.|.+||..+.... .+ +.|+.||.
T Consensus 2 ~~C~~CGy~y~~~~------------~~-~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------AP-WVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CC-CcCcCCCC
Confidence 56777776554332 33 77777775
No 48
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.64 E-value=0.025 Score=38.87 Aligned_cols=63 Identities=21% Similarity=0.337 Sum_probs=53.7
Q ss_pred CceecCcchhhcCCchHHHHHHH--HhcCCC--CCeeCC--CCCcccCCchHHHHHHHHhcCCCCcccccC
Q psy7447 24 FRYTCDSCGKVYKLKRSLYRHRT--LECGKE--PRYQCP--HCPYRGKQKVHLKTHVAIKHQGPEMLSVKH 88 (114)
Q Consensus 24 k~~~C~~C~~~f~~~~~l~~h~~--~h~~~~--k~~~C~--~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~ 88 (114)
.++.|..|...|.....+..|.+ .|.+ + +++.|+ .|++.|.+...+..|...+++..+ ..+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~-~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 356 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSG-ESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP-AKEKL 356 (467)
T ss_pred cCCCCccccCCcccccccccccccccccc-ccCCceeeeccCCCccccccccccCCcccccCCCc-ccccc
Confidence 46788999999999999999999 7888 7 899998 799999999999999999988776 55554
No 49
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.32 E-value=0.12 Score=22.89 Aligned_cols=22 Identities=18% Similarity=0.409 Sum_probs=12.8
Q ss_pred ceecCcchhhcCCchHHHHHHH
Q psy7447 25 RYTCDSCGKVYKLKRSLYRHRT 46 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~~l~~h~~ 46 (114)
+|.|..|+..|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4556666666665555555544
No 50
>KOG1146|consensus
Probab=91.28 E-value=0.17 Score=40.25 Aligned_cols=64 Identities=25% Similarity=0.450 Sum_probs=50.5
Q ss_pred CCCCccccCCCCCCceecCcchhhcCCchHHHHHHHHh-------------------------cCCCCCeeCCCCCcccC
Q psy7447 11 NLPPHTLFNPLLQFRYTCDSCGKVYKLKRSLYRHRTLE-------------------------CGKEPRYQCPHCPYRGK 65 (114)
Q Consensus 11 ~l~~h~~~~h~~~k~~~C~~C~~~f~~~~~l~~h~~~h-------------------------~~~~k~~~C~~c~~~~~ 65 (114)
.+-.++...++..+.+.|..|+..++....|..||+.- .+ .++|.|..|..++.
T Consensus 451 ~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~-~~p~~C~~C~~stt 529 (1406)
T KOG1146|consen 451 SLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCP-GKPYPCRACNYSTT 529 (1406)
T ss_pred ccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCC-CCcccceeeeeeee
Confidence 33456666678889999999999999999999999971 11 57788888888888
Q ss_pred CchHHHHHHH
Q psy7447 66 QKVHLKTHVA 75 (114)
Q Consensus 66 ~~~~l~~h~~ 75 (114)
...+|.+|+.
T Consensus 530 tng~Lsihlq 539 (1406)
T KOG1146|consen 530 TNGNLSIHLQ 539 (1406)
T ss_pred cchHHHHHHH
Confidence 8788887765
No 51
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.00 E-value=0.28 Score=26.84 Aligned_cols=26 Identities=19% Similarity=0.537 Sum_probs=22.2
Q ss_pred ceecCcchhhcCCchHHHHHHHHhcC
Q psy7447 25 RYTCDSCGKVYKLKRSLYRHRTLECG 50 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~~l~~h~~~h~~ 50 (114)
.+.|..|++.|.....|..|++.+..
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccC
Confidence 68999999999999999999997543
No 52
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.11 E-value=0.39 Score=21.84 Aligned_cols=10 Identities=10% Similarity=0.149 Sum_probs=5.3
Q ss_pred ccccCCCccc
Q psy7447 84 LSVKHQGPEM 93 (114)
Q Consensus 84 ~~C~~C~~~f 93 (114)
..|..|+..|
T Consensus 26 vrC~~C~~~f 35 (37)
T PF13719_consen 26 VRCPKCGHVF 35 (37)
T ss_pred EECCCCCcEe
Confidence 4555555544
No 53
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=88.43 E-value=0.9 Score=26.95 Aligned_cols=60 Identities=15% Similarity=0.105 Sum_probs=33.6
Q ss_pred CCCCceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCccccccc
Q psy7447 21 LLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSIK 97 (114)
Q Consensus 21 ~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~~ 97 (114)
...+-|+|.+|..+...... -||-+| ||...-..- -.....+....| .|+.|..+|.+.+
T Consensus 76 ~d~~lYeCnIC~etS~ee~F-----------LKPneC--CgY~iCn~C--ya~LWK~~~~yp--vCPvCkTSFKss~ 135 (140)
T PF05290_consen 76 LDPKLYECNICKETSAEERF-----------LKPNEC--CGYSICNAC--YANLWKFCNLYP--VCPVCKTSFKSSS 135 (140)
T ss_pred cCCCceeccCcccccchhhc-----------CCcccc--cchHHHHHH--HHHHHHHcccCC--CCCcccccccccc
Confidence 44588999999877553322 344444 554322211 112222333445 8999999998654
No 54
>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=88.28 E-value=0.45 Score=21.21 Aligned_cols=8 Identities=13% Similarity=-0.039 Sum_probs=4.5
Q ss_pred ccccCCCc
Q psy7447 84 LSVKHQGP 91 (114)
Q Consensus 84 ~~C~~C~~ 91 (114)
..|+.||.
T Consensus 19 ~~CP~Cg~ 26 (34)
T cd00729 19 EKCPICGA 26 (34)
T ss_pred CcCcCCCC
Confidence 55666654
No 55
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=88.09 E-value=0.33 Score=29.94 Aligned_cols=26 Identities=19% Similarity=0.370 Sum_probs=18.8
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCc
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGP 91 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~ 91 (114)
++.|.|.+||.. +.| .+|-.|+.||-
T Consensus 132 ~~~~vC~vCGy~-------------~~g-e~P~~CPiCga 157 (166)
T COG1592 132 GKVWVCPVCGYT-------------HEG-EAPEVCPICGA 157 (166)
T ss_pred CCEEEcCCCCCc-------------ccC-CCCCcCCCCCC
Confidence 346999999863 345 44599999994
No 56
>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=87.81 E-value=0.47 Score=27.15 Aligned_cols=13 Identities=23% Similarity=0.488 Sum_probs=5.8
Q ss_pred CeeCCCCCcccCC
Q psy7447 54 RYQCPHCPYRGKQ 66 (114)
Q Consensus 54 ~~~C~~c~~~~~~ 66 (114)
|..|+.||..|..
T Consensus 26 PivCP~CG~~~~~ 38 (108)
T PF09538_consen 26 PIVCPKCGTEFPP 38 (108)
T ss_pred CccCCCCCCccCc
Confidence 4444444444443
No 57
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=87.78 E-value=0.076 Score=34.05 Aligned_cols=13 Identities=15% Similarity=0.095 Sum_probs=10.5
Q ss_pred ccccCCCcccccc
Q psy7447 84 LSVKHQGPEMLSI 96 (114)
Q Consensus 84 ~~C~~C~~~f~~~ 96 (114)
+.|+.||.+|...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 6899999888744
No 58
>KOG4317|consensus
Probab=86.68 E-value=0.23 Score=33.60 Aligned_cols=30 Identities=17% Similarity=0.102 Sum_probs=24.7
Q ss_pred ccccCCCcccccccccCCCccccccccccC
Q psy7447 84 LSVKHQGPEMLSIKHQGPETLSIKHQFSQD 113 (114)
Q Consensus 84 ~~C~~C~~~f~~~~~~~~~~~~~~~~~~~~ 113 (114)
|.|+.|+..+.+++.+..|..++.+.+=.|
T Consensus 20 YtCPRCn~~YCsl~CYr~h~~~CsE~Fyrd 49 (383)
T KOG4317|consen 20 YTCPRCNLLYCSLKCYRNHKHSCSEKFYRD 49 (383)
T ss_pred ccCCCCCccceeeeeecCCCccchHHHHHH
Confidence 899999999999999888888887765443
No 59
>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=85.62 E-value=1.2 Score=27.19 Aligned_cols=33 Identities=12% Similarity=0.165 Sum_probs=26.3
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
..-|.|+.|+..|+...++. .. |.|+.||....
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~-F~Cp~Cg~~L~ 139 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LN-FTCPRCGAMLD 139 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cC-CcCCCCCCEee
Confidence 56789999999888887774 13 99999997644
No 60
>KOG2186|consensus
Probab=85.35 E-value=0.61 Score=30.67 Aligned_cols=50 Identities=20% Similarity=0.418 Sum_probs=34.0
Q ss_pred eecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcC
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQ 79 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~ 79 (114)
|.|..||....-+ .+..|+..-.+ .-|.|..|+..|... ....|...-+-
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn--~~fSCIDC~k~F~~~-sYknH~kCITE 53 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN--AYFSCIDCGKTFERV-SYKNHTKCITE 53 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC--CeeEEeecccccccc-hhhhhhhhcch
Confidence 6789999887654 45667665443 458888999999884 44566554443
No 61
>KOG2893|consensus
Probab=84.32 E-value=0.27 Score=32.08 Aligned_cols=45 Identities=18% Similarity=0.427 Sum_probs=32.5
Q ss_pred CCceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHH
Q psy7447 23 QFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTH 73 (114)
Q Consensus 23 ~k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h 73 (114)
.|+| |=+|++.|.....|.+|++ .|.|.|-+|-+.+.+...|..|
T Consensus 9 ~kpw-cwycnrefddekiliqhqk-----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQK-----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred CCce-eeecccccchhhhhhhhhh-----hccceeeeehhhhccCCCceee
Confidence 4666 5688889988888888887 6678898888765554445444
No 62
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.91 E-value=1.1 Score=20.28 Aligned_cols=10 Identities=10% Similarity=0.172 Sum_probs=4.8
Q ss_pred ccccCCCccc
Q psy7447 84 LSVKHQGPEM 93 (114)
Q Consensus 84 ~~C~~C~~~f 93 (114)
..|..|+..|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 4455554443
No 63
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.43 E-value=4.3 Score=23.42 Aligned_cols=71 Identities=13% Similarity=-0.016 Sum_probs=36.8
Q ss_pred CceecCcchhhcCCchHHHHHHH---HhcCC-CCC-------eeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcc
Q psy7447 24 FRYTCDSCGKVYKLKRSLYRHRT---LECGK-EPR-------YQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPE 92 (114)
Q Consensus 24 k~~~C~~C~~~f~~~~~l~~h~~---~h~~~-~k~-------~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~ 92 (114)
-|..|..|+-+......|.+.-- ..... +.+ ..|-.|...|....... ......... |.|+.|...
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~--~~~~~~~~~-y~C~~C~~~ 90 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSP--FDELKDSHR-YVCAVCKNV 90 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccc--ccccccccc-eeCCCCCCc
Confidence 46788889887776666654211 00000 111 13667777776532111 000111224 889999988
Q ss_pred ccccc
Q psy7447 93 MLSIK 97 (114)
Q Consensus 93 f~~~~ 97 (114)
|-..-
T Consensus 91 FC~dC 95 (112)
T TIGR00622 91 FCVDC 95 (112)
T ss_pred ccccc
Confidence 87443
No 64
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=82.24 E-value=0.38 Score=26.31 Aligned_cols=31 Identities=19% Similarity=0.354 Sum_probs=20.9
Q ss_pred CCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 53 PRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 53 k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
..+.|+.|++. ...+.-+| - |.|..||..|+
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~G--I-W~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIATG--I-WKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCc--------ceeeeccC--e-EEcCCCCCeec
Confidence 46789999863 12233333 3 89999999887
No 65
>KOG2186|consensus
Probab=82.12 E-value=0.79 Score=30.15 Aligned_cols=39 Identities=15% Similarity=0.255 Sum_probs=31.2
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCccccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLS 95 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~ 95 (114)
-|.|.+||....-+ .+.+|+-..++ .- |.|.-|+..|-.
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~-fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AY-FSCIDCGKTFER 41 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-Ce-eEEeeccccccc
Confidence 36899999887764 46678887777 44 999999999986
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=81.59 E-value=1.1 Score=22.35 Aligned_cols=31 Identities=23% Similarity=0.420 Sum_probs=22.3
Q ss_pred CCCCCceecCcchhhcCCchHHHHHHHHhcC
Q psy7447 20 PLLQFRYTCDSCGKVYKLKRSLYRHRTLECG 50 (114)
Q Consensus 20 h~~~k~~~C~~C~~~f~~~~~l~~h~~~h~~ 50 (114)
..++.-+.|+.|+..|....++..|..-..+
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 4577778888888888877777777554333
No 67
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=81.00 E-value=2 Score=26.81 Aligned_cols=33 Identities=15% Similarity=0.272 Sum_probs=25.2
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
..-|.|+.|+..|....++. .. |.|+.||....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~-F~Cp~Cg~~L~ 147 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YG-FRCPQCGEMLE 147 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cC-CcCCCCCCCCe
Confidence 46789999998888876653 23 99999997655
No 68
>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=80.88 E-value=1.3 Score=19.94 Aligned_cols=10 Identities=10% Similarity=0.046 Sum_probs=4.9
Q ss_pred ccccCCCccc
Q psy7447 84 LSVKHQGPEM 93 (114)
Q Consensus 84 ~~C~~C~~~f 93 (114)
..|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4555555444
No 69
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=80.72 E-value=1.7 Score=20.63 Aligned_cols=11 Identities=18% Similarity=0.386 Sum_probs=6.3
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
..|+.||...+
T Consensus 20 irC~~CG~rIl 30 (44)
T smart00659 20 VRCRECGYRIL 30 (44)
T ss_pred eECCCCCceEE
Confidence 56666665444
No 70
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=80.12 E-value=3.9 Score=24.61 Aligned_cols=38 Identities=16% Similarity=0.331 Sum_probs=25.7
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
...|.|+.|+..|.....+. ....... |.|+.||....
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~----~~d~~~~-f~Cp~Cg~~l~ 134 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQ----LLDMDGT-FTCPRCGEELE 134 (147)
T ss_pred CcEEECcCCCCEeeHHHHHH----hcCCCCc-EECCCCCCEEE
Confidence 56789999998888654432 1112333 99999998664
No 71
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.55 E-value=1.2 Score=21.07 Aligned_cols=11 Identities=18% Similarity=0.208 Sum_probs=6.4
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
..|++||..+.
T Consensus 22 ~~Cp~CG~~~~ 32 (46)
T PRK00398 22 VRCPYCGYRIL 32 (46)
T ss_pred eECCCCCCeEE
Confidence 56666665444
No 72
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=78.41 E-value=0.27 Score=36.84 Aligned_cols=62 Identities=19% Similarity=0.436 Sum_probs=40.2
Q ss_pred ecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccccc
Q psy7447 27 TCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSI 96 (114)
Q Consensus 27 ~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~ 96 (114)
.|..||-+|+....|-.-+..-+. ..--.|+.|.+.+....+.+.|. +| ..|+.||....-.
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM-~~F~lC~~C~~EY~dP~nRRfHA------Qp-~aCp~CGP~~~l~ 186 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSM-ADFPLCPFCDKEYKDPLNRRFHA------QP-IACPKCGPHLFLV 186 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCcc-ccCcCCHHHHHHhcCcccccccc------cc-ccCcccCCCeEEE
Confidence 588999998876655443332233 33447888888787776554332 24 8999999865533
No 73
>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=77.86 E-value=0.89 Score=20.73 Aligned_cols=12 Identities=25% Similarity=0.631 Sum_probs=6.1
Q ss_pred eeCCCCCcccCC
Q psy7447 55 YQCPHCPYRGKQ 66 (114)
Q Consensus 55 ~~C~~c~~~~~~ 66 (114)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 455555554443
No 74
>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=77.03 E-value=1.6 Score=25.98 Aligned_cols=26 Identities=27% Similarity=0.361 Sum_probs=15.5
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCC
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPE 82 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p 82 (114)
-..|-+||+.|.. |.+|.+.|+|.-|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCCcccch---HHHHHHHccCCCH
Confidence 4578888888877 5788888877654
No 75
>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=76.80 E-value=2.1 Score=25.20 Aligned_cols=30 Identities=10% Similarity=0.047 Sum_probs=17.6
Q ss_pred eecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCc
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQK 67 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~ 67 (114)
..|..||+.|-- .+ ..|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYD-----------Ln-k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD-----------LN-RRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc-----------cC-CCCccCCCcCCccCcc
Confidence 357777766531 12 4566777777766554
No 76
>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=75.88 E-value=1.1 Score=21.75 Aligned_cols=12 Identities=33% Similarity=0.750 Sum_probs=6.0
Q ss_pred eeCCCCCcccCC
Q psy7447 55 YQCPHCPYRGKQ 66 (114)
Q Consensus 55 ~~C~~c~~~~~~ 66 (114)
|.|..|+..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 455555554443
No 77
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=75.87 E-value=2.3 Score=21.55 Aligned_cols=34 Identities=15% Similarity=0.271 Sum_probs=18.7
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCc
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGP 91 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~ 91 (114)
...|.|+.||+.-.....-- | ....+ |.|+.||.
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~C---R--k~g~~-Y~Cp~CGF 58 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKC---R--KLGNP-YRCPKCGF 58 (61)
T ss_pred eeEeeCCCCCceeeehhhhH---H--HcCCc-eECCCcCc
Confidence 44578888885444322111 1 12234 88888885
No 78
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=74.45 E-value=2.1 Score=20.84 Aligned_cols=11 Identities=36% Similarity=1.123 Sum_probs=5.5
Q ss_pred ceecCcchhhc
Q psy7447 25 RYTCDSCGKVY 35 (114)
Q Consensus 25 ~~~C~~C~~~f 35 (114)
.|.|..||+.+
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 34555555444
No 79
>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=74.44 E-value=2.4 Score=18.68 Aligned_cols=11 Identities=18% Similarity=0.377 Sum_probs=5.1
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
..|+.||..-+
T Consensus 18 irC~~CG~RIl 28 (32)
T PF03604_consen 18 IRCPECGHRIL 28 (32)
T ss_dssp SSBSSSS-SEE
T ss_pred EECCcCCCeEE
Confidence 55555554433
No 80
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=74.11 E-value=6 Score=23.47 Aligned_cols=15 Identities=27% Similarity=0.749 Sum_probs=9.2
Q ss_pred ceecCcchhhcCCch
Q psy7447 25 RYTCDSCGKVYKLKR 39 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~ 39 (114)
|.+|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 456777777766543
No 81
>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=73.91 E-value=3.5 Score=23.35 Aligned_cols=26 Identities=35% Similarity=0.823 Sum_probs=22.2
Q ss_pred CeeC----CCCCcccCCchHHHHHHHHhcC
Q psy7447 54 RYQC----PHCPYRGKQKVHLKTHVAIKHQ 79 (114)
Q Consensus 54 ~~~C----~~c~~~~~~~~~l~~h~~~~~~ 79 (114)
.|.| ..|+....+...+..|++.++|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4688 8899999999999999988775
No 82
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=73.60 E-value=1.7 Score=29.88 Aligned_cols=45 Identities=11% Similarity=0.053 Sum_probs=38.8
Q ss_pred CCeeCCCCCcccCCchHHHHHHH--HhcCC--CCccccc--CCCcccccccc
Q psy7447 53 PRYQCPHCPYRGKQKVHLKTHVA--IKHQG--PEMLSVK--HQGPEMLSIKH 98 (114)
Q Consensus 53 k~~~C~~c~~~~~~~~~l~~h~~--~~~~~--~p~~~C~--~C~~~f~~~~~ 98 (114)
.++.|..|...|.....+..|.+ .|.++ ++ +.|+ .|+..|....-
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~ 338 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDA 338 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCc-eeeeccCCCcccccccc
Confidence 46788899999999999999999 79998 77 9999 79998886553
No 83
>PF14353 CpXC: CpXC protein
Probab=73.08 E-value=4.1 Score=23.77 Aligned_cols=10 Identities=40% Similarity=1.205 Sum_probs=5.4
Q ss_pred ecCcchhhcC
Q psy7447 27 TCDSCGKVYK 36 (114)
Q Consensus 27 ~C~~C~~~f~ 36 (114)
.|+.|+..|.
T Consensus 3 tCP~C~~~~~ 12 (128)
T PF14353_consen 3 TCPHCGHEFE 12 (128)
T ss_pred CCCCCCCeeE
Confidence 4666665543
No 84
>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=72.42 E-value=2.1 Score=17.88 Aligned_cols=11 Identities=18% Similarity=0.096 Sum_probs=7.2
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 46777777663
No 85
>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=72.18 E-value=4.6 Score=16.73 Aligned_cols=19 Identities=26% Similarity=0.567 Sum_probs=10.9
Q ss_pred eCCCCCcccCCchHHHHHHH
Q psy7447 56 QCPHCPYRGKQKVHLKTHVA 75 (114)
Q Consensus 56 ~C~~c~~~~~~~~~l~~h~~ 75 (114)
.|++|++.+ ....++.|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 466776666 3345555554
No 86
>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=70.54 E-value=3 Score=26.89 Aligned_cols=29 Identities=21% Similarity=0.368 Sum_probs=21.9
Q ss_pred CCCceecCcchhhcCCchHHHHHHHHhcC
Q psy7447 22 LQFRYTCDSCGKVYKLKRSLYRHRTLECG 50 (114)
Q Consensus 22 ~~k~~~C~~C~~~f~~~~~l~~h~~~h~~ 50 (114)
.+..|.|..|+|.|.....+..|+..-+.
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 45679999999999999999999886543
No 87
>KOG2231|consensus
Probab=69.06 E-value=1.2 Score=33.40 Aligned_cols=30 Identities=20% Similarity=0.248 Sum_probs=15.7
Q ss_pred eCCCCCcccCCchHHHHHHHHhcCCCCcccccCCC
Q psy7447 56 QCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQG 90 (114)
Q Consensus 56 ~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~ 90 (114)
.|..|...|.....+..|++.++ |-|.+|+
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h-----~~chfC~ 213 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH-----EFCHFCD 213 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce-----eheeecC
Confidence 45555555555555555555433 4455553
No 88
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=68.93 E-value=5.4 Score=20.20 Aligned_cols=32 Identities=16% Similarity=0.211 Sum_probs=17.1
Q ss_pred CCeeCCCCCcc-cCCchHHHHHHHHhcCCCCcccccCCCc
Q psy7447 53 PRYQCPHCPYR-GKQKVHLKTHVAIKHQGPEMLSVKHQGP 91 (114)
Q Consensus 53 k~~~C~~c~~~-~~~~~~l~~h~~~~~~~~p~~~C~~C~~ 91 (114)
..|.|+.||.. ..+-..- |. ...+ |.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~~C----Rk--~~~~-Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEKC----RK--QSNP-YTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeechhH----Hh--cCCc-eECCCCCC
Confidence 45778888765 2222111 11 1133 88888875
No 89
>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=67.87 E-value=1.9 Score=27.76 Aligned_cols=29 Identities=28% Similarity=0.520 Sum_probs=22.6
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcCC
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQG 80 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~~ 80 (114)
+..|.|..|++.|.-......|+..-|.+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 44689999999999999999999987765
No 90
>KOG2593|consensus
Probab=66.27 E-value=6.6 Score=28.01 Aligned_cols=39 Identities=18% Similarity=0.396 Sum_probs=27.4
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
...|.|+.|.+.|.....++ +...+.-.|.|..|+....
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~----L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQ----LLDNETGEFHCENCGGELV 164 (436)
T ss_pred cccccCCccccchhhhHHHH----hhcccCceEEEecCCCchh
Confidence 56799999999998876553 3332222399999997654
No 91
>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=64.47 E-value=3.5 Score=30.01 Aligned_cols=15 Identities=27% Similarity=0.208 Sum_probs=9.1
Q ss_pred ccccCCCcccccccc
Q psy7447 84 LSVKHQGPEMLSIKH 98 (114)
Q Consensus 84 ~~C~~C~~~f~~~~~ 98 (114)
..|+.|+...+...+
T Consensus 254 ~~Cp~C~s~~l~~~g 268 (505)
T TIGR00595 254 KTCPQCGSEDLVYKG 268 (505)
T ss_pred CCCCCCCCCeeEeec
Confidence 778888765444333
No 92
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=63.21 E-value=2.1 Score=32.60 Aligned_cols=23 Identities=30% Similarity=0.397 Sum_probs=14.4
Q ss_pred cccccCCCcccccccccCCCccccc
Q psy7447 83 MLSVKHQGPEMLSIKHQGPETLSIK 107 (114)
Q Consensus 83 ~~~C~~C~~~f~~~~~~~~~~~~~~ 107 (114)
|..|+.||.. .+...|..+-.+.
T Consensus 475 p~~Cp~Cgs~--~L~~~G~Gterie 497 (730)
T COG1198 475 PQSCPECGSE--HLRAVGPGTERIE 497 (730)
T ss_pred CCCCCCCCCC--eeEEecccHHHHH
Confidence 4899999986 4444455444433
No 93
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=60.95 E-value=11 Score=26.25 Aligned_cols=43 Identities=23% Similarity=0.158 Sum_probs=27.6
Q ss_pred ccCccCCCCccccCCCCC----CceecCcchhhcCCchHHHHHHHHhc
Q psy7447 6 RFSEFNLPPHTLFNPLLQ----FRYTCDSCGKVYKLKRSLYRHRTLEC 49 (114)
Q Consensus 6 ~~~~~~l~~h~~~~h~~~----k~~~C~~C~~~f~~~~~l~~h~~~h~ 49 (114)
.|++..|+.|.-. ...+ ..-.|..|...|-....|..|++...
T Consensus 198 lF~~~~Lr~H~~~-G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 198 LFRSSTLRDHKNG-GLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred eeecccccccccC-CccccCcCCCchhhhccceecChHHHHHHHHhhh
Confidence 3566666666544 2222 23368888888888888888888544
No 94
>KOG2893|consensus
Probab=60.42 E-value=4.4 Score=26.67 Aligned_cols=42 Identities=17% Similarity=0.184 Sum_probs=30.8
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCccccccccc
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSIKHQ 99 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~~~~ 99 (114)
.|+| |=.|++.|....-|..|++..+ |+|.+|-+...+-.+.
T Consensus 9 ~kpw-cwycnrefddekiliqhqkakh-----fkchichkkl~sgpgl 50 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKAKH-----FKCHICHKKLFSGPGL 50 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhhcc-----ceeeeehhhhccCCCc
Confidence 3454 5668899999888888887643 9999998766544443
No 95
>KOG2785|consensus
Probab=60.33 E-value=17 Score=25.60 Aligned_cols=55 Identities=20% Similarity=0.216 Sum_probs=40.2
Q ss_pred ceecCcchhhcCCchHHHHHHHHhcCC----------------------CCCeeCCCCC---cccCCchHHHHHHHHhcC
Q psy7447 25 RYTCDSCGKVYKLKRSLYRHRTLECGK----------------------EPRYQCPHCP---YRGKQKVHLKTHVAIKHQ 79 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~~l~~h~~~h~~~----------------------~k~~~C~~c~---~~~~~~~~l~~h~~~~~~ 79 (114)
|-.|..|++.+.....-..||..++|. .+.+.|-.|+ +.|.+..+.+.|+.....
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~H 245 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKGH 245 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhccC
Confidence 457888998888777777788877654 3445676777 888888888888875433
No 96
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=60.27 E-value=3.7 Score=20.60 Aligned_cols=10 Identities=30% Similarity=0.577 Sum_probs=4.7
Q ss_pred ecCcchhhcC
Q psy7447 27 TCDSCGKVYK 36 (114)
Q Consensus 27 ~C~~C~~~f~ 36 (114)
.|..|++.+.
T Consensus 4 kC~lCdk~~~ 13 (56)
T PF09963_consen 4 KCILCDKKEE 13 (56)
T ss_pred EEEecCCEEE
Confidence 3455554443
No 97
>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=59.98 E-value=4.3 Score=16.61 Aligned_cols=7 Identities=14% Similarity=0.344 Sum_probs=4.3
Q ss_pred ccccCCC
Q psy7447 84 LSVKHQG 90 (114)
Q Consensus 84 ~~C~~C~ 90 (114)
|.|+.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 6666665
No 98
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=59.93 E-value=1.9 Score=26.35 Aligned_cols=11 Identities=36% Similarity=0.945 Sum_probs=4.6
Q ss_pred eecCcchhhcC
Q psy7447 26 YTCDSCGKVYK 36 (114)
Q Consensus 26 ~~C~~C~~~f~ 36 (114)
++|..||.+|.
T Consensus 29 ~~c~~c~~~f~ 39 (154)
T PRK00464 29 RECLACGKRFT 39 (154)
T ss_pred eeccccCCcce
Confidence 34444444443
No 99
>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=59.73 E-value=8.4 Score=17.80 Aligned_cols=13 Identities=46% Similarity=0.887 Sum_probs=5.0
Q ss_pred CceecCcchhhcC
Q psy7447 24 FRYTCDSCGKVYK 36 (114)
Q Consensus 24 k~~~C~~C~~~f~ 36 (114)
....|..|++.+.
T Consensus 15 ~~a~C~~C~~~~~ 27 (45)
T PF02892_consen 15 KKAKCKYCGKVIK 27 (45)
T ss_dssp S-EEETTTTEE--
T ss_pred CeEEeCCCCeEEe
Confidence 3345555554443
No 100
>KOG1146|consensus
Probab=58.72 E-value=0.87 Score=36.53 Aligned_cols=74 Identities=19% Similarity=0.221 Sum_probs=46.3
Q ss_pred CcchhhcCCchHHHHHHH-HhcCCCCCeeCCCCCcccCCchHHHHHHHHhcC-------------------------CCC
Q psy7447 29 DSCGKVYKLKRSLYRHRT-LECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQ-------------------------GPE 82 (114)
Q Consensus 29 ~~C~~~f~~~~~l~~h~~-~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~-------------------------~~p 82 (114)
..++..+.....+..++. .+.- .+.+.|+.|+..|.....|-.|+|..+. .++
T Consensus 440 ~~~e~~~~s~r~~~~~t~~L~S~-~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p 518 (1406)
T KOG1146|consen 440 TKAEPLLESKRSLEGQTVVLHSF-FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP 518 (1406)
T ss_pred cchhhhhhhhcccccceeeeecc-cccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc
Confidence 334444444443433333 2333 6788999999999999999999998221 134
Q ss_pred cccccCCCcccccccccCCCcc
Q psy7447 83 MLSVKHQGPEMLSIKHQGPETL 104 (114)
Q Consensus 83 ~~~C~~C~~~f~~~~~~~~~~~ 104 (114)
|.|..|..++.....--.|..
T Consensus 519 -~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 519 -YPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred -ccceeeeeeeecchHHHHHHH
Confidence 888888887775433333333
No 101
>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=56.83 E-value=4.5 Score=18.78 Aligned_cols=18 Identities=11% Similarity=0.150 Sum_probs=13.8
Q ss_pred ccccCCCcccccccccCC
Q psy7447 84 LSVKHQGPEMLSIKHQGP 101 (114)
Q Consensus 84 ~~C~~C~~~f~~~~~~~~ 101 (114)
|.|..||..|-.+.....
T Consensus 6 y~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE 23 (42)
T ss_pred EEeCCCCCEEEEEEEcCC
Confidence 899999998886655433
No 102
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=56.47 E-value=9.3 Score=21.20 Aligned_cols=14 Identities=14% Similarity=0.543 Sum_probs=8.7
Q ss_pred CCeeCCCCCcccCC
Q psy7447 53 PRYQCPHCPYRGKQ 66 (114)
Q Consensus 53 k~~~C~~c~~~~~~ 66 (114)
+|..|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 45566667666655
No 103
>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=56.18 E-value=5.9 Score=18.27 Aligned_cols=14 Identities=29% Similarity=0.335 Sum_probs=9.4
Q ss_pred CcccccCCCccccc
Q psy7447 82 EMLSVKHQGPEMLS 95 (114)
Q Consensus 82 p~~~C~~C~~~f~~ 95 (114)
|.+.|+.||..+.+
T Consensus 31 p~~~C~~CGE~~~~ 44 (46)
T TIGR03831 31 PALVCPQCGEEYLD 44 (46)
T ss_pred CccccccCCCEeeC
Confidence 44678888776654
No 104
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=54.62 E-value=6.1 Score=18.09 Aligned_cols=14 Identities=14% Similarity=0.233 Sum_probs=11.8
Q ss_pred ccccCCCccccccc
Q psy7447 84 LSVKHQGPEMLSIK 97 (114)
Q Consensus 84 ~~C~~C~~~f~~~~ 97 (114)
+.|..|+..|-...
T Consensus 13 f~C~~C~~~FC~~H 26 (39)
T smart00154 13 FKCRHCGNLFCGEH 26 (39)
T ss_pred eECCccCCcccccc
Confidence 99999999998553
No 105
>PHA00626 hypothetical protein
Probab=54.36 E-value=6.3 Score=19.76 Aligned_cols=14 Identities=7% Similarity=-0.311 Sum_probs=11.7
Q ss_pred cccccCCCcccccc
Q psy7447 83 MLSVKHQGPEMLSI 96 (114)
Q Consensus 83 ~~~C~~C~~~f~~~ 96 (114)
.|.|+.||..|...
T Consensus 23 rYkCkdCGY~ft~~ 36 (59)
T PHA00626 23 DYVCCDCGYNDSKD 36 (59)
T ss_pred ceEcCCCCCeechh
Confidence 39999999998854
No 106
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=54.16 E-value=8.1 Score=18.81 Aligned_cols=10 Identities=10% Similarity=-0.077 Sum_probs=6.2
Q ss_pred ccccCCCccc
Q psy7447 84 LSVKHQGPEM 93 (114)
Q Consensus 84 ~~C~~C~~~f 93 (114)
+.|..||..+
T Consensus 38 ~~C~~Cgyt~ 47 (50)
T PRK00432 38 WHCGKCGYTE 47 (50)
T ss_pred EECCCcCCEE
Confidence 6666666544
No 107
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.77 E-value=5.9 Score=23.57 Aligned_cols=15 Identities=20% Similarity=0.406 Sum_probs=9.7
Q ss_pred CCeeCCCCCcccCCc
Q psy7447 53 PRYQCPHCPYRGKQK 67 (114)
Q Consensus 53 k~~~C~~c~~~~~~~ 67 (114)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 346777787766553
No 108
>KOG4167|consensus
Probab=53.70 E-value=3.9 Score=31.17 Aligned_cols=28 Identities=25% Similarity=0.386 Sum_probs=23.8
Q ss_pred CCceecCcchhhcCCchHHHHHHHHhcC
Q psy7447 23 QFRYTCDSCGKVYKLKRSLYRHRTLECG 50 (114)
Q Consensus 23 ~k~~~C~~C~~~f~~~~~l~~h~~~h~~ 50 (114)
..-|.|.+|++.|....++..||+.|..
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 3468999999999988889999999854
No 109
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=53.60 E-value=19 Score=17.21 Aligned_cols=8 Identities=25% Similarity=0.580 Sum_probs=4.3
Q ss_pred hHHHHHHH
Q psy7447 68 VHLKTHVA 75 (114)
Q Consensus 68 ~~l~~h~~ 75 (114)
++|.+|+.
T Consensus 37 s~L~rHl~ 44 (50)
T smart00614 37 SNLRRHLR 44 (50)
T ss_pred HHHHHHHH
Confidence 45555555
No 110
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=53.39 E-value=8.3 Score=23.06 Aligned_cols=24 Identities=21% Similarity=0.128 Sum_probs=13.5
Q ss_pred eCCCCCcccCCchHHHHHHHHhcCCCC
Q psy7447 56 QCPHCPYRGKQKVHLKTHVAIKHQGPE 82 (114)
Q Consensus 56 ~C~~c~~~~~~~~~l~~h~~~~~~~~p 82 (114)
.|-++|+.|.+ |.+|..+|.|.-|
T Consensus 78 icLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 78 ICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEeccCcchHH---HHHHHhcccCCCH
Confidence 45555655554 5666666655433
No 111
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=53.13 E-value=10 Score=21.47 Aligned_cols=15 Identities=27% Similarity=0.693 Sum_probs=10.8
Q ss_pred ceecCcchhhcCCch
Q psy7447 25 RYTCDSCGKVYKLKR 39 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~ 39 (114)
|.+|..||..|...+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 457888888887643
No 112
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=53.04 E-value=4.2 Score=24.39 Aligned_cols=33 Identities=18% Similarity=0.386 Sum_probs=18.4
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCccccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLS 95 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~ 95 (114)
.|.|..|+..+... .+. .... |.|..|+..+..
T Consensus 123 ~~~C~~C~~~~~r~------~~~--~~~~-~~C~~C~~~l~~ 155 (157)
T PF10263_consen 123 VYRCPSCGREYKRH------RRS--KRKR-YRCGRCGGPLVQ 155 (157)
T ss_pred EEEcCCCCCEeeee------ccc--chhh-EECCCCCCEEEE
Confidence 46777777655332 122 2223 788888866543
No 113
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=51.44 E-value=8.9 Score=18.87 Aligned_cols=20 Identities=30% Similarity=0.551 Sum_probs=8.6
Q ss_pred hHHHHHHHHhcCCCCCeeCCC
Q psy7447 39 RSLYRHRTLECGKEPRYQCPH 59 (114)
Q Consensus 39 ~~l~~h~~~h~~~~k~~~C~~ 59 (114)
..|..|....-. ..+..|..
T Consensus 24 ~~l~~H~~~~C~-~~~v~C~~ 43 (60)
T PF02176_consen 24 KELDDHLENECP-KRPVPCPY 43 (60)
T ss_dssp CCHHHHHHTTST-TSEEE-SS
T ss_pred HHHHHHHHccCC-CCcEECCC
Confidence 345555554333 44444444
No 114
>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=50.95 E-value=24 Score=23.72 Aligned_cols=72 Identities=15% Similarity=0.274 Sum_probs=39.3
Q ss_pred CCCCCceecCcchhhcCCchHHHHHHHH--hcCCCCCeeCCCCCcccCCc------hHHHHHHHH----hcCCCCccccc
Q psy7447 20 PLLQFRYTCDSCGKVYKLKRSLYRHRTL--ECGKEPRYQCPHCPYRGKQK------VHLKTHVAI----KHQGPEMLSVK 87 (114)
Q Consensus 20 h~~~k~~~C~~C~~~f~~~~~l~~h~~~--h~~~~k~~~C~~c~~~~~~~------~~l~~h~~~----~~~~~p~~~C~ 87 (114)
..+.+.|+|..|....-....+ .|+.. ... ...|.|..|++.-..+ .....|.+. ....++ +.|+
T Consensus 137 ~hGGrif~CsfC~~flCEDDQF-EHQAsCQvLe-~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~-~PCP 213 (314)
T PF06524_consen 137 DHGGRIFKCSFCDNFLCEDDQF-EHQASCQVLE-SETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKP-IPCP 213 (314)
T ss_pred cCCCeEEEeecCCCeeeccchh-hhhhhhhhhh-cccccccccccccchhhhheeeeehhhhhhhcccccccCCC-CCCC
Confidence 3467889999998665444433 45442 122 3356777666532221 112234442 233455 9999
Q ss_pred CCCcccc
Q psy7447 88 HQGPEML 94 (114)
Q Consensus 88 ~C~~~f~ 94 (114)
.||....
T Consensus 214 KCg~et~ 220 (314)
T PF06524_consen 214 KCGYETQ 220 (314)
T ss_pred CCCCccc
Confidence 9996544
No 115
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=49.12 E-value=7.5 Score=23.72 Aligned_cols=36 Identities=14% Similarity=0.348 Sum_probs=20.2
Q ss_pred CCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 53 PRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 53 k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
-+|.|. |+..+... .+|-.+--|+ . |.|..|+....
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~-YrC~~C~gkL~ 151 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-V-YRCGKCGGKLV 151 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-e-EEeccCCceEE
Confidence 467777 77665543 2332333344 5 88888876443
No 116
>PRK14873 primosome assembly protein PriA; Provisional
Probab=48.97 E-value=19 Score=27.38 Aligned_cols=55 Identities=16% Similarity=0.320 Sum_probs=28.4
Q ss_pred ecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccccccccC
Q psy7447 27 TCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSIKHQG 100 (114)
Q Consensus 27 ~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~~~~~ 100 (114)
.|..||..+.-... ...+..|.. .....|..||.. ..| +.|+.||.......+.|
T Consensus 385 ~C~~Cg~~~~C~~C-~~~L~~h~~-~~~l~Ch~CG~~----------------~~p-~~Cp~Cgs~~l~~~g~G 439 (665)
T PRK14873 385 ACARCRTPARCRHC-TGPLGLPSA-GGTPRCRWCGRA----------------APD-WRCPRCGSDRLRAVVVG 439 (665)
T ss_pred EhhhCcCeeECCCC-CCceeEecC-CCeeECCCCcCC----------------CcC-ccCCCCcCCcceeeecc
Confidence 56666554433211 111233333 445678777741 113 89999987655444444
No 117
>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=48.40 E-value=12 Score=21.63 Aligned_cols=27 Identities=11% Similarity=0.213 Sum_probs=17.9
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEM 93 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f 93 (114)
...|..|+..|..... - +.|+.||...
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~-~~CP~Cgs~~ 96 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------L-YRCPKCHGIM 96 (115)
T ss_pred EEEcccCCCEEecCCc------------C-ccCcCCcCCC
Confidence 3578888877665421 2 7788888644
No 118
>PRK05580 primosome assembly protein PriA; Validated
Probab=48.16 E-value=8.5 Score=29.20 Aligned_cols=13 Identities=15% Similarity=0.021 Sum_probs=8.1
Q ss_pred ccccCCCcccccc
Q psy7447 84 LSVKHQGPEMLSI 96 (114)
Q Consensus 84 ~~C~~C~~~f~~~ 96 (114)
..|+.||......
T Consensus 422 ~~Cp~Cg~~~l~~ 434 (679)
T PRK05580 422 KACPECGSTDLVP 434 (679)
T ss_pred CCCCCCcCCeeEE
Confidence 6777777654433
No 119
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=48.11 E-value=9.2 Score=22.01 Aligned_cols=26 Identities=15% Similarity=0.070 Sum_probs=16.7
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPE 92 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~ 92 (114)
...|..|+..|.... . .+.|+.||..
T Consensus 70 ~~~C~~Cg~~~~~~~------------~-~~~CP~Cgs~ 95 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ------------H-DAQCPHCHGE 95 (113)
T ss_pred EEEcccCCCEEecCC------------c-CccCcCCCCC
Confidence 457888886666532 1 2678888853
No 120
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=48.09 E-value=25 Score=16.21 Aligned_cols=22 Identities=23% Similarity=0.356 Sum_probs=10.1
Q ss_pred eCCCCCcccC--CchHHHHHHHHh
Q psy7447 56 QCPHCPYRGK--QKVHLKTHVAIK 77 (114)
Q Consensus 56 ~C~~c~~~~~--~~~~l~~h~~~~ 77 (114)
.|+.||..|. .......|.+.|
T Consensus 15 ~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 15 TCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCCCCEECCCCHHHHHHHHHHH
Confidence 5566665443 233344444433
No 121
>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=47.67 E-value=6.7 Score=18.19 Aligned_cols=10 Identities=10% Similarity=0.086 Sum_probs=7.3
Q ss_pred ccccCCCccc
Q psy7447 84 LSVKHQGPEM 93 (114)
Q Consensus 84 ~~C~~C~~~f 93 (114)
-.|++|+..|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 6778887765
No 122
>KOG2231|consensus
Probab=47.52 E-value=22 Score=27.10 Aligned_cols=48 Identities=23% Similarity=0.380 Sum_probs=34.0
Q ss_pred eecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCC------CcccCCchHHHHHHHHhc
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHC------PYRGKQKVHLKTHVAIKH 78 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c------~~~~~~~~~l~~h~~~~~ 78 (114)
..|..|...|.....+..|++.+. +.|..| +..|..-..|..|.+..|
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h-----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH-----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce-----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 468888888888888888887543 244444 345677778888888765
No 123
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=46.94 E-value=8.8 Score=22.11 Aligned_cols=28 Identities=11% Similarity=0.112 Sum_probs=15.9
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEM 93 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f 93 (114)
...|..|+..|...... .+.|+.||...
T Consensus 70 ~~~C~~Cg~~~~~~~~~------------~~~CP~Cgs~~ 97 (114)
T PRK03681 70 ECWCETCQQYVTLLTQR------------VRRCPQCHGDM 97 (114)
T ss_pred EEEcccCCCeeecCCcc------------CCcCcCcCCCC
Confidence 35777787655442110 15688888543
No 124
>KOG3507|consensus
Probab=46.92 E-value=13 Score=18.82 Aligned_cols=27 Identities=41% Similarity=0.936 Sum_probs=15.2
Q ss_pred ceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcc
Q psy7447 25 RYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYR 63 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~ 63 (114)
.|.|.+|+.....+. .-.+.|..||..
T Consensus 20 iYiCgdC~~en~lk~------------~D~irCReCG~R 46 (62)
T KOG3507|consen 20 IYICGDCGQENTLKR------------GDVIRCRECGYR 46 (62)
T ss_pred EEEeccccccccccC------------CCcEehhhcchH
Confidence 467777775433211 335677777753
No 125
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=46.59 E-value=2 Score=19.84 Aligned_cols=8 Identities=13% Similarity=0.119 Sum_probs=3.4
Q ss_pred ccccCCCc
Q psy7447 84 LSVKHQGP 91 (114)
Q Consensus 84 ~~C~~C~~ 91 (114)
|.|..|+.
T Consensus 29 y~C~~C~~ 36 (40)
T smart00440 29 YVCTKCGH 36 (40)
T ss_pred EEeCCCCC
Confidence 44444443
No 126
>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=46.59 E-value=6.4 Score=18.34 Aligned_cols=15 Identities=20% Similarity=0.206 Sum_probs=9.4
Q ss_pred cccccCCCccccccc
Q psy7447 83 MLSVKHQGPEMLSIK 97 (114)
Q Consensus 83 ~~~C~~C~~~f~~~~ 97 (114)
++.|..|+..|-...
T Consensus 13 ~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKH 27 (43)
T ss_dssp HEE-TTTS-EE-TTT
T ss_pred CeECCCCCcccCccc
Confidence 399999999999543
No 127
>KOG3362|consensus
Probab=45.46 E-value=8.1 Score=23.33 Aligned_cols=20 Identities=15% Similarity=0.177 Sum_probs=15.3
Q ss_pred ccccCCCcccccccccCCCc
Q psy7447 84 LSVKHQGPEMLSIKHQGPET 103 (114)
Q Consensus 84 ~~C~~C~~~f~~~~~~~~~~ 103 (114)
|.|.-||..+.++....-|.
T Consensus 130 ysC~~CG~kyCsv~C~~~Hn 149 (156)
T KOG3362|consen 130 YSCVNCGTKYCSVRCLKTHN 149 (156)
T ss_pred hHHHhcCCceeechhhhhcc
Confidence 88999998888887655443
No 128
>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=45.40 E-value=24 Score=15.86 Aligned_cols=10 Identities=20% Similarity=0.179 Sum_probs=5.3
Q ss_pred ccccCCCccc
Q psy7447 84 LSVKHQGPEM 93 (114)
Q Consensus 84 ~~C~~C~~~f 93 (114)
-.|+.||..+
T Consensus 22 ~~Cd~cg~~L 31 (36)
T PF05191_consen 22 GVCDNCGGEL 31 (36)
T ss_dssp TBCTTTTEBE
T ss_pred CccCCCCCee
Confidence 4566665533
No 129
>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=45.32 E-value=11 Score=19.17 Aligned_cols=11 Identities=9% Similarity=0.102 Sum_probs=4.1
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
+.|..||..|-
T Consensus 26 hhCr~CG~~vC 36 (69)
T PF01363_consen 26 HHCRNCGRVVC 36 (69)
T ss_dssp EE-TTT--EEE
T ss_pred EccCCCCCEEC
Confidence 45555555444
No 130
>KOG2482|consensus
Probab=44.03 E-value=15 Score=25.69 Aligned_cols=24 Identities=29% Similarity=0.576 Sum_probs=21.4
Q ss_pred ceecCcchhhcCCchHHHHHHHHh
Q psy7447 25 RYTCDSCGKVYKLKRSLYRHRTLE 48 (114)
Q Consensus 25 ~~~C~~C~~~f~~~~~l~~h~~~h 48 (114)
.++|-.|.+.|..+..|..||+..
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhc
Confidence 468999999999999999999854
No 131
>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=43.10 E-value=12 Score=21.09 Aligned_cols=14 Identities=43% Similarity=0.925 Sum_probs=11.1
Q ss_pred CceecCcchhhcCC
Q psy7447 24 FRYTCDSCGKVYKL 37 (114)
Q Consensus 24 k~~~C~~C~~~f~~ 37 (114)
++.+|..||..|..
T Consensus 78 ~~~rC~eCG~~fkL 91 (97)
T cd00924 78 KPKRCPECGHVFKL 91 (97)
T ss_pred CceeCCCCCcEEEE
Confidence 78888888887763
No 132
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.76 E-value=19 Score=20.85 Aligned_cols=29 Identities=10% Similarity=0.165 Sum_probs=17.1
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
...|..|+..|..... .-+.|+.||....
T Consensus 71 ~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~~~ 99 (117)
T PRK00564 71 ELECKDCSHVFKPNAL------------DYGVCEKCHSKNV 99 (117)
T ss_pred EEEhhhCCCccccCCc------------cCCcCcCCCCCce
Confidence 3578888866655321 1034888886544
No 133
>KOG4167|consensus
Probab=41.71 E-value=5.4 Score=30.51 Aligned_cols=26 Identities=15% Similarity=0.232 Sum_probs=22.5
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcC
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQ 79 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~ 79 (114)
.|-|.+|++.|...-.++.|++.|..
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 47899999999988889999998854
No 134
>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=41.66 E-value=7.3 Score=22.37 Aligned_cols=28 Identities=18% Similarity=0.258 Sum_probs=16.6
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
...|..|+..|..... .+.|+.||....
T Consensus 70 ~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~~~ 97 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEF-------------DFSCPRCGSPDV 97 (113)
T ss_dssp EEEETTTS-EEECHHC-------------CHH-SSSSSS-E
T ss_pred cEECCCCCCEEecCCC-------------CCCCcCCcCCCc
Confidence 3578888887776432 156888887653
No 135
>PLN02294 cytochrome c oxidase subunit Vb
Probab=41.64 E-value=13 Score=23.20 Aligned_cols=15 Identities=20% Similarity=0.698 Sum_probs=10.9
Q ss_pred CCceecCcchhhcCC
Q psy7447 23 QFRYTCDSCGKVYKL 37 (114)
Q Consensus 23 ~k~~~C~~C~~~f~~ 37 (114)
.++.+|.+||..|..
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 467788888877763
No 136
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.63 E-value=3.6 Score=26.89 Aligned_cols=10 Identities=0% Similarity=-0.403 Sum_probs=6.8
Q ss_pred ccccCCCccc
Q psy7447 84 LSVKHQGPEM 93 (114)
Q Consensus 84 ~~C~~C~~~f 93 (114)
+.|+.|+.+.
T Consensus 63 vvCP~C~yAa 72 (267)
T COG1655 63 VVCPICYYAA 72 (267)
T ss_pred EEcchhhHHH
Confidence 4788887543
No 137
>KOG3408|consensus
Probab=40.58 E-value=23 Score=20.78 Aligned_cols=26 Identities=15% Similarity=0.262 Sum_probs=16.1
Q ss_pred CCCCceecCcchhhcCCchHHHHHHH
Q psy7447 21 LLQFRYTCDSCGKVYKLKRSLYRHRT 46 (114)
Q Consensus 21 ~~~k~~~C~~C~~~f~~~~~l~~h~~ 46 (114)
+|...|.|-.|.+-|.....|..|.+
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHh
Confidence 34455667777777766666666654
No 138
>PF15269 zf-C2H2_7: Zinc-finger
Probab=40.45 E-value=23 Score=16.90 Aligned_cols=21 Identities=38% Similarity=0.940 Sum_probs=11.3
Q ss_pred eeCCCCCcccCCchHHHHHHH
Q psy7447 55 YQCPHCPYRGKQKVHLKTHVA 75 (114)
Q Consensus 55 ~~C~~c~~~~~~~~~l~~h~~ 75 (114)
|.|-.|..+...++.|-.|++
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 345555555555555555554
No 139
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.35 E-value=18 Score=21.42 Aligned_cols=17 Identities=12% Similarity=0.032 Sum_probs=14.3
Q ss_pred ccccCCCcccccccccC
Q psy7447 84 LSVKHQGPEMLSIKHQG 100 (114)
Q Consensus 84 ~~C~~C~~~f~~~~~~~ 100 (114)
|.|..|++.|....+..
T Consensus 54 yrC~~C~~tf~~~~~~~ 70 (129)
T COG3677 54 YKCKSCGSTFTVETGSP 70 (129)
T ss_pred cccCCcCcceeeeccCc
Confidence 99999999999776643
No 140
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=39.90 E-value=11 Score=18.35 Aligned_cols=15 Identities=27% Similarity=0.344 Sum_probs=10.2
Q ss_pred ccccCCCcccccccc
Q psy7447 84 LSVKHQGPEMLSIKH 98 (114)
Q Consensus 84 ~~C~~C~~~f~~~~~ 98 (114)
+.|.-||..|....+
T Consensus 5 l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 5 LTCKDCGAEFVFTAG 19 (49)
T ss_pred EEcccCCCeEEEehh
Confidence 677778877775443
No 141
>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=39.48 E-value=11 Score=18.39 Aligned_cols=11 Identities=9% Similarity=-0.016 Sum_probs=5.2
Q ss_pred cccCCCccccc
Q psy7447 85 SVKHQGPEMLS 95 (114)
Q Consensus 85 ~C~~C~~~f~~ 95 (114)
.|+.|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 78888887764
No 142
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=38.76 E-value=13 Score=18.09 Aligned_cols=9 Identities=11% Similarity=0.036 Sum_probs=6.0
Q ss_pred ccccCCCcc
Q psy7447 84 LSVKHQGPE 92 (114)
Q Consensus 84 ~~C~~C~~~ 92 (114)
|.|..||..
T Consensus 38 ~~CGkCgyT 46 (51)
T COG1998 38 WACGKCGYT 46 (51)
T ss_pred eEeccccce
Confidence 777777653
No 143
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=38.73 E-value=12 Score=19.85 Aligned_cols=8 Identities=25% Similarity=0.816 Sum_probs=3.8
Q ss_pred ecCcchhh
Q psy7447 27 TCDSCGKV 34 (114)
Q Consensus 27 ~C~~C~~~ 34 (114)
.|..||..
T Consensus 3 ~CP~Cg~~ 10 (72)
T PRK09678 3 HCPLCQHA 10 (72)
T ss_pred cCCCCCCc
Confidence 35555543
No 144
>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=38.55 E-value=16 Score=17.15 Aligned_cols=11 Identities=9% Similarity=-0.100 Sum_probs=8.2
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
=.|..|++.|.
T Consensus 9 K~C~~C~rpf~ 19 (42)
T PF10013_consen 9 KICPVCGRPFT 19 (42)
T ss_pred CcCcccCCcch
Confidence 46788888776
No 145
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=38.47 E-value=24 Score=25.34 Aligned_cols=13 Identities=23% Similarity=0.889 Sum_probs=6.7
Q ss_pred CeeCCCCCcccCC
Q psy7447 54 RYQCPHCPYRGKQ 66 (114)
Q Consensus 54 ~~~C~~c~~~~~~ 66 (114)
-|.|+.|+..+..
T Consensus 367 g~rC~kCg~~~~~ 379 (421)
T COG1571 367 GFRCKKCGTRARE 379 (421)
T ss_pred CcccccccccCCc
Confidence 4555555554444
No 146
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=37.54 E-value=36 Score=16.56 Aligned_cols=12 Identities=33% Similarity=0.899 Sum_probs=5.6
Q ss_pred eeCCCCCcccCC
Q psy7447 55 YQCPHCPYRGKQ 66 (114)
Q Consensus 55 ~~C~~c~~~~~~ 66 (114)
+.|..|+..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 355555444443
No 147
>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 COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=35.95 E-value=63 Score=20.33 Aligned_cols=33 Identities=15% Similarity=0.371 Sum_probs=21.1
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
..-|.|+.|...++...+.. . .|.|+.||....
T Consensus 111 ~~~y~C~~~~~r~sfdeA~~------~----~F~Cp~Cg~~L~ 143 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAME------L----GFTCPKCGEDLE 143 (176)
T ss_pred CCceeCCCCCCcccHHHHHH------h----CCCCCCCCchhh
Confidence 66788877776666544332 1 289999986543
No 149
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=35.95 E-value=19 Score=19.91 Aligned_cols=17 Identities=24% Similarity=0.175 Sum_probs=12.5
Q ss_pred CCCcccccCCCcccccc
Q psy7447 80 GPEMLSVKHQGPEMLSI 96 (114)
Q Consensus 80 ~~p~~~C~~C~~~f~~~ 96 (114)
.-|...|..||..+.+.
T Consensus 32 nVPa~~C~~CGe~y~~d 48 (89)
T TIGR03829 32 ETPSISCSHCGMEYQDD 48 (89)
T ss_pred cCCcccccCCCcEeecH
Confidence 34668899999887753
No 150
>COG1773 Rubredoxin [Energy production and conversion]
Probab=35.89 E-value=20 Score=17.94 Aligned_cols=13 Identities=31% Similarity=0.825 Sum_probs=9.8
Q ss_pred CeeCCCCCcccCC
Q psy7447 54 RYQCPHCPYRGKQ 66 (114)
Q Consensus 54 ~~~C~~c~~~~~~ 66 (114)
.|+|.+||..|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 5788888887765
No 151
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=35.84 E-value=36 Score=16.41 Aligned_cols=9 Identities=44% Similarity=1.243 Sum_probs=4.3
Q ss_pred cCcchhhcC
Q psy7447 28 CDSCGKVYK 36 (114)
Q Consensus 28 C~~C~~~f~ 36 (114)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 445554443
No 152
>PRK12496 hypothetical protein; Provisional
Probab=34.99 E-value=29 Score=21.37 Aligned_cols=12 Identities=42% Similarity=0.946 Sum_probs=7.4
Q ss_pred ceecCcchhhcC
Q psy7447 25 RYTCDSCGKVYK 36 (114)
Q Consensus 25 ~~~C~~C~~~f~ 36 (114)
.+.|.-|++.|.
T Consensus 127 ~~~C~gC~~~~~ 138 (164)
T PRK12496 127 RKVCKGCKKKYP 138 (164)
T ss_pred eEECCCCCcccc
Confidence 456777766654
No 153
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=34.81 E-value=4 Score=27.41 Aligned_cols=9 Identities=33% Similarity=0.752 Sum_probs=3.6
Q ss_pred eecCcchhh
Q psy7447 26 YTCDSCGKV 34 (114)
Q Consensus 26 ~~C~~C~~~ 34 (114)
-.|..||..
T Consensus 173 g~CPvCGs~ 181 (290)
T PF04216_consen 173 GYCPVCGSP 181 (290)
T ss_dssp SS-TTT---
T ss_pred CcCCCCCCc
Confidence 368888854
No 154
>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=34.81 E-value=15 Score=16.63 Aligned_cols=13 Identities=15% Similarity=0.227 Sum_probs=7.1
Q ss_pred ccccCCCcccccc
Q psy7447 84 LSVKHQGPEMLSI 96 (114)
Q Consensus 84 ~~C~~C~~~f~~~ 96 (114)
|+|..||..+.-+
T Consensus 7 YkC~~CGniVev~ 19 (36)
T PF06397_consen 7 YKCEHCGNIVEVV 19 (36)
T ss_dssp EE-TTT--EEEEE
T ss_pred EEccCCCCEEEEE
Confidence 7888888876544
No 155
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=34.03 E-value=25 Score=21.01 Aligned_cols=10 Identities=10% Similarity=0.199 Sum_probs=6.5
Q ss_pred ccccCCCccc
Q psy7447 84 LSVKHQGPEM 93 (114)
Q Consensus 84 ~~C~~C~~~f 93 (114)
|.|..|+..+
T Consensus 134 y~C~~C~g~l 143 (146)
T smart00731 134 YRCGKCGGKL 143 (146)
T ss_pred EEcCCCCCEE
Confidence 6777776654
No 156
>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=34.02 E-value=33 Score=17.44 Aligned_cols=15 Identities=20% Similarity=0.791 Sum_probs=7.6
Q ss_pred CCCeeCCCCCcccCC
Q psy7447 52 EPRYQCPHCPYRGKQ 66 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~ 66 (114)
.+.+.|+.||.....
T Consensus 44 ~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 44 GRVFTCPNCGFEMDR 58 (69)
T ss_pred cceEEcCCCCCEECc
Confidence 344555556554443
No 157
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.31 E-value=19 Score=18.42 Aligned_cols=11 Identities=0% Similarity=-0.176 Sum_probs=8.0
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
-.|++|+..|.
T Consensus 49 v~CPYC~t~y~ 59 (62)
T COG4391 49 VVCPYCSTRYR 59 (62)
T ss_pred EecCccccEEE
Confidence 67788877664
No 158
>KOG2071|consensus
Probab=33.30 E-value=31 Score=25.83 Aligned_cols=28 Identities=21% Similarity=0.415 Sum_probs=19.3
Q ss_pred CCCeeCCCCCcccCCchHHHHHHHHhcC
Q psy7447 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQ 79 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~~~l~~h~~~~~~ 79 (114)
..+-+|..||..|........|+..|..
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhh
Confidence 4456788888888877766666666543
No 159
>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=33.04 E-value=2.3 Score=32.33 Aligned_cols=60 Identities=20% Similarity=0.441 Sum_probs=33.1
Q ss_pred ecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 27 TCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 27 ~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
.|..||-+|+....|-.-. ..+.-..--.|+.|.+-+..+.+.+.| . .+ -.|..||....
T Consensus 92 nCt~CGPr~~i~~~lpydr-~~t~m~~f~~C~~C~~ey~~p~~rr~h----~--~~-~~C~~Cgp~l~ 151 (711)
T TIGR00143 92 SCTHCGPRFTIIEALPYDR-ENTSMADFPLCPDCAKEYKDPLDRRFH----A--QP-IACPRCGPQLN 151 (711)
T ss_pred cccCCCCCeEEeecCCCCC-CCcCCCCCcCCHHHHHHhcCCccccCC----C--CC-ccCCCCCcEEE
Confidence 5888888877654433221 122202223677777666655433222 1 23 79999997664
No 160
>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=32.83 E-value=78 Score=17.93 Aligned_cols=38 Identities=8% Similarity=0.118 Sum_probs=23.9
Q ss_pred CceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcc
Q psy7447 24 FRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYR 63 (114)
Q Consensus 24 k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~ 63 (114)
+.|.|..-+..|..-..+...+..-. .+.|.|...|+.
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y~--~~vwtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILYN--QRVWTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHHh--CCeeEEecCCCC
Confidence 45667777777777666655555432 566777776653
No 161
>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=32.58 E-value=26 Score=23.71 Aligned_cols=32 Identities=25% Similarity=0.529 Sum_probs=18.9
Q ss_pred eecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCc
Q psy7447 26 YTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQK 67 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~ 67 (114)
.+|..|+...-.+. .. ..-+.|+.|+.-|...
T Consensus 27 ~~c~~c~~~~~~~~-----l~-----~~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 27 TKCPKCGQVLYTKE-----LE-----RNLEVCPKCDHHMRMD 58 (285)
T ss_pred eECCCCcchhhHHH-----HH-----hhCCCCCCCCCcCcCC
Confidence 36888876643211 11 2235788898877654
No 162
>PRK04351 hypothetical protein; Provisional
Probab=32.54 E-value=19 Score=21.86 Aligned_cols=34 Identities=15% Similarity=0.192 Sum_probs=19.6
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEMLSI 96 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~~~ 96 (114)
.|.|..|+..+... .+ +.... |.|..|+..+...
T Consensus 112 ~Y~C~~Cg~~~~r~------Rr--~n~~~-yrCg~C~g~L~~~ 145 (149)
T PRK04351 112 LYECQSCGQQYLRK------RR--INTKR-YRCGKCRGKLKLI 145 (149)
T ss_pred EEECCCCCCEeeee------ee--cCCCc-EEeCCCCcEeeec
Confidence 46787777554432 11 12344 8888888666543
No 163
>KOG2636|consensus
Probab=32.26 E-value=37 Score=24.67 Aligned_cols=27 Identities=37% Similarity=0.755 Sum_probs=16.1
Q ss_pred CCCCCceecCcch-hhcCCchHHHHHHH
Q psy7447 20 PLLQFRYTCDSCG-KVYKLKRSLYRHRT 46 (114)
Q Consensus 20 h~~~k~~~C~~C~-~~f~~~~~l~~h~~ 46 (114)
|.-..-|.|.+|| .++..+..+.+|-.
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 4444556777777 55555666666644
No 164
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=32.08 E-value=59 Score=15.87 Aligned_cols=13 Identities=8% Similarity=-0.013 Sum_probs=7.4
Q ss_pred cCCCCcccccCCCc
Q psy7447 78 HQGPEMLSVKHQGP 91 (114)
Q Consensus 78 ~~~~p~~~C~~C~~ 91 (114)
.+.+- ..|+.||+
T Consensus 42 ~~~~i-~~Cp~CgR 54 (56)
T PF02591_consen 42 KGDEI-VFCPNCGR 54 (56)
T ss_pred cCCCe-EECcCCCc
Confidence 33344 66777765
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=32.02 E-value=24 Score=16.01 Aligned_cols=11 Identities=0% Similarity=-0.266 Sum_probs=5.1
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
|-|++|+.-+.
T Consensus 4 yyCdyC~~~~~ 14 (38)
T PF06220_consen 4 YYCDYCKKYLT 14 (38)
T ss_dssp -B-TTT--B-S
T ss_pred eecccccceec
Confidence 89999998884
No 166
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=31.72 E-value=26 Score=17.27 Aligned_cols=13 Identities=8% Similarity=0.107 Sum_probs=9.6
Q ss_pred ccccCCCcccccc
Q psy7447 84 LSVKHQGPEMLSI 96 (114)
Q Consensus 84 ~~C~~C~~~f~~~ 96 (114)
+.|++||..+..+
T Consensus 1 i~CPyCge~~~~~ 13 (52)
T PF14255_consen 1 IQCPYCGEPIEIL 13 (52)
T ss_pred CCCCCCCCeeEEE
Confidence 3689999877644
No 167
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=31.17 E-value=7.9 Score=21.87 Aligned_cols=15 Identities=33% Similarity=0.700 Sum_probs=10.0
Q ss_pred CCCceecCcchhhcC
Q psy7447 22 LQFRYTCDSCGKVYK 36 (114)
Q Consensus 22 ~~k~~~C~~C~~~f~ 36 (114)
-.+.|.|..|+..-.
T Consensus 19 L~k~FtCp~Cghe~v 33 (104)
T COG4888 19 LPKTFTCPRCGHEKV 33 (104)
T ss_pred CCceEecCccCCeee
Confidence 456788888875533
No 168
>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=30.62 E-value=28 Score=14.99 Aligned_cols=8 Identities=38% Similarity=1.070 Sum_probs=3.6
Q ss_pred CeeCCCCC
Q psy7447 54 RYQCPHCP 61 (114)
Q Consensus 54 ~~~C~~c~ 61 (114)
.+.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34444444
No 169
>PF14369 zf-RING_3: zinc-finger
Probab=30.14 E-value=27 Score=15.51 Aligned_cols=10 Identities=0% Similarity=-0.054 Sum_probs=7.0
Q ss_pred cccCCCcccc
Q psy7447 85 SVKHQGPEML 94 (114)
Q Consensus 85 ~C~~C~~~f~ 94 (114)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4777777775
No 170
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.91 E-value=18 Score=21.34 Aligned_cols=14 Identities=29% Similarity=0.430 Sum_probs=6.6
Q ss_pred CCeeCCCCCcccCC
Q psy7447 53 PRYQCPHCPYRGKQ 66 (114)
Q Consensus 53 k~~~C~~c~~~~~~ 66 (114)
.|.-|.-||+.|.+
T Consensus 67 ~psfchncgs~fpw 80 (160)
T COG4306 67 PPSFCHNCGSRFPW 80 (160)
T ss_pred CcchhhcCCCCCCc
Confidence 34444445555544
No 171
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=29.49 E-value=15 Score=26.76 Aligned_cols=15 Identities=33% Similarity=0.738 Sum_probs=9.7
Q ss_pred CCCeeCCCCCcccCC
Q psy7447 52 EPRYQCPHCPYRGKQ 66 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~ 66 (114)
...|+|..|+..+..
T Consensus 423 ~~~~~c~~c~~~yd~ 437 (479)
T PRK05452 423 GPRMQCSVCQWIYDP 437 (479)
T ss_pred CCeEEECCCCeEECC
Confidence 345677777766654
No 172
>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=29.40 E-value=21 Score=20.31 Aligned_cols=11 Identities=27% Similarity=0.564 Sum_probs=6.1
Q ss_pred CceecCcchhh
Q psy7447 24 FRYTCDSCGKV 34 (114)
Q Consensus 24 k~~~C~~C~~~ 34 (114)
||..|..||..
T Consensus 1 ~p~~CpYCg~~ 11 (102)
T PF11672_consen 1 KPIICPYCGGP 11 (102)
T ss_pred CCcccCCCCCe
Confidence 34556666643
No 173
>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=29.24 E-value=30 Score=16.82 Aligned_cols=15 Identities=7% Similarity=-0.124 Sum_probs=11.0
Q ss_pred ccccCCCcccccccc
Q psy7447 84 LSVKHQGPEMLSIKH 98 (114)
Q Consensus 84 ~~C~~C~~~f~~~~~ 98 (114)
|.|..||..+....|
T Consensus 2 y~C~~CgyiYd~~~G 16 (50)
T cd00730 2 YECRICGYIYDPAEG 16 (50)
T ss_pred cCCCCCCeEECCCCC
Confidence 788888887775443
No 174
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.86 E-value=19 Score=19.31 Aligned_cols=32 Identities=16% Similarity=0.358 Sum_probs=19.0
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEM 93 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f 93 (114)
.|+|..|+..|.--. + ..+.|.-.|+.|+-.+
T Consensus 12 ~Y~c~~cg~~~dvvq----~----~~ddplt~ce~c~a~~ 43 (82)
T COG2331 12 SYECTECGNRFDVVQ----A----MTDDPLTTCEECGARL 43 (82)
T ss_pred EEeecccchHHHHHH----h----cccCccccChhhChHH
Confidence 478888887654421 1 2233435788888544
No 175
>PRK04023 DNA polymerase II large subunit; Validated
Probab=28.59 E-value=59 Score=26.33 Aligned_cols=10 Identities=60% Similarity=1.178 Sum_probs=6.1
Q ss_pred ceecCcchhh
Q psy7447 25 RYTCDSCGKV 34 (114)
Q Consensus 25 ~~~C~~C~~~ 34 (114)
...|..||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 3457777755
No 176
>PRK11823 DNA repair protein RadA; Provisional
Probab=28.43 E-value=54 Score=23.66 Aligned_cols=13 Identities=31% Similarity=0.846 Sum_probs=9.2
Q ss_pred CCceecCcchhhc
Q psy7447 23 QFRYTCDSCGKVY 35 (114)
Q Consensus 23 ~k~~~C~~C~~~f 35 (114)
...|.|..||...
T Consensus 5 ~~~y~C~~Cg~~~ 17 (446)
T PRK11823 5 KTAYVCQECGAES 17 (446)
T ss_pred CCeEECCcCCCCC
Confidence 3568898888654
No 177
>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=28.39 E-value=26 Score=16.83 Aligned_cols=15 Identities=13% Similarity=-0.173 Sum_probs=10.6
Q ss_pred ccccCCCcccccccc
Q psy7447 84 LSVKHQGPEMLSIKH 98 (114)
Q Consensus 84 ~~C~~C~~~f~~~~~ 98 (114)
|.|..|+..+....+
T Consensus 2 y~C~~CgyvYd~~~G 16 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKG 16 (47)
T ss_dssp EEETTTSBEEETTTB
T ss_pred cCCCCCCEEEcCCcC
Confidence 778888877665544
No 178
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=28.26 E-value=54 Score=23.79 Aligned_cols=23 Identities=26% Similarity=0.774 Sum_probs=15.8
Q ss_pred CceecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCC
Q psy7447 24 FRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCP 61 (114)
Q Consensus 24 k~~~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~ 61 (114)
..|.|..||.... ..-+.|+.|+
T Consensus 6 ~~y~C~~Cg~~~~---------------~~~g~Cp~C~ 28 (454)
T TIGR00416 6 SKFVCQHCGADSP---------------KWQGKCPACH 28 (454)
T ss_pred CeEECCcCCCCCc---------------cccEECcCCC
Confidence 4589999986543 3345788885
No 179
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=28.00 E-value=61 Score=16.20 Aligned_cols=14 Identities=21% Similarity=0.785 Sum_probs=9.4
Q ss_pred CCCeeCCCCCcccC
Q psy7447 52 EPRYQCPHCPYRGK 65 (114)
Q Consensus 52 ~k~~~C~~c~~~~~ 65 (114)
...|.|+.||-.+-
T Consensus 12 ~v~~~Cp~cGipth 25 (55)
T PF13824_consen 12 HVNFECPDCGIPTH 25 (55)
T ss_pred ccCCcCCCCCCcCc
Confidence 56678888875443
No 180
>KOG4173|consensus
Probab=27.62 E-value=41 Score=21.80 Aligned_cols=68 Identities=18% Similarity=0.320 Sum_probs=33.6
Q ss_pred ceecCc--chhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCchHHHHHHHHhc---------CCCCcccccC--CCc
Q psy7447 25 RYTCDS--CGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKTHVAIKH---------QGPEMLSVKH--QGP 91 (114)
Q Consensus 25 ~~~C~~--C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~~~l~~h~~~~~---------~~~p~~~C~~--C~~ 91 (114)
.+.|.+ |-+.|.....+..|--+..+ -.|..|.+.|....-|..|+--.+ ..++.|.|=. |+.
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~----~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~ 154 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG----NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTE 154 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc----chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhh
Confidence 344544 44555544444444332222 256667777776666666644222 1244466653 555
Q ss_pred ccccc
Q psy7447 92 EMLSI 96 (114)
Q Consensus 92 ~f~~~ 96 (114)
.|-..
T Consensus 155 KFkT~ 159 (253)
T KOG4173|consen 155 KFKTS 159 (253)
T ss_pred hhhhh
Confidence 55433
No 181
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.55 E-value=25 Score=20.60 Aligned_cols=34 Identities=18% Similarity=0.343 Sum_probs=18.0
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
...| .|+..|.....-..+ -.+.+.|+.||....
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~------~~~~~~CP~Cgs~~~ 103 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDH------YAAVIECPVCGNKRA 103 (124)
T ss_pred eEEe-eCcCcccccccchhc------cccCCcCcCCCCCCC
Confidence 4588 888776654210000 011267999985443
No 182
>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=27.42 E-value=20 Score=15.34 Aligned_cols=13 Identities=15% Similarity=0.207 Sum_probs=6.9
Q ss_pred ccccCCCcccccc
Q psy7447 84 LSVKHQGPEMLSI 96 (114)
Q Consensus 84 ~~C~~C~~~f~~~ 96 (114)
|.|+.|+..+-++
T Consensus 14 Y~Cp~C~~~~CSl 26 (30)
T PF04438_consen 14 YRCPRCGARYCSL 26 (30)
T ss_dssp EE-TTT--EESSH
T ss_pred EECCCcCCceeCc
Confidence 7777777766554
No 183
>PHA02998 RNA polymerase subunit; Provisional
Probab=27.11 E-value=12 Score=23.49 Aligned_cols=11 Identities=0% Similarity=-0.055 Sum_probs=7.4
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
|.|..||..|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 67777776665
No 184
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=26.48 E-value=35 Score=23.31 Aligned_cols=14 Identities=29% Similarity=0.558 Sum_probs=9.4
Q ss_pred CeeCCCCCcccCCc
Q psy7447 54 RYQCPHCPYRGKQK 67 (114)
Q Consensus 54 ~~~C~~c~~~~~~~ 67 (114)
-+.|+.|+.-|...
T Consensus 57 ~~vcp~c~~h~rlt 70 (296)
T CHL00174 57 MNICEQCGYHLKMS 70 (296)
T ss_pred CCCCCCCCCCcCCC
Confidence 35778888766654
No 185
>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=26.30 E-value=42 Score=19.28 Aligned_cols=13 Identities=31% Similarity=0.881 Sum_probs=6.6
Q ss_pred CeeCCCCCcccCC
Q psy7447 54 RYQCPHCPYRGKQ 66 (114)
Q Consensus 54 ~~~C~~c~~~~~~ 66 (114)
.+.|+.|+..|..
T Consensus 19 ~~iCpeC~~EW~~ 31 (109)
T TIGR00686 19 QLICPSCLYEWNE 31 (109)
T ss_pred eeECccccccccc
Confidence 3555555554443
No 186
>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=26.28 E-value=36 Score=14.78 Aligned_cols=15 Identities=7% Similarity=-0.017 Sum_probs=11.3
Q ss_pred ccccCCCcccccccc
Q psy7447 84 LSVKHQGPEMLSIKH 98 (114)
Q Consensus 84 ~~C~~C~~~f~~~~~ 98 (114)
|+|..||..+..+..
T Consensus 5 ykC~~CGniv~v~~~ 19 (34)
T cd00974 5 YKCEICGNIVEVLNV 19 (34)
T ss_pred EEcCCCCcEEEEEEC
Confidence 788888888776643
No 187
>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=26.16 E-value=52 Score=19.96 Aligned_cols=8 Identities=13% Similarity=0.144 Sum_probs=4.9
Q ss_pred cccCCCcc
Q psy7447 85 SVKHQGPE 92 (114)
Q Consensus 85 ~C~~C~~~ 92 (114)
.|+.||..
T Consensus 132 ~Cp~C~~~ 139 (146)
T PF07295_consen 132 PCPKCGHT 139 (146)
T ss_pred CCCCCCCC
Confidence 66666653
No 188
>PRK05978 hypothetical protein; Provisional
Probab=26.06 E-value=42 Score=20.45 Aligned_cols=13 Identities=8% Similarity=-0.025 Sum_probs=8.4
Q ss_pred ccccCCCcccccc
Q psy7447 84 LSVKHQGPEMLSI 96 (114)
Q Consensus 84 ~~C~~C~~~f~~~ 96 (114)
-.|+.||..|...
T Consensus 53 ~~C~~CG~~~~~~ 65 (148)
T PRK05978 53 DHCAACGEDFTHH 65 (148)
T ss_pred CCccccCCccccC
Confidence 4777777766633
No 189
>KOG1842|consensus
Probab=26.06 E-value=39 Score=24.55 Aligned_cols=27 Identities=19% Similarity=0.128 Sum_probs=21.7
Q ss_pred CceecCcchhhcCCchHHHHHHHHhcC
Q psy7447 24 FRYTCDSCGKVYKLKRSLYRHRTLECG 50 (114)
Q Consensus 24 k~~~C~~C~~~f~~~~~l~~h~~~h~~ 50 (114)
+-|.|+.|..-|...+.|..|....+.
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcc
Confidence 457899999999998999998775444
No 190
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.98 E-value=62 Score=26.89 Aligned_cols=11 Identities=9% Similarity=0.093 Sum_probs=6.2
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
..|+.|+....
T Consensus 710 ~~CP~CGtplv 720 (1337)
T PRK14714 710 VECPRCDVELT 720 (1337)
T ss_pred ccCCCCCCccc
Confidence 45666664433
No 191
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=25.84 E-value=36 Score=14.75 Aligned_cols=14 Identities=7% Similarity=0.029 Sum_probs=10.8
Q ss_pred ccccCCCccccccc
Q psy7447 84 LSVKHQGPEMLSIK 97 (114)
Q Consensus 84 ~~C~~C~~~f~~~~ 97 (114)
|+|..||..+..+.
T Consensus 8 ykC~~Cgniv~v~~ 21 (34)
T TIGR00319 8 YKCEVCGNIVEVLH 21 (34)
T ss_pred EEcCCCCcEEEEEE
Confidence 88888888777554
No 192
>KOG1280|consensus
Probab=25.51 E-value=75 Score=22.37 Aligned_cols=26 Identities=31% Similarity=0.643 Sum_probs=13.1
Q ss_pred CeeCCCCCcccCCchHHHHHHHHhcC
Q psy7447 54 RYQCPHCPYRGKQKVHLKTHVAIKHQ 79 (114)
Q Consensus 54 ~~~C~~c~~~~~~~~~l~~h~~~~~~ 79 (114)
-|.|+.|+..-.....+..|.-..+.
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hp 104 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHP 104 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCc
Confidence 34555555554444555555544443
No 193
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=25.24 E-value=16 Score=21.10 Aligned_cols=11 Identities=9% Similarity=-0.025 Sum_probs=6.9
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
|.|..||..+.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 66666766553
No 194
>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=24.55 E-value=70 Score=19.16 Aligned_cols=47 Identities=13% Similarity=0.244 Sum_probs=26.4
Q ss_pred eecCcchhhcCCchH--HHHH--HHHhcCCCCCeeCCCCCcccCCchHHHH
Q psy7447 26 YTCDSCGKVYKLKRS--LYRH--RTLECGKEPRYQCPHCPYRGKQKVHLKT 72 (114)
Q Consensus 26 ~~C~~C~~~f~~~~~--l~~h--~~~h~~~~k~~~C~~c~~~~~~~~~l~~ 72 (114)
-.|..|+..+...+. +..- ..+......-+.|+.|++.|...++..+
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHH
Confidence 479999876543211 1100 0011110346799999999988776553
No 195
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=24.05 E-value=41 Score=15.23 Aligned_cols=13 Identities=8% Similarity=-0.205 Sum_probs=7.2
Q ss_pred ccccCCCcccccc
Q psy7447 84 LSVKHQGPEMLSI 96 (114)
Q Consensus 84 ~~C~~C~~~f~~~ 96 (114)
-.|..|++.|--.
T Consensus 3 ~~CprC~kg~Hwa 15 (36)
T PF14787_consen 3 GLCPRCGKGFHWA 15 (36)
T ss_dssp -C-TTTSSSCS-T
T ss_pred ccCcccCCCcchh
Confidence 3578888877533
No 196
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=23.99 E-value=43 Score=17.25 Aligned_cols=9 Identities=22% Similarity=0.261 Sum_probs=5.7
Q ss_pred ccccCCCcc
Q psy7447 84 LSVKHQGPE 92 (114)
Q Consensus 84 ~~C~~C~~~ 92 (114)
|.|++||..
T Consensus 1 y~C~KCg~~ 9 (64)
T PF09855_consen 1 YKCPKCGNE 9 (64)
T ss_pred CCCCCCCCc
Confidence 567777743
No 197
>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=23.77 E-value=27 Score=19.37 Aligned_cols=31 Identities=19% Similarity=0.475 Sum_probs=19.9
Q ss_pred CCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 53 PRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 53 k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
..|.|+.|++.--. +.-+| - |.|..|+..|+
T Consensus 34 ~ky~Cp~Cgk~~vk--------R~a~G--I-W~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK--------RVATG--I-WKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEE--------EEETT--E-EEETTTTEEEE
T ss_pred CCCcCCCCCCceeE--------EeeeE--E-eecCCCCCEEe
Confidence 46899999864211 11222 2 99999999887
No 198
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=23.74 E-value=11 Score=16.87 Aligned_cols=6 Identities=33% Similarity=1.270 Sum_probs=2.1
Q ss_pred eCCCCC
Q psy7447 56 QCPHCP 61 (114)
Q Consensus 56 ~C~~c~ 61 (114)
.|..||
T Consensus 23 sC~~CG 28 (35)
T PF07503_consen 23 SCTNCG 28 (35)
T ss_dssp -BTTCC
T ss_pred cCCCCC
Confidence 344444
No 199
>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=23.31 E-value=83 Score=14.09 Aligned_cols=14 Identities=36% Similarity=0.980 Sum_probs=6.8
Q ss_pred HHhcCCCCCeeCCCC
Q psy7447 46 TLECGKEPRYQCPHC 60 (114)
Q Consensus 46 ~~h~~~~k~~~C~~c 60 (114)
....| ...|.|..|
T Consensus 22 ~~~~G-~qryrC~~C 35 (36)
T PF03811_consen 22 KSPSG-HQRYRCKDC 35 (36)
T ss_pred CCCCC-CEeEecCcC
Confidence 33344 445666554
No 200
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=23.01 E-value=96 Score=21.36 Aligned_cols=10 Identities=40% Similarity=0.992 Sum_probs=6.7
Q ss_pred ceecCcchhh
Q psy7447 25 RYTCDSCGKV 34 (114)
Q Consensus 25 ~~~C~~C~~~ 34 (114)
.-.|..||..
T Consensus 184 ~~~CPvCGs~ 193 (305)
T TIGR01562 184 RTLCPACGSP 193 (305)
T ss_pred CCcCCCCCCh
Confidence 3468888844
No 201
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=22.49 E-value=47 Score=22.65 Aligned_cols=31 Identities=29% Similarity=0.565 Sum_probs=18.4
Q ss_pred ecCcchhhcCCchHHHHHHHHhcCCCCCeeCCCCCcccCCc
Q psy7447 27 TCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQK 67 (114)
Q Consensus 27 ~C~~C~~~f~~~~~l~~h~~~h~~~~k~~~C~~c~~~~~~~ 67 (114)
+|..|+...-.+. .. ..-+.|+.|+.-|...
T Consensus 29 ~c~~c~~~~~~~~-----l~-----~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 29 KCPSCGQVLYRKE-----LE-----ANLNVCPKCGHHMRIS 59 (292)
T ss_pred ECCCccchhhHHH-----HH-----hcCCCCCCCCCCeeCC
Confidence 6888876532211 11 2235888999877654
No 202
>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=22.42 E-value=32 Score=20.65 Aligned_cols=16 Identities=44% Similarity=0.883 Sum_probs=12.5
Q ss_pred CCceecCcchhhcCCc
Q psy7447 23 QFRYTCDSCGKVYKLK 38 (114)
Q Consensus 23 ~k~~~C~~C~~~f~~~ 38 (114)
.++.+|..||..|...
T Consensus 110 g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLK 125 (136)
T ss_dssp TSEEEETTTEEEEEEE
T ss_pred CCccCCCCCCeEEEEE
Confidence 4688999999888643
No 203
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=22.29 E-value=75 Score=22.07 Aligned_cols=12 Identities=8% Similarity=-0.036 Sum_probs=7.5
Q ss_pred ccccCCCccccc
Q psy7447 84 LSVKHQGPEMLS 95 (114)
Q Consensus 84 ~~C~~C~~~f~~ 95 (114)
|.|..|...|..
T Consensus 389 Y~Ce~CK~~FC~ 400 (421)
T COG5151 389 YQCELCKSTFCS 400 (421)
T ss_pred eechhhhhhhhh
Confidence 666666666654
No 204
>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=22.03 E-value=37 Score=14.98 Aligned_cols=11 Identities=9% Similarity=0.178 Sum_probs=7.6
Q ss_pred ccccCCCcccc
Q psy7447 84 LSVKHQGPEML 94 (114)
Q Consensus 84 ~~C~~C~~~f~ 94 (114)
+.|+.|++.+.
T Consensus 5 ~~C~nC~R~v~ 15 (33)
T PF08209_consen 5 VECPNCGRPVA 15 (33)
T ss_dssp EE-TTTSSEEE
T ss_pred EECCCCcCCcc
Confidence 67888888665
No 205
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=21.98 E-value=44 Score=22.38 Aligned_cols=27 Identities=19% Similarity=0.252 Sum_probs=17.9
Q ss_pred eCCCCCcccCCchHHHHHHHHhcCCCCcccccCCC
Q psy7447 56 QCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQG 90 (114)
Q Consensus 56 ~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~ 90 (114)
.|+.||..+.....+. --. .|+|+.|-
T Consensus 222 ~CP~Cg~~W~L~~plh--~iF------dFKCD~CR 248 (258)
T PF10071_consen 222 KCPSCGGDWRLKEPLH--DIF------DFKCDPCR 248 (258)
T ss_pred CCCCCCCccccCCchh--hce------eccCCcce
Confidence 6888888777766652 111 28888874
No 206
>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=21.89 E-value=41 Score=16.51 Aligned_cols=15 Identities=0% Similarity=-0.265 Sum_probs=7.2
Q ss_pred ccccCCCcccccccc
Q psy7447 84 LSVKHQGPEMLSIKH 98 (114)
Q Consensus 84 ~~C~~C~~~f~~~~~ 98 (114)
|.|+.|...|-..-.
T Consensus 22 y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCD 36 (51)
T ss_dssp E--TTTT--B-HHHH
T ss_pred EECCCCCCccccCcC
Confidence 999999988874433
No 207
>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=21.62 E-value=38 Score=15.10 Aligned_cols=13 Identities=8% Similarity=0.128 Sum_probs=6.8
Q ss_pred ccccCCCcccccc
Q psy7447 84 LSVKHQGPEMLSI 96 (114)
Q Consensus 84 ~~C~~C~~~f~~~ 96 (114)
-.|..|++.|+..
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 3688899988843
No 208
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=21.30 E-value=43 Score=22.05 Aligned_cols=17 Identities=29% Similarity=0.835 Sum_probs=13.8
Q ss_pred CCCceecCcchhhcCCc
Q psy7447 22 LQFRYTCDSCGKVYKLK 38 (114)
Q Consensus 22 ~~k~~~C~~C~~~f~~~ 38 (114)
..++.+|.+||..|...
T Consensus 178 EGkpqRCpECGqVFKLV 194 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCCccCCCCCcEEEEE
Confidence 45788999999998754
No 209
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=21.29 E-value=18 Score=24.63 Aligned_cols=10 Identities=10% Similarity=0.255 Sum_probs=6.1
Q ss_pred ccccCCCccc
Q psy7447 84 LSVKHQGPEM 93 (114)
Q Consensus 84 ~~C~~C~~~f 93 (114)
|.|..||..+
T Consensus 287 ~~C~~Cg~~w 296 (299)
T TIGR01385 287 VTCEECGNRW 296 (299)
T ss_pred EEcCCCCCee
Confidence 5666666544
No 210
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=21.17 E-value=41 Score=14.77 Aligned_cols=10 Identities=10% Similarity=0.016 Sum_probs=6.4
Q ss_pred ccccCCCccc
Q psy7447 84 LSVKHQGPEM 93 (114)
Q Consensus 84 ~~C~~C~~~f 93 (114)
+.|..|+..|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 5666666655
No 211
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.99 E-value=1e+02 Score=20.62 Aligned_cols=16 Identities=19% Similarity=0.760 Sum_probs=10.1
Q ss_pred CCCeeCCCCCcccCCc
Q psy7447 52 EPRYQCPHCPYRGKQK 67 (114)
Q Consensus 52 ~k~~~C~~c~~~~~~~ 67 (114)
.+.+.|+.||..+...
T Consensus 320 ~r~~~C~~cg~~~~rD 335 (364)
T COG0675 320 GRLFKCPRCGFVHDRD 335 (364)
T ss_pred ceeEECCCCCCeehhh
Confidence 4456777777665554
No 212
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=20.97 E-value=44 Score=15.79 Aligned_cols=12 Identities=17% Similarity=0.083 Sum_probs=9.7
Q ss_pred ccccCCCccccc
Q psy7447 84 LSVKHQGPEMLS 95 (114)
Q Consensus 84 ~~C~~C~~~f~~ 95 (114)
+.|+.||..+..
T Consensus 21 ~vC~~Cg~~~~~ 32 (52)
T smart00661 21 FVCRKCGYEEPI 32 (52)
T ss_pred EECCcCCCeEEC
Confidence 899999987653
No 213
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=20.65 E-value=70 Score=22.55 Aligned_cols=10 Identities=30% Similarity=0.926 Sum_probs=4.7
Q ss_pred CceecCcchh
Q psy7447 24 FRYTCDSCGK 33 (114)
Q Consensus 24 k~~~C~~C~~ 33 (114)
..++|+.|+.
T Consensus 13 ~~g~cp~c~~ 22 (372)
T cd01121 13 WLGKCPECGE 22 (372)
T ss_pred ccEECcCCCC
Confidence 3345555543
No 214
>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=20.49 E-value=53 Score=15.81 Aligned_cols=8 Identities=0% Similarity=-0.246 Sum_probs=2.9
Q ss_pred ccccCCCc
Q psy7447 84 LSVKHQGP 91 (114)
Q Consensus 84 ~~C~~C~~ 91 (114)
|.|+.|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 77777764
No 215
>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=20.37 E-value=44 Score=18.59 Aligned_cols=31 Identities=16% Similarity=0.417 Sum_probs=20.2
Q ss_pred CCeeCCCCCcccCCchHHHHHHHHhcCCCCcccccCCCcccc
Q psy7447 53 PRYQCPHCPYRGKQKVHLKTHVAIKHQGPEMLSVKHQGPEML 94 (114)
Q Consensus 53 k~~~C~~c~~~~~~~~~l~~h~~~~~~~~p~~~C~~C~~~f~ 94 (114)
..|.|+.|++.--. +.-+| . |.|..|+..|+
T Consensus 34 a~y~CpfCgk~~vk--------R~a~G--I-W~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKTVK--------RGSTG--I-WTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCceE--------EEeeE--E-EEcCCCCCEEe
Confidence 46899999852111 22222 3 99999999887
No 216
>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=20.20 E-value=40 Score=16.55 Aligned_cols=16 Identities=13% Similarity=0.507 Sum_probs=8.8
Q ss_pred CCCCceecCcchhhcC
Q psy7447 21 LLQFRYTCDSCGKVYK 36 (114)
Q Consensus 21 ~~~k~~~C~~C~~~f~ 36 (114)
.....++|.+|++.+.
T Consensus 31 ~~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 31 KEPIKLRCHYCERIIT 46 (52)
T ss_dssp TTTCEEEETTT--EEE
T ss_pred CCCCEEEeeCCCCEec
Confidence 3455677777776654
Done!