Query 023000
Match_columns 289
No_of_seqs 321 out of 2165
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 07:43:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023000.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023000hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3183 Predicted Zn-finger pr 100.0 6.6E-34 1.4E-38 239.7 5.8 136 3-138 1-138 (250)
2 KOG2462 C2H2-type Zn-finger pr 99.8 8.9E-20 1.9E-24 158.1 5.4 55 218-281 211-265 (279)
3 KOG2462 C2H2-type Zn-finger pr 99.7 2.7E-17 5.9E-22 142.7 6.0 55 221-284 186-240 (279)
4 KOG1074 Transcriptional repres 99.4 1.1E-12 2.4E-17 128.1 8.3 54 221-283 604-657 (958)
5 KOG1074 Transcriptional repres 99.1 1.4E-10 3.1E-15 113.6 9.4 55 222-285 879-933 (958)
6 KOG3623 Homeobox transcription 99.1 9.5E-12 2.1E-16 119.9 0.7 53 218-279 918-970 (1007)
7 PF01428 zf-AN1: AN1-like Zinc 99.1 5.5E-11 1.2E-15 76.3 2.3 40 13-52 1-40 (43)
8 KOG3608 Zn finger proteins [Ge 99.0 6.1E-11 1.3E-15 106.2 -0.5 82 31-144 185-273 (467)
9 KOG3576 Ovo and related transc 99.0 5.4E-11 1.2E-15 99.1 -1.4 55 221-284 144-198 (267)
10 KOG3623 Homeobox transcription 98.9 3.7E-10 8E-15 109.1 0.9 53 219-280 278-330 (1007)
11 smart00154 ZnF_AN1 AN1-like Zi 98.9 1.6E-09 3.5E-14 67.7 2.6 34 17-50 3-37 (39)
12 KOG3608 Zn finger proteins [Ge 98.8 1.2E-09 2.6E-14 97.9 1.7 208 6-287 112-349 (467)
13 PHA02768 hypothetical protein; 98.8 2.9E-09 6.2E-14 71.0 1.8 45 222-277 5-49 (55)
14 KOG3576 Ovo and related transc 98.6 9.5E-08 2.1E-12 80.0 5.4 59 218-285 113-171 (267)
15 PHA00733 hypothetical protein 98.5 1.2E-07 2.5E-12 75.5 5.2 54 220-284 71-124 (128)
16 PF01428 zf-AN1: AN1-like Zinc 98.3 2.7E-07 5.9E-12 59.1 2.2 39 101-141 1-39 (43)
17 KOG3993 Transcription factor ( 98.2 2.9E-07 6.3E-12 84.6 -0.4 53 26-84 268-320 (500)
18 PF13465 zf-H2C2_2: Zinc-finge 98.2 1.1E-06 2.3E-11 50.0 1.8 26 237-271 1-26 (26)
19 PLN03086 PRLI-interacting fact 98.1 3.9E-06 8.4E-11 81.6 4.9 55 219-284 501-565 (567)
20 PHA00732 hypothetical protein 98.0 3.6E-06 7.7E-11 61.1 2.8 46 222-281 1-46 (79)
21 PF05605 zf-Di19: Drought indu 98.0 1.2E-05 2.6E-10 54.0 4.5 53 222-284 2-54 (54)
22 PHA00616 hypothetical protein 97.9 5.2E-06 1.1E-10 52.8 1.7 34 222-264 1-34 (44)
23 PLN03086 PRLI-interacting fact 97.9 3.8E-05 8.3E-10 74.8 8.0 51 221-282 477-537 (567)
24 PHA00616 hypothetical protein 97.6 2.9E-05 6.3E-10 49.4 1.7 28 259-286 1-28 (44)
25 smart00154 ZnF_AN1 AN1-like Zi 97.6 3.6E-05 7.7E-10 48.1 1.8 33 106-139 4-36 (39)
26 PF00096 zf-C2H2: Zinc finger, 97.6 4.1E-05 8.8E-10 41.9 1.5 22 260-281 1-22 (23)
27 PHA02768 hypothetical protein; 97.5 6.2E-05 1.3E-09 50.3 1.8 25 259-283 5-29 (55)
28 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00013 2.9E-09 39.8 1.8 24 260-283 1-24 (24)
29 PF13912 zf-C2H2_6: C2H2-type 97.3 0.00011 2.4E-09 41.8 1.2 26 259-284 1-26 (27)
30 KOG3993 Transcription factor ( 97.2 0.00015 3.3E-09 67.0 2.2 62 222-284 295-381 (500)
31 PF00096 zf-C2H2: Zinc finger, 97.2 0.00021 4.5E-09 39.0 1.7 23 223-246 1-23 (23)
32 PHA00733 hypothetical protein 97.0 0.00035 7.6E-09 55.6 1.8 55 220-282 38-96 (128)
33 PF13912 zf-C2H2_6: C2H2-type 96.5 0.0016 3.5E-08 36.9 1.7 25 222-247 1-25 (27)
34 COG5189 SFP1 Putative transcri 96.5 0.0008 1.7E-08 60.3 0.5 61 219-279 346-418 (423)
35 PF13894 zf-C2H2_4: C2H2-type 96.4 0.003 6.4E-08 34.2 2.1 23 223-246 1-23 (24)
36 smart00355 ZnF_C2H2 zinc finge 96.2 0.0042 9E-08 34.1 2.4 23 260-282 1-23 (26)
37 PF12756 zf-C2H2_2: C2H2 type 96.2 0.0024 5.2E-08 47.6 1.8 59 224-282 1-73 (100)
38 PF09237 GAGA: GAGA factor; I 96.1 0.0025 5.3E-08 41.6 1.1 26 259-284 24-49 (54)
39 COG3582 Predicted nucleic acid 95.8 0.01 2.2E-07 48.8 3.7 122 17-142 5-137 (162)
40 PF13465 zf-H2C2_2: Zinc-finge 95.8 0.0038 8.3E-08 35.2 0.9 16 219-234 11-26 (26)
41 smart00355 ZnF_C2H2 zinc finge 95.6 0.013 2.8E-07 32.0 2.5 24 223-247 1-24 (26)
42 PHA00732 hypothetical protein 95.1 0.015 3.2E-07 42.2 2.1 26 259-284 1-26 (79)
43 KOG3183 Predicted Zn-finger pr 95.0 0.009 1.9E-07 51.6 0.9 40 99-140 9-48 (250)
44 PF13909 zf-H2C2_5: C2H2-type 94.9 0.017 3.7E-07 31.6 1.6 23 260-283 1-23 (24)
45 PRK04860 hypothetical protein; 94.9 0.012 2.7E-07 48.5 1.3 40 221-273 118-157 (160)
46 PF09237 GAGA: GAGA factor; I 94.4 0.037 8E-07 36.2 2.4 31 219-250 21-51 (54)
47 PF12874 zf-met: Zinc-finger o 94.3 0.022 4.8E-07 31.4 1.1 21 260-280 1-21 (25)
48 COG5189 SFP1 Putative transcri 93.7 0.05 1.1E-06 49.0 2.7 54 22-75 346-416 (423)
49 PF12874 zf-met: Zinc-finger o 93.1 0.058 1.3E-06 29.7 1.4 21 223-243 1-21 (25)
50 PF12171 zf-C2H2_jaz: Zinc-fin 92.8 0.038 8.3E-07 31.2 0.4 21 260-280 2-22 (27)
51 PF13913 zf-C2HC_2: zinc-finge 92.2 0.12 2.6E-06 28.8 1.9 20 260-280 3-22 (25)
52 PF10571 UPF0547: Uncharacteri 90.7 0.15 3.3E-06 28.7 1.3 10 59-68 2-11 (26)
53 TIGR02098 MJ0042_CXXC MJ0042 f 90.6 0.092 2E-06 32.2 0.4 13 58-70 3-15 (38)
54 PF13909 zf-H2C2_5: C2H2-type 90.4 0.19 4.2E-06 27.3 1.6 20 223-243 1-20 (24)
55 PRK14890 putative Zn-ribbon RN 90.3 0.13 2.8E-06 34.8 1.0 10 114-123 47-56 (59)
56 PF13913 zf-C2HC_2: zinc-finge 90.1 0.27 5.9E-06 27.3 2.0 20 223-243 3-22 (25)
57 PF13717 zinc_ribbon_4: zinc-r 90.0 0.15 3.2E-06 31.1 0.9 13 58-70 3-15 (36)
58 COG2888 Predicted Zn-ribbon RN 89.9 0.14 2.9E-06 34.6 0.8 9 114-122 49-57 (61)
59 smart00451 ZnF_U1 U1-like zinc 89.8 0.24 5.2E-06 29.4 1.8 22 259-280 3-24 (35)
60 PF09538 FYDLN_acid: Protein o 89.7 0.19 4.1E-06 38.7 1.6 30 26-70 10-39 (108)
61 PF13717 zinc_ribbon_4: zinc-r 89.6 0.23 5E-06 30.2 1.6 33 26-67 3-35 (36)
62 PF13719 zinc_ribbon_5: zinc-r 89.1 0.17 3.6E-06 31.0 0.7 13 58-70 3-15 (37)
63 TIGR00622 ssl1 transcription f 89.0 0.62 1.3E-05 36.0 3.9 27 115-141 81-110 (112)
64 PF12171 zf-C2H2_jaz: Zinc-fin 88.6 0.17 3.7E-06 28.5 0.5 21 223-243 2-22 (27)
65 PF09538 FYDLN_acid: Protein o 88.0 0.29 6.4E-06 37.6 1.6 13 115-127 26-38 (108)
66 PF07975 C1_4: TFIIH C1-like d 86.8 0.41 8.9E-06 31.6 1.5 27 115-141 21-50 (51)
67 PF05605 zf-Di19: Drought indu 86.6 0.78 1.7E-05 30.4 2.8 28 259-287 2-29 (54)
68 PF03604 DNA_RNApol_7kD: DNA d 84.7 0.83 1.8E-05 27.0 2.0 11 58-68 1-11 (32)
69 smart00834 CxxC_CXXC_SSSS Puta 84.6 0.68 1.5E-05 28.6 1.7 31 26-67 6-36 (41)
70 PRK00398 rpoP DNA-directed RNA 84.2 0.77 1.7E-05 29.4 1.8 32 24-69 2-33 (46)
71 COG5048 FOG: Zn-finger [Genera 83.7 0.25 5.4E-06 46.0 -0.9 56 221-284 288-348 (467)
72 PHA00626 hypothetical protein 82.9 0.83 1.8E-05 30.5 1.6 14 114-127 22-35 (59)
73 KOG1146 Homeobox protein [Gene 82.9 1 2.2E-05 48.1 3.0 63 219-281 462-540 (1406)
74 smart00451 ZnF_U1 U1-like zinc 82.8 1 2.3E-05 26.6 1.9 22 222-243 3-24 (35)
75 PF04236 Transp_Tc5_C: Tc5 tra 82.5 1.2 2.5E-05 30.8 2.3 39 7-47 24-63 (63)
76 cd00350 rubredoxin_like Rubred 82.3 0.83 1.8E-05 27.1 1.3 24 26-65 2-25 (33)
77 TIGR02300 FYDLN_acid conserved 82.1 0.81 1.8E-05 36.0 1.6 29 26-69 10-38 (129)
78 PRK04023 DNA polymerase II lar 80.8 1.4 3.1E-05 45.9 3.2 11 269-279 823-833 (1121)
79 smart00659 RPOLCX RNA polymera 80.8 1.3 2.8E-05 28.2 1.9 10 58-67 3-12 (44)
80 PF07975 C1_4: TFIIH C1-like d 80.8 0.7 1.5E-05 30.5 0.7 27 23-49 19-48 (51)
81 PF09986 DUF2225: Uncharacteri 80.4 1.2 2.5E-05 38.6 2.1 23 57-79 5-27 (214)
82 COG2888 Predicted Zn-ribbon RN 79.9 1.4 3.1E-05 29.8 1.9 33 23-64 25-57 (61)
83 COG3582 Predicted nucleic acid 79.9 0.93 2E-05 37.3 1.3 37 17-53 102-138 (162)
84 COG4049 Uncharacterized protei 79.6 1 2.2E-05 30.1 1.1 29 219-247 14-42 (65)
85 KOG3173 Predicted Zn-finger pr 79.1 1.1 2.4E-05 37.2 1.5 38 12-51 107-144 (167)
86 COG4049 Uncharacterized protei 78.1 0.96 2.1E-05 30.2 0.7 26 259-284 17-42 (65)
87 PRK04860 hypothetical protein; 76.3 1.1 2.4E-05 37.0 0.7 13 115-127 143-155 (160)
88 PF06524 NOA36: NOA36 protein; 75.4 2 4.3E-05 38.0 2.1 23 221-243 208-230 (314)
89 TIGR02300 FYDLN_acid conserved 74.5 1.8 4E-05 34.0 1.5 12 115-126 26-37 (129)
90 PF14353 CpXC: CpXC protein 74.3 0.99 2.1E-05 35.6 -0.1 15 115-129 38-52 (128)
91 cd00729 rubredoxin_SM Rubredox 74.1 1.9 4E-05 25.8 1.1 24 26-65 3-26 (34)
92 PF12756 zf-C2H2_2: C2H2 type 72.8 3 6.5E-05 30.5 2.3 23 221-243 49-71 (100)
93 PF14353 CpXC: CpXC protein 71.9 1.3 2.7E-05 35.0 0.0 40 26-70 2-51 (128)
94 KOG1813 Predicted E3 ubiquitin 71.6 2 4.4E-05 38.6 1.3 47 21-67 237-285 (313)
95 PF09723 Zn-ribbon_8: Zinc rib 70.0 3.2 7E-05 26.0 1.6 29 115-143 5-35 (42)
96 TIGR01206 lysW lysine biosynth 69.3 3.7 8.1E-05 27.4 1.9 13 58-70 23-35 (54)
97 KOG2807 RNA polymerase II tran 68.8 4.1 8.9E-05 37.2 2.6 36 106-141 336-374 (378)
98 PF09986 DUF2225: Uncharacteri 68.1 2.9 6.3E-05 36.2 1.5 44 25-68 5-59 (214)
99 COG1198 PriA Primosomal protei 65.6 3.8 8.3E-05 41.9 2.0 40 26-66 445-484 (730)
100 PRK12496 hypothetical protein; 65.1 4.6 9.9E-05 33.5 2.0 28 26-69 128-155 (164)
101 COG5151 SSL1 RNA polymerase II 63.7 4.7 0.0001 36.6 1.9 23 221-243 387-409 (421)
102 COG1997 RPL43A Ribosomal prote 63.2 4.5 9.8E-05 29.7 1.4 12 115-126 53-64 (89)
103 PF04236 Transp_Tc5_C: Tc5 tra 62.2 4.2 9.1E-05 28.1 1.1 36 98-137 27-63 (63)
104 TIGR00622 ssl1 transcription f 62.2 13 0.00028 28.7 3.9 23 221-243 80-102 (112)
105 COG4530 Uncharacterized protei 61.7 4 8.7E-05 31.2 1.0 28 27-69 11-38 (129)
106 PF13240 zinc_ribbon_2: zinc-r 59.9 5.8 0.00013 21.5 1.2 8 60-67 2-9 (23)
107 PRK12380 hydrogenase nickel in 58.8 5.9 0.00013 30.6 1.5 25 26-66 71-95 (113)
108 COG5151 SSL1 RNA polymerase II 58.0 3.8 8.3E-05 37.1 0.4 28 115-142 388-418 (421)
109 PRK00464 nrdR transcriptional 57.9 8.1 0.00018 31.7 2.2 39 26-68 1-39 (154)
110 KOG2893 Zn finger protein [Gen 57.6 3.4 7.4E-05 36.1 -0.0 45 221-279 10-54 (341)
111 TIGR02605 CxxC_CxxC_SSSS putat 57.1 7.8 0.00017 25.2 1.7 29 115-143 5-35 (52)
112 PRK04023 DNA polymerase II lar 56.8 11 0.00024 39.6 3.5 57 4-70 620-676 (1121)
113 TIGR00595 priA primosomal prot 56.6 10 0.00022 37.2 3.2 21 116-142 241-261 (505)
114 COG1592 Rubrerythrin [Energy p 56.5 6.2 0.00013 32.7 1.3 24 222-267 134-157 (166)
115 PRK14873 primosome assembly pr 56.4 8.1 0.00018 39.3 2.4 46 20-66 377-431 (665)
116 PF07754 DUF1610: Domain of un 54.7 6.9 0.00015 21.5 0.9 10 56-65 15-24 (24)
117 TIGR00100 hypA hydrogenase nic 54.5 7.8 0.00017 30.0 1.5 25 26-66 71-95 (115)
118 PF02176 zf-TRAF: TRAF-type zi 54.3 5.7 0.00012 26.5 0.7 27 56-89 8-36 (60)
119 PF08274 PhnA_Zn_Ribbon: PhnA 53.9 5 0.00011 23.4 0.3 10 56-65 18-27 (30)
120 PF06524 NOA36: NOA36 protein; 53.9 8.3 0.00018 34.2 1.8 52 17-75 176-227 (314)
121 PRK14714 DNA polymerase II lar 53.6 14 0.0003 40.0 3.5 37 25-68 667-703 (1337)
122 PF14446 Prok-RING_1: Prokaryo 53.0 11 0.00025 25.1 1.9 27 25-67 5-31 (54)
123 COG5048 FOG: Zn-finger [Genera 52.9 15 0.00033 33.8 3.6 59 219-286 30-90 (467)
124 smart00614 ZnF_BED BED zinc fi 52.8 9.7 0.00021 24.6 1.6 20 224-243 20-44 (50)
125 PF01096 TFIIS_C: Transcriptio 52.7 10 0.00022 23.3 1.6 11 115-125 28-38 (39)
126 PF01155 HypA: Hydrogenase exp 52.3 4.8 0.0001 31.1 0.0 25 26-66 71-95 (113)
127 PF14205 Cys_rich_KTR: Cystein 52.2 11 0.00023 25.2 1.6 11 58-68 5-15 (55)
128 PRK03824 hypA hydrogenase nick 51.6 11 0.00024 30.1 2.1 40 24-66 69-116 (135)
129 smart00734 ZnF_Rad18 Rad18-lik 50.6 13 0.00027 20.8 1.6 19 261-280 3-21 (26)
130 PRK00415 rps27e 30S ribosomal 50.3 11 0.00024 25.6 1.6 42 22-77 8-50 (59)
131 PF02892 zf-BED: BED zinc fing 49.9 14 0.00031 23.0 2.0 23 221-243 15-41 (45)
132 PF01286 XPA_N: XPA protein N- 49.5 12 0.00025 22.5 1.4 17 26-43 4-20 (34)
133 PF05443 ROS_MUCR: ROS/MUCR tr 48.9 9.6 0.00021 30.4 1.3 22 260-284 73-94 (132)
134 smart00647 IBR In Between Ring 48.1 20 0.00043 23.9 2.7 33 100-132 20-57 (64)
135 PF13248 zf-ribbon_3: zinc-rib 47.3 11 0.00024 20.9 1.0 9 59-67 4-12 (26)
136 PRK14873 primosome assembly pr 47.0 14 0.0003 37.6 2.4 8 118-125 395-402 (665)
137 KOG1146 Homeobox protein [Gene 46.5 20 0.00044 38.8 3.5 62 219-280 515-610 (1406)
138 PRK00564 hypA hydrogenase nick 46.4 11 0.00025 29.2 1.4 13 25-37 71-83 (117)
139 COG1996 RPC10 DNA-directed RNA 46.3 11 0.00024 24.6 1.0 32 24-69 5-36 (49)
140 cd00730 rubredoxin Rubredoxin; 45.8 20 0.00042 23.5 2.2 11 26-36 2-12 (50)
141 smart00531 TFIIE Transcription 45.1 17 0.00038 29.3 2.3 37 221-270 98-134 (147)
142 PF03833 PolC_DP2: DNA polymer 45.0 7.1 0.00015 40.2 0.0 37 24-67 654-690 (900)
143 smart00440 ZnF_C2C2 C2C2 Zinc 44.8 18 0.00039 22.4 1.8 11 115-125 28-38 (40)
144 TIGR00373 conserved hypothetic 44.3 8.2 0.00018 31.7 0.3 30 115-144 109-138 (158)
145 PRK06266 transcription initiat 44.2 9.1 0.0002 32.1 0.5 31 115-145 117-147 (178)
146 PF01485 IBR: IBR domain; Int 43.1 18 0.0004 24.0 1.9 32 100-131 20-56 (64)
147 PRK09678 DNA-binding transcrip 42.5 14 0.0003 26.2 1.2 12 115-126 27-40 (72)
148 PRK03681 hypA hydrogenase nick 42.2 14 0.00031 28.6 1.3 11 26-36 71-81 (114)
149 PF12013 DUF3505: Protein of u 42.1 18 0.00039 27.4 1.9 21 223-243 81-105 (109)
150 smart00661 RPOL9 RNA polymeras 42.1 23 0.00049 22.8 2.1 13 115-127 20-32 (52)
151 PF00301 Rubredoxin: Rubredoxi 41.8 20 0.00044 23.1 1.8 39 26-66 2-43 (47)
152 COG2051 RPS27A Ribosomal prote 39.9 15 0.00033 25.5 1.0 42 22-77 16-58 (67)
153 TIGR00280 L37a ribosomal prote 38.2 23 0.00049 26.3 1.8 11 115-125 53-63 (91)
154 PF04438 zf-HIT: HIT zinc fing 37.5 16 0.00034 21.2 0.7 18 18-37 8-25 (30)
155 PF04959 ARS2: Arsenite-resist 37.4 22 0.00047 30.8 1.8 29 219-247 74-102 (214)
156 COG1773 Rubredoxin [Energy pro 37.2 31 0.00067 23.1 2.1 41 25-65 3-44 (55)
157 PF05191 ADK_lid: Adenylate ki 36.9 9.1 0.0002 23.2 -0.4 31 26-68 2-32 (36)
158 KOG2186 Cell growth-regulating 36.3 11 0.00024 33.3 -0.2 37 58-126 4-40 (276)
159 TIGR00686 phnA alkylphosphonat 36.3 20 0.00044 27.4 1.2 13 115-127 19-31 (109)
160 COG1198 PriA Primosomal protei 36.3 29 0.00062 35.7 2.7 10 115-124 475-484 (730)
161 COG2331 Uncharacterized protei 35.8 17 0.00038 25.9 0.8 33 222-270 12-44 (82)
162 PTZ00255 60S ribosomal protein 35.2 28 0.0006 25.8 1.8 11 115-125 54-64 (90)
163 KOG2186 Cell growth-regulating 34.6 11 0.00025 33.2 -0.4 49 25-87 3-52 (276)
164 COG3357 Predicted transcriptio 34.5 34 0.00075 25.3 2.2 28 114-142 57-84 (97)
165 PF07295 DUF1451: Protein of u 34.3 24 0.00051 28.7 1.5 13 26-38 113-125 (146)
166 TIGR00595 priA primosomal prot 34.3 26 0.00057 34.3 2.1 39 27-66 224-262 (505)
167 PF04423 Rad50_zn_hook: Rad50 33.7 15 0.00032 24.2 0.2 10 59-68 22-31 (54)
168 smart00249 PHD PHD zinc finger 33.5 44 0.00095 20.1 2.4 14 22-35 11-24 (47)
169 PRK10220 hypothetical protein; 33.1 28 0.00061 26.7 1.6 12 115-126 20-31 (111)
170 PLN00209 ribosomal protein S27 32.6 29 0.00063 25.4 1.5 44 22-78 33-76 (86)
171 PRK05580 primosome assembly pr 32.6 30 0.00065 35.3 2.2 40 26-66 391-430 (679)
172 PF04606 Ogr_Delta: Ogr/Delta- 32.3 17 0.00037 23.2 0.3 10 59-68 1-10 (47)
173 KOG0320 Predicted E3 ubiquitin 32.1 18 0.0004 30.2 0.5 24 119-142 149-175 (187)
174 KOG3173 Predicted Zn-finger pr 32.1 24 0.00053 29.3 1.2 39 97-139 104-142 (167)
175 PRK03976 rpl37ae 50S ribosomal 32.0 34 0.00073 25.4 1.8 12 115-126 54-65 (90)
176 PF09788 Tmemb_55A: Transmembr 31.9 1.2E+02 0.0026 27.0 5.5 45 99-143 124-186 (256)
177 COG5222 Uncharacterized conser 31.9 15 0.00032 33.2 -0.1 65 4-79 268-332 (427)
178 PF05129 Elf1: Transcription e 31.8 14 0.00029 26.9 -0.3 12 115-126 46-57 (81)
179 KOG2231 Predicted E3 ubiquitin 31.4 45 0.00097 33.8 3.1 61 223-283 100-206 (669)
180 KOG2807 RNA polymerase II tran 30.8 63 0.0014 29.7 3.7 40 115-159 276-315 (378)
181 PF01927 Mut7-C: Mut7-C RNAse 30.6 32 0.00069 27.7 1.7 13 115-127 124-136 (147)
182 KOG3408 U1-like Zn-finger-cont 30.1 32 0.00069 26.9 1.4 26 255-280 53-78 (129)
183 TIGR00515 accD acetyl-CoA carb 29.8 19 0.00041 32.6 0.2 14 115-128 45-58 (285)
184 KOG3507 DNA-directed RNA polym 29.7 22 0.00049 24.0 0.5 15 115-129 37-51 (62)
185 COG1656 Uncharacterized conser 29.1 23 0.0005 29.3 0.6 12 115-126 130-141 (165)
186 COG0846 SIR2 NAD-dependent pro 29.1 32 0.0007 30.5 1.6 39 22-68 119-158 (250)
187 PHA02998 RNA polymerase subuni 28.6 40 0.00087 28.2 1.9 12 115-126 171-182 (195)
188 PRK12722 transcriptional activ 28.5 38 0.00082 28.7 1.8 31 26-68 135-165 (187)
189 PTZ00083 40S ribosomal protein 28.4 37 0.00081 24.8 1.5 44 22-78 32-75 (85)
190 PF01363 FYVE: FYVE zinc finge 28.3 32 0.00069 23.5 1.1 13 56-68 8-20 (69)
191 PRK00418 DNA gyrase inhibitor; 28.0 35 0.00077 23.4 1.2 14 56-69 5-18 (62)
192 PF08209 Sgf11: Sgf11 (transcr 27.9 16 0.00035 21.7 -0.4 20 57-83 4-23 (33)
193 PRK12860 transcriptional activ 27.8 39 0.00085 28.6 1.8 28 26-65 135-162 (189)
194 CHL00174 accD acetyl-CoA carbo 27.5 22 0.00047 32.4 0.2 14 115-128 57-70 (296)
195 COG3024 Uncharacterized protei 26.9 30 0.00065 23.8 0.7 13 57-69 7-19 (65)
196 PRK14714 DNA polymerase II lar 26.7 78 0.0017 34.5 4.0 28 115-144 692-719 (1337)
197 PF11238 DUF3039: Protein of u 26.7 20 0.00043 24.2 -0.2 11 57-67 44-54 (58)
198 KOG1842 FYVE finger-containing 26.6 15 0.00032 35.2 -1.1 15 54-68 177-191 (505)
199 PF09963 DUF2197: Uncharacteri 26.5 12 0.00027 25.1 -1.2 41 26-69 3-43 (56)
200 COG1655 Uncharacterized protei 26.3 33 0.00072 30.0 1.1 14 25-38 19-32 (267)
201 PRK01343 zinc-binding protein; 26.3 32 0.00069 23.2 0.8 13 56-68 8-20 (57)
202 PF04959 ARS2: Arsenite-resist 26.1 40 0.00087 29.2 1.6 25 259-283 77-101 (214)
203 PF12172 DUF35_N: Rubredoxin-l 26.1 24 0.00051 21.2 0.1 13 23-35 9-21 (37)
204 PRK05654 acetyl-CoA carboxylas 25.9 23 0.0005 32.2 0.1 14 115-128 46-59 (292)
205 PF09862 DUF2089: Protein of u 25.9 31 0.00068 26.7 0.8 11 115-125 12-22 (113)
206 PF15616 TerY-C: TerY-C metal 25.8 49 0.0011 26.3 1.9 25 116-143 90-114 (131)
207 COG4338 Uncharacterized protei 25.8 20 0.00043 23.2 -0.3 13 58-70 13-25 (54)
208 PF13451 zf-trcl: Probable zin 25.5 50 0.0011 21.6 1.5 39 221-267 3-41 (49)
209 PF03884 DUF329: Domain of unk 25.5 29 0.00063 23.4 0.5 12 58-69 3-14 (57)
210 PF05741 zf-nanos: Nanos RNA b 25.5 26 0.00056 23.5 0.2 12 55-66 31-42 (55)
211 cd00065 FYVE FYVE domain; Zinc 25.3 55 0.0012 21.3 1.8 25 118-145 5-29 (57)
212 PF10013 DUF2256: Uncharacteri 25.1 35 0.00075 21.5 0.7 12 59-70 10-21 (42)
213 PF07191 zinc-ribbons_6: zinc- 25.0 41 0.00089 23.7 1.2 13 56-68 29-41 (70)
214 KOG4317 Predicted Zn-finger pr 24.8 37 0.0008 31.0 1.1 13 115-127 19-31 (383)
215 PF09845 DUF2072: Zn-ribbon co 24.6 51 0.0011 26.2 1.7 11 25-35 1-11 (131)
216 COG1779 C4-type Zn-finger prot 24.2 42 0.00092 28.6 1.3 40 26-68 15-54 (201)
217 PF08271 TF_Zn_Ribbon: TFIIB z 24.1 22 0.00048 22.1 -0.3 9 117-125 2-10 (43)
218 PF14319 Zn_Tnp_IS91: Transpos 24.1 53 0.0011 25.2 1.8 34 20-67 37-70 (111)
219 PF05876 Terminase_GpA: Phage 23.7 64 0.0014 32.1 2.7 41 25-68 200-240 (557)
220 PF04810 zf-Sec23_Sec24: Sec23 23.5 35 0.00076 21.0 0.5 34 25-68 2-35 (40)
221 KOG1812 Predicted E3 ubiquitin 23.5 38 0.00081 32.1 1.0 27 12-38 235-271 (384)
222 PRK14559 putative protein seri 23.3 76 0.0017 32.2 3.1 47 27-123 3-49 (645)
223 TIGR00599 rad18 DNA repair pro 23.1 29 0.00063 33.0 0.2 25 58-89 182-206 (397)
224 PRK00432 30S ribosomal protein 22.9 49 0.0011 21.6 1.2 23 118-142 23-45 (50)
225 PF08882 Acetone_carb_G: Aceto 22.6 37 0.00081 26.1 0.6 43 24-67 23-84 (112)
226 TIGR03830 CxxCG_CxxCG_HTH puta 22.6 59 0.0013 24.9 1.8 13 114-126 30-42 (127)
227 PF09332 Mcm10: Mcm10 replicat 22.4 35 0.00075 31.8 0.5 27 115-142 285-311 (344)
228 PLN03208 E3 ubiquitin-protein 22.2 1.4E+02 0.003 25.4 4.0 11 57-67 18-28 (193)
229 PRK00762 hypA hydrogenase nick 21.9 46 0.001 26.1 1.1 12 25-37 70-81 (124)
230 PF12760 Zn_Tnp_IS1595: Transp 21.7 53 0.0012 20.7 1.1 26 115-142 18-45 (46)
231 COG1594 RPB9 DNA-directed RNA 21.5 1.4E+02 0.0029 23.1 3.6 15 56-70 21-35 (113)
232 PF14787 zf-CCHC_5: GAG-polypr 21.1 72 0.0016 19.4 1.5 13 58-70 3-15 (36)
233 PF12907 zf-met2: Zinc-binding 20.5 24 0.00051 22.0 -0.7 27 223-249 2-31 (40)
234 KOG2272 Focal adhesion protein 20.4 26 0.00057 31.0 -0.7 16 115-131 221-236 (332)
235 PF12013 DUF3505: Protein of u 20.4 79 0.0017 23.8 2.1 22 263-284 88-109 (109)
236 KOG4167 Predicted DNA-binding 20.3 29 0.00063 35.3 -0.5 28 255-282 788-815 (907)
237 PF06397 Desulfoferrod_N: Desu 20.2 48 0.001 20.1 0.6 13 56-68 5-17 (36)
No 1
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=6.6e-34 Score=239.73 Aligned_cols=136 Identities=53% Similarity=1.069 Sum_probs=129.6
Q ss_pred CCCcCcccCcCCcCCCCCcccccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccccCCCCCCccccccc
Q 023000 3 TPQFPDLGKHCSLPDCKQIDFLPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLRPDENPHITWENH 82 (289)
Q Consensus 3 ~~~~~~~g~~C~~~~C~~~dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~~~~~~~H 82 (289)
+|||||||+||++++|+|||||||+|+.|+..||++|+.++.|.|+.....++++.+||+|.++++...+..++..|..|
T Consensus 1 ~~efpDlGkHCs~~~CkqlDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~~~~de~~~~~v~~h 80 (250)
T KOG3183|consen 1 TMEFPDLGKHCSVPYCKQLDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVPTKKDEAPDKVVEPH 80 (250)
T ss_pred CCcccccccccCcchhhhccccceeeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCCCCCCCcchhhhhchh
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCC--CCcccCcccCCCCCCCCcceeeecccccCCcccccccccCcCCCCCCCC
Q 023000 83 VNVDCDP--SNYDKVTKKRKCPVRGCKEILVFSNTIKCRDCTVDHCLKHRFAPDHSCP 138 (289)
Q Consensus 83 ~~~~c~~--~~~~~~~~~~~C~~~~ck~~~~~~~~~~C~~C~~~fc~~hr~~~~h~C~ 138 (289)
+...|++ ..++...+.++|+..+|++++.+.+.++|.+|+..||++||++.+|.|.
T Consensus 81 ~~~dC~~~~~~~~~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~ 138 (250)
T KOG3183|consen 81 ISNDCDRHPEQKKRKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCN 138 (250)
T ss_pred hccccccCchhhhcccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhh
Confidence 9999997 4555666788899999999999888899999999999999999999998
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.79 E-value=8.9e-20 Score=158.07 Aligned_cols=55 Identities=27% Similarity=0.572 Sum_probs=52.2
Q ss_pred CCCCccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHh
Q 023000 218 GTGGTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVER 281 (289)
Q Consensus 218 ~~~kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~ 281 (289)
.|||||.|+.|+|+|+..++|..||+ +|.+.| +|+|..|+|.|+..+.|.+|...
T Consensus 211 TGEKPF~C~hC~kAFADRSNLRAHmQ-THS~~K--------~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 211 TGEKPFSCPHCGKAFADRSNLRAHMQ-THSDVK--------KHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cCCCCccCCcccchhcchHHHHHHHH-hhcCCc--------cccCcchhhHHHHHHHHHHhhhh
Confidence 37799999999999999999999999 999999 99999999999999999999853
No 3
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.69 E-value=2.7e-17 Score=142.70 Aligned_cols=55 Identities=27% Similarity=0.482 Sum_probs=52.8
Q ss_pred CccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHhhcC
Q 023000 221 GTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
-|++|.+|||.|.+.|-|+.|+| +|+||| ||.|+.|+|+|.+++||+.||++|.+
T Consensus 186 l~c~C~iCGKaFSRPWLLQGHiR-THTGEK--------PF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQGHIR-THTGEK--------PFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred CCcccccccccccchHHhhcccc-cccCCC--------CccCCcccchhcchHHHHHHHHhhcC
Confidence 48999999999999999999999 999999 99999999999999999999999864
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.37 E-value=1.1e-12 Score=128.08 Aligned_cols=54 Identities=20% Similarity=0.314 Sum_probs=51.3
Q ss_pred CccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHhhc
Q 023000 221 GTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVERDH 283 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~hh 283 (289)
.|.+|-+|-+..+-++.|+.|+| +|+||+ ||+|.+||+.|.++.+|+.||.+|-
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyr-tHtGER--------PFkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYR-THTGER--------PFKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred Cccceeeeeecccchhhhhhhhh-cccCcC--------ccccccccchhccccchhhcccccc
Confidence 57899999999999999999999 999999 9999999999999999999997763
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.14 E-value=1.4e-10 Score=113.57 Aligned_cols=55 Identities=25% Similarity=0.417 Sum_probs=52.0
Q ss_pred ccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHhhcCC
Q 023000 222 TELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVERDHGG 285 (289)
Q Consensus 222 p~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~hh~g 285 (289)
...|.+||+.|...+.|..|++ +|+++| ||.|..|++.|..+.+|+.||.+|+..
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~r-THtg~K--------PF~C~fC~~aFttrgnLKvHMgtH~w~ 933 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMR-THTGPK--------PFFCHFCEEAFTTRGNLKVHMGTHMWV 933 (958)
T ss_pred hhhhccchhcccchHHHHHhhh-cCCCCC--------Cccchhhhhhhhhhhhhhhhhcccccc
Confidence 3779999999999999999999 999999 999999999999999999999988754
No 6
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.13 E-value=9.5e-12 Score=119.90 Aligned_cols=53 Identities=23% Similarity=0.399 Sum_probs=51.3
Q ss_pred CCCCccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHH
Q 023000 218 GTGGTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHV 279 (289)
Q Consensus 218 ~~~kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~ 279 (289)
+|.+||+|.+|.|+|+.+.+|+.|+| .|.||| ||+|+.|+|+|+.......||
T Consensus 918 sGqRPyqC~iCkKAFKHKHHLtEHkR-LHSGEK--------PfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 918 SGQRPYQCIICKKAFKHKHHLTEHKR-LHSGEK--------PFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cCCCCcccchhhHhhhhhhhhhhhhh-hccCCC--------cchhhhhhhhcccccchHhhh
Confidence 37799999999999999999999999 999999 999999999999999999999
No 7
>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=99.08 E-value=5.5e-11 Score=76.30 Aligned_cols=40 Identities=53% Similarity=1.217 Sum_probs=31.0
Q ss_pred CCcCCCCCcccccccCCccCcccccCCCccccccCCCCCC
Q 023000 13 CSLPDCKQIDFLPFTCDCCHKVFCLDHRSYNQHQCPKAER 52 (289)
Q Consensus 13 C~~~~C~~~dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~ 52 (289)
|++++|+++|||||+|+.|++.||.+|+.++.|.|.....
T Consensus 1 C~~~~C~~~~~~~~~C~~C~~~FC~~Hr~~e~H~C~~~~~ 40 (43)
T PF01428_consen 1 CSFPGCKKKDFLPFKCKHCGKSFCLKHRLPEDHNCSKLQK 40 (43)
T ss_dssp -SSTTT--BCTSHEE-TTTS-EE-TTTHSTTTCT-SSTTS
T ss_pred CccCcCcCccCCCeECCCCCcccCccccCccccCCcchhh
Confidence 7899999999999999999999999999999999987754
No 8
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.99 E-value=6.1e-11 Score=106.15 Aligned_cols=82 Identities=20% Similarity=0.347 Sum_probs=53.5
Q ss_pred cCcccccCCCccccccCCCCCCCcceeecCCCCCCccccCCCCCCccccccccccCCCCCCcccCcccCCCCCCCCccee
Q 023000 31 CHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLRPDENPHITWENHVNVDCDPSNYDKVTKKRKCPVRGCKEIL 110 (289)
Q Consensus 31 C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~~~~~~~H~~~~c~~~~~~~~~~~~~C~~~~ck~~~ 110 (289)
|.+.| .+...+..|.-.+.+ ++++-||.||..|+.. ..|-.|+++ +.+
T Consensus 185 Ct~~~-~~k~~LreH~r~Hs~---eKvvACp~Cg~~F~~~------tkl~DH~rR----------------------qt~ 232 (467)
T KOG3608|consen 185 CTKHM-GNKYRLREHIRTHSN---EKVVACPHCGELFRTK------TKLFDHLRR----------------------QTE 232 (467)
T ss_pred hhhhh-ccHHHHHHHHHhcCC---CeEEecchHHHHhccc------cHHHHHHHh----------------------hhh
Confidence 66666 333455666655554 4678999999999743 344445543 223
Q ss_pred eecccccCCccccccccc-------CcCCCCCCCCCCCCCC
Q 023000 111 VFSNTIKCRDCTVDHCLK-------HRFAPDHSCPGPKKLD 144 (289)
Q Consensus 111 ~~~~~~~C~~C~~~fc~~-------hr~~~~h~C~~~~~~~ 144 (289)
++.|+|.|.+|.|.|..+ -|+-..|.|+.|...-
T Consensus 233 l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc 273 (467)
T KOG3608|consen 233 LNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTC 273 (467)
T ss_pred hcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCC
Confidence 444699999999999644 2666778888776633
No 9
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.97 E-value=5.4e-11 Score=99.14 Aligned_cols=55 Identities=27% Similarity=0.574 Sum_probs=38.2
Q ss_pred CccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHhhcC
Q 023000 221 GTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
+.|.|..||+.|...-.|++|+| +|+|.+ ||+|..|+|.|.++-.|..|++..|+
T Consensus 144 kr~lct~cgkgfndtfdlkrh~r-thtgvr--------pykc~~c~kaftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 144 KRHLCTFCGKGFNDTFDLKRHTR-THTGVR--------PYKCSLCEKAFTQRCSLESHLKKVHG 198 (267)
T ss_pred HHHHHhhccCcccchhhhhhhhc-cccCcc--------ccchhhhhHHHHhhccHHHHHHHHcC
Confidence 45667777777777777777776 777777 77777777777777777777665554
No 10
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.89 E-value=3.7e-10 Score=109.14 Aligned_cols=53 Identities=26% Similarity=0.495 Sum_probs=50.0
Q ss_pred CCCccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHH
Q 023000 219 TGGTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVE 280 (289)
Q Consensus 219 ~~kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~ 280 (289)
..+.|+|.+|||+|+.+.+|+.|+| +|.||| ||.|+.|+|+|+.......||.
T Consensus 278 ~lRKFKCtECgKAFKfKHHLKEHlR-IHSGEK--------PfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 278 LLRKFKCTECGKAFKFKHHLKEHLR-IHSGEK--------PFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhccccccccchhhhhHHHHHhhhe-eecCCC--------CcCCcccccccccCCccccccc
Confidence 4478999999999999999999999 999999 9999999999999999999983
No 11
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=98.85 E-value=1.6e-09 Score=67.72 Aligned_cols=34 Identities=35% Similarity=0.802 Sum_probs=32.1
Q ss_pred CCCCcccc-cccCCccCcccccCCCccccccCCCC
Q 023000 17 DCKQIDFL-PFTCDCCHKVFCLDHRSYNQHQCPKA 50 (289)
Q Consensus 17 ~C~~~dfL-Pf~C~~C~k~Fc~~h~~~~~H~c~~~ 50 (289)
.|+++||| ||+|+.|++.||.+|+.++.|.|...
T Consensus 3 ~C~~~~~l~~f~C~~C~~~FC~~HR~~e~H~C~~~ 37 (39)
T smart00154 3 FCRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGD 37 (39)
T ss_pred ccCCcccccCeECCccCCccccccCCccccCCccc
Confidence 59999999 99999999999999999999999764
No 12
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.82 E-value=1.2e-09 Score=97.91 Aligned_cols=208 Identities=18% Similarity=0.326 Sum_probs=130.6
Q ss_pred cCcccC-cCCcCCCCCccccc--ccCC--ccCcccccC---------CCccccccCCCCCCCcceeecCCC--CCCcccc
Q 023000 6 FPDLGK-HCSLPDCKQIDFLP--FTCD--CCHKVFCLD---------HRSYNQHQCPKAERHDVTVVICPL--CAKGVRL 69 (289)
Q Consensus 6 ~~~~g~-~C~~~~C~~~dfLP--f~C~--~C~k~Fc~~---------h~~~~~H~c~~~~~~~~~~~~Cp~--C~k~~~~ 69 (289)
-+|||+ -|.++.|+.+--|| |.|. .|+..|-+- |...-.+.....++...-++.|.- |-+.+
T Consensus 112 ~~dig~c~~~f~~~~~ip~~g~~f~C~WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~-- 189 (467)
T KOG3608|consen 112 HPDIGACTAPFRLMEKIPALGQNFRCGWEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHM-- 189 (467)
T ss_pred CCCcCcccCCcchhhccccchhhhccChhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhh--
Confidence 356776 57888899988888 8885 599999532 333223332333433334455653 55544
Q ss_pred CCCCCCccccccccccCCCCCCcccCcccCCCCCCCCcceeeecccccCCccccccccc-----C------cCCCCCCCC
Q 023000 70 RPDENPHITWENHVNVDCDPSNYDKVTKKRKCPVRGCKEILVFSNTIKCRDCTVDHCLK-----H------RFAPDHSCP 138 (289)
Q Consensus 70 ~~~~~~~~~~~~H~~~~c~~~~~~~~~~~~~C~~~~ck~~~~~~~~~~C~~C~~~fc~~-----h------r~~~~h~C~ 138 (289)
+....|.+|++++.+.+ -+.|+.||..|..+ | -...+|+|.
T Consensus 190 ----~~k~~LreH~r~Hs~eK------------------------vvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~ 241 (467)
T KOG3608|consen 190 ----GNKYRLREHIRTHSNEK------------------------VVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCA 241 (467)
T ss_pred ----ccHHHHHHHHHhcCCCe------------------------EEecchHHHHhccccHHHHHHHhhhhhcCCchHHH
Confidence 34566788988877654 45699999999744 2 124589999
Q ss_pred CCCCCCCccchhhhhc-cCCCCCCCCCCCCCCCCCCccccccccchhhhhhhhcccCccchhhhhhhhhhcCCCCCCCCC
Q 023000 139 GPKKLDTGFAFMSLLN-RSRKEEPKPKQSPATSSTKWTSSFLNAASSFRASAEAGMSKLSNEISQKLQIAKDGAGQSSSS 217 (289)
Q Consensus 139 ~~~~~~~~~~~~a~l~-r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 (289)
.|-|-+.....+..+. |+...+..+-.+- .-..+ +........ . .
T Consensus 242 ~C~KrFaTeklL~~Hv~rHvn~ykCplCdm--------------tc~~~-----------ssL~~H~r~-r--------H 287 (467)
T KOG3608|consen 242 QCFKRFATEKLLKSHVVRHVNCYKCPLCDM--------------TCSSA-----------SSLTTHIRY-R--------H 287 (467)
T ss_pred HHHHHHhHHHHHHHHHHHhhhccccccccc--------------CCCCh-----------HHHHHHHHh-h--------h
Confidence 8877665544443333 3333333332211 00000 001111111 0 1
Q ss_pred CCCCccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccc--cCcccCChhhHHHHHHhhcCCCC
Q 023000 218 GTGGTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPK--CSQGFCDPVALVEHVERDHGGTS 287 (289)
Q Consensus 218 ~~~kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~--C~k~F~~~~~L~~H~~~hh~g~~ 287 (289)
+..|||+|+.|+++|...+.|.+|+. +|+ +. .|.|.. |...|.+..+|++|++.+|.|.+
T Consensus 288 s~dkpfKCd~Cd~~c~~esdL~kH~~-~HS-~~--------~y~C~h~~C~~s~r~~~q~~~H~~evhEg~n 349 (467)
T KOG3608|consen 288 SKDKPFKCDECDTRCVRESDLAKHVQ-VHS-KT--------VYQCEHPDCHYSVRTYTQMRRHFLEVHEGNN 349 (467)
T ss_pred ccCCCccccchhhhhccHHHHHHHHH-hcc-cc--------ceecCCCCCcHHHHHHHHHHHHHHHhccCCC
Confidence 12389999999999999999999988 888 44 699977 99999999999999988886643
No 13
>PHA02768 hypothetical protein; Provisional
Probab=98.77 E-value=2.9e-09 Score=70.99 Aligned_cols=45 Identities=20% Similarity=0.361 Sum_probs=41.4
Q ss_pred ccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHH
Q 023000 222 TELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVE 277 (289)
Q Consensus 222 p~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~ 277 (289)
-|+|++||+.|...++|..|++ +|+ + +|+|..|++.|.+.+.|+.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r-~H~--k--------~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLR-KHN--T--------NLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHH-hcC--C--------cccCCcccceecccceeEE
Confidence 4899999999999999999999 898 7 8999999999999888753
No 14
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.56 E-value=9.5e-08 Score=79.96 Aligned_cols=59 Identities=25% Similarity=0.523 Sum_probs=54.6
Q ss_pred CCCCccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHhhcCC
Q 023000 218 GTGGTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVERDHGG 285 (289)
Q Consensus 218 ~~~kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~hh~g 285 (289)
++...|.|.+|+|.|.....|.+|+. -|...+ .|.|..|||+|.....|.+|+|+|+|-
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~k-ch~~vk--------r~lct~cgkgfndtfdlkrh~rthtgv 171 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLK-CHSDVK--------RHLCTFCGKGFNDTFDLKRHTRTHTGV 171 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhh-hccHHH--------HHHHhhccCcccchhhhhhhhccccCc
Confidence 34568999999999999999999999 999988 899999999999999999999999874
No 15
>PHA00733 hypothetical protein
Probab=98.54 E-value=1.2e-07 Score=75.50 Aligned_cols=54 Identities=30% Similarity=0.615 Sum_probs=49.5
Q ss_pred CCccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHhhcC
Q 023000 220 GGTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 220 ~kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
++||.|+.||+.|.....|..|++ .| +. +|.|++|++.|.....|.+|+...|+
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r-~h--~~--------~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIR-YT--EH--------SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHh-cC--Cc--------CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 479999999999999999999988 66 46 89999999999999999999988775
No 16
>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=98.34 E-value=2.7e-07 Score=59.06 Aligned_cols=39 Identities=38% Similarity=0.943 Sum_probs=28.0
Q ss_pred CCCCCCcceeeecccccCCcccccccccCcCCCCCCCCCCC
Q 023000 101 CPVRGCKEILVFSNTIKCRDCTVDHCLKHRFAPDHSCPGPK 141 (289)
Q Consensus 101 C~~~~ck~~~~~~~~~~C~~C~~~fc~~hr~~~~h~C~~~~ 141 (289)
|++.+|++.+.. ||+|+.|++.||++||++..|.|....
T Consensus 1 C~~~~C~~~~~~--~~~C~~C~~~FC~~Hr~~e~H~C~~~~ 39 (43)
T PF01428_consen 1 CSFPGCKKKDFL--PFKCKHCGKSFCLKHRLPEDHNCSKLQ 39 (43)
T ss_dssp -SSTTT--BCTS--HEE-TTTS-EE-TTTHSTTTCT-SSTT
T ss_pred CccCcCcCccCC--CeECCCCCcccCccccCccccCCcchh
Confidence 677889988763 999999999999999999999998543
No 17
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.18 E-value=2.9e-07 Score=84.62 Aligned_cols=53 Identities=26% Similarity=0.652 Sum_probs=46.2
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccccCCCCCCccccccccc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLRPDENPHITWENHVN 84 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~~~~~~~H~~ 84 (289)
|.|..|...| .|-+.+..|+|+-...-+ |.||+|+|.|....++-.|.+| |.-
T Consensus 268 yiCqLCK~kY-eD~F~LAQHrC~RIV~vE---YrCPEC~KVFsCPANLASHRRW--HKP 320 (500)
T KOG3993|consen 268 YICQLCKEKY-EDAFALAQHRCPRIVHVE---YRCPECDKVFSCPANLASHRRW--HKP 320 (500)
T ss_pred HHHHHHHHhh-hhHHHHhhccCCeeEEee---ecCCcccccccCchhhhhhhcc--cCC
Confidence 8899999999 788889999998776543 8999999999999999999998 643
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.16 E-value=1.1e-06 Score=50.00 Aligned_cols=26 Identities=27% Similarity=0.613 Sum_probs=23.9
Q ss_pred HHHHHHHhhcCCCCCCCCCCCCcccccccCcccCC
Q 023000 237 TLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCD 271 (289)
Q Consensus 237 ~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~ 271 (289)
+|.+|++ +|++++ ||.|++|++.|.+
T Consensus 1 ~l~~H~~-~H~~~k--------~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMR-THTGEK--------PYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHH-HHSSSS--------SEEESSSSEEESS
T ss_pred CHHHHhh-hcCCCC--------CCCCCCCcCeeCc
Confidence 5889999 999999 9999999999974
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.07 E-value=3.9e-06 Score=81.58 Aligned_cols=55 Identities=20% Similarity=0.254 Sum_probs=43.7
Q ss_pred CCCccccCccCcccC----------ChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHhhcC
Q 023000 219 TGGTELCPQCGARFS----------SVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 219 ~~kp~~C~~Cgk~F~----------~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
+++|+.|+.|++.|. ....|..|.. +. |.+ ++.|..||+.|..+. |..|+...|.
T Consensus 501 p~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~-~C-G~r--------t~~C~~Cgk~Vrlrd-m~~H~~~~h~ 565 (567)
T PLN03086 501 PLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHES-IC-GSR--------TAPCDSCGRSVMLKE-MDIHQIAVHQ 565 (567)
T ss_pred CCCceeCCCCCCccccCccccchhhhhhhHHHHHH-hc-CCc--------ceEccccCCeeeehh-HHHHHHHhhc
Confidence 458999999999995 2458999977 54 888 999999999888655 6788765554
No 20
>PHA00732 hypothetical protein
Probab=98.03 E-value=3.6e-06 Score=61.14 Aligned_cols=46 Identities=26% Similarity=0.591 Sum_probs=38.8
Q ss_pred ccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHh
Q 023000 222 TELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVER 281 (289)
Q Consensus 222 p~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~ 281 (289)
||.|+.||+.|.....|..|++..|. ++.|+.|++.|. .|..|+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~-----------~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT-----------LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC-----------CCccCCCCCEeC---Chhhhhcc
Confidence 68999999999999999999872243 578999999998 58888754
No 21
>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=97.97 E-value=1.2e-05 Score=54.03 Aligned_cols=53 Identities=34% Similarity=0.640 Sum_probs=42.7
Q ss_pred ccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHhhcC
Q 023000 222 TELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 222 p~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
.|.||.|++. .....|..|+...|..+. ..+.||+|...+. .+|..|+..+|+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~-------~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSES-------KNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCC-------CCccCCCchhhhh--hHHHHHHHHhcC
Confidence 4899999995 556789999886777653 1699999998755 499999988774
No 22
>PHA00616 hypothetical protein
Probab=97.91 E-value=5.2e-06 Score=52.80 Aligned_cols=34 Identities=21% Similarity=0.312 Sum_probs=30.2
Q ss_pred ccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccc
Q 023000 222 TELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPK 264 (289)
Q Consensus 222 p~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~ 264 (289)
||+|+.||+.|...+.|.+|++ .|+|++ ++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r-~~hg~~--------~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLL-SVHKQN--------KLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHH-HhcCCC--------ccceeE
Confidence 6899999999999999999998 899888 888764
No 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.89 E-value=3.8e-05 Score=74.77 Aligned_cols=51 Identities=18% Similarity=0.300 Sum_probs=42.9
Q ss_pred CccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCC----------hhhHHHHHHhh
Q 023000 221 GTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCD----------PVALVEHVERD 282 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~----------~~~L~~H~~~h 282 (289)
+|+.|+ ||+.+ ....|..|++ +|..++ |+.|+.|++.|.. ...|..|..+.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~-thCp~K--------pi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C 537 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQA-STCPLR--------LITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC 537 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhh-ccCCCC--------ceeCCCCCCccccCccccchhhhhhhHHHHHHhc
Confidence 589999 99765 6689999988 899999 9999999999952 35799998764
No 24
>PHA00616 hypothetical protein
Probab=97.62 E-value=2.9e-05 Score=49.40 Aligned_cols=28 Identities=21% Similarity=0.399 Sum_probs=26.2
Q ss_pred cccccccCcccCChhhHHHHHHhhcCCC
Q 023000 259 VDVCPKCSQGFCDPVALVEHVERDHGGT 286 (289)
Q Consensus 259 p~~C~~C~k~F~~~~~L~~H~~~hh~g~ 286 (289)
||+|+.||+.|....+|+.|++.||+..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~ 28 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQN 28 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCC
Confidence 6999999999999999999999999864
No 25
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=97.59 E-value=3.6e-05 Score=48.06 Aligned_cols=33 Identities=39% Similarity=0.977 Sum_probs=27.1
Q ss_pred CcceeeecccccCCcccccccccCcCCCCCCCCC
Q 023000 106 CKEILVFSNTIKCRDCTVDHCLKHRFAPDHSCPG 139 (289)
Q Consensus 106 ck~~~~~~~~~~C~~C~~~fc~~hr~~~~h~C~~ 139 (289)
|++..... ||+|+.|++.||++||....|.|..
T Consensus 4 C~~~~~l~-~f~C~~C~~~FC~~HR~~e~H~C~~ 36 (39)
T smart00154 4 CRKKVGLT-GFKCRHCGNLFCGEHRLPEDHDCPG 36 (39)
T ss_pred cCCccccc-CeECCccCCccccccCCccccCCcc
Confidence 44443322 9999999999999999999999974
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.56 E-value=4.1e-05 Score=41.88 Aligned_cols=22 Identities=32% Similarity=0.718 Sum_probs=13.7
Q ss_pred ccccccCcccCChhhHHHHHHh
Q 023000 260 DVCPKCSQGFCDPVALVEHVER 281 (289)
Q Consensus 260 ~~C~~C~k~F~~~~~L~~H~~~ 281 (289)
|.|++|++.|.++..|..|++.
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 4566666666666666666654
No 27
>PHA02768 hypothetical protein; Provisional
Probab=97.47 E-value=6.2e-05 Score=50.30 Aligned_cols=25 Identities=16% Similarity=0.526 Sum_probs=24.0
Q ss_pred cccccccCcccCChhhHHHHHHhhc
Q 023000 259 VDVCPKCSQGFCDPVALVEHVERDH 283 (289)
Q Consensus 259 p~~C~~C~k~F~~~~~L~~H~~~hh 283 (289)
-|+|+.||+.|++.++|..|+++|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC
Confidence 5999999999999999999999998
No 28
>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=97.32 E-value=0.00013 Score=39.80 Aligned_cols=24 Identities=29% Similarity=0.645 Sum_probs=15.4
Q ss_pred ccccccCcccCChhhHHHHHHhhc
Q 023000 260 DVCPKCSQGFCDPVALVEHVERDH 283 (289)
Q Consensus 260 ~~C~~C~k~F~~~~~L~~H~~~hh 283 (289)
|.|++|++.|.+...|..|+++||
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 467777777777777777776654
No 29
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.29 E-value=0.00011 Score=41.81 Aligned_cols=26 Identities=27% Similarity=0.416 Sum_probs=17.0
Q ss_pred cccccccCcccCChhhHHHHHHhhcC
Q 023000 259 VDVCPKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 259 p~~C~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
||+|..|++.|.....|..|++.|+.
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 46666777777777777777665543
No 30
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.24 E-value=0.00015 Score=67.04 Aligned_cols=62 Identities=23% Similarity=0.387 Sum_probs=48.6
Q ss_pred ccccCccCcccCChHHHHHHHHhhcC--------CCCC-CCC----------------CCCCcccccccCcccCChhhHH
Q 023000 222 TELCPQCGARFSSVTTLIEHVEKIHD--------RSGN-QAR----------------PKVTVDVCPKCSQGFCDPVALV 276 (289)
Q Consensus 222 p~~C~~Cgk~F~~~~~L~~H~~~~h~--------~~k~-~~~----------------~~~~p~~C~~C~k~F~~~~~L~ 276 (289)
-|.|++|+|.|+-..+|..|.| -|. +..+ ... +..+.|.|.+|+|.|.+...|+
T Consensus 295 EYrCPEC~KVFsCPANLASHRR-WHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLr 373 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRR-WHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLR 373 (500)
T ss_pred eecCCcccccccCchhhhhhhc-ccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHH
Confidence 4899999999999999999977 452 1111 000 1245799999999999999999
Q ss_pred HHHHhhcC
Q 023000 277 EHVERDHG 284 (289)
Q Consensus 277 ~H~~~hh~ 284 (289)
.|+.+|+.
T Consensus 374 KHqlthq~ 381 (500)
T KOG3993|consen 374 KHQLTHQR 381 (500)
T ss_pred HhHHhhhc
Confidence 99888874
No 31
>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=97.21 E-value=0.00021 Score=38.98 Aligned_cols=23 Identities=43% Similarity=0.804 Sum_probs=21.2
Q ss_pred cccCccCcccCChHHHHHHHHhhc
Q 023000 223 ELCPQCGARFSSVTTLIEHVEKIH 246 (289)
Q Consensus 223 ~~C~~Cgk~F~~~~~L~~H~~~~h 246 (289)
|.|+.|++.|.....|.+|++ .|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~-~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR-RH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH-HH
T ss_pred CCCCCCCCccCCHHHHHHHHh-HC
Confidence 689999999999999999998 54
No 32
>PHA00733 hypothetical protein
Probab=97.00 E-value=0.00035 Score=55.58 Aligned_cols=55 Identities=18% Similarity=0.210 Sum_probs=44.2
Q ss_pred CCccccCccCcccCChHHHHHH--HH--hhcCCCCCCCCCCCCcccccccCcccCChhhHHHHHHhh
Q 023000 220 GGTELCPQCGARFSSVTTLIEH--VE--KIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHVERD 282 (289)
Q Consensus 220 ~kp~~C~~Cgk~F~~~~~L~~H--~~--~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~h 282 (289)
.+++.|.+|.+.|.....|..+ ++ ..+.+.+ ||.|+.|++.|....+|..|++.+
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~k--------Py~C~~Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVS--------PYVCPLCLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCC--------CccCCCCCCcCCCHHHHHHHHhcC
Confidence 4789999999999888777766 22 0223466 999999999999999999999864
No 33
>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=96.51 E-value=0.0016 Score=36.87 Aligned_cols=25 Identities=40% Similarity=0.662 Sum_probs=22.8
Q ss_pred ccccCccCcccCChHHHHHHHHhhcC
Q 023000 222 TELCPQCGARFSSVTTLIEHVEKIHD 247 (289)
Q Consensus 222 p~~C~~Cgk~F~~~~~L~~H~~~~h~ 247 (289)
||+|..|++.|.....|..|++ .|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~-~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKR-SHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHC-TTT
T ss_pred CCCCCccCCccCChhHHHHHhH-Hhc
Confidence 6899999999999999999987 664
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.50 E-value=0.0008 Score=60.25 Aligned_cols=61 Identities=20% Similarity=0.336 Sum_probs=45.9
Q ss_pred CCCccccCc--cCcccCChHHHHHHHHhhcCCC----CCC------CCCCCCcccccccCcccCChhhHHHHH
Q 023000 219 TGGTELCPQ--CGARFSSVTTLIEHVEKIHDRS----GNQ------ARPKVTVDVCPKCSQGFCDPVALVEHV 279 (289)
Q Consensus 219 ~~kp~~C~~--Cgk~F~~~~~L~~H~~~~h~~~----k~~------~~~~~~p~~C~~C~k~F~~~~~L~~H~ 279 (289)
++|||+|++ |.|+|+..-.|+-|+.--|... .|. -.+..+||.|++|+|++.....|+.|.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 359999987 9999999999999965223111 000 012456999999999999999999887
No 35
>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=96.35 E-value=0.003 Score=34.22 Aligned_cols=23 Identities=39% Similarity=0.791 Sum_probs=19.1
Q ss_pred cccCccCcccCChHHHHHHHHhhc
Q 023000 223 ELCPQCGARFSSVTTLIEHVEKIH 246 (289)
Q Consensus 223 ~~C~~Cgk~F~~~~~L~~H~~~~h 246 (289)
|.|++|++.|.....|..|++ .|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~-~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR-TH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH-HH
T ss_pred CCCcCCCCcCCcHHHHHHHHH-hh
Confidence 689999999999999999998 54
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.25 E-value=0.0042 Score=34.09 Aligned_cols=23 Identities=35% Similarity=0.655 Sum_probs=13.1
Q ss_pred ccccccCcccCChhhHHHHHHhh
Q 023000 260 DVCPKCSQGFCDPVALVEHVERD 282 (289)
Q Consensus 260 ~~C~~C~k~F~~~~~L~~H~~~h 282 (289)
|.|+.|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 34555666666666666665533
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.24 E-value=0.0024 Score=47.64 Aligned_cols=59 Identities=36% Similarity=0.569 Sum_probs=21.1
Q ss_pred ccCccCcccCChHHHHHHHHhhcCCCCCC-------CC------CCCC-cccccccCcccCChhhHHHHHHhh
Q 023000 224 LCPQCGARFSSVTTLIEHVEKIHDRSGNQ-------AR------PKVT-VDVCPKCSQGFCDPVALVEHVERD 282 (289)
Q Consensus 224 ~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~-------~~------~~~~-p~~C~~C~k~F~~~~~L~~H~~~h 282 (289)
+|..|+..|.....|..|+...|.-..+. .. ..+. .+.|.+|++.|.....|..||+.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 58999999999999999997556422110 00 0122 589999999999999999999864
No 38
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.12 E-value=0.0025 Score=41.65 Aligned_cols=26 Identities=27% Similarity=0.424 Sum_probs=17.4
Q ss_pred cccccccCcccCChhhHHHHHHhhcC
Q 023000 259 VDVCPKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 259 p~~C~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
|-.|++|+..+++..+|++|++++|+
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred CCCCCcchhhccchhhHHHHHHHHhc
Confidence 77788888888888888888877765
No 39
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=95.84 E-value=0.01 Score=48.76 Aligned_cols=122 Identities=18% Similarity=0.160 Sum_probs=67.1
Q ss_pred CCCCcccccccCCccCcccccCCCccccccCCCC------CC-CcceeecCCCCCCccccC-CCCCCccccccccccCCC
Q 023000 17 DCKQIDFLPFTCDCCHKVFCLDHRSYNQHQCPKA------ER-HDVTVVICPLCAKGVRLR-PDENPHITWENHVNVDCD 88 (289)
Q Consensus 17 ~C~~~dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~------~~-~~~~~~~Cp~C~k~~~~~-~~~~~~~~~~~H~~~~c~ 88 (289)
.|-..-=||++|+.|.|.|+.++...--+.+.-. .. ....++++-.|.-.+... ++.......++=++ .
T Consensus 5 s~~~~~~lP~r~~~~~kv~s~~~~~~~~~~f~~~i~~~~r~~i~k~~~~~~~~~~p~i~~~~~~~~~~~~~k~s~~---~ 81 (162)
T COG3582 5 SRVSETRLPSRGNITAKVSSTDNSLTLFSPFKLFIQLCDRKKIKKPDPGQAMKCLPLISSAVSNPSNTDTPKRSTR---V 81 (162)
T ss_pred ccceeccCCccccceeeeccCccccccccccchhhhhhhhhccccCCCcchhhhcceEEEEeeccccccCcccccc---c
Confidence 3445556999999999999999887777766553 11 112344455454444321 11111111111110 0
Q ss_pred CCCcccCccc---CCCCCCCCcceeeecccccCCcccccccccCcCCCCCCCCCCCC
Q 023000 89 PSNYDKVTKK---RKCPVRGCKEILVFSNTIKCRDCTVDHCLKHRFAPDHSCPGPKK 142 (289)
Q Consensus 89 ~~~~~~~~~~---~~C~~~~ck~~~~~~~~~~C~~C~~~fc~~hr~~~~h~C~~~~~ 142 (289)
+.+....... ..|....|.-+.... +++|+.|+-.||..|+++..|.|.....
T Consensus 82 ~~~~~~~~~~~~t~~~a~~~~~g~~s~l-~~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 82 PLNGPFDSGKGITDRCATPQCTGKGSTL-AGKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred ccccccccccccceeeecceeccCCccc-cccccCCCCcceeceecccccccccHHH
Confidence 1111111111 134443333222222 8999999999999999999999986444
No 40
>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=95.83 E-value=0.0038 Score=35.18 Aligned_cols=16 Identities=38% Similarity=0.777 Sum_probs=14.0
Q ss_pred CCCccccCccCcccCC
Q 023000 219 TGGTELCPQCGARFSS 234 (289)
Q Consensus 219 ~~kp~~C~~Cgk~F~~ 234 (289)
+++||.|++|+++|..
T Consensus 11 ~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 11 GEKPYKCPYCGKSFSN 26 (26)
T ss_dssp SSSSEEESSSSEEESS
T ss_pred CCCCCCCCCCcCeeCc
Confidence 5599999999999963
No 41
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.56 E-value=0.013 Score=32.02 Aligned_cols=24 Identities=42% Similarity=0.843 Sum_probs=21.8
Q ss_pred cccCccCcccCChHHHHHHHHhhcC
Q 023000 223 ELCPQCGARFSSVTTLIEHVEKIHD 247 (289)
Q Consensus 223 ~~C~~Cgk~F~~~~~L~~H~~~~h~ 247 (289)
|+|+.|++.|.....|..|++ .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhc
Confidence 679999999999999999988 765
No 42
>PHA00732 hypothetical protein
Probab=95.11 E-value=0.015 Score=42.24 Aligned_cols=26 Identities=31% Similarity=0.525 Sum_probs=22.9
Q ss_pred cccccccCcccCChhhHHHHHHhhcC
Q 023000 259 VDVCPKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 259 p~~C~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
||.|+.|++.|.+..+|..|++.+|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~ 26 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT 26 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC
Confidence 68999999999999999999985443
No 43
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=95.03 E-value=0.009 Score=51.62 Aligned_cols=40 Identities=35% Similarity=0.808 Sum_probs=35.0
Q ss_pred CCCCCCCCcceeeecccccCCcccccccccCcCCCCCCCCCC
Q 023000 99 RKCPVRGCKEILVFSNTIKCRDCTVDHCLKHRFAPDHSCPGP 140 (289)
Q Consensus 99 ~~C~~~~ck~~~~~~~~~~C~~C~~~fc~~hr~~~~h~C~~~ 140 (289)
..|+..-|++.... ||+|+-|+.-||+.||....|.|+..
T Consensus 9 kHCs~~~CkqlDFL--Pf~Cd~C~~~FC~eHrsye~H~Cp~~ 48 (250)
T KOG3183|consen 9 KHCSVPYCKQLDFL--PFKCDGCSGIFCLEHRSYESHHCPKG 48 (250)
T ss_pred cccCcchhhhcccc--ceeeCCccchhhhccchHhhcCCCcc
Confidence 46888889988654 99999999999999999999999863
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.93 E-value=0.017 Score=31.61 Aligned_cols=23 Identities=35% Similarity=0.673 Sum_probs=12.8
Q ss_pred ccccccCcccCChhhHHHHHHhhc
Q 023000 260 DVCPKCSQGFCDPVALVEHVERDH 283 (289)
Q Consensus 260 ~~C~~C~k~F~~~~~L~~H~~~hh 283 (289)
|+|+.|+.... ...|.+|++++|
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 45666666555 666666666655
No 45
>PRK04860 hypothetical protein; Provisional
Probab=94.87 E-value=0.012 Score=48.52 Aligned_cols=40 Identities=18% Similarity=0.280 Sum_probs=34.6
Q ss_pred CccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChh
Q 023000 221 GTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPV 273 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~ 273 (289)
-+|.|. |++ ....+.+|.+ +|++++ +|.|..|++.|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~r-i~~g~~--------~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNR-VVRGEA--------VYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHH-HhcCCc--------cEECCCCCceeEEec
Confidence 479998 998 6667899999 999999 999999999887543
No 46
>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=94.39 E-value=0.037 Score=36.23 Aligned_cols=31 Identities=29% Similarity=0.524 Sum_probs=22.3
Q ss_pred CCCccccCccCcccCChHHHHHHHHhhcCCCC
Q 023000 219 TGGTELCPQCGARFSSVTTLIEHVEKIHDRSG 250 (289)
Q Consensus 219 ~~kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k 250 (289)
.+.|..|++|+..+.+..+|.+|+. .+.+.+
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle-~~H~~k 51 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLE-IRHFKK 51 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHH-HHTTTS
T ss_pred cCCCCCCCcchhhccchhhHHHHHH-HHhccc
Confidence 3479999999999999999999998 666665
No 47
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.35 E-value=0.022 Score=31.40 Aligned_cols=21 Identities=24% Similarity=0.561 Sum_probs=13.1
Q ss_pred ccccccCcccCChhhHHHHHH
Q 023000 260 DVCPKCSQGFCDPVALVEHVE 280 (289)
Q Consensus 260 ~~C~~C~k~F~~~~~L~~H~~ 280 (289)
|.|.+|++.|.....|..|++
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 456666666666666666664
No 48
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=93.70 E-value=0.05 Score=49.03 Aligned_cols=54 Identities=22% Similarity=0.439 Sum_probs=34.9
Q ss_pred ccccccCCc--cCcccccC----------CCccccccCCCCCCCc-----ceeecCCCCCCccccCCCCCC
Q 023000 22 DFLPFTCDC--CHKVFCLD----------HRSYNQHQCPKAERHD-----VTVVICPLCAKGVRLRPDENP 75 (289)
Q Consensus 22 dfLPf~C~~--C~k~Fc~~----------h~~~~~H~c~~~~~~~-----~~~~~Cp~C~k~~~~~~~~~~ 75 (289)
|-.||+|+. |+|.|-.. |-..+.|.-+.....+ .+||.|++|+|.+.-.-+++-
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCcccee
Confidence 458999986 99999544 3333333333332221 489999999998875555443
No 49
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.10 E-value=0.058 Score=29.65 Aligned_cols=21 Identities=33% Similarity=0.624 Sum_probs=19.8
Q ss_pred cccCccCcccCChHHHHHHHH
Q 023000 223 ELCPQCGARFSSVTTLIEHVE 243 (289)
Q Consensus 223 ~~C~~Cgk~F~~~~~L~~H~~ 243 (289)
|.|..|++.|.....|..|++
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 679999999999999999987
No 50
>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=92.81 E-value=0.038 Score=31.21 Aligned_cols=21 Identities=24% Similarity=0.505 Sum_probs=15.5
Q ss_pred ccccccCcccCChhhHHHHHH
Q 023000 260 DVCPKCSQGFCDPVALVEHVE 280 (289)
Q Consensus 260 ~~C~~C~k~F~~~~~L~~H~~ 280 (289)
|.|..|++.|.+..+|..|++
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 667777777777777777764
No 51
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.19 E-value=0.12 Score=28.78 Aligned_cols=20 Identities=35% Similarity=0.775 Sum_probs=11.3
Q ss_pred ccccccCcccCChhhHHHHHH
Q 023000 260 DVCPKCSQGFCDPVALVEHVE 280 (289)
Q Consensus 260 ~~C~~C~k~F~~~~~L~~H~~ 280 (289)
..|+.||+.| ....|.+|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3466666666 4555556653
No 52
>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=90.66 E-value=0.15 Score=28.70 Aligned_cols=10 Identities=40% Similarity=0.966 Sum_probs=7.6
Q ss_pred cCCCCCCccc
Q 023000 59 ICPLCAKGVR 68 (289)
Q Consensus 59 ~Cp~C~k~~~ 68 (289)
.||.|++.++
T Consensus 2 ~CP~C~~~V~ 11 (26)
T PF10571_consen 2 TCPECGAEVP 11 (26)
T ss_pred cCCCCcCCch
Confidence 4888888774
No 53
>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=90.60 E-value=0.092 Score=32.18 Aligned_cols=13 Identities=31% Similarity=0.858 Sum_probs=10.4
Q ss_pred ecCCCCCCccccC
Q 023000 58 VICPLCAKGVRLR 70 (289)
Q Consensus 58 ~~Cp~C~k~~~~~ 70 (289)
+.||.|+..|...
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 6799999988754
No 54
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=90.41 E-value=0.19 Score=27.30 Aligned_cols=20 Identities=30% Similarity=0.610 Sum_probs=16.6
Q ss_pred cccCccCcccCChHHHHHHHH
Q 023000 223 ELCPQCGARFSSVTTLIEHVE 243 (289)
Q Consensus 223 ~~C~~Cgk~F~~~~~L~~H~~ 243 (289)
|.|+.|+.... ...|.+|++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~ 20 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLK 20 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHH
Confidence 68999999988 899999998
No 55
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=90.32 E-value=0.13 Score=34.78 Aligned_cols=10 Identities=30% Similarity=0.830 Sum_probs=8.1
Q ss_pred ccccCCcccc
Q 023000 114 NTIKCRDCTV 123 (289)
Q Consensus 114 ~~~~C~~C~~ 123 (289)
++|+|++||-
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 4899999983
No 56
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=90.10 E-value=0.27 Score=27.32 Aligned_cols=20 Identities=35% Similarity=0.781 Sum_probs=17.1
Q ss_pred cccCccCcccCChHHHHHHHH
Q 023000 223 ELCPQCGARFSSVTTLIEHVE 243 (289)
Q Consensus 223 ~~C~~Cgk~F~~~~~L~~H~~ 243 (289)
..|+.||+.| ....|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4799999999 6778999975
No 57
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=90.02 E-value=0.15 Score=31.10 Aligned_cols=13 Identities=23% Similarity=0.774 Sum_probs=10.2
Q ss_pred ecCCCCCCccccC
Q 023000 58 VICPLCAKGVRLR 70 (289)
Q Consensus 58 ~~Cp~C~k~~~~~ 70 (289)
+.||.|+..|...
T Consensus 3 i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 3 ITCPNCQAKYEID 15 (36)
T ss_pred EECCCCCCEEeCC
Confidence 5799999988754
No 58
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=89.88 E-value=0.14 Score=34.65 Aligned_cols=9 Identities=33% Similarity=1.014 Sum_probs=7.9
Q ss_pred ccccCCccc
Q 023000 114 NTIKCRDCT 122 (289)
Q Consensus 114 ~~~~C~~C~ 122 (289)
++|+|++||
T Consensus 49 ~~Y~Cp~CG 57 (61)
T COG2888 49 NPYRCPKCG 57 (61)
T ss_pred CceECCCcC
Confidence 499999998
No 59
>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=89.85 E-value=0.24 Score=29.43 Aligned_cols=22 Identities=23% Similarity=0.508 Sum_probs=18.7
Q ss_pred cccccccCcccCChhhHHHHHH
Q 023000 259 VDVCPKCSQGFCDPVALVEHVE 280 (289)
Q Consensus 259 p~~C~~C~k~F~~~~~L~~H~~ 280 (289)
+|.|.+|++.|....++..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 6889999999998888888874
No 60
>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=89.75 E-value=0.19 Score=38.66 Aligned_cols=30 Identities=27% Similarity=0.709 Sum_probs=22.0
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccccC
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLR 70 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~ 70 (289)
..|..||+.| |. -+..|.+||.||..|...
T Consensus 10 R~Cp~CG~kF------YD---------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKF------YD---------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchh------cc---------CCCCCccCCCCCCccCcc
Confidence 4699999999 22 122567899999999754
No 61
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.55 E-value=0.23 Score=30.23 Aligned_cols=33 Identities=24% Similarity=0.591 Sum_probs=22.6
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGV 67 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~ 67 (289)
+.|+.|+..|-.+ +-+-+..+ +...|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~-----d~~ip~~g----~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEID-----DEKIPPKG----RKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCC-----HHHCCCCC----cEEECCCCCCEe
Confidence 6899999999433 33323222 458999999877
No 62
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.10 E-value=0.17 Score=31.02 Aligned_cols=13 Identities=31% Similarity=0.889 Sum_probs=10.6
Q ss_pred ecCCCCCCccccC
Q 023000 58 VICPLCAKGVRLR 70 (289)
Q Consensus 58 ~~Cp~C~k~~~~~ 70 (289)
..||.|+..|.+.
T Consensus 3 i~CP~C~~~f~v~ 15 (37)
T PF13719_consen 3 ITCPNCQTRFRVP 15 (37)
T ss_pred EECCCCCceEEcC
Confidence 5799999999754
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=88.96 E-value=0.62 Score=35.96 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=22.3
Q ss_pred cccCCccccccccc---CcCCCCCCCCCCC
Q 023000 115 TIKCRDCTVDHCLK---HRFAPDHSCPGPK 141 (289)
Q Consensus 115 ~~~C~~C~~~fc~~---hr~~~~h~C~~~~ 141 (289)
.|.|+.|.+.||+. --++.-|+|+.|.
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred ceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 78999999999855 5667889998765
No 64
>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=88.57 E-value=0.17 Score=28.46 Aligned_cols=21 Identities=33% Similarity=0.611 Sum_probs=19.4
Q ss_pred cccCccCcccCChHHHHHHHH
Q 023000 223 ELCPQCGARFSSVTTLIEHVE 243 (289)
Q Consensus 223 ~~C~~Cgk~F~~~~~L~~H~~ 243 (289)
|.|..|++.|.....|..|++
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 789999999999999998876
No 65
>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=88.04 E-value=0.29 Score=37.61 Aligned_cols=13 Identities=23% Similarity=0.542 Sum_probs=10.3
Q ss_pred cccCCcccccccc
Q 023000 115 TIKCRDCTVDHCL 127 (289)
Q Consensus 115 ~~~C~~C~~~fc~ 127 (289)
|++|++||..|-+
T Consensus 26 PivCP~CG~~~~~ 38 (108)
T PF09538_consen 26 PIVCPKCGTEFPP 38 (108)
T ss_pred CccCCCCCCccCc
Confidence 8888888888843
No 66
>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=86.80 E-value=0.41 Score=31.56 Aligned_cols=27 Identities=26% Similarity=0.760 Sum_probs=17.0
Q ss_pred cccCCccccccccc---CcCCCCCCCCCCC
Q 023000 115 TIKCRDCTVDHCLK---HRFAPDHSCPGPK 141 (289)
Q Consensus 115 ~~~C~~C~~~fc~~---hr~~~~h~C~~~~ 141 (289)
.|.|+.|++.||+. .-++.-|+|+.|.
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred eEECCCCCCccccCcChhhhccccCCcCCC
Confidence 79999999999865 7788889999763
No 67
>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=86.58 E-value=0.78 Score=30.44 Aligned_cols=28 Identities=43% Similarity=0.822 Sum_probs=22.3
Q ss_pred cccccccCcccCChhhHHHHHHhhcCCCC
Q 023000 259 VDVCPKCSQGFCDPVALVEHVERDHGGTS 287 (289)
Q Consensus 259 p~~C~~C~k~F~~~~~L~~H~~~hh~g~~ 287 (289)
.|.||.|++.| +...|..|....|....
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~~H~~~~ 29 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCEDEHRSES 29 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHhHCcCCC
Confidence 58999999954 56789999988776543
No 68
>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=84.68 E-value=0.83 Score=27.04 Aligned_cols=11 Identities=36% Similarity=0.745 Sum_probs=7.8
Q ss_pred ecCCCCCCccc
Q 023000 58 VICPLCAKGVR 68 (289)
Q Consensus 58 ~~Cp~C~k~~~ 68 (289)
|+|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 67888888774
No 69
>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=84.61 E-value=0.68 Score=28.55 Aligned_cols=31 Identities=26% Similarity=0.697 Sum_probs=19.8
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGV 67 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~ 67 (289)
|+|..||+.|-..... . +.....||.||..+
T Consensus 6 y~C~~Cg~~fe~~~~~------~-----~~~~~~CP~Cg~~~ 36 (41)
T smart00834 6 YRCEDCGHTFEVLQKI------S-----DDPLATCPECGGDV 36 (41)
T ss_pred EEcCCCCCEEEEEEec------C-----CCCCCCCCCCCCcc
Confidence 7999999999433211 0 01235799999854
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=84.15 E-value=0.77 Score=29.38 Aligned_cols=32 Identities=28% Similarity=0.618 Sum_probs=22.7
Q ss_pred ccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcccc
Q 023000 24 LPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRL 69 (289)
Q Consensus 24 LPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~ 69 (289)
+.|+|+.||..|-.+-.. ....||.||..+-.
T Consensus 2 ~~y~C~~CG~~~~~~~~~--------------~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 2 AEYKCARCGREVELDEYG--------------TGVRCPYCGYRILF 33 (46)
T ss_pred CEEECCCCCCEEEECCCC--------------CceECCCCCCeEEE
Confidence 579999999999443211 13689999987754
No 71
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=83.71 E-value=0.25 Score=46.03 Aligned_cols=56 Identities=25% Similarity=0.352 Sum_probs=50.3
Q ss_pred CccccCccCcccCChHHHHHHHHh-hcCCC--CCCCCCCCCccccc--ccCcccCChhhHHHHHHhhcC
Q 023000 221 GTELCPQCGARFSSVTTLIEHVEK-IHDRS--GNQARPKVTVDVCP--KCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~~-~h~~~--k~~~~~~~~p~~C~--~C~k~F~~~~~L~~H~~~hh~ 284 (289)
.++.|..|...|.....|..|.+. .|.++ + |+.|+ .|++.|.+...|..|..+|.+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~--------~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 348 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLK--------PFSCPYSLCGKLFSRNDALKRHILLHTS 348 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCC--------ceeeeccCCCccccccccccCCcccccC
Confidence 478999999999999999999874 58888 8 99999 799999999999999977764
No 72
>PHA00626 hypothetical protein
Probab=82.89 E-value=0.83 Score=30.51 Aligned_cols=14 Identities=21% Similarity=0.565 Sum_probs=11.7
Q ss_pred ccccCCcccccccc
Q 023000 114 NTIKCRDCTVDHCL 127 (289)
Q Consensus 114 ~~~~C~~C~~~fc~ 127 (289)
+.|+|+.||..|..
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 38999999999953
No 73
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=82.87 E-value=1 Score=48.14 Aligned_cols=63 Identities=22% Similarity=0.251 Sum_probs=49.9
Q ss_pred CCCccccCccCcccCChHHHHHHHHhhcCCCC----------------CCCCCCCCcccccccCcccCChhhHHHHHHh
Q 023000 219 TGGTELCPQCGARFSSVTTLIEHVEKIHDRSG----------------NQARPKVTVDVCPKCSQGFCDPVALVEHVER 281 (289)
Q Consensus 219 ~~kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k----------------~~~~~~~~p~~C~~C~k~F~~~~~L~~H~~~ 281 (289)
-.+.|.|+.|+-.|.....|..|+|..|.... ..-..+.+||.|..|...++...+|..|+..
T Consensus 462 ~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 462 FFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 34789999999999999999999995443211 1112357799999999999999999999863
No 74
>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=82.78 E-value=1 Score=26.56 Aligned_cols=22 Identities=18% Similarity=0.489 Sum_probs=20.2
Q ss_pred ccccCccCcccCChHHHHHHHH
Q 023000 222 TELCPQCGARFSSVTTLIEHVE 243 (289)
Q Consensus 222 p~~C~~Cgk~F~~~~~L~~H~~ 243 (289)
+|.|..|++.|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 6899999999999999999976
No 75
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=82.46 E-value=1.2 Score=30.82 Aligned_cols=39 Identities=26% Similarity=0.841 Sum_probs=33.0
Q ss_pred CcccCcCCcCCCCCcccccccCCccCcccccCCCcc-ccccC
Q 023000 7 PDLGKHCSLPDCKQIDFLPFTCDCCHKVFCLDHRSY-NQHQC 47 (289)
Q Consensus 7 ~~~g~~C~~~~C~~~dfLPf~C~~C~k~Fc~~h~~~-~~H~c 47 (289)
.+....|...+|+.+.|+ +|..|.|.+|-+|.-. +.|.|
T Consensus 24 ~~~~~~C~~~gC~~~s~I--~C~~Ckk~~Cf~Hfiv~~~H~C 63 (63)
T PF04236_consen 24 KNVAGDCDITGCNNTSFI--RCAYCKKSLCFNHFIVSEYHLC 63 (63)
T ss_pred CCCcCcCCCCCCCCcCEE--EccccCCcccccceeeeeeEcC
Confidence 456678999999999995 8999999999999885 56765
No 76
>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=82.35 E-value=0.83 Score=27.10 Aligned_cols=24 Identities=21% Similarity=0.825 Sum_probs=16.4
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCC
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAK 65 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k 65 (289)
|+|..||-.+-.+. .+..||+||-
T Consensus 2 ~~C~~CGy~y~~~~----------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE----------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc----------------CCCcCcCCCC
Confidence 67888887773222 2357999986
No 77
>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=82.13 E-value=0.81 Score=35.97 Aligned_cols=29 Identities=14% Similarity=0.266 Sum_probs=21.2
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcccc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRL 69 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~ 69 (289)
..|+.||+.| +. -+..|.+||.||..|..
T Consensus 10 r~Cp~cg~kF------YD---------Lnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 10 RICPNTGSKF------YD---------LNRRPAVSPYTGEQFPP 38 (129)
T ss_pred ccCCCcCccc------cc---------cCCCCccCCCcCCccCc
Confidence 4689999999 21 12356899999998864
No 78
>PRK04023 DNA polymerase II large subunit; Validated
Probab=80.82 E-value=1.4 Score=45.88 Aligned_cols=11 Identities=18% Similarity=0.262 Sum_probs=6.2
Q ss_pred cCChhhHHHHH
Q 023000 269 FCDPVALVEHV 279 (289)
Q Consensus 269 F~~~~~L~~H~ 279 (289)
......|+.|+
T Consensus 823 ~~~~eDLiGhL 833 (1121)
T PRK04023 823 VEKREDLIGHL 833 (1121)
T ss_pred CCChhhcccce
Confidence 34556666665
No 79
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=80.79 E-value=1.3 Score=28.25 Aligned_cols=10 Identities=30% Similarity=0.723 Sum_probs=5.6
Q ss_pred ecCCCCCCcc
Q 023000 58 VICPLCAKGV 67 (289)
Q Consensus 58 ~~Cp~C~k~~ 67 (289)
|.|..||..|
T Consensus 3 Y~C~~Cg~~~ 12 (44)
T smart00659 3 YICGECGREN 12 (44)
T ss_pred EECCCCCCEe
Confidence 5555555544
No 80
>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=80.76 E-value=0.7 Score=30.47 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=14.7
Q ss_pred cccccCCccCcccccC---CCccccccCCC
Q 023000 23 FLPFTCDCCHKVFCLD---HRSYNQHQCPK 49 (289)
Q Consensus 23 fLPf~C~~C~k~Fc~~---h~~~~~H~c~~ 49 (289)
-..|+|+.|++.||.+ -.++.-|+|+-
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~CPG 48 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHNCPG 48 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-SSST
T ss_pred CCeEECCCCCCccccCcChhhhccccCCcC
Confidence 3679999999999988 33377777764
No 81
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=80.35 E-value=1.2 Score=38.62 Aligned_cols=23 Identities=22% Similarity=0.556 Sum_probs=16.6
Q ss_pred eecCCCCCCccccCCCCCCcccc
Q 023000 57 VVICPLCAKGVRLRPDENPHITW 79 (289)
Q Consensus 57 ~~~Cp~C~k~~~~~~~~~~~~~~ 79 (289)
.++||+|++.|.........+++
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceE
Confidence 47899999999866555555544
No 82
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=79.93 E-value=1.4 Score=29.80 Aligned_cols=33 Identities=30% Similarity=0.671 Sum_probs=16.9
Q ss_pred cccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCC
Q 023000 23 FLPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCA 64 (289)
Q Consensus 23 fLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~ 64 (289)
+--|.|+.||+.- -.+-.+|-+.+ .+|+||.||
T Consensus 25 ~v~F~CPnCGe~~-----I~Rc~~CRk~g----~~Y~Cp~CG 57 (61)
T COG2888 25 AVKFPCPNCGEVE-----IYRCAKCRKLG----NPYRCPKCG 57 (61)
T ss_pred eeEeeCCCCCcee-----eehhhhHHHcC----CceECCCcC
Confidence 3446777776432 12222233322 358888887
No 83
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=79.90 E-value=0.93 Score=37.33 Aligned_cols=37 Identities=24% Similarity=0.463 Sum_probs=32.0
Q ss_pred CCCCcccccccCCccCcccccCCCccccccCCCCCCC
Q 023000 17 DCKQIDFLPFTCDCCHKVFCLDHRSYNQHQCPKAERH 53 (289)
Q Consensus 17 ~C~~~dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~ 53 (289)
-|..-.-||++|+.|+-.||.+|+....|-|.-..+.
T Consensus 102 ~~g~~s~l~~~c~~c~g~fc~~h~lp~nhdc~~L~s~ 138 (162)
T COG3582 102 CTGKGSTLAGKCNYCTGYFCAEHRLPENHDCNGLGSL 138 (162)
T ss_pred eccCCccccccccCCCCcceeceecccccccccHHHh
Confidence 4556678999999999999999999999999876653
No 84
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=79.58 E-value=1 Score=30.09 Aligned_cols=29 Identities=34% Similarity=0.621 Sum_probs=24.4
Q ss_pred CCCccccCccCcccCChHHHHHHHHhhcC
Q 023000 219 TGGTELCPQCGARFSSVTTLIEHVEKIHD 247 (289)
Q Consensus 219 ~~kp~~C~~Cgk~F~~~~~L~~H~~~~h~ 247 (289)
||.-+.|+-||..|.......+|+...|.
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 56788999999999999999999885553
No 85
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=79.14 E-value=1.1 Score=37.22 Aligned_cols=38 Identities=32% Similarity=0.666 Sum_probs=30.6
Q ss_pred cCCcCCCCCcccccccCCccCcccccCCCccccccCCCCC
Q 023000 12 HCSLPDCKQIDFLPFTCDCCHKVFCLDHRSYNQHQCPKAE 51 (289)
Q Consensus 12 ~C~~~~C~~~dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~ 51 (289)
+|..-. ++++...|.|. ||..||..|+..+.|.|.-..
T Consensus 107 rC~~C~-kk~gltgf~Cr-CG~~fC~~HRy~e~H~C~fDy 144 (167)
T KOG3173|consen 107 RCFKCR-KKVGLTGFKCR-CGNTFCGTHRYPEQHDCSFDY 144 (167)
T ss_pred hhhhhh-hhhcccccccc-cCCcccccccCCccccccccH
Confidence 355333 67788899995 999999999999999997554
No 86
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=78.08 E-value=0.96 Score=30.18 Aligned_cols=26 Identities=31% Similarity=0.691 Sum_probs=23.0
Q ss_pred cccccccCcccCChhhHHHHHHhhcC
Q 023000 259 VDVCPKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 259 p~~C~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
-+.||.|+..|...-..++|+..-|+
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 89999999999999999999866553
No 87
>PRK04860 hypothetical protein; Provisional
Probab=76.30 E-value=1.1 Score=37.02 Aligned_cols=13 Identities=23% Similarity=0.680 Sum_probs=10.3
Q ss_pred cccCCcccccccc
Q 023000 115 TIKCRDCTVDHCL 127 (289)
Q Consensus 115 ~~~C~~C~~~fc~ 127 (289)
+|.|..|++.|..
T Consensus 143 ~YrC~~C~~~l~~ 155 (160)
T PRK04860 143 VYRCRRCGETLVF 155 (160)
T ss_pred cEECCCCCceeEE
Confidence 7888888888854
No 88
>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=75.38 E-value=2 Score=37.97 Aligned_cols=23 Identities=22% Similarity=0.430 Sum_probs=14.3
Q ss_pred CccccCccCcccCChHHHHHHHH
Q 023000 221 GTELCPQCGARFSSVTTLIEHVE 243 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~ 243 (289)
+++.||.||.-......|..-.|
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR 230 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTR 230 (314)
T ss_pred CCCCCCCCCCcccccccceeeee
Confidence 46667777766666666655544
No 89
>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=74.50 E-value=1.8 Score=34.03 Aligned_cols=12 Identities=0% Similarity=-0.324 Sum_probs=11.0
Q ss_pred cccCCccccccc
Q 023000 115 TIKCRDCTVDHC 126 (289)
Q Consensus 115 ~~~C~~C~~~fc 126 (289)
|++|++||..|-
T Consensus 26 p~vcP~cg~~~~ 37 (129)
T TIGR02300 26 PAVSPYTGEQFP 37 (129)
T ss_pred CccCCCcCCccC
Confidence 999999999994
No 90
>PF14353 CpXC: CpXC protein
Probab=74.27 E-value=0.99 Score=35.57 Aligned_cols=15 Identities=20% Similarity=0.518 Sum_probs=12.6
Q ss_pred cccCCcccccccccC
Q 023000 115 TIKCRDCTVDHCLKH 129 (289)
Q Consensus 115 ~~~C~~C~~~fc~~h 129 (289)
.|+|+.||..|.+.+
T Consensus 38 ~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEY 52 (128)
T ss_pred EEECCCCCCceecCC
Confidence 789999999996643
No 91
>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=74.07 E-value=1.9 Score=25.84 Aligned_cols=24 Identities=21% Similarity=0.686 Sum_probs=15.7
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCC
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAK 65 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k 65 (289)
|+|..||-.+-.++ .+..||+||.
T Consensus 3 ~~C~~CG~i~~g~~----------------~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGEE----------------APEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECCc----------------CCCcCcCCCC
Confidence 67888887662221 2347999987
No 92
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=72.78 E-value=3 Score=30.52 Aligned_cols=23 Identities=35% Similarity=0.645 Sum_probs=20.6
Q ss_pred CccccCccCcccCChHHHHHHHH
Q 023000 221 GTELCPQCGARFSSVTTLIEHVE 243 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~ 243 (289)
..+.|..|++.|.....|..|++
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHH
T ss_pred CCCCCCccCCCCcCHHHHHHHHc
Confidence 36999999999999999999998
No 93
>PF14353 CpXC: CpXC protein
Probab=71.92 E-value=1.3 Score=34.98 Aligned_cols=40 Identities=25% Similarity=0.560 Sum_probs=24.8
Q ss_pred ccCCccCcccccCCCccccccCCCCCC----------CcceeecCCCCCCccccC
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAER----------HDVTVVICPLCAKGVRLR 70 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~----------~~~~~~~Cp~C~k~~~~~ 70 (289)
.+|+.|+..|-.+-+. -..... ...-.++||.||..|...
T Consensus 2 itCP~C~~~~~~~v~~-----~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWT-----SINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCCCCCCCeeEEEEEe-----EEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 4799999999544211 111111 113468999999999753
No 94
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.62 E-value=2 Score=38.59 Aligned_cols=47 Identities=23% Similarity=0.492 Sum_probs=29.0
Q ss_pred cccccccCCccCcccccC-CCccccccCCCCCCCccee-ecCCCCCCcc
Q 023000 21 IDFLPFTCDCCHKVFCLD-HRSYNQHQCPKAERHDVTV-VICPLCAKGV 67 (289)
Q Consensus 21 ~dfLPf~C~~C~k~Fc~~-h~~~~~H~c~~~~~~~~~~-~~Cp~C~k~~ 67 (289)
++.|||.|..|.+.|-.. -+.-..|=|....-+..+. ..|.+|++..
T Consensus 237 ~~~~Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t 285 (313)
T KOG1813|consen 237 IELLPFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQT 285 (313)
T ss_pred cccCCccccccccccccchhhcCCceeehhhhccccccCCcceeccccc
Confidence 678999999999999433 1112233344444444333 5688888755
No 95
>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=69.97 E-value=3.2 Score=26.00 Aligned_cols=29 Identities=14% Similarity=0.413 Sum_probs=21.1
Q ss_pred cccCCcccccccccCcC--CCCCCCCCCCCC
Q 023000 115 TIKCRDCTVDHCLKHRF--APDHSCPGPKKL 143 (289)
Q Consensus 115 ~~~C~~C~~~fc~~hr~--~~~h~C~~~~~~ 143 (289)
-|+|..||..|-.-... ...-.|+.|+..
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGST 35 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCC
Confidence 58899999999644333 457888888763
No 96
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=69.29 E-value=3.7 Score=27.39 Aligned_cols=13 Identities=31% Similarity=0.723 Sum_probs=8.3
Q ss_pred ecCCCCCCccccC
Q 023000 58 VICPLCAKGVRLR 70 (289)
Q Consensus 58 ~~Cp~C~k~~~~~ 70 (289)
+.||.||..+.+.
T Consensus 23 V~Cp~CGaeleVv 35 (54)
T TIGR01206 23 VICDECGAELEVV 35 (54)
T ss_pred EeCCCCCCEEEEE
Confidence 5677777766543
No 97
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=68.79 E-value=4.1 Score=37.19 Aligned_cols=36 Identities=31% Similarity=0.706 Sum_probs=25.9
Q ss_pred CcceeeecccccCCccccccccc---CcCCCCCCCCCCC
Q 023000 106 CKEILVFSNTIKCRDCTVDHCLK---HRFAPDHSCPGPK 141 (289)
Q Consensus 106 ck~~~~~~~~~~C~~C~~~fc~~---hr~~~~h~C~~~~ 141 (289)
|...++...-|.|..|...||+. --++.-|.|+.|.
T Consensus 336 C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCe 374 (378)
T KOG2807|consen 336 CQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCE 374 (378)
T ss_pred eccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcC
Confidence 43343444479999999999976 3556678898776
No 98
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=68.14 E-value=2.9 Score=36.18 Aligned_cols=44 Identities=25% Similarity=0.508 Sum_probs=25.3
Q ss_pred cccCCccCcccccCCCc---c-----ccccCCCCCCC---cceeecCCCCCCccc
Q 023000 25 PFTCDCCHKVFCLDHRS---Y-----NQHQCPKAERH---DVTVVICPLCAKGVR 68 (289)
Q Consensus 25 Pf~C~~C~k~Fc~~h~~---~-----~~H~c~~~~~~---~~~~~~Cp~C~k~~~ 68 (289)
-++|+.|++.|-.+-.. . +.=-|+....- -..+.+||.||-++-
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~ 59 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAF 59 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccc
Confidence 47899999999654100 0 00011211111 146778999999885
No 99
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=65.60 E-value=3.8 Score=41.89 Aligned_cols=40 Identities=20% Similarity=0.454 Sum_probs=31.4
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKG 66 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~ 66 (289)
++|+.|+-.+ .-|.....-.|+..+.....|..||.||..
T Consensus 445 ~~Cp~Cd~~l-t~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPL-TLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcce-EEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 5777777766 446666777888888877788999999987
No 100
>PRK12496 hypothetical protein; Provisional
Probab=65.09 E-value=4.6 Score=33.46 Aligned_cols=28 Identities=25% Similarity=0.594 Sum_probs=18.7
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcccc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRL 69 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~ 69 (289)
|+|..|++.|-..- .. -.||+||..+..
T Consensus 128 ~~C~gC~~~~~~~~------------~~----~~C~~CG~~~~r 155 (164)
T PRK12496 128 KVCKGCKKKYPEDY------------PD----DVCEICGSPVKR 155 (164)
T ss_pred EECCCCCccccCCC------------CC----CcCCCCCChhhh
Confidence 67999999982111 11 259999987754
No 101
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=63.68 E-value=4.7 Score=36.60 Aligned_cols=23 Identities=26% Similarity=0.476 Sum_probs=18.4
Q ss_pred CccccCccCcccCChHHHHHHHH
Q 023000 221 GTELCPQCGARFSSVTTLIEHVE 243 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~ 243 (289)
..|.|+.|...|-.--..-.|..
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHET 409 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHH
Confidence 36999999999988877777755
No 102
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=63.21 E-value=4.5 Score=29.65 Aligned_cols=12 Identities=33% Similarity=0.803 Sum_probs=9.4
Q ss_pred cccCCccccccc
Q 023000 115 TIKCRDCTVDHC 126 (289)
Q Consensus 115 ~~~C~~C~~~fc 126 (289)
-.+|+.||..|.
T Consensus 53 IW~C~kCg~~fA 64 (89)
T COG1997 53 IWKCRKCGAKFA 64 (89)
T ss_pred eEEcCCCCCeec
Confidence 467999998883
No 103
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=62.21 E-value=4.2 Score=28.06 Aligned_cols=36 Identities=28% Similarity=0.762 Sum_probs=27.4
Q ss_pred cCCCCCCCCcceeeecccccCCcccccccccCcC-CCCCCC
Q 023000 98 KRKCPVRGCKEILVFSNTIKCRDCTVDHCLKHRF-APDHSC 137 (289)
Q Consensus 98 ~~~C~~~~ck~~~~~~~~~~C~~C~~~fc~~hr~-~~~h~C 137 (289)
...|...||.+.. -++|..|.+.+|..|-. ...|.|
T Consensus 27 ~~~C~~~gC~~~s----~I~C~~Ckk~~Cf~Hfiv~~~H~C 63 (63)
T PF04236_consen 27 AGDCDITGCNNTS----FIRCAYCKKSLCFNHFIVSEYHLC 63 (63)
T ss_pred cCcCCCCCCCCcC----EEEccccCCcccccceeeeeeEcC
Confidence 3457777888773 57899999999999987 355654
No 104
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.17 E-value=13 Score=28.73 Aligned_cols=23 Identities=17% Similarity=0.346 Sum_probs=15.6
Q ss_pred CccccCccCcccCChHHHHHHHH
Q 023000 221 GTELCPQCGARFSSVTTLIEHVE 243 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~ 243 (289)
..|+|+.|...|-..-.+-.|..
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred cceeCCCCCCccccccchhhhhh
Confidence 35777777777776666666643
No 105
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.66 E-value=4 Score=31.20 Aligned_cols=28 Identities=18% Similarity=0.197 Sum_probs=19.8
Q ss_pred cCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcccc
Q 023000 27 TCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRL 69 (289)
Q Consensus 27 ~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~ 69 (289)
.|+.|++.| + .-+++|.+||.||+.|+.
T Consensus 11 idPetg~KF------Y---------DLNrdPiVsPytG~s~P~ 38 (129)
T COG4530 11 IDPETGKKF------Y---------DLNRDPIVSPYTGKSYPR 38 (129)
T ss_pred cCccccchh------h---------ccCCCccccCcccccchH
Confidence 366777777 1 123567899999999964
No 106
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=59.92 E-value=5.8 Score=21.49 Aligned_cols=8 Identities=38% Similarity=1.248 Sum_probs=4.5
Q ss_pred CCCCCCcc
Q 023000 60 CPLCAKGV 67 (289)
Q Consensus 60 Cp~C~k~~ 67 (289)
||.||+.+
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 55565544
No 107
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=58.76 E-value=5.9 Score=30.64 Aligned_cols=25 Identities=24% Similarity=0.481 Sum_probs=17.5
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKG 66 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~ 66 (289)
++|..|+..|-.+. ..+.||.||..
T Consensus 71 ~~C~~Cg~~~~~~~----------------~~~~CP~Cgs~ 95 (113)
T PRK12380 71 AWCWDCSQVVEIHQ----------------HDAQCPHCHGE 95 (113)
T ss_pred EEcccCCCEEecCC----------------cCccCcCCCCC
Confidence 78999998884332 12469999863
No 108
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=58.01 E-value=3.8 Score=37.14 Aligned_cols=28 Identities=21% Similarity=0.443 Sum_probs=21.3
Q ss_pred cccCCccccccccc---CcCCCCCCCCCCCC
Q 023000 115 TIKCRDCTVDHCLK---HRFAPDHSCPGPKK 142 (289)
Q Consensus 115 ~~~C~~C~~~fc~~---hr~~~~h~C~~~~~ 142 (289)
.|.|+.|...||+. --++.-|.|..|.-
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh~C~gCe~ 418 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLHFCIGCEL 418 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHhhCCCCcC
Confidence 79999999999865 34556678876653
No 109
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=57.92 E-value=8.1 Score=31.67 Aligned_cols=39 Identities=13% Similarity=0.136 Sum_probs=21.0
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVR 68 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~ 68 (289)
.+|+.||-.+..- .....+ ..+..-.|-++||.||+.|.
T Consensus 1 m~cp~c~~~~~~~--~~s~~~--~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 1 MRCPFCGHPDTRV--IDSRPA--EDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred CcCCCCCCCCCEe--Eecccc--CCCCceeeeeeccccCCcce
Confidence 3788888765111 111110 11212234599999999996
No 110
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=57.59 E-value=3.4 Score=36.06 Aligned_cols=45 Identities=22% Similarity=0.365 Sum_probs=34.5
Q ss_pred CccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccCChhhHHHHH
Q 023000 221 GTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFCDPVALVEHV 279 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~~~~~L~~H~ 279 (289)
||| |=.|++-|-....|++|+. .| -|+|-+|.|..-+--.|.-|.
T Consensus 10 kpw-cwycnrefddekiliqhqk-----ak--------hfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEKILIQHQK-----AK--------HFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred Cce-eeecccccchhhhhhhhhh-----hc--------cceeeeehhhhccCCCceeeh
Confidence 443 7889999999999999976 45 799999987655555565554
No 111
>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=57.10 E-value=7.8 Score=25.16 Aligned_cols=29 Identities=17% Similarity=0.430 Sum_probs=19.9
Q ss_pred cccCCcccccccccCcC--CCCCCCCCCCCC
Q 023000 115 TIKCRDCTVDHCLKHRF--APDHSCPGPKKL 143 (289)
Q Consensus 115 ~~~C~~C~~~fc~~hr~--~~~h~C~~~~~~ 143 (289)
-|+|.+||..|-..... ...-.|+.|+..
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGE 35 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCC
Confidence 58899999999654332 234568887763
No 112
>PRK04023 DNA polymerase II large subunit; Validated
Probab=56.80 E-value=11 Score=39.62 Aligned_cols=57 Identities=18% Similarity=0.357 Sum_probs=38.0
Q ss_pred CCcCcccCcCCcCCCCCcccccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccccC
Q 023000 4 PQFPDLGKHCSLPDCKQIDFLPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLR 70 (289)
Q Consensus 4 ~~~~~~g~~C~~~~C~~~dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~ 70 (289)
.+++--...|. .|+..-+ -|.|+.||.. ....+.|+..+.. ..+|.||.||....-.
T Consensus 620 ~eVEVg~RfCp--sCG~~t~-~frCP~CG~~------Te~i~fCP~CG~~-~~~y~CPKCG~El~~~ 676 (1121)
T PRK04023 620 IEVEIGRRKCP--SCGKETF-YRRCPFCGTH------TEPVYRCPRCGIE-VEEDECEKCGREPTPY 676 (1121)
T ss_pred eeecccCccCC--CCCCcCC-cccCCCCCCC------CCcceeCccccCc-CCCCcCCCCCCCCCcc
Confidence 34444456677 8888754 3889888876 3456677777654 3358899999877533
No 113
>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=56.65 E-value=10 Score=37.19 Aligned_cols=21 Identities=19% Similarity=0.611 Sum_probs=9.6
Q ss_pred ccCCcccccccccCcCCCCCCCCCCCC
Q 023000 116 IKCRDCTVDHCLKHRFAPDHSCPGPKK 142 (289)
Q Consensus 116 ~~C~~C~~~fc~~hr~~~~h~C~~~~~ 142 (289)
.+|..||... ..+..|+.|+.
T Consensus 241 l~Ch~Cg~~~------~~~~~Cp~C~s 261 (505)
T TIGR00595 241 LRCHYCGYQE------PIPKTCPQCGS 261 (505)
T ss_pred EEcCCCcCcC------CCCCCCCCCCC
Confidence 3455555333 33444555443
No 114
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=56.46 E-value=6.2 Score=32.73 Aligned_cols=24 Identities=38% Similarity=1.002 Sum_probs=19.3
Q ss_pred ccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCc
Q 023000 222 TELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQ 267 (289)
Q Consensus 222 p~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k 267 (289)
-|.|++||.. +-|+. |.+||+||-
T Consensus 134 ~~vC~vCGy~--------------~~ge~--------P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT--------------HEGEA--------PEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc--------------ccCCC--------CCcCCCCCC
Confidence 6999999854 44566 999999984
No 115
>PRK14873 primosome assembly protein PriA; Provisional
Probab=56.45 E-value=8.1 Score=39.27 Aligned_cols=46 Identities=17% Similarity=0.337 Sum_probs=27.0
Q ss_pred Ccccccc-cCCccCcccc--------cCCCccccccCCCCCCCcceeecCCCCCCc
Q 023000 20 QIDFLPF-TCDCCHKVFC--------LDHRSYNQHQCPKAERHDVTVVICPLCAKG 66 (289)
Q Consensus 20 ~~dfLPf-~C~~C~k~Fc--------~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~ 66 (289)
+..|-|| .|..||..+- .-|.....-.|+..+... .+..||.||..
T Consensus 377 RrGyap~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 377 RRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred CCCCCCeeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCC-cCccCCCCcCC
Confidence 3445554 5555555551 115444455577777654 57889999875
No 116
>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=54.72 E-value=6.9 Score=21.54 Aligned_cols=10 Identities=30% Similarity=0.683 Sum_probs=7.1
Q ss_pred eeecCCCCCC
Q 023000 56 TVVICPLCAK 65 (289)
Q Consensus 56 ~~~~Cp~C~k 65 (289)
-+|.||.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 3578888874
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=54.49 E-value=7.8 Score=30.05 Aligned_cols=25 Identities=20% Similarity=0.523 Sum_probs=18.2
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKG 66 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~ 66 (289)
++|..|++.|-.... .+.||.||..
T Consensus 71 ~~C~~Cg~~~~~~~~----------------~~~CP~Cgs~ 95 (115)
T TIGR00100 71 CECEDCSEEVSPEID----------------LYRCPKCHGI 95 (115)
T ss_pred EEcccCCCEEecCCc----------------CccCcCCcCC
Confidence 889999999844321 2579999874
No 118
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=54.33 E-value=5.7 Score=26.47 Aligned_cols=27 Identities=22% Similarity=0.593 Sum_probs=16.0
Q ss_pred eeecCCC--CCCccccCCCCCCccccccccccCCCC
Q 023000 56 TVVICPL--CAKGVRLRPDENPHITWENHVNVDCDP 89 (289)
Q Consensus 56 ~~~~Cp~--C~k~~~~~~~~~~~~~~~~H~~~~c~~ 89 (289)
+++.||. |...|. ...|+.|+...|..
T Consensus 8 ~~v~C~~~cc~~~i~-------r~~l~~H~~~~C~~ 36 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-------RKELDDHLENECPK 36 (60)
T ss_dssp SEEE-TT--S-BEEE-------CCCHHHHHHTTSTT
T ss_pred CEeeCCCCCccccee-------HHHHHHHHHccCCC
Confidence 3578888 666564 23567788776754
No 119
>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=53.92 E-value=5 Score=23.35 Aligned_cols=10 Identities=30% Similarity=1.182 Sum_probs=6.8
Q ss_pred eeecCCCCCC
Q 023000 56 TVVICPLCAK 65 (289)
Q Consensus 56 ~~~~Cp~C~k 65 (289)
..++||.|+-
T Consensus 18 ~~~vCp~C~~ 27 (30)
T PF08274_consen 18 ELLVCPECGH 27 (30)
T ss_dssp SSEEETTTTE
T ss_pred CEEeCCcccc
Confidence 4477888764
No 120
>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=53.90 E-value=8.3 Score=34.17 Aligned_cols=52 Identities=21% Similarity=0.524 Sum_probs=34.6
Q ss_pred CCCCcccccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccccCCCCCC
Q 023000 17 DCKQIDFLPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLRPDENP 75 (289)
Q Consensus 17 ~C~~~dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~ 75 (289)
+||+|. -|.|-.|.-.||-+|..-+..+= ++ .+++.||.||-......++..
T Consensus 176 SCNrlG--q~sCLRCK~cfCddHvrrKg~ky----~k-~k~~PCPKCg~et~eTkdLSm 227 (314)
T PF06524_consen 176 SCNRLG--QYSCLRCKICFCDDHVRRKGFKY----EK-GKPIPCPKCGYETQETKDLSM 227 (314)
T ss_pred cccccc--chhhhheeeeehhhhhhhccccc----cc-CCCCCCCCCCCccccccccee
Confidence 566654 35666677789999977554322 12 267999999998876655543
No 121
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=53.57 E-value=14 Score=39.96 Aligned_cols=37 Identities=30% Similarity=0.731 Sum_probs=23.6
Q ss_pred cccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccc
Q 023000 25 PFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVR 68 (289)
Q Consensus 25 Pf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~ 68 (289)
-++|+.||..= .. ..|+..+..-..+|.||.||..+.
T Consensus 667 ~rkCPkCG~~t------~~-~fCP~CGs~te~vy~CPsCGaev~ 703 (1337)
T PRK14714 667 RRRCPSCGTET------YE-NRCPDCGTHTEPVYVCPDCGAEVP 703 (1337)
T ss_pred EEECCCCCCcc------cc-ccCcccCCcCCCceeCccCCCccC
Confidence 57888888731 11 156666655455678888888653
No 122
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=53.03 E-value=11 Score=25.05 Aligned_cols=27 Identities=30% Similarity=0.646 Sum_probs=17.8
Q ss_pred cccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcc
Q 023000 25 PFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGV 67 (289)
Q Consensus 25 Pf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~ 67 (289)
--+|+.|++.|-.+ ...++||.|+.+.
T Consensus 5 ~~~C~~Cg~~~~~~----------------dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG----------------DDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccCC----------------CCEEECCCCCCcc
Confidence 34677888888211 1247899998866
No 123
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=52.90 E-value=15 Score=33.84 Aligned_cols=59 Identities=25% Similarity=0.623 Sum_probs=50.7
Q ss_pred CCCccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccc--cCcccCChhhHHHHHHhhcCCC
Q 023000 219 TGGTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPK--CSQGFCDPVALVEHVERDHGGT 286 (289)
Q Consensus 219 ~~kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~--C~k~F~~~~~L~~H~~~hh~g~ 286 (289)
...++.|+.|...|.....+..|++ .|.+++ ++.|.. |...|.....+.+|.+.++.+.
T Consensus 30 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (467)
T COG5048 30 APRPDSCPNCTDSFSRLEHLTRHIR-SHTGEK--------PSQCSYSGCDKSFSRPLELSRHLRTHHNNP 90 (467)
T ss_pred CCchhhcccccccccccchhhhhcc-cccccC--------CccccccccccccCCcchhhhhcccccccc
Confidence 3467899999999999999999999 999999 999954 6778888999999988777543
No 124
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=52.76 E-value=9.7 Score=24.63 Aligned_cols=20 Identities=30% Similarity=0.712 Sum_probs=10.1
Q ss_pred ccCccCcccCCh-----HHHHHHHH
Q 023000 224 LCPQCGARFSSV-----TTLIEHVE 243 (289)
Q Consensus 224 ~C~~Cgk~F~~~-----~~L~~H~~ 243 (289)
.|..|++.+... ++|.+|++
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 455565555443 34555544
No 125
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=52.69 E-value=10 Score=23.31 Aligned_cols=11 Identities=18% Similarity=0.431 Sum_probs=9.6
Q ss_pred cccCCcccccc
Q 023000 115 TIKCRDCTVDH 125 (289)
Q Consensus 115 ~~~C~~C~~~f 125 (289)
-|.|..|++.|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 78899999877
No 126
>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=52.30 E-value=4.8 Score=31.10 Aligned_cols=25 Identities=28% Similarity=0.588 Sum_probs=16.1
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKG 66 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~ 66 (289)
++|..|+..|..+... +.||.||..
T Consensus 71 ~~C~~Cg~~~~~~~~~----------------~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFD----------------FSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHHCC----------------HH-SSSSSS
T ss_pred EECCCCCCEEecCCCC----------------CCCcCCcCC
Confidence 7899999999443211 468999885
No 127
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=52.16 E-value=11 Score=25.18 Aligned_cols=11 Identities=36% Similarity=1.337 Sum_probs=8.6
Q ss_pred ecCCCCCCccc
Q 023000 58 VICPLCAKGVR 68 (289)
Q Consensus 58 ~~Cp~C~k~~~ 68 (289)
+.||+||..-+
T Consensus 5 i~CP~CgnKTR 15 (55)
T PF14205_consen 5 ILCPICGNKTR 15 (55)
T ss_pred EECCCCCCccc
Confidence 67999997554
No 128
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=51.60 E-value=11 Score=30.06 Aligned_cols=40 Identities=23% Similarity=0.491 Sum_probs=23.1
Q ss_pred ccccCCccCcccccC--CCc------cccccCCCCCCCcceeecCCCCCCc
Q 023000 24 LPFTCDCCHKVFCLD--HRS------YNQHQCPKAERHDVTVVICPLCAKG 66 (289)
Q Consensus 24 LPf~C~~C~k~Fc~~--h~~------~~~H~c~~~~~~~~~~~~Cp~C~k~ 66 (289)
.-+.|..||..|-.+ +.. ...|--+.. ....+.||.||..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEV---VHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccc---cccCcCCcCCCCC
Confidence 458999999999664 111 111211211 1233679999974
No 129
>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=50.61 E-value=13 Score=20.76 Aligned_cols=19 Identities=21% Similarity=0.564 Sum_probs=12.8
Q ss_pred cccccCcccCChhhHHHHHH
Q 023000 261 VCPKCSQGFCDPVALVEHVE 280 (289)
Q Consensus 261 ~C~~C~k~F~~~~~L~~H~~ 280 (289)
.||+|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577887777 4566667763
No 130
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=50.26 E-value=11 Score=25.56 Aligned_cols=42 Identities=29% Similarity=0.525 Sum_probs=29.1
Q ss_pred ccccccCCccCcccc-cCCCccccccCCCCCCCcceeecCCCCCCccccCCCCCCcc
Q 023000 22 DFLPFTCDCCHKVFC-LDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLRPDENPHI 77 (289)
Q Consensus 22 dfLPf~C~~C~k~Fc-~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~~~ 77 (289)
-||-.+|+.|+..=. -.| ...+..|..||..+..+.+.+..+
T Consensus 8 ~F~~VkCp~C~n~q~vFsh--------------a~t~V~C~~Cg~~L~~PtGGKa~i 50 (59)
T PRK00415 8 RFLKVKCPDCGNEQVVFSH--------------ASTVVRCLVCGKTLAEPTGGKAKI 50 (59)
T ss_pred eEEEEECCCCCCeEEEEec--------------CCcEEECcccCCCcccCCCcceee
Confidence 588899999986420 011 224578999999998887765543
No 131
>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=49.90 E-value=14 Score=23.00 Aligned_cols=23 Identities=22% Similarity=0.483 Sum_probs=12.7
Q ss_pred CccccCccCcccCCh----HHHHHHHH
Q 023000 221 GTELCPQCGARFSSV----TTLIEHVE 243 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~----~~L~~H~~ 243 (289)
.-..|..|++.+... +.|.+|++
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 456788888776653 66777764
No 132
>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=49.53 E-value=12 Score=22.49 Aligned_cols=17 Identities=41% Similarity=0.690 Sum_probs=7.7
Q ss_pred ccCCccCcccccCCCccc
Q 023000 26 FTCDCCHKVFCLDHRSYN 43 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~ 43 (289)
-.|..|++.| .+-++.+
T Consensus 4 ~~C~eC~~~f-~dSyL~~ 20 (34)
T PF01286_consen 4 PKCDECGKPF-MDSYLLN 20 (34)
T ss_dssp EE-TTT--EE-S-SSCCC
T ss_pred chHhHhCCHH-HHHHHHH
Confidence 3677888888 4444444
No 133
>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=48.89 E-value=9.6 Score=30.39 Aligned_cols=22 Identities=32% Similarity=0.756 Sum_probs=10.5
Q ss_pred ccccccCcccCChhhHHHHHHhhcC
Q 023000 260 DVCPKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 260 ~~C~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
..|-+||+.|.. |.+|++.|||
T Consensus 73 i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-
T ss_pred eEEccCCcccch---HHHHHHHccC
Confidence 446666666654 4666666654
No 134
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=48.12 E-value=20 Score=23.86 Aligned_cols=33 Identities=21% Similarity=0.808 Sum_probs=23.0
Q ss_pred CCCCCCCcceeeec-----ccccCCcccccccccCcCC
Q 023000 100 KCPVRGCKEILVFS-----NTIKCRDCTVDHCLKHRFA 132 (289)
Q Consensus 100 ~C~~~~ck~~~~~~-----~~~~C~~C~~~fc~~hr~~ 132 (289)
.|+..+|....... ..++|+.|+..||.....+
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCc
Confidence 46666776554332 2688999999999876544
No 135
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=47.34 E-value=11 Score=20.86 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=5.1
Q ss_pred cCCCCCCcc
Q 023000 59 ICPLCAKGV 67 (289)
Q Consensus 59 ~Cp~C~k~~ 67 (289)
.||.||+.+
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 466666633
No 136
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.05 E-value=14 Score=37.61 Aligned_cols=8 Identities=50% Similarity=1.028 Sum_probs=3.3
Q ss_pred CCcccccc
Q 023000 118 CRDCTVDH 125 (289)
Q Consensus 118 C~~C~~~f 125 (289)
|+.|+-..
T Consensus 395 C~~C~~~L 402 (665)
T PRK14873 395 CRHCTGPL 402 (665)
T ss_pred CCCCCCce
Confidence 44444333
No 137
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=46.50 E-value=20 Score=38.78 Aligned_cols=62 Identities=18% Similarity=0.191 Sum_probs=43.9
Q ss_pred CCCccccCccCcccCChHHHHHHHHhh-cCCC----------------------CCCCC-------C----CCCcccccc
Q 023000 219 TGGTELCPQCGARFSSVTTLIEHVEKI-HDRS----------------------GNQAR-------P----KVTVDVCPK 264 (289)
Q Consensus 219 ~~kp~~C~~Cgk~F~~~~~L~~H~~~~-h~~~----------------------k~~~~-------~----~~~p~~C~~ 264 (289)
+.+||.|..|...+..+.+|.+|+... |..+ .+... . ...+|.|.+
T Consensus 515 ~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~~C~v 594 (1406)
T KOG1146|consen 515 PGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSWRCEV 594 (1406)
T ss_pred CCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCcchhh
Confidence 558999999999999999999998631 2111 00000 0 133689999
Q ss_pred cCcccCChhhHHHHHH
Q 023000 265 CSQGFCDPVALVEHVE 280 (289)
Q Consensus 265 C~k~F~~~~~L~~H~~ 280 (289)
|+..-+-..+|+-||.
T Consensus 595 c~yetniarnlrihmt 610 (1406)
T KOG1146|consen 595 CSYETNIARNLRIHMT 610 (1406)
T ss_pred hcchhhhhhccccccc
Confidence 9988888888888874
No 138
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.41 E-value=11 Score=29.21 Aligned_cols=13 Identities=31% Similarity=0.703 Sum_probs=10.3
Q ss_pred cccCCccCccccc
Q 023000 25 PFTCDCCHKVFCL 37 (289)
Q Consensus 25 Pf~C~~C~k~Fc~ 37 (289)
-+.|..|+..|-.
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 4889999988843
No 139
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=46.34 E-value=11 Score=24.58 Aligned_cols=32 Identities=22% Similarity=0.700 Sum_probs=21.0
Q ss_pred ccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcccc
Q 023000 24 LPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRL 69 (289)
Q Consensus 24 LPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~ 69 (289)
.-|+|-.|++.|-..- ....+.||.||-.+-.
T Consensus 5 ~~Y~C~~Cg~~~~~~~--------------~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 5 MEYKCARCGREVELDQ--------------ETRGIRCPYCGSRILV 36 (49)
T ss_pred EEEEhhhcCCeeehhh--------------ccCceeCCCCCcEEEE
Confidence 3588999999991111 1123789999987743
No 140
>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=45.81 E-value=20 Score=23.50 Aligned_cols=11 Identities=18% Similarity=0.851 Sum_probs=9.3
Q ss_pred ccCCccCcccc
Q 023000 26 FTCDCCHKVFC 36 (289)
Q Consensus 26 f~C~~C~k~Fc 36 (289)
|+|..|+-.|-
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 78999998884
No 141
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=45.08 E-value=17 Score=29.29 Aligned_cols=37 Identities=19% Similarity=0.604 Sum_probs=25.2
Q ss_pred CccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccC
Q 023000 221 GTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFC 270 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~ 270 (289)
.-|.|+.|+..|.....+ ...+. .. -|.|+.||....
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~----~~~d~-~~--------~f~Cp~Cg~~l~ 134 (147)
T smart00531 98 AYYKCPNCQSKYTFLEAN----QLLDM-DG--------TFTCPRCGEELE 134 (147)
T ss_pred cEEECcCCCCEeeHHHHH----HhcCC-CC--------cEECCCCCCEEE
Confidence 579999999999854322 20122 33 599999998753
No 142
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=45.02 E-value=7.1 Score=40.22 Aligned_cols=37 Identities=30% Similarity=0.572 Sum_probs=0.0
Q ss_pred ccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcc
Q 023000 24 LPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGV 67 (289)
Q Consensus 24 LPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~ 67 (289)
--++|+.|++.- -...|+..+..-...|.||.|+..+
T Consensus 654 ~~r~Cp~Cg~~t-------~~~~Cp~CG~~T~~~~~Cp~C~~~~ 690 (900)
T PF03833_consen 654 GRRRCPKCGKET-------FYNRCPECGSHTEPVYVCPDCGIEV 690 (900)
T ss_dssp --------------------------------------------
T ss_pred ecccCcccCCcc-------hhhcCcccCCccccceecccccccc
Confidence 346677777642 1223555555545556677666644
No 143
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=44.79 E-value=18 Score=22.39 Aligned_cols=11 Identities=18% Similarity=0.440 Sum_probs=9.6
Q ss_pred cccCCcccccc
Q 023000 115 TIKCRDCTVDH 125 (289)
Q Consensus 115 ~~~C~~C~~~f 125 (289)
-|+|..|++.|
T Consensus 28 fy~C~~C~~~w 38 (40)
T smart00440 28 FYVCTKCGHRW 38 (40)
T ss_pred EEEeCCCCCEe
Confidence 78999999877
No 144
>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=44.34 E-value=8.2 Score=31.70 Aligned_cols=30 Identities=13% Similarity=0.317 Sum_probs=24.3
Q ss_pred cccCCcccccccccCcCCCCCCCCCCCCCC
Q 023000 115 TIKCRDCTVDHCLKHRFAPDHSCPGPKKLD 144 (289)
Q Consensus 115 ~~~C~~C~~~fc~~hr~~~~h~C~~~~~~~ 144 (289)
-|.|+.|+..|...-..+..|.|+.||...
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAMELNFTCPRCGAML 138 (158)
T ss_pred eEECCCCCcEeeHHHHHHcCCcCCCCCCEe
Confidence 689999999997665556789999988754
No 145
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=44.24 E-value=9.1 Score=32.14 Aligned_cols=31 Identities=13% Similarity=0.389 Sum_probs=25.1
Q ss_pred cccCCcccccccccCcCCCCCCCCCCCCCCC
Q 023000 115 TIKCRDCTVDHCLKHRFAPDHSCPGPKKLDT 145 (289)
Q Consensus 115 ~~~C~~C~~~fc~~hr~~~~h~C~~~~~~~~ 145 (289)
.|.|+.|+..|-..-..+..|.|+.||....
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCCCCCe
Confidence 7899999999976655667899999987553
No 146
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=43.10 E-value=18 Score=23.97 Aligned_cols=32 Identities=25% Similarity=0.690 Sum_probs=19.2
Q ss_pred CCCCCCCcceeeecc---c--ccCCcccccccccCcC
Q 023000 100 KCPVRGCKEILVFSN---T--IKCRDCTVDHCLKHRF 131 (289)
Q Consensus 100 ~C~~~~ck~~~~~~~---~--~~C~~C~~~fc~~hr~ 131 (289)
.|...+|........ . ++|+.|+..||...+.
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~ 56 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGE 56 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEECSSSTS
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCc
Confidence 677777776654333 3 8899999999987554
No 147
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=42.49 E-value=14 Score=26.20 Aligned_cols=12 Identities=17% Similarity=0.681 Sum_probs=9.1
Q ss_pred cccCC--ccccccc
Q 023000 115 TIKCR--DCTVDHC 126 (289)
Q Consensus 115 ~~~C~--~C~~~fc 126 (289)
-+.|. +||..|-
T Consensus 27 Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 27 YHQCQNVNCSATFI 40 (72)
T ss_pred eeecCCCCCCCEEE
Confidence 45676 8999994
No 148
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=42.15 E-value=14 Score=28.55 Aligned_cols=11 Identities=18% Similarity=0.670 Sum_probs=9.2
Q ss_pred ccCCccCcccc
Q 023000 26 FTCDCCHKVFC 36 (289)
Q Consensus 26 f~C~~C~k~Fc 36 (289)
++|..|+..|-
T Consensus 71 ~~C~~Cg~~~~ 81 (114)
T PRK03681 71 CWCETCQQYVT 81 (114)
T ss_pred EEcccCCCeee
Confidence 78999998883
No 149
>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=42.12 E-value=18 Score=27.45 Aligned_cols=21 Identities=33% Similarity=0.556 Sum_probs=14.7
Q ss_pred ccc----CccCcccCChHHHHHHHH
Q 023000 223 ELC----PQCGARFSSVTTLIEHVE 243 (289)
Q Consensus 223 ~~C----~~Cgk~F~~~~~L~~H~~ 243 (289)
|.| ..|+........+.+|++
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~ 105 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWR 105 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHH
Confidence 667 667777777777777766
No 150
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=42.12 E-value=23 Score=22.75 Aligned_cols=13 Identities=23% Similarity=0.715 Sum_probs=9.2
Q ss_pred cccCCcccccccc
Q 023000 115 TIKCRDCTVDHCL 127 (289)
Q Consensus 115 ~~~C~~C~~~fc~ 127 (289)
-+.|+.||..+..
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 4668888877743
No 151
>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=41.79 E-value=20 Score=23.10 Aligned_cols=39 Identities=21% Similarity=0.582 Sum_probs=18.2
Q ss_pred ccCCccCcccccCCCccccccCCCCCC-C-c-ceeecCCCCCCc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAER-H-D-VTVVICPLCAKG 66 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~-~-~-~~~~~Cp~C~k~ 66 (289)
|+|..|+-.|-.+ .....+..+ .+- . + -.-+.||+|+-.
T Consensus 2 y~C~~CgyvYd~~-~Gd~~~~i~-pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPE-KGDPENGIP-PGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETT-TBBGGGTB--TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCC-cCCcccCcC-CCCCHHHCCCCCcCcCCCCc
Confidence 7899999888433 222222222 111 0 0 022689999763
No 152
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=39.95 E-value=15 Score=25.50 Aligned_cols=42 Identities=26% Similarity=0.521 Sum_probs=28.8
Q ss_pred ccccccCCccCcccc-cCCCccccccCCCCCCCcceeecCCCCCCccccCCCCCCcc
Q 023000 22 DFLPFTCDCCHKVFC-LDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLRPDENPHI 77 (289)
Q Consensus 22 dfLPf~C~~C~k~Fc-~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~~~ 77 (289)
-||-.+|+.|+..=. -.| .-.+..|..||..+..+.+.+..+
T Consensus 16 ~Fl~VkCpdC~N~q~vFsh--------------ast~V~C~~CG~~l~~PTGGka~i 58 (67)
T COG2051 16 RFLRVKCPDCGNEQVVFSH--------------ASTVVTCLICGTTLAEPTGGKAKI 58 (67)
T ss_pred eEEEEECCCCCCEEEEecc--------------CceEEEecccccEEEecCCCeEEe
Confidence 488899999986421 122 224578999999998887765443
No 153
>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=38.20 E-value=23 Score=26.31 Aligned_cols=11 Identities=27% Similarity=0.767 Sum_probs=8.2
Q ss_pred cccCCcccccc
Q 023000 115 TIKCRDCTVDH 125 (289)
Q Consensus 115 ~~~C~~C~~~f 125 (289)
...|..|++.|
T Consensus 53 IW~C~~C~~~~ 63 (91)
T TIGR00280 53 IWTCRKCGAKF 63 (91)
T ss_pred EEEcCCCCCEE
Confidence 46688888777
No 154
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=37.50 E-value=16 Score=21.16 Aligned_cols=18 Identities=22% Similarity=0.763 Sum_probs=9.6
Q ss_pred CCCcccccccCCccCccccc
Q 023000 18 CKQIDFLPFTCDCCHKVFCL 37 (289)
Q Consensus 18 C~~~dfLPf~C~~C~k~Fc~ 37 (289)
|+. +-.|+|+.|+..||+
T Consensus 8 C~~--~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 8 CGN--PAKYRCPRCGARYCS 25 (30)
T ss_dssp SSS--EESEE-TTT--EESS
T ss_pred CcC--CCEEECCCcCCceeC
Confidence 555 566777777776664
No 155
>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=37.43 E-value=22 Score=30.84 Aligned_cols=29 Identities=24% Similarity=0.450 Sum_probs=22.1
Q ss_pred CCCccccCccCcccCChHHHHHHHHhhcC
Q 023000 219 TGGTELCPQCGARFSSVTTLIEHVEKIHD 247 (289)
Q Consensus 219 ~~kp~~C~~Cgk~F~~~~~L~~H~~~~h~ 247 (289)
.+..|.|+.|+|.|.-......||...|.
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 34569999999999999999999986565
No 156
>COG1773 Rubredoxin [Energy production and conversion]
Probab=37.17 E-value=31 Score=23.08 Aligned_cols=41 Identities=20% Similarity=0.446 Sum_probs=22.7
Q ss_pred cccCCccCcccccCCCccccccCCCCCCCcc-eeecCCCCCC
Q 023000 25 PFTCDCCHKVFCLDHRSYNQHQCPKAERHDV-TVVICPLCAK 65 (289)
Q Consensus 25 Pf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~-~~~~Cp~C~k 65 (289)
-|+|..||-.|--+.-.+..=.++.....+. --..||+||-
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred ceEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCCC
Confidence 4789999999965553333333332221111 1246888874
No 157
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=36.86 E-value=9.1 Score=23.21 Aligned_cols=31 Identities=16% Similarity=0.554 Sum_probs=17.8
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVR 68 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~ 68 (289)
..|..||+.|-..... + ...-+|..||-.+.
T Consensus 2 r~C~~Cg~~Yh~~~~p------P------~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNP------P------KVEGVCDNCGGELV 32 (36)
T ss_dssp EEETTTTEEEETTTB--------------SSTTBCTTTTEBEB
T ss_pred cCcCCCCCccccccCC------C------CCCCccCCCCCeeE
Confidence 3688899988333211 1 12246888887653
No 158
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=36.32 E-value=11 Score=33.30 Aligned_cols=37 Identities=24% Similarity=0.638 Sum_probs=26.4
Q ss_pred ecCCCCCCccccCCCCCCccccccccccCCCCCCcccCcccCCCCCCCCcceeeecccccCCccccccc
Q 023000 58 VICPLCAKGVRLRPDENPHITWENHVNVDCDPSNYDKVTKKRKCPVRGCKEILVFSNTIKCRDCTVDHC 126 (289)
Q Consensus 58 ~~Cp~C~k~~~~~~~~~~~~~~~~H~~~~c~~~~~~~~~~~~~C~~~~ck~~~~~~~~~~C~~C~~~fc 126 (289)
+.|..||..+. ...+.+|+ .+|+ .. -|.|=.|++.|-
T Consensus 4 FtCnvCgEsvK-------Kp~vekH~---------------srCr-----n~-----~fSCIDC~k~F~ 40 (276)
T KOG2186|consen 4 FTCNVCGESVK-------KPQVEKHM---------------SRCR-----NA-----YFSCIDCGKTFE 40 (276)
T ss_pred Eehhhhhhhcc-------ccchHHHH---------------Hhcc-----CC-----eeEEeecccccc
Confidence 67999999884 44566675 2333 22 788999999994
No 159
>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=36.29 E-value=20 Score=27.40 Aligned_cols=13 Identities=15% Similarity=0.468 Sum_probs=10.7
Q ss_pred cccCCcccccccc
Q 023000 115 TIKCRDCTVDHCL 127 (289)
Q Consensus 115 ~~~C~~C~~~fc~ 127 (289)
-|+|++|+..+..
T Consensus 19 ~~iCpeC~~EW~~ 31 (109)
T TIGR00686 19 QLICPSCLYEWNE 31 (109)
T ss_pred eeECccccccccc
Confidence 6789999999843
No 160
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=36.26 E-value=29 Score=35.70 Aligned_cols=10 Identities=20% Similarity=0.790 Sum_probs=5.9
Q ss_pred cccCCccccc
Q 023000 115 TIKCRDCTVD 124 (289)
Q Consensus 115 ~~~C~~C~~~ 124 (289)
|..|++||-.
T Consensus 475 p~~Cp~Cgs~ 484 (730)
T COG1198 475 PQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCC
Confidence 5556666655
No 161
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.78 E-value=17 Score=25.90 Aligned_cols=33 Identities=21% Similarity=0.704 Sum_probs=22.7
Q ss_pred ccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCcccC
Q 023000 222 TELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQGFC 270 (289)
Q Consensus 222 p~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k~F~ 270 (289)
.|+|..||..| .+.+||. +.| .-.|+.|+..|.
T Consensus 12 ~Y~c~~cg~~~----dvvq~~~-----ddp-------lt~ce~c~a~~k 44 (82)
T COG2331 12 SYECTECGNRF----DVVQAMT-----DDP-------LTTCEECGARLK 44 (82)
T ss_pred EEeecccchHH----HHHHhcc-----cCc-------cccChhhChHHH
Confidence 59999999888 4555654 230 356999987654
No 162
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=35.21 E-value=28 Score=25.82 Aligned_cols=11 Identities=18% Similarity=0.682 Sum_probs=7.7
Q ss_pred cccCCcccccc
Q 023000 115 TIKCRDCTVDH 125 (289)
Q Consensus 115 ~~~C~~C~~~f 125 (289)
...|..|++.|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PTZ00255 54 IWRCKGCKKTV 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 45677777777
No 163
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=34.58 E-value=11 Score=33.19 Aligned_cols=49 Identities=22% Similarity=0.480 Sum_probs=31.6
Q ss_pred cccCCccCcccccCCCccc-cccCCCCCCCcceeecCCCCCCccccCCCCCCccccccccccCC
Q 023000 25 PFTCDCCHKVFCLDHRSYN-QHQCPKAERHDVTVVICPLCAKGVRLRPDENPHITWENHVNVDC 87 (289)
Q Consensus 25 Pf~C~~C~k~Fc~~h~~~~-~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~~~~~~~H~~~~c 87 (289)
-|.|+.||..--.- ..++ -.+|... .|.|-.|++.|- ......|+.-+.
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn~------~fSCIDC~k~F~-------~~sYknH~kCIT 52 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRNA------YFSCIDCGKTFE-------RVSYKNHTKCIT 52 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccCC------eeEEeecccccc-------cchhhhhhhhcc
Confidence 38999999987332 2333 2356553 389999999994 345566765433
No 164
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=34.54 E-value=34 Score=25.32 Aligned_cols=28 Identities=18% Similarity=0.526 Sum_probs=21.4
Q ss_pred ccccCCcccccccccCcCCCCCCCCCCCC
Q 023000 114 NTIKCRDCTVDHCLKHRFAPDHSCPGPKK 142 (289)
Q Consensus 114 ~~~~C~~C~~~fc~~hr~~~~h~C~~~~~ 142 (289)
.|-.|..||-.|.. -....+..|+.|+.
T Consensus 57 ~Pa~CkkCGfef~~-~~ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRD-DKIKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCccccc-cccCCcccCCcchh
Confidence 39999999999965 34566888887654
No 165
>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=34.34 E-value=24 Score=28.68 Aligned_cols=13 Identities=23% Similarity=0.623 Sum_probs=7.6
Q ss_pred ccCCccCcccccC
Q 023000 26 FTCDCCHKVFCLD 38 (289)
Q Consensus 26 f~C~~C~k~Fc~~ 38 (289)
|.|..||..-...
T Consensus 113 l~C~~Cg~~~~~~ 125 (146)
T PF07295_consen 113 LVCENCGHEVELT 125 (146)
T ss_pred EecccCCCEEEec
Confidence 5666666655433
No 166
>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=34.30 E-value=26 Score=34.34 Aligned_cols=39 Identities=18% Similarity=0.476 Sum_probs=24.8
Q ss_pred cCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCc
Q 023000 27 TCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKG 66 (289)
Q Consensus 27 ~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~ 66 (289)
+|+.|+-.- .-|.....-.|+..+.....+..||.|+..
T Consensus 224 ~C~~C~~~l-~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSL-TYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCce-EEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 444444332 225555566777777766667789999874
No 167
>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=33.74 E-value=15 Score=24.17 Aligned_cols=10 Identities=40% Similarity=1.218 Sum_probs=5.5
Q ss_pred cCCCCCCccc
Q 023000 59 ICPLCAKGVR 68 (289)
Q Consensus 59 ~Cp~C~k~~~ 68 (289)
.||+|+..|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 7999999884
No 168
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PRK10220 hypothetical protein; Provisional
Probab=33.10 E-value=28 Score=26.67 Aligned_cols=12 Identities=17% Similarity=0.559 Sum_probs=10.2
Q ss_pred cccCCccccccc
Q 023000 115 TIKCRDCTVDHC 126 (289)
Q Consensus 115 ~~~C~~C~~~fc 126 (289)
-|+|++|+..+-
T Consensus 20 ~~vCpeC~hEW~ 31 (111)
T PRK10220 20 MYICPECAHEWN 31 (111)
T ss_pred eEECCcccCcCC
Confidence 678999999883
No 170
>PLN00209 ribosomal protein S27; Provisional
Probab=32.62 E-value=29 Score=25.40 Aligned_cols=44 Identities=23% Similarity=0.448 Sum_probs=29.1
Q ss_pred ccccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccccCCCCCCccc
Q 023000 22 DFLPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLRPDENPHIT 78 (289)
Q Consensus 22 dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~~~~ 78 (289)
-|+-.+|+.|++.=. - ......++.|..||..+..+.+.+..+.
T Consensus 33 ~Fm~VkCp~C~n~q~-------V------FShA~t~V~C~~Cg~~L~~PTGGKa~l~ 76 (86)
T PLN00209 33 FFMDVKCQGCFNITT-------V------FSHSQTVVVCGSCQTVLCQPTGGKARLT 76 (86)
T ss_pred EEEEEECCCCCCeeE-------E------EecCceEEEccccCCEeeccCCCCeEec
Confidence 478888998887420 0 0112245789999999988877765543
No 171
>PRK05580 primosome assembly protein PriA; Validated
Probab=32.56 E-value=30 Score=35.32 Aligned_cols=40 Identities=20% Similarity=0.462 Sum_probs=25.4
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKG 66 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~ 66 (289)
++|+.|+-.. .-|.....-.|+..+.....+..||.||..
T Consensus 391 ~~C~~C~~~l-~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASL-TLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCce-eEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 4566666544 334445555677777665566789999875
No 172
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=32.28 E-value=17 Score=23.24 Aligned_cols=10 Identities=40% Similarity=1.019 Sum_probs=7.2
Q ss_pred cCCCCCCccc
Q 023000 59 ICPLCAKGVR 68 (289)
Q Consensus 59 ~Cp~C~k~~~ 68 (289)
.||.||...+
T Consensus 1 ~CP~Cg~~a~ 10 (47)
T PF04606_consen 1 RCPHCGSKAR 10 (47)
T ss_pred CcCCCCCeeE
Confidence 3888988654
No 173
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.10 E-value=18 Score=30.22 Aligned_cols=24 Identities=25% Similarity=0.636 Sum_probs=15.4
Q ss_pred Cccccccc---ccCcCCCCCCCCCCCC
Q 023000 119 RDCTVDHC---LKHRFAPDHSCPGPKK 142 (289)
Q Consensus 119 ~~C~~~fc---~~hr~~~~h~C~~~~~ 142 (289)
.+||.-|| ++-.....+.|+.|++
T Consensus 149 TkCGHvFC~~Cik~alk~~~~CP~C~k 175 (187)
T KOG0320|consen 149 TKCGHVFCSQCIKDALKNTNKCPTCRK 175 (187)
T ss_pred cccchhHHHHHHHHHHHhCCCCCCccc
Confidence 46777774 4455566677777765
No 174
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=32.08 E-value=24 Score=29.28 Aligned_cols=39 Identities=31% Similarity=0.655 Sum_probs=28.5
Q ss_pred ccCCCCCCCCcceeeecccccCCcccccccccCcCCCCCCCCC
Q 023000 97 KKRKCPVRGCKEILVFSNTIKCRDCTVDHCLKHRFAPDHSCPG 139 (289)
Q Consensus 97 ~~~~C~~~~ck~~~~~~~~~~C~~C~~~fc~~hr~~~~h~C~~ 139 (289)
+..+|...+ |+.-++ .|.| .||..||-.||....|.|..
T Consensus 104 ~~~rC~~C~-kk~glt--gf~C-rCG~~fC~~HRy~e~H~C~f 142 (167)
T KOG3173|consen 104 KKKRCFKCR-KKVGLT--GFKC-RCGNTFCGTHRYPEQHDCSF 142 (167)
T ss_pred cchhhhhhh-hhhccc--cccc-ccCCcccccccCCccccccc
Confidence 445566544 333232 6888 59999999999999999984
No 175
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=31.98 E-value=34 Score=25.37 Aligned_cols=12 Identities=25% Similarity=0.747 Sum_probs=8.7
Q ss_pred cccCCccccccc
Q 023000 115 TIKCRDCTVDHC 126 (289)
Q Consensus 115 ~~~C~~C~~~fc 126 (289)
...|..|++.|.
T Consensus 54 IW~C~~C~~~~A 65 (90)
T PRK03976 54 IWECRKCGAKFA 65 (90)
T ss_pred EEEcCCCCCEEe
Confidence 466888888873
No 176
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=31.92 E-value=1.2e+02 Score=26.95 Aligned_cols=45 Identities=22% Similarity=0.527 Sum_probs=30.1
Q ss_pred CCCCCCCCcceeeecc-----------------cccCCcccccccccCcC-CCCCCCCCCCCC
Q 023000 99 RKCPVRGCKEILVFSN-----------------TIKCRDCTVDHCLKHRF-APDHSCPGPKKL 143 (289)
Q Consensus 99 ~~C~~~~ck~~~~~~~-----------------~~~C~~C~~~fc~~hr~-~~~h~C~~~~~~ 143 (289)
--|...+||.+++..- .++|..|...|-...-. ..-..|++|+|.
T Consensus 124 IaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKv 186 (256)
T PF09788_consen 124 IACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKV 186 (256)
T ss_pred ccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCcee
Confidence 3477788887754322 46799999999655322 345688888773
No 177
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=31.91 E-value=15 Score=33.24 Aligned_cols=65 Identities=25% Similarity=0.478 Sum_probs=44.0
Q ss_pred CCcCcccCcCCcCCCCCcccccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccccCCCCCCcccc
Q 023000 4 PQFPDLGKHCSLPDCKQIDFLPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLRPDENPHITW 79 (289)
Q Consensus 4 ~~~~~~g~~C~~~~C~~~dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~~~~~ 79 (289)
|.+++|.-.|- .|+-|---|.+=.-|+..||.+-.. ....+.| ++||.|...--+..++.+++..
T Consensus 268 ~~~~~i~LkCp--lc~~Llrnp~kT~cC~~~fc~eci~------~al~dsD---f~CpnC~rkdvlld~l~pD~dk 332 (427)
T COG5222 268 MQPPNISLKCP--LCHCLLRNPMKTPCCGHTFCDECIG------TALLDSD---FKCPNCSRKDVLLDGLTPDIDK 332 (427)
T ss_pred cCCCCccccCc--chhhhhhCcccCccccchHHHHHHh------hhhhhcc---ccCCCcccccchhhccCccHHH
Confidence 67888888898 7887878888878899999876311 1111223 7899998855555555555543
No 178
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=31.83 E-value=14 Score=26.86 Aligned_cols=12 Identities=25% Similarity=0.614 Sum_probs=7.9
Q ss_pred cccCCccccccc
Q 023000 115 TIKCRDCTVDHC 126 (289)
Q Consensus 115 ~~~C~~C~~~fc 126 (289)
-+.|..||..|-
T Consensus 46 ~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 46 ILSCRVCGESFQ 57 (81)
T ss_dssp EEEESSS--EEE
T ss_pred EEEecCCCCeEE
Confidence 567999998884
No 179
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.43 E-value=45 Score=33.83 Aligned_cols=61 Identities=28% Similarity=0.437 Sum_probs=0.0
Q ss_pred cccCccCcccC---------------ChHHHHHHHHhhcCCCCCCCCCC-----------------------CCc-----
Q 023000 223 ELCPQCGARFS---------------SVTTLIEHVEKIHDRSGNQARPK-----------------------VTV----- 259 (289)
Q Consensus 223 ~~C~~Cgk~F~---------------~~~~L~~H~~~~h~~~k~~~~~~-----------------------~~p----- 259 (289)
+.|..|+++|. ....|..|++..|..-....... ..|
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~ 179 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESC 179 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccc
Q ss_pred ---ccccccCcccCChhhHHHHHHhhc
Q 023000 260 ---DVCPKCSQGFCDPVALVEHVERDH 283 (289)
Q Consensus 260 ---~~C~~C~k~F~~~~~L~~H~~~hh 283 (289)
-.|..|...|.....|.+|++.+|
T Consensus 180 rGhp~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 180 RGHPLCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred cCCccchhhhhhhccHHHHHHhhccce
No 180
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=30.81 E-value=63 Score=29.75 Aligned_cols=40 Identities=13% Similarity=0.132 Sum_probs=26.7
Q ss_pred cccCCcccccccccCcCCCCCCCCCCCCCCCccchhhhhccCCCC
Q 023000 115 TIKCRDCTVDHCLKHRFAPDHSCPGPKKLDTGFAFMSLLNRSRKE 159 (289)
Q Consensus 115 ~~~C~~C~~~fc~~hr~~~~h~C~~~~~~~~~~~~~a~l~r~~~~ 159 (289)
.|.|++|+-..|. .|-.|+.|+-.....+.++.-.++-..
T Consensus 276 Gy~CP~CkakvCs-----LP~eCpiC~ltLVss~hLARSyhhL~P 315 (378)
T KOG2807|consen 276 GYFCPQCKAKVCS-----LPIECPICSLTLVSSPHLARSYHHLFP 315 (378)
T ss_pred ceeCCcccCeeec-----CCccCCccceeEecchHHHHHHHhhcC
Confidence 6888888888873 466777777766665666555554433
No 181
>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=30.64 E-value=32 Score=27.73 Aligned_cols=13 Identities=15% Similarity=0.215 Sum_probs=11.0
Q ss_pred cccCCcccccccc
Q 023000 115 TIKCRDCTVDHCL 127 (289)
Q Consensus 115 ~~~C~~C~~~fc~ 127 (289)
-+.|+.||+-|..
T Consensus 124 f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 124 FWRCPGCGKIYWE 136 (147)
T ss_pred EEECCCCCCEecc
Confidence 5789999999964
No 182
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=30.09 E-value=32 Score=26.93 Aligned_cols=26 Identities=31% Similarity=0.466 Sum_probs=19.1
Q ss_pred CCCCcccccccCcccCChhhHHHHHH
Q 023000 255 PKVTVDVCPKCSQGFCDPVALVEHVE 280 (289)
Q Consensus 255 ~~~~p~~C~~C~k~F~~~~~L~~H~~ 280 (289)
+|.+.|.|-.|-+-|.+...|..|.+
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHh
Confidence 44556778888888888888877765
No 183
>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=29.83 E-value=19 Score=32.63 Aligned_cols=14 Identities=14% Similarity=0.361 Sum_probs=11.2
Q ss_pred cccCCccccccccc
Q 023000 115 TIKCRDCTVDHCLK 128 (289)
Q Consensus 115 ~~~C~~C~~~fc~~ 128 (289)
-++|++|+.+|.+.
T Consensus 45 ~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 45 LEVCPKCDHHMRMD 58 (285)
T ss_pred CCCCCCCCCcCcCC
Confidence 57799999999653
No 184
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=29.75 E-value=22 Score=24.01 Aligned_cols=15 Identities=33% Similarity=0.771 Sum_probs=10.5
Q ss_pred cccCCcccccccccC
Q 023000 115 TIKCRDCTVDHCLKH 129 (289)
Q Consensus 115 ~~~C~~C~~~fc~~h 129 (289)
.|.|.+||..--.|-
T Consensus 37 ~irCReCG~RIlyKk 51 (62)
T KOG3507|consen 37 VIRCRECGYRILYKK 51 (62)
T ss_pred cEehhhcchHHHHHH
Confidence 677888887665443
No 185
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=29.12 E-value=23 Score=29.28 Aligned_cols=12 Identities=17% Similarity=0.351 Sum_probs=10.3
Q ss_pred cccCCccccccc
Q 023000 115 TIKCRDCTVDHC 126 (289)
Q Consensus 115 ~~~C~~C~~~fc 126 (289)
-+.|+.||+.|.
T Consensus 130 f~~C~~CgkiYW 141 (165)
T COG1656 130 FYRCPKCGKIYW 141 (165)
T ss_pred eeECCCCccccc
Confidence 567999999995
No 186
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=29.09 E-value=32 Score=30.50 Aligned_cols=39 Identities=18% Similarity=0.399 Sum_probs=24.7
Q ss_pred ccccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCC-ccc
Q 023000 22 DFLPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAK-GVR 68 (289)
Q Consensus 22 dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k-~~~ 68 (289)
.++.++|..|+..|-.+... + +.. +..++.||.||. .++
T Consensus 119 sl~~~~C~~C~~~~~~~~~~-~---~~~----~~~~p~C~~Cg~~~lr 158 (250)
T COG0846 119 SLKRVRCSKCGNQYYDEDVI-K---FIE----DGLIPRCPKCGGPVLR 158 (250)
T ss_pred ceeeeEeCCCcCccchhhhh-h---hcc----cCCCCcCccCCCcccc
Confidence 46778999999888433211 1 111 124689999999 554
No 187
>PHA02998 RNA polymerase subunit; Provisional
Probab=28.63 E-value=40 Score=28.23 Aligned_cols=12 Identities=33% Similarity=0.708 Sum_probs=10.7
Q ss_pred cccCCccccccc
Q 023000 115 TIKCRDCTVDHC 126 (289)
Q Consensus 115 ~~~C~~C~~~fc 126 (289)
.|+|..||+.|.
T Consensus 171 FYkC~~CG~~wk 182 (195)
T PHA02998 171 RHACRDCKKHFK 182 (195)
T ss_pred EEEcCCCCCccC
Confidence 789999999994
No 188
>PRK12722 transcriptional activator FlhC; Provisional
Probab=28.49 E-value=38 Score=28.68 Aligned_cols=31 Identities=32% Similarity=0.778 Sum_probs=20.2
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVR 68 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~ 68 (289)
-.|..|+-.| ..|..+- ...|+||+|+-+-+
T Consensus 135 ~~C~~Cgg~f-v~~~~e~-----------~~~f~CplC~~psR 165 (187)
T PRK12722 135 SSCNCCGGHF-VTHAHDP-----------VGSFVCGLCQPPSR 165 (187)
T ss_pred ccCCCCCCCe-ecccccc-----------CCCCcCCCCCCccc
Confidence 4589999999 4443311 23389999988443
No 189
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=28.43 E-value=37 Score=24.78 Aligned_cols=44 Identities=23% Similarity=0.455 Sum_probs=29.0
Q ss_pred ccccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccccCCCCCCccc
Q 023000 22 DFLPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLRPDENPHIT 78 (289)
Q Consensus 22 dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~~~~ 78 (289)
-|+-.+|+.|++.=. - ......++.|..|+..+..+++.+..+.
T Consensus 32 ~Fm~VkCp~C~n~q~-------V------FShA~t~V~C~~Cg~~L~~PTGGKa~l~ 75 (85)
T PTZ00083 32 YFMDVKCPGCSQITT-------V------FSHAQTVVLCGGCSSQLCQPTGGKAKLT 75 (85)
T ss_pred eEEEEECCCCCCeeE-------E------EecCceEEEccccCCEeeccCCCCeEec
Confidence 477888998887420 0 0112245789999999988877765543
No 190
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=28.29 E-value=32 Score=23.54 Aligned_cols=13 Identities=23% Similarity=0.567 Sum_probs=5.6
Q ss_pred eeecCCCCCCccc
Q 023000 56 TVVICPLCAKGVR 68 (289)
Q Consensus 56 ~~~~Cp~C~k~~~ 68 (289)
..-.|.+|++.|.
T Consensus 8 ~~~~C~~C~~~F~ 20 (69)
T PF01363_consen 8 EASNCMICGKKFS 20 (69)
T ss_dssp G-SB-TTT--B-B
T ss_pred CCCcCcCcCCcCC
Confidence 4457888888885
No 191
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=27.96 E-value=35 Score=23.41 Aligned_cols=14 Identities=43% Similarity=0.821 Sum_probs=10.8
Q ss_pred eeecCCCCCCcccc
Q 023000 56 TVVICPLCAKGVRL 69 (289)
Q Consensus 56 ~~~~Cp~C~k~~~~ 69 (289)
..+.||+|+|.+.+
T Consensus 5 ~~v~CP~C~k~~~w 18 (62)
T PRK00418 5 ITVNCPTCGKPVEW 18 (62)
T ss_pred ccccCCCCCCcccc
Confidence 34789999998754
No 192
>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=27.95 E-value=16 Score=21.73 Aligned_cols=20 Identities=30% Similarity=0.655 Sum_probs=13.2
Q ss_pred eecCCCCCCccccCCCCCCcccccccc
Q 023000 57 VVICPLCAKGVRLRPDENPHITWENHV 83 (289)
Q Consensus 57 ~~~Cp~C~k~~~~~~~~~~~~~~~~H~ 83 (289)
.+.||.|++.|. ..++..|+
T Consensus 4 ~~~C~nC~R~v~-------a~RfA~HL 23 (33)
T PF08209_consen 4 YVECPNCGRPVA-------ASRFAPHL 23 (33)
T ss_dssp EEE-TTTSSEEE-------GGGHHHHH
T ss_pred eEECCCCcCCcc-------hhhhHHHH
Confidence 478999999884 34455565
No 193
>PRK12860 transcriptional activator FlhC; Provisional
Probab=27.84 E-value=39 Score=28.63 Aligned_cols=28 Identities=25% Similarity=0.553 Sum_probs=18.6
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCC
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAK 65 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k 65 (289)
-.|..|+-.| ..|.. + ....|+||+|.-
T Consensus 135 ~~C~~Cgg~f-v~~~~-e----------~~~~f~CplC~~ 162 (189)
T PRK12860 135 ARCCRCGGKF-VTHAH-D----------LRHNFVCGLCQP 162 (189)
T ss_pred ccCCCCCCCe-ecccc-c----------cCCCCcCCCCCC
Confidence 4688999999 44433 1 123489999984
No 194
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=27.47 E-value=22 Score=32.42 Aligned_cols=14 Identities=14% Similarity=0.363 Sum_probs=11.0
Q ss_pred cccCCccccccccc
Q 023000 115 TIKCRDCTVDHCLK 128 (289)
Q Consensus 115 ~~~C~~C~~~fc~~ 128 (289)
-++|++|+.+|.+.
T Consensus 57 ~~vcp~c~~h~rlt 70 (296)
T CHL00174 57 MNICEQCGYHLKMS 70 (296)
T ss_pred CCCCCCCCCCcCCC
Confidence 57799999988654
No 195
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.93 E-value=30 Score=23.84 Aligned_cols=13 Identities=46% Similarity=0.843 Sum_probs=10.7
Q ss_pred eecCCCCCCcccc
Q 023000 57 VVICPLCAKGVRL 69 (289)
Q Consensus 57 ~~~Cp~C~k~~~~ 69 (289)
...||+|||.+.+
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 4689999998865
No 196
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.74 E-value=78 Score=34.52 Aligned_cols=28 Identities=18% Similarity=0.229 Sum_probs=16.2
Q ss_pred cccCCcccccccccCcCCCCCCCCCCCCCC
Q 023000 115 TIKCRDCTVDHCLKHRFAPDHSCPGPKKLD 144 (289)
Q Consensus 115 ~~~C~~C~~~fc~~hr~~~~h~C~~~~~~~ 144 (289)
+|.|+.||...-..-.. .-.|+.|+...
T Consensus 692 vy~CPsCGaev~~des~--a~~CP~CGtpl 719 (1337)
T PRK14714 692 VYVCPDCGAEVPPDESG--RVECPRCDVEL 719 (1337)
T ss_pred ceeCccCCCccCCCccc--cccCCCCCCcc
Confidence 67788888865322111 23577777544
No 197
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.70 E-value=20 Score=24.22 Aligned_cols=11 Identities=27% Similarity=0.739 Sum_probs=7.4
Q ss_pred eecCCCCCCcc
Q 023000 57 VVICPLCAKGV 67 (289)
Q Consensus 57 ~~~Cp~C~k~~ 67 (289)
.++||.|.+.+
T Consensus 44 ~PVCP~Ck~iy 54 (58)
T PF11238_consen 44 FPVCPECKEIY 54 (58)
T ss_pred CCCCcCHHHHH
Confidence 46788886644
No 198
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=26.60 E-value=15 Score=35.15 Aligned_cols=15 Identities=40% Similarity=0.857 Sum_probs=12.3
Q ss_pred cceeecCCCCCCccc
Q 023000 54 DVTVVICPLCAKGVR 68 (289)
Q Consensus 54 ~~~~~~Cp~C~k~~~ 68 (289)
|..+.-||+|++.|.
T Consensus 177 Ds~V~~CP~Ca~~F~ 191 (505)
T KOG1842|consen 177 DSSVQFCPECANSFG 191 (505)
T ss_pred CCcccccccccchhh
Confidence 456778999999994
No 199
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=26.54 E-value=12 Score=25.08 Aligned_cols=41 Identities=17% Similarity=0.391 Sum_probs=29.2
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcccc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRL 69 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~ 69 (289)
.+|-.|+|.+-.+..++.+-+-- ..+...|.|+.|...+..
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLr---nrPi~tYmC~eC~~RI~~ 43 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLR---NRPIHTYMCDECKERIRE 43 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhh---cCCCcceeChhHHHHHhH
Confidence 47889999998776555543322 235677999999887764
No 200
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.30 E-value=33 Score=29.96 Aligned_cols=14 Identities=21% Similarity=0.660 Sum_probs=11.4
Q ss_pred cccCCccCcccccC
Q 023000 25 PFTCDCCHKVFCLD 38 (289)
Q Consensus 25 Pf~C~~C~k~Fc~~ 38 (289)
-+.|+.|+..|-.+
T Consensus 19 ~ieCPvC~tkFkke 32 (267)
T COG1655 19 TIECPVCNTKFKKE 32 (267)
T ss_pred eeccCcccchhhhh
Confidence 47899999999544
No 201
>PRK01343 zinc-binding protein; Provisional
Probab=26.27 E-value=32 Score=23.20 Aligned_cols=13 Identities=31% Similarity=0.621 Sum_probs=10.1
Q ss_pred eeecCCCCCCccc
Q 023000 56 TVVICPLCAKGVR 68 (289)
Q Consensus 56 ~~~~Cp~C~k~~~ 68 (289)
....||+|+|.+.
T Consensus 8 p~~~CP~C~k~~~ 20 (57)
T PRK01343 8 PTRPCPECGKPST 20 (57)
T ss_pred CCCcCCCCCCcCc
Confidence 3467999999873
No 202
>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=26.13 E-value=40 Score=29.19 Aligned_cols=25 Identities=28% Similarity=0.505 Sum_probs=20.1
Q ss_pred cccccccCcccCChhhHHHHHHhhc
Q 023000 259 VDVCPKCSQGFCDPVALVEHVERDH 283 (289)
Q Consensus 259 p~~C~~C~k~F~~~~~L~~H~~~hh 283 (289)
.|.|+.|+|.|.-.....+|+..-|
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred EECCCCCCcccCChHHHHHHHhhcC
Confidence 6999999999999999999997655
No 203
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=26.08 E-value=24 Score=21.15 Aligned_cols=13 Identities=31% Similarity=0.595 Sum_probs=4.6
Q ss_pred cccccCCccCccc
Q 023000 23 FLPFTCDCCHKVF 35 (289)
Q Consensus 23 fLPf~C~~C~k~F 35 (289)
|+=-+|..|+..+
T Consensus 9 l~~~rC~~Cg~~~ 21 (37)
T PF12172_consen 9 LLGQRCRDCGRVQ 21 (37)
T ss_dssp EEEEE-TTT--EE
T ss_pred EEEEEcCCCCCEe
Confidence 3334555555553
No 204
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=25.94 E-value=23 Score=32.18 Aligned_cols=14 Identities=14% Similarity=0.323 Sum_probs=11.1
Q ss_pred cccCCccccccccc
Q 023000 115 TIKCRDCTVDHCLK 128 (289)
Q Consensus 115 ~~~C~~C~~~fc~~ 128 (289)
-++|++|+.+|.+.
T Consensus 46 ~~vc~~c~~h~rl~ 59 (292)
T PRK05654 46 LNVCPKCGHHMRIS 59 (292)
T ss_pred CCCCCCCCCCeeCC
Confidence 56799999999654
No 205
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=25.89 E-value=31 Score=26.68 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=8.1
Q ss_pred cccCCcccccc
Q 023000 115 TIKCRDCTVDH 125 (289)
Q Consensus 115 ~~~C~~C~~~f 125 (289)
.++|+.|+-..
T Consensus 12 ~l~C~~C~t~i 22 (113)
T PF09862_consen 12 RLKCPSCGTEI 22 (113)
T ss_pred EEEcCCCCCEE
Confidence 56788887766
No 206
>PF15616 TerY-C: TerY-C metal binding domain
Probab=25.82 E-value=49 Score=26.35 Aligned_cols=25 Identities=20% Similarity=0.489 Sum_probs=18.5
Q ss_pred ccCCcccccccccCcCCCCCCCCCCCCC
Q 023000 116 IKCRDCTVDHCLKHRFAPDHSCPGPKKL 143 (289)
Q Consensus 116 ~~C~~C~~~fc~~hr~~~~h~C~~~~~~ 143 (289)
..| .|||.||..- +..-.|+-|++.
T Consensus 90 a~C-~CGkl~Ci~g--~~~~~CPwCg~~ 114 (131)
T PF15616_consen 90 AVC-GCGKLFCIDG--EGEVTCPWCGNE 114 (131)
T ss_pred EEe-cCCCEEEeCC--CCCEECCCCCCe
Confidence 347 7999999754 557788888773
No 207
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.79 E-value=20 Score=23.23 Aligned_cols=13 Identities=38% Similarity=1.012 Sum_probs=10.6
Q ss_pred ecCCCCCCccccC
Q 023000 58 VICPLCAKGVRLR 70 (289)
Q Consensus 58 ~~Cp~C~k~~~~~ 70 (289)
-+||.|+.+|.+.
T Consensus 13 KICpvCqRPFsWR 25 (54)
T COG4338 13 KICPVCQRPFSWR 25 (54)
T ss_pred hhhhhhcCchHHH
Confidence 3799999999753
No 208
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=25.51 E-value=50 Score=21.55 Aligned_cols=39 Identities=26% Similarity=0.426 Sum_probs=24.0
Q ss_pred CccccCccCcccCChHHHHHHHHhhcCCCCCCCCCCCCcccccccCc
Q 023000 221 GTELCPQCGARFSSVTTLIEHVEKIHDRSGNQARPKVTVDVCPKCSQ 267 (289)
Q Consensus 221 kp~~C~~Cgk~F~~~~~L~~H~~~~h~~~k~~~~~~~~p~~C~~C~k 267 (289)
+++.|..||..|.....=..... . .|-. ..|-.|+.|.+
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~fy~-e-Kgf~------n~p~RC~~CR~ 41 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKFYA-E-KGFD------NEPKRCPSCRQ 41 (49)
T ss_pred eeEEcccCCCeEEEehhHHHHHH-h-cCCc------CCCccCHHHHH
Confidence 67899999999887665444432 1 2210 11777888743
No 209
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=25.51 E-value=29 Score=23.41 Aligned_cols=12 Identities=50% Similarity=1.107 Sum_probs=6.8
Q ss_pred ecCCCCCCcccc
Q 023000 58 VICPLCAKGVRL 69 (289)
Q Consensus 58 ~~Cp~C~k~~~~ 69 (289)
+.||+|+|.+.+
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 579999998865
No 210
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=25.47 E-value=26 Score=23.47 Aligned_cols=12 Identities=25% Similarity=0.952 Sum_probs=4.9
Q ss_pred ceeecCCCCCCc
Q 023000 55 VTVVICPLCAKG 66 (289)
Q Consensus 55 ~~~~~Cp~C~k~ 66 (289)
.|.|+||+||..
T Consensus 31 Lr~y~Cp~CgAt 42 (55)
T PF05741_consen 31 LRKYVCPICGAT 42 (55)
T ss_dssp GGG---TTT---
T ss_pred HhcCcCCCCcCc
Confidence 477999999873
No 211
>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=25.31 E-value=55 Score=21.28 Aligned_cols=25 Identities=20% Similarity=0.406 Sum_probs=15.6
Q ss_pred CCcccccccccCcCCCCCCCCCCCCCCC
Q 023000 118 CRDCTVDHCLKHRFAPDHSCPGPKKLDT 145 (289)
Q Consensus 118 C~~C~~~fc~~hr~~~~h~C~~~~~~~~ 145 (289)
|..|++.|-+ +.+.|.|..|+..+.
T Consensus 5 C~~C~~~F~~---~~rk~~Cr~Cg~~~C 29 (57)
T cd00065 5 CMGCGKPFTL---TRRRHHCRNCGRIFC 29 (57)
T ss_pred CcccCccccC---CccccccCcCcCCcC
Confidence 6667777754 455577776666543
No 212
>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=25.12 E-value=35 Score=21.49 Aligned_cols=12 Identities=42% Similarity=1.162 Sum_probs=10.1
Q ss_pred cCCCCCCccccC
Q 023000 59 ICPLCAKGVRLR 70 (289)
Q Consensus 59 ~Cp~C~k~~~~~ 70 (289)
+|+.|+.+|...
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 699999999753
No 213
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=25.02 E-value=41 Score=23.68 Aligned_cols=13 Identities=23% Similarity=0.731 Sum_probs=6.9
Q ss_pred eeecCCCCCCccc
Q 023000 56 TVVICPLCAKGVR 68 (289)
Q Consensus 56 ~~~~Cp~C~k~~~ 68 (289)
....||.|++.+.
T Consensus 29 ~~a~CPdC~~~Le 41 (70)
T PF07191_consen 29 KEAFCPDCGQPLE 41 (70)
T ss_dssp EEEE-TTT-SB-E
T ss_pred ecccCCCcccHHH
Confidence 4467888888664
No 214
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=24.76 E-value=37 Score=31.03 Aligned_cols=13 Identities=23% Similarity=0.682 Sum_probs=9.2
Q ss_pred cccCCcccccccc
Q 023000 115 TIKCRDCTVDHCL 127 (289)
Q Consensus 115 ~~~C~~C~~~fc~ 127 (289)
.|+|+.|+-.||.
T Consensus 19 ~YtCPRCn~~YCs 31 (383)
T KOG4317|consen 19 EYTCPRCNLLYCS 31 (383)
T ss_pred cccCCCCCcccee
Confidence 5677777777764
No 215
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=24.62 E-value=51 Score=26.20 Aligned_cols=11 Identities=45% Similarity=1.192 Sum_probs=10.0
Q ss_pred cccCCccCccc
Q 023000 25 PFTCDCCHKVF 35 (289)
Q Consensus 25 Pf~C~~C~k~F 35 (289)
|.+|..||+.|
T Consensus 1 PH~Ct~Cg~~f 11 (131)
T PF09845_consen 1 PHQCTKCGRVF 11 (131)
T ss_pred CcccCcCCCCc
Confidence 77899999999
No 216
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=24.18 E-value=42 Score=28.59 Aligned_cols=40 Identities=15% Similarity=0.322 Sum_probs=29.9
Q ss_pred ccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccc
Q 023000 26 FTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVR 68 (289)
Q Consensus 26 f~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~ 68 (289)
..|+.|+..| .-| ...+.-+..++--...+.|..||..++
T Consensus 15 ~~CPvCg~~l-~~~--~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 15 IDCPVCGGTL-KAH--MYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred ecCCccccee-eEE--EeeecCCccceEEEEEEEccccCCccc
Confidence 5699999955 333 456677777776678889999999775
No 217
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=24.10 E-value=22 Score=22.15 Aligned_cols=9 Identities=33% Similarity=0.973 Sum_probs=4.3
Q ss_pred cCCcccccc
Q 023000 117 KCRDCTVDH 125 (289)
Q Consensus 117 ~C~~C~~~f 125 (289)
+|+.|+...
T Consensus 2 ~Cp~Cg~~~ 10 (43)
T PF08271_consen 2 KCPNCGSKE 10 (43)
T ss_dssp SBTTTSSSE
T ss_pred CCcCCcCCc
Confidence 355555443
No 218
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=24.08 E-value=53 Score=25.21 Aligned_cols=34 Identities=21% Similarity=0.597 Sum_probs=21.9
Q ss_pred CcccccccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCcc
Q 023000 20 QIDFLPFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGV 67 (289)
Q Consensus 20 ~~dfLPf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~ 67 (289)
.++|.-+.|+.||... .-.+.|-+. -||.|+..-
T Consensus 37 ~~G~~~~~C~~Cg~~~------~~~~SCk~R--------~CP~C~~~~ 70 (111)
T PF14319_consen 37 ALGFHRYRCEDCGHEK------IVYNSCKNR--------HCPSCQAKA 70 (111)
T ss_pred cCCcceeecCCCCceE------EecCcccCc--------CCCCCCChH
Confidence 4577778888877655 345555433 488888743
No 219
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=23.72 E-value=64 Score=32.14 Aligned_cols=41 Identities=20% Similarity=0.456 Sum_probs=26.6
Q ss_pred cccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccc
Q 023000 25 PFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVR 68 (289)
Q Consensus 25 Pf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~ 68 (289)
=..|++|+..|-++-..++- +.....+.-.|+||.||..+.
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w---~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKW---DKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EccCCCCCCCccccccceee---cCCCCccceEEECCCCcCCCC
Confidence 46899999999776322221 111022345699999999885
No 220
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=23.53 E-value=35 Score=20.98 Aligned_cols=34 Identities=18% Similarity=0.489 Sum_probs=15.2
Q ss_pred cccCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccc
Q 023000 25 PFTCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVR 68 (289)
Q Consensus 25 Pf~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~ 68 (289)
|.+|..|+-.. .-..... .+.+..+|++|+..-.
T Consensus 2 p~rC~~C~ayl-Np~~~~~---------~~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 2 PVRCRRCRAYL-NPFCQFD---------DGGKTWICNFCGTKNP 35 (40)
T ss_dssp S-B-TTT--BS--TTSEEE---------TTTTEEEETTT--EEE
T ss_pred ccccCCCCCEE-CCcceEc---------CCCCEEECcCCCCcCC
Confidence 67888887765 2211111 1234689999998554
No 221
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.50 E-value=38 Score=32.09 Aligned_cols=27 Identities=30% Similarity=0.828 Sum_probs=20.5
Q ss_pred cCCcCCCCCcccccc----------cCCccCcccccC
Q 023000 12 HCSLPDCKQIDFLPF----------TCDCCHKVFCLD 38 (289)
Q Consensus 12 ~C~~~~C~~~dfLPf----------~C~~C~k~Fc~~ 38 (289)
.|.++.|-.+-++.. .|..|+..||.+
T Consensus 235 ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~ 271 (384)
T KOG1812|consen 235 YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVK 271 (384)
T ss_pred cCCCCCchHhhhhhhhccchhhcccccccCCCceeec
Confidence 677888866665444 688999999876
No 222
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.28 E-value=76 Score=32.25 Aligned_cols=47 Identities=26% Similarity=0.581 Sum_probs=0.0
Q ss_pred cCCccCcccccCCCccccccCCCCCCCcceeecCCCCCCccccCCCCCCccccccccccCCCCCCcccCcccCCCCCCCC
Q 023000 27 TCDCCHKVFCLDHRSYNQHQCPKAERHDVTVVICPLCAKGVRLRPDENPHITWENHVNVDCDPSNYDKVTKKRKCPVRGC 106 (289)
Q Consensus 27 ~C~~C~k~Fc~~h~~~~~H~c~~~~~~~~~~~~Cp~C~k~~~~~~~~~~~~~~~~H~~~~c~~~~~~~~~~~~~C~~~~c 106 (289)
.|+.|+..- ...+.-|...| .....-.||.||..++....+
T Consensus 3 ~Cp~Cg~~n-----~~~akFC~~CG-~~l~~~~Cp~CG~~~~~~~~f--------------------------------- 43 (645)
T PRK14559 3 ICPQCQFEN-----PNNNRFCQKCG-TSLTHKPCPQCGTEVPVDEAH--------------------------------- 43 (645)
T ss_pred cCCCCCCcC-----CCCCccccccC-CCCCCCcCCCCCCCCCccccc---------------------------------
Q ss_pred cceeeecccccCCcccc
Q 023000 107 KEILVFSNTIKCRDCTV 123 (289)
Q Consensus 107 k~~~~~~~~~~C~~C~~ 123 (289)
|++||.
T Consensus 44 -----------C~~CG~ 49 (645)
T PRK14559 44 -----------CPNCGA 49 (645)
T ss_pred -----------ccccCC
No 223
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.13 E-value=29 Score=32.95 Aligned_cols=25 Identities=28% Similarity=0.716 Sum_probs=20.1
Q ss_pred ecCCCCCCccccCCCCCCccccccccccCCCC
Q 023000 58 VICPLCAKGVRLRPDENPHITWENHVNVDCDP 89 (289)
Q Consensus 58 ~~Cp~C~k~~~~~~~~~~~~~~~~H~~~~c~~ 89 (289)
+.||+|++.+. ...|.+|+++.|-.
T Consensus 182 v~CPiC~~~~~-------~~~i~~Hld~~Cl~ 206 (397)
T TIGR00599 182 VQCPICQQRMP-------EKAVERHLDSECLG 206 (397)
T ss_pred ccCCCcccccC-------HHHHHHHHhccCCC
Confidence 68999999884 55678999987764
No 224
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=22.86 E-value=49 Score=21.56 Aligned_cols=23 Identities=17% Similarity=0.336 Sum_probs=11.7
Q ss_pred CCcccccccccCcCCCCCCCCCCCC
Q 023000 118 CRDCTVDHCLKHRFAPDHSCPGPKK 142 (289)
Q Consensus 118 C~~C~~~fc~~hr~~~~h~C~~~~~ 142 (289)
|+.||..|...|. .-+.|..|+.
T Consensus 23 CP~Cg~~~m~~~~--~r~~C~~Cgy 45 (50)
T PRK00432 23 CPRCGSGFMAEHL--DRWHCGKCGY 45 (50)
T ss_pred CcCCCcchheccC--CcEECCCcCC
Confidence 6666655444333 3455555544
No 225
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=22.62 E-value=37 Score=26.11 Aligned_cols=43 Identities=16% Similarity=0.397 Sum_probs=25.5
Q ss_pred ccccCCccCcccccCCCccccccCCCCCC-------------------CcceeecCCCCCCcc
Q 023000 24 LPFTCDCCHKVFCLDHRSYNQHQCPKAER-------------------HDVTVVICPLCAKGV 67 (289)
Q Consensus 24 LPf~C~~C~k~Fc~~h~~~~~H~c~~~~~-------------------~~~~~~~Cp~C~k~~ 67 (289)
.-.+| .||-.||.-.-+.|.|.-..... .-.+-|-||.||-.+
T Consensus 23 k~vkc-~CGh~f~d~r~NwK~~alv~vRd~~E~~~~iYp~~~aPdp~w~~irEyyCP~Cgt~l 84 (112)
T PF08882_consen 23 KVVKC-DCGHEFCDARENWKLGALVYVRDPEEIHPEIYPFTMAPDPEWQVIREYYCPGCGTQL 84 (112)
T ss_pred ceeec-cCCCeecChhcChhhCcEEEecChHHhhhhhcccccCCCCCcEEEEEEECCCCccee
Confidence 35677 59999986644444332221111 114778899999865
No 226
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=22.61 E-value=59 Score=24.91 Aligned_cols=13 Identities=15% Similarity=0.314 Sum_probs=10.5
Q ss_pred ccccCCccccccc
Q 023000 114 NTIKCRDCTVDHC 126 (289)
Q Consensus 114 ~~~~C~~C~~~fc 126 (289)
.-+.|++||..|-
T Consensus 30 ~~~~C~~CGe~~~ 42 (127)
T TIGR03830 30 PGWYCPACGEELL 42 (127)
T ss_pred eeeECCCCCCEEE
Confidence 3578999999884
No 227
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=22.43 E-value=35 Score=31.78 Aligned_cols=27 Identities=22% Similarity=0.477 Sum_probs=14.8
Q ss_pred cccCCcccccccccCcCCCCCCCCCCCC
Q 023000 115 TIKCRDCTVDHCLKHRFAPDHSCPGPKK 142 (289)
Q Consensus 115 ~~~C~~C~~~fc~~hr~~~~h~C~~~~~ 142 (289)
.|+|..|++....-.+.+. ..|..|+.
T Consensus 285 FFkC~~C~~Rt~sl~r~P~-~~C~~Cg~ 311 (344)
T PF09332_consen 285 FFKCKDCGNRTISLERLPK-KHCSNCGS 311 (344)
T ss_dssp EEE-T-TS-EEEESSSS---S--TTT-S
T ss_pred eEECCCCCCeeeecccCCC-CCCCcCCc
Confidence 7999999998765577644 78888775
No 228
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=22.20 E-value=1.4e+02 Score=25.43 Aligned_cols=11 Identities=27% Similarity=0.606 Sum_probs=8.3
Q ss_pred eecCCCCCCcc
Q 023000 57 VVICPLCAKGV 67 (289)
Q Consensus 57 ~~~Cp~C~k~~ 67 (289)
.+.||+|...+
T Consensus 18 ~~~CpICld~~ 28 (193)
T PLN03208 18 DFDCNICLDQV 28 (193)
T ss_pred ccCCccCCCcC
Confidence 47899987765
No 229
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.94 E-value=46 Score=26.07 Aligned_cols=12 Identities=17% Similarity=0.323 Sum_probs=9.5
Q ss_pred cccCCccCccccc
Q 023000 25 PFTCDCCHKVFCL 37 (289)
Q Consensus 25 Pf~C~~C~k~Fc~ 37 (289)
-+.| .|+..|-.
T Consensus 70 ~~~C-~Cg~~~~~ 81 (124)
T PRK00762 70 EIEC-ECGYEGVV 81 (124)
T ss_pred eEEe-eCcCcccc
Confidence 4899 99998844
No 230
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=21.69 E-value=53 Score=20.72 Aligned_cols=26 Identities=23% Similarity=0.391 Sum_probs=14.0
Q ss_pred cccCCccccc--ccccCcCCCCCCCCCCCC
Q 023000 115 TIKCRDCTVD--HCLKHRFAPDHSCPGPKK 142 (289)
Q Consensus 115 ~~~C~~C~~~--fc~~hr~~~~h~C~~~~~ 142 (289)
.|+|+.||.. +.++. ...|.|..|++
T Consensus 18 g~~CP~Cg~~~~~~~~~--~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKT--RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCeeeEEeCC--CCeEECCCCCC
Confidence 4567777753 22222 45566666554
No 231
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=21.47 E-value=1.4e+02 Score=23.09 Aligned_cols=15 Identities=13% Similarity=0.375 Sum_probs=12.3
Q ss_pred eeecCCCCCCccccC
Q 023000 56 TVVICPLCAKGVRLR 70 (289)
Q Consensus 56 ~~~~Cp~C~k~~~~~ 70 (289)
..++|+.||..+...
T Consensus 21 ~~l~C~kCgye~~~~ 35 (113)
T COG1594 21 GKLVCRKCGYEEEAS 35 (113)
T ss_pred cEEECCCCCcchhcc
Confidence 478999999988755
No 232
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=21.11 E-value=72 Score=19.36 Aligned_cols=13 Identities=38% Similarity=0.963 Sum_probs=7.9
Q ss_pred ecCCCCCCccccC
Q 023000 58 VICPLCAKGVRLR 70 (289)
Q Consensus 58 ~~Cp~C~k~~~~~ 70 (289)
-.||.|+|.|.+.
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 3699999988443
No 233
>PF12907 zf-met2: Zinc-binding
Probab=20.49 E-value=24 Score=22.01 Aligned_cols=27 Identities=30% Similarity=0.577 Sum_probs=14.3
Q ss_pred cccCccCcccC---ChHHHHHHHHhhcCCC
Q 023000 223 ELCPQCGARFS---SVTTLIEHVEKIHDRS 249 (289)
Q Consensus 223 ~~C~~Cgk~F~---~~~~L~~H~~~~h~~~ 249 (289)
+.|.+|-.+|. ....|..|....|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 45666664443 3344666655445544
No 234
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=20.38 E-value=26 Score=30.98 Aligned_cols=16 Identities=31% Similarity=0.683 Sum_probs=12.3
Q ss_pred cccCCcccccccccCcC
Q 023000 115 TIKCRDCTVDHCLKHRF 131 (289)
Q Consensus 115 ~~~C~~C~~~fc~~hr~ 131 (289)
-|+|..|.+-| +-||+
T Consensus 221 HFvCa~CekPF-lGHrH 236 (332)
T KOG2272|consen 221 HFVCAKCEKPF-LGHRH 236 (332)
T ss_pred heeehhcCCcc-cchhh
Confidence 58899999999 44554
No 235
>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=20.37 E-value=79 Score=23.85 Aligned_cols=22 Identities=23% Similarity=0.487 Sum_probs=20.0
Q ss_pred cccCcccCChhhHHHHHHhhcC
Q 023000 263 PKCSQGFCDPVALVEHVERDHG 284 (289)
Q Consensus 263 ~~C~k~F~~~~~L~~H~~~hh~ 284 (289)
..|+....+...+.+|.+.+|+
T Consensus 88 ~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCcEeccHHHHHHHHHHhcC
Confidence 7889999999999999998885
No 236
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=20.27 E-value=29 Score=35.33 Aligned_cols=28 Identities=14% Similarity=0.292 Sum_probs=0.0
Q ss_pred CCCCcccccccCcccCChhhHHHHHHhh
Q 023000 255 PKVTVDVCPKCSQGFCDPVALVEHVERD 282 (289)
Q Consensus 255 ~~~~p~~C~~C~k~F~~~~~L~~H~~~h 282 (289)
.+.+-|.|..|+|.|-.--++..||++|
T Consensus 788 ~~~giFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 788 DPTGIFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred CCCceeehHHHHHHHHHHhhhhHHHHHH
No 237
>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=20.16 E-value=48 Score=20.15 Aligned_cols=13 Identities=23% Similarity=0.462 Sum_probs=8.1
Q ss_pred eeecCCCCCCccc
Q 023000 56 TVVICPLCAKGVR 68 (289)
Q Consensus 56 ~~~~Cp~C~k~~~ 68 (289)
..|+|.+||..+-
T Consensus 5 ~~YkC~~CGniVe 17 (36)
T PF06397_consen 5 EFYKCEHCGNIVE 17 (36)
T ss_dssp EEEE-TTT--EEE
T ss_pred cEEEccCCCCEEE
Confidence 5799999999774
Done!