Query 007898
Match_columns 585
No_of_seqs 471 out of 3630
Neff 6.9
Searched_HMMs 46136
Date Thu Mar 28 16:49:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007898hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 99.9 4.6E-24 9.9E-29 210.8 3.1 136 89-254 127-264 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.9 2.4E-23 5.2E-28 205.8 5.7 133 61-215 127-264 (279)
3 KOG3576 Ovo and related transc 99.7 2.6E-17 5.5E-22 155.6 6.0 115 87-221 112-239 (267)
4 KOG1074 Transcriptional repres 99.6 9.6E-17 2.1E-21 177.3 4.2 66 51-116 340-405 (958)
5 KOG1074 Transcriptional repres 99.6 1.5E-16 3.2E-21 175.8 4.2 82 169-257 606-692 (958)
6 KOG3608 Zn finger proteins [Ge 99.6 1.8E-16 4E-21 160.4 2.6 193 68-275 183-394 (467)
7 KOG3623 Homeobox transcription 99.5 1.2E-15 2.6E-20 166.0 2.4 169 91-277 209-394 (1007)
8 KOG3576 Ovo and related transc 99.5 2E-15 4.2E-20 142.9 -1.1 122 130-258 114-237 (267)
9 KOG3623 Homeobox transcription 99.4 1.6E-13 3.5E-18 149.6 2.7 104 133-254 210-330 (1007)
10 KOG3608 Zn finger proteins [Ge 99.3 4.9E-13 1.1E-17 135.8 0.1 138 93-257 178-345 (467)
11 PLN03086 PRLI-interacting fact 99.1 8.5E-11 1.8E-15 129.7 6.2 103 90-218 451-564 (567)
12 PHA00733 hypothetical protein 98.8 2.9E-09 6.2E-14 97.2 4.5 83 130-220 37-125 (128)
13 PLN03086 PRLI-interacting fact 98.8 5.1E-09 1.1E-13 115.8 6.6 129 92-245 407-553 (567)
14 PHA00733 hypothetical protein 98.8 5.2E-09 1.1E-13 95.5 4.1 87 87-192 35-124 (128)
15 KOG3993 Transcription factor ( 98.6 7.7E-09 1.7E-13 107.9 -0.4 147 92-258 267-483 (500)
16 PHA02768 hypothetical protein; 98.5 2.7E-08 5.8E-13 76.3 1.5 42 169-211 6-48 (55)
17 PHA02768 hypothetical protein; 98.3 1.4E-07 3E-12 72.4 1.1 44 133-185 5-48 (55)
18 KOG3993 Transcription factor ( 98.3 9.2E-08 2E-12 100.0 -1.7 138 76-220 279-484 (500)
19 PF13465 zf-H2C2_2: Zinc-finge 98.2 5.1E-07 1.1E-11 59.1 0.6 26 155-180 1-26 (26)
20 PF01352 KRAB: KRAB box; Inte 97.7 1.7E-05 3.8E-10 57.6 2.3 26 4-29 16-41 (41)
21 COG5189 SFP1 Putative transcri 97.7 1E-05 2.2E-10 82.1 0.2 49 166-214 347-418 (423)
22 PHA00616 hypothetical protein 97.6 2E-05 4.3E-10 57.8 1.4 31 169-199 2-33 (44)
23 PHA00732 hypothetical protein 97.6 2.9E-05 6.2E-10 64.9 2.3 45 133-190 1-46 (79)
24 PF13465 zf-H2C2_2: Zinc-finge 97.6 3.3E-05 7.2E-10 50.5 2.0 24 183-206 1-26 (26)
25 COG5189 SFP1 Putative transcri 97.6 1.5E-05 3.4E-10 80.8 0.1 56 130-190 346-420 (423)
26 PHA00616 hypothetical protein 97.5 3.1E-05 6.8E-10 56.8 0.2 40 133-179 1-40 (44)
27 PHA00732 hypothetical protein 97.4 0.0001 2.2E-09 61.6 2.3 44 168-216 1-46 (79)
28 PF05605 zf-Di19: Drought indu 97.2 0.00042 9E-09 53.6 4.1 47 169-218 3-53 (54)
29 KOG1146 Homeobox protein [Gene 97.1 0.00083 1.8E-08 79.8 6.9 25 90-114 463-487 (1406)
30 PF05605 zf-Di19: Drought indu 96.9 0.0008 1.7E-08 52.0 3.2 50 133-192 2-54 (54)
31 PF00096 zf-C2H2: Zinc finger, 96.9 0.00068 1.5E-08 42.6 2.1 21 196-216 1-22 (23)
32 PF12756 zf-C2H2_2: C2H2 type 96.8 0.00073 1.6E-08 57.9 2.6 72 94-190 1-72 (100)
33 PF00096 zf-C2H2: Zinc finger, 96.7 0.00086 1.9E-08 42.1 1.5 22 169-190 1-22 (23)
34 COG5048 FOG: Zn-finger [Genera 96.4 0.0023 5.1E-08 68.3 3.5 137 91-256 288-441 (467)
35 PF13894 zf-C2H2_4: C2H2-type 96.4 0.0027 5.9E-08 39.7 2.4 22 196-217 1-23 (24)
36 PF12756 zf-C2H2_2: C2H2 type 96.4 0.0024 5.2E-08 54.6 2.6 73 135-218 1-74 (100)
37 PF13912 zf-C2H2_6: C2H2-type 96.2 0.0021 4.6E-08 42.0 1.1 23 195-217 1-24 (27)
38 PF13894 zf-C2H2_4: C2H2-type 96.0 0.0041 9E-08 38.8 1.8 22 169-190 1-22 (24)
39 PF13912 zf-C2H2_6: C2H2-type 95.9 0.0021 4.6E-08 42.0 0.1 25 92-116 1-25 (27)
40 KOG2231 Predicted E3 ubiquitin 95.8 0.0058 1.3E-07 69.2 3.2 22 92-113 99-135 (669)
41 PF09237 GAGA: GAGA factor; I 95.4 0.013 2.8E-07 44.3 2.6 31 165-195 21-52 (54)
42 COG5048 FOG: Zn-finger [Genera 95.3 0.016 3.4E-07 61.9 4.0 132 65-214 290-438 (467)
43 PRK04860 hypothetical protein; 94.9 0.0093 2E-07 56.6 0.7 36 168-207 119-156 (160)
44 PRK04860 hypothetical protein; 94.8 0.014 3.1E-07 55.3 1.6 39 132-181 118-156 (160)
45 smart00355 ZnF_C2H2 zinc finge 94.7 0.025 5.5E-07 35.6 2.2 22 196-217 1-23 (26)
46 smart00355 ZnF_C2H2 zinc finge 94.5 0.033 7.1E-07 35.0 2.4 23 169-191 1-23 (26)
47 KOG1146 Homeobox protein [Gene 94.3 0.019 4E-07 68.8 1.4 139 95-255 439-611 (1406)
48 PF09237 GAGA: GAGA factor; I 94.2 0.028 6.1E-07 42.5 1.7 32 130-168 21-52 (54)
49 PF12874 zf-met: Zinc-finger o 92.5 0.03 6.4E-07 35.8 -0.4 23 93-115 1-23 (25)
50 PF12874 zf-met: Zinc-finger o 92.0 0.074 1.6E-06 33.9 1.0 20 170-189 2-21 (25)
51 PF13909 zf-H2C2_5: C2H2-type 91.7 0.16 3.4E-06 32.2 2.3 22 196-218 1-23 (24)
52 KOG2893 Zn finger protein [Gen 91.6 0.077 1.7E-06 52.5 1.1 44 166-213 9-53 (341)
53 PF12171 zf-C2H2_jaz: Zinc-fin 91.6 0.061 1.3E-06 35.2 0.3 24 92-115 1-24 (27)
54 PF12171 zf-C2H2_jaz: Zinc-fin 90.5 0.073 1.6E-06 34.8 -0.1 21 169-189 2-22 (27)
55 COG5236 Uncharacterized conser 89.8 0.2 4.3E-06 52.2 2.2 65 148-216 228-303 (493)
56 PF13909 zf-H2C2_5: C2H2-type 89.7 0.25 5.4E-06 31.2 1.9 21 169-190 1-21 (24)
57 KOG2482 Predicted C2H2-type Zn 89.6 0.26 5.7E-06 51.3 2.9 118 131-254 142-355 (423)
58 KOG2932 E3 ubiquitin ligase in 89.2 4.4 9.4E-05 42.1 11.2 115 91-218 52-171 (389)
59 KOG4173 Alpha-SNAP protein [In 88.0 0.23 5.1E-06 48.2 1.2 83 130-220 76-172 (253)
60 KOG2482 Predicted C2H2-type Zn 87.3 0.37 8E-06 50.3 2.2 48 169-216 280-356 (423)
61 PF13913 zf-C2HC_2: zinc-finge 86.2 0.59 1.3E-05 30.2 2.0 19 197-216 4-23 (25)
62 KOG2231 Predicted E3 ubiquitin 84.0 0.67 1.5E-05 53.0 2.5 72 133-218 182-263 (669)
63 KOG2893 Zn finger protein [Gen 83.9 0.26 5.7E-06 48.8 -0.7 41 136-187 13-53 (341)
64 smart00451 ZnF_U1 U1-like zinc 83.5 0.79 1.7E-05 31.4 1.8 23 168-190 3-25 (35)
65 KOG2186 Cell growth-regulating 82.6 0.79 1.7E-05 46.1 2.0 44 169-214 4-48 (276)
66 PF13913 zf-C2HC_2: zinc-finge 82.6 1.1 2.3E-05 29.0 2.0 21 169-190 3-23 (25)
67 TIGR00622 ssl1 transcription f 80.0 3.3 7.1E-05 36.9 4.8 78 166-256 13-104 (112)
68 smart00451 ZnF_U1 U1-like zinc 79.8 1.6 3.5E-05 29.9 2.3 22 195-216 3-25 (35)
69 KOG2785 C2H2-type Zn-finger pr 79.4 0.41 8.9E-06 50.8 -1.2 154 92-254 3-241 (390)
70 COG4049 Uncharacterized protei 77.8 1 2.3E-05 34.7 0.9 30 163-192 12-42 (65)
71 KOG4124 Putative transcription 74.5 5.9 0.00013 41.8 5.5 25 89-113 346-372 (442)
72 COG1997 RPL43A Ribosomal prote 74.2 1.6 3.4E-05 36.9 1.1 34 130-180 32-65 (89)
73 COG4049 Uncharacterized protei 73.7 1.8 3.8E-05 33.5 1.2 29 191-219 13-42 (65)
74 PF09986 DUF2225: Uncharacteri 73.0 1.9 4.2E-05 42.9 1.7 25 90-114 3-27 (214)
75 COG5236 Uncharacterized conser 72.4 4.7 0.0001 42.3 4.3 112 92-216 151-273 (493)
76 cd00350 rubredoxin_like Rubred 71.8 2.4 5.2E-05 29.2 1.4 10 167-176 16-25 (33)
77 PF06524 NOA36: NOA36 protein; 71.0 4 8.8E-05 41.3 3.3 89 162-252 136-228 (314)
78 KOG2071 mRNA cleavage and poly 70.3 2.5 5.5E-05 47.5 1.9 28 89-116 415-442 (579)
79 COG1592 Rubrerythrin [Energy p 67.1 3.2 6.8E-05 39.7 1.6 26 131-176 132-157 (166)
80 PF09986 DUF2225: Uncharacteri 66.0 2.8 6E-05 41.8 1.1 44 131-181 3-61 (214)
81 PF04959 ARS2: Arsenite-resist 66.0 2.3 4.9E-05 42.4 0.4 29 165-193 74-103 (214)
82 KOG4173 Alpha-SNAP protein [In 65.7 1.5 3.3E-05 42.8 -0.8 80 90-192 77-171 (253)
83 PRK00464 nrdR transcriptional 64.9 3 6.4E-05 39.4 1.0 16 168-183 28-43 (154)
84 cd00729 rubredoxin_SM Rubredox 64.3 4.6 9.9E-05 28.1 1.6 10 167-176 17-26 (34)
85 COG1198 PriA Primosomal protei 63.6 4.5 9.9E-05 47.3 2.4 11 94-104 437-447 (730)
86 KOG2186 Cell growth-regulating 63.2 3.6 7.8E-05 41.5 1.2 48 133-190 3-50 (276)
87 PF09538 FYDLN_acid: Protein o 62.2 4.7 0.0001 35.8 1.7 15 167-181 25-39 (108)
88 KOG4124 Putative transcription 61.3 2.1 4.6E-05 44.9 -0.8 26 86-112 207-232 (442)
89 PF04216 FdhE: Protein involve 61.2 2.7 5.9E-05 43.8 -0.0 33 169-201 212-245 (290)
90 PF09723 Zn-ribbon_8: Zinc rib 58.6 5.4 0.00012 29.0 1.2 29 92-140 5-33 (42)
91 KOG1819 FYVE finger-containing 58.0 9.1 0.0002 42.0 3.2 15 90-104 899-913 (990)
92 PF09416 UPF1_Zn_bind: RNA hel 57.9 7.8 0.00017 36.4 2.4 26 165-190 11-42 (152)
93 PRK04023 DNA polymerase II lar 56.6 9.3 0.0002 45.7 3.3 13 89-101 623-635 (1121)
94 PF09538 FYDLN_acid: Protein o 56.3 5.5 0.00012 35.3 1.1 29 169-207 10-39 (108)
95 PF09845 DUF2072: Zn-ribbon co 56.2 5.6 0.00012 36.4 1.1 15 92-106 1-15 (131)
96 TIGR02605 CxxC_CxxC_SSSS putat 55.7 6.4 0.00014 29.7 1.2 14 92-105 5-18 (52)
97 smart00834 CxxC_CXXC_SSSS Puta 55.1 6.9 0.00015 27.8 1.3 15 92-106 5-19 (41)
98 PF12013 DUF3505: Protein of u 54.6 21 0.00045 31.4 4.5 24 196-219 81-109 (109)
99 COG1592 Rubrerythrin [Energy p 54.3 7 0.00015 37.4 1.5 24 91-140 133-156 (166)
100 PRK14890 putative Zn-ribbon RN 54.0 14 0.00031 29.0 2.9 30 168-202 25-56 (59)
101 PF02892 zf-BED: BED zinc fing 53.1 9.1 0.0002 27.8 1.7 24 166-189 14-41 (45)
102 PF12013 DUF3505: Protein of u 53.0 14 0.00031 32.4 3.2 24 169-192 81-109 (109)
103 PHA00626 hypothetical protein 52.9 7.5 0.00016 30.2 1.2 11 169-179 24-34 (59)
104 PRK00398 rpoP DNA-directed RNA 51.6 9 0.0002 28.3 1.4 15 91-105 2-16 (46)
105 PTZ00255 60S ribosomal protein 51.4 6.9 0.00015 33.5 0.9 14 167-180 53-66 (90)
106 COG2888 Predicted Zn-ribbon RN 49.4 8.5 0.00019 30.3 1.0 8 194-201 49-57 (61)
107 KOG1280 Uncharacterized conser 48.9 13 0.00029 39.2 2.6 32 166-197 77-109 (381)
108 TIGR00280 L37a ribosomal prote 48.0 7.4 0.00016 33.4 0.6 14 167-180 52-65 (91)
109 PRK14873 primosome assembly pr 47.9 11 0.00023 44.0 2.0 10 167-176 409-418 (665)
110 smart00531 TFIIE Transcription 47.9 19 0.00041 33.6 3.3 12 168-179 99-110 (147)
111 COG1996 RPC10 DNA-directed RNA 47.7 8.6 0.00019 29.2 0.8 13 90-102 4-16 (49)
112 PF03833 PolC_DP2: DNA polymer 47.0 6.4 0.00014 46.2 0.0 9 92-100 655-663 (900)
113 TIGR02300 FYDLN_acid conserved 46.6 13 0.00028 33.9 1.8 14 194-207 25-39 (129)
114 TIGR00622 ssl1 transcription f 46.1 31 0.00067 30.9 4.1 90 90-190 13-103 (112)
115 PF01780 Ribosomal_L37ae: Ribo 45.6 6.3 0.00014 33.8 -0.2 33 130-179 32-64 (90)
116 smart00531 TFIIE Transcription 43.8 12 0.00025 35.0 1.2 41 128-179 94-134 (147)
117 PRK09678 DNA-binding transcrip 43.6 11 0.00023 31.0 0.8 13 194-206 26-41 (72)
118 PF13717 zinc_ribbon_4: zinc-r 43.3 17 0.00037 25.6 1.7 10 169-178 26-35 (36)
119 KOG2071 mRNA cleavage and poly 43.0 17 0.00036 41.2 2.5 25 166-190 416-440 (579)
120 TIGR00595 priA primosomal prot 42.7 16 0.00034 41.2 2.3 14 164-177 236-249 (505)
121 TIGR02300 FYDLN_acid conserved 42.5 13 0.00028 33.9 1.2 34 132-183 8-41 (129)
122 PRK03976 rpl37ae 50S ribosomal 42.5 10 0.00022 32.5 0.5 14 167-180 53-66 (90)
123 PRK06266 transcription initiat 41.9 11 0.00025 36.4 0.9 33 130-178 114-146 (178)
124 PRK14714 DNA polymerase II lar 41.2 21 0.00046 43.9 3.0 10 92-101 667-676 (1337)
125 KOG2593 Transcription initiati 41.0 22 0.00047 38.8 2.9 34 166-202 126-161 (436)
126 KOG4377 Zn-finger protein [Gen 40.9 13 0.00027 40.2 1.1 28 89-116 268-297 (480)
127 TIGR00373 conserved hypothetic 40.3 13 0.00029 35.2 1.0 33 130-178 106-138 (158)
128 COG1594 RPB9 DNA-directed RNA 40.1 17 0.00037 32.5 1.6 17 90-106 20-36 (113)
129 PF13719 zinc_ribbon_5: zinc-r 39.9 20 0.00044 25.3 1.7 12 167-178 24-35 (37)
130 COG3364 Zn-ribbon containing p 39.8 11 0.00023 32.9 0.3 15 92-106 2-16 (112)
131 smart00614 ZnF_BED BED zinc fi 39.5 19 0.00042 27.0 1.6 21 169-189 19-44 (50)
132 PF14353 CpXC: CpXC protein 39.4 27 0.00059 31.5 2.9 13 169-181 39-51 (128)
133 TIGR02098 MJ0042_CXXC MJ0042 f 39.1 16 0.00035 25.6 1.1 15 93-107 3-17 (38)
134 COG1198 PriA Primosomal protei 38.8 20 0.00043 42.2 2.4 28 162-203 456-484 (730)
135 PF15135 UPF0515: Uncharacteri 38.2 17 0.00036 36.8 1.3 59 130-207 109-168 (278)
136 KOG0782 Predicted diacylglycer 38.1 5.4 0.00012 44.5 -2.2 72 130-208 218-290 (1004)
137 PF04959 ARS2: Arsenite-resist 37.3 23 0.00049 35.4 2.2 30 192-221 74-104 (214)
138 COG0068 HypF Hydrogenase matur 37.2 8.4 0.00018 44.5 -1.0 55 135-202 125-181 (750)
139 PF05191 ADK_lid: Adenylate ki 37.1 21 0.00046 25.2 1.4 27 93-140 2-28 (36)
140 PRK09678 DNA-binding transcrip 36.7 12 0.00026 30.8 0.1 15 166-180 25-41 (72)
141 TIGR00373 conserved hypothetic 36.5 21 0.00046 33.8 1.8 34 164-205 105-139 (158)
142 PF05443 ROS_MUCR: ROS/MUCR tr 34.8 20 0.00043 33.0 1.2 25 168-195 72-97 (132)
143 COG4530 Uncharacterized protei 34.1 28 0.00061 30.8 2.0 13 166-178 24-36 (129)
144 PRK06266 transcription initiat 34.0 24 0.00052 34.1 1.7 33 166-206 115-148 (178)
145 PRK00464 nrdR transcriptional 33.7 24 0.00052 33.4 1.6 21 90-110 26-46 (154)
146 COG1656 Uncharacterized conser 33.7 31 0.00067 32.9 2.3 24 166-189 128-151 (165)
147 COG3091 SprT Zn-dependent meta 33.4 19 0.00042 33.8 0.9 34 166-204 115-150 (156)
148 KOG3002 Zn finger protein [Gen 32.9 31 0.00066 36.3 2.4 60 166-240 78-143 (299)
149 PF03604 DNA_RNApol_7kD: DNA d 32.7 31 0.00068 23.7 1.6 11 93-103 1-11 (32)
150 PRK05580 primosome assembly pr 32.4 30 0.00064 40.6 2.4 11 167-177 407-417 (679)
151 cd07765 KRAB_A-box KRAB (Krupp 32.3 49 0.0011 19.9 2.6 23 5-27 17-39 (40)
152 PF05443 ROS_MUCR: ROS/MUCR tr 31.6 27 0.00059 32.1 1.6 29 130-168 69-97 (132)
153 PRK03824 hypA hydrogenase nick 31.5 27 0.00058 32.2 1.5 16 90-105 68-83 (135)
154 COG3357 Predicted transcriptio 31.2 27 0.00059 29.9 1.4 15 90-104 56-70 (97)
155 PF00301 Rubredoxin: Rubredoxi 31.2 49 0.0011 24.9 2.6 16 92-107 1-16 (47)
156 KOG1280 Uncharacterized conser 31.1 14 0.0003 39.1 -0.5 60 193-252 77-138 (381)
157 PF06524 NOA36: NOA36 protein; 30.9 25 0.00054 35.8 1.3 73 130-211 139-226 (314)
158 COG1571 Predicted DNA-binding 30.5 29 0.00062 38.0 1.7 29 170-208 352-381 (421)
159 KOG4167 Predicted DNA-binding 30.5 17 0.00036 42.1 -0.0 27 90-116 790-816 (907)
160 TIGR01562 FdhE formate dehydro 29.6 21 0.00046 37.5 0.6 10 130-139 207-216 (305)
161 PF01096 TFIIS_C: Transcriptio 27.1 19 0.00041 25.8 -0.2 10 169-178 29-38 (39)
162 smart00659 RPOLCX RNA polymera 27.0 38 0.00083 25.0 1.4 12 167-178 18-29 (44)
163 PRK04023 DNA polymerase II lar 26.9 40 0.00088 40.7 2.2 11 167-177 650-660 (1121)
164 PF15269 zf-C2H2_7: Zinc-finge 26.9 47 0.001 24.7 1.8 21 196-216 21-42 (54)
165 PRK14873 primosome assembly pr 26.8 31 0.00068 40.3 1.3 6 135-140 385-390 (665)
166 KOG4167 Predicted DNA-binding 26.1 17 0.00037 42.0 -0.9 26 195-220 792-818 (907)
167 PF04216 FdhE: Protein involve 25.8 15 0.00033 38.2 -1.3 52 133-207 172-224 (290)
168 PF04810 zf-Sec23_Sec24: Sec23 25.8 34 0.00074 24.6 0.9 23 156-178 12-34 (40)
169 COG3677 Transposase and inacti 25.6 35 0.00075 31.3 1.1 16 166-181 51-66 (129)
170 COG1571 Predicted DNA-binding 25.4 40 0.00087 36.9 1.7 35 131-183 348-382 (421)
171 KOG2932 E3 ubiquitin ligase in 25.0 45 0.00099 34.8 2.0 29 164-192 140-172 (389)
172 KOG2785 C2H2-type Zn-finger pr 24.6 62 0.0013 34.8 2.9 73 133-216 166-242 (390)
173 KOG1701 Focal adhesion adaptor 24.6 13 0.00028 40.4 -2.1 23 91-113 301-323 (468)
174 KOG2593 Transcription initiati 24.5 24 0.00052 38.5 -0.2 40 129-178 124-163 (436)
175 PF12760 Zn_Tnp_IS1595: Transp 24.2 40 0.00088 24.8 1.1 11 166-176 35-45 (46)
176 TIGR00595 priA primosomal prot 24.2 42 0.00092 37.8 1.7 18 159-176 244-261 (505)
177 smart00440 ZnF_C2C2 C2C2 Zinc 24.1 31 0.00068 24.8 0.5 11 169-179 29-39 (40)
178 PF05290 Baculo_IE-1: Baculovi 24.1 30 0.00066 31.8 0.5 18 89-106 77-94 (140)
179 KOG2461 Transcription factor B 23.9 1.8E+02 0.0038 31.9 6.3 32 85-116 203-234 (396)
180 TIGR01384 TFS_arch transcripti 23.8 45 0.00097 28.9 1.5 15 91-105 15-29 (104)
181 PRK12380 hydrogenase nickel in 23.4 41 0.00088 30.0 1.2 15 90-104 68-82 (113)
182 TIGR03826 YvyF flagellar opero 23.3 26 0.00056 32.5 -0.2 11 94-104 5-15 (137)
183 PF07800 DUF1644: Protein of u 23.1 1.5E+02 0.0032 28.2 4.8 50 168-219 80-133 (162)
184 COG4957 Predicted transcriptio 22.1 31 0.00066 31.8 0.1 20 94-116 78-97 (148)
185 PRK05978 hypothetical protein; 22.0 53 0.0012 30.9 1.7 33 133-181 33-65 (148)
186 PF11672 DUF3268: Protein of u 21.6 53 0.0011 28.9 1.5 9 132-140 1-9 (102)
187 PF07975 C1_4: TFIIH C1-like d 21.5 38 0.00082 26.0 0.5 27 90-116 19-45 (51)
188 PF10263 SprT-like: SprT-like 21.4 26 0.00056 32.5 -0.6 31 168-205 123-154 (157)
189 KOG2807 RNA polymerase II tran 21.2 68 0.0015 33.8 2.4 69 93-200 277-373 (378)
190 KOG3507 DNA-directed RNA polym 20.7 39 0.00085 26.6 0.4 14 167-180 36-49 (62)
191 TIGR01562 FdhE formate dehydro 20.7 69 0.0015 33.8 2.3 28 163-203 205-233 (305)
192 PRK03564 formate dehydrogenase 20.4 73 0.0016 33.6 2.5 49 130-201 184-233 (309)
193 TIGR03831 YgiT_finger YgiT-typ 20.3 52 0.0011 23.6 1.0 15 166-180 30-44 (46)
194 KOG4377 Zn-finger protein [Gen 20.2 34 0.00075 37.0 0.0 76 130-217 268-368 (480)
195 PHA02998 RNA polymerase subuni 20.1 52 0.0011 31.7 1.2 11 169-179 172-182 (195)
196 TIGR01206 lysW lysine biosynth 20.0 65 0.0014 25.0 1.5 13 92-104 2-14 (54)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.88 E-value=4.6e-24 Score=210.85 Aligned_cols=136 Identities=19% Similarity=0.403 Sum_probs=125.7
Q ss_pred ccCcccccccCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccCCcc
Q 007898 89 ATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKK 168 (585)
Q Consensus 89 ~~kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekp 168 (585)
...+|+|.+|||.|.+..+|.+|..+|.. ....+.+.|++|| |.|.....|+.|+|+|+ -+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~----------~~s~ka~~C~~C~-------K~YvSmpALkMHirTH~--l~ 187 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRS----------LDSKKAFSCKYCG-------KVYVSMPALKMHIRTHT--LP 187 (279)
T ss_pred cCCceeccccccccccccccchhhccccc----------ccccccccCCCCC-------ceeeehHHHhhHhhccC--CC
Confidence 45789999999999999999999999961 1157889999996 99999999999999997 57
Q ss_pred ccccccCCcccChhHHHHHHHH-hCCcceecC-CCCccCChHHHHHHHHHhhhccccccccccCCCCccCCCCCCCCCcC
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRRDSFITHRAFCDALAEESTRAITGTNPILSSSSHHQPGIV 246 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F~~~s~L~~H~~~h~~~~~~~~r~ht~ekp~~cs~c~~sf~~~ 246 (585)
++|.+|||.|.+..-|..|+|+ +|||||.|. |+|.|..+++|+.|+ .+|++.|.|+|..|+++|+..
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHm-----------QTHS~~K~~qC~~C~KsFsl~ 256 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHM-----------QTHSDVKKHQCPRCGKSFALK 256 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHH-----------HhhcCCccccCcchhhHHHHH
Confidence 9999999999999999999999 899999999 999999999999999 677889999999999999999
Q ss_pred CCcccccc
Q 007898 247 AGASSHVN 254 (585)
Q Consensus 247 s~l~sH~~ 254 (585)
+-|..|+-
T Consensus 257 SyLnKH~E 264 (279)
T KOG2462|consen 257 SYLNKHSE 264 (279)
T ss_pred HHHHHhhh
Confidence 99999964
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.88 E-value=2.4e-23 Score=205.78 Aligned_cols=133 Identities=23% Similarity=0.412 Sum_probs=121.2
Q ss_pred CcccccCCCCCCCCCCchhhccCccccc---ccCcccccccCcccccccccchhcccccCccccccchhhhccccccccC
Q 007898 61 PPAKKKRNLPGNPDPDAEVIALSPKTLM---ATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCP 137 (585)
Q Consensus 61 ~p~k~k~~~~~~~~~~~~~~~~~~k~~~---~~kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~ 137 (585)
...+.++..|++.......+..|..+|- ..+.+.|++|+|.|.....|+.|+|+|+ -+++|.
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~---------------l~c~C~ 191 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT---------------LPCECG 191 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC---------------CCcccc
Confidence 4556677778887777788888888773 3789999999999999999999999996 578999
Q ss_pred CCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHH-hCCcceecC-CCCccCChHHHHHHHH
Q 007898 138 EPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRRDSFITHRA 215 (585)
Q Consensus 138 ~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F~~~s~L~~H~~ 215 (585)
+|| |.|.+..-|+-|+|+|+|||||.|..|+|+|..+++|+.||++ .+.|+|.|. |+|+|.+++.|.+|..
T Consensus 192 iCG-------KaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 192 ICG-------KAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred ccc-------ccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 996 9999999999999999999999999999999999999999999 588999999 9999999999999984
No 3
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.68 E-value=2.6e-17 Score=155.56 Aligned_cols=115 Identities=23% Similarity=0.526 Sum_probs=105.5
Q ss_pred ccccCcccccccCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccCC
Q 007898 87 LMATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGE 166 (585)
Q Consensus 87 ~~~~kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htge 166 (585)
-.+...|.|.+|+|.|....-|.+|++.|. .-|.|-|..|| |.|.+.-+|++|+|+|+|.
T Consensus 112 ssd~d~ftCrvCgK~F~lQRmlnrh~kch~-------------~vkr~lct~cg-------kgfndtfdlkrh~rthtgv 171 (267)
T KOG3576|consen 112 SSDQDSFTCRVCGKKFGLQRMLNRHLKCHS-------------DVKRHLCTFCG-------KGFNDTFDLKRHTRTHTGV 171 (267)
T ss_pred CCCCCeeeeehhhhhhhHHHHHHHHhhhcc-------------HHHHHHHhhcc-------CcccchhhhhhhhccccCc
Confidence 344678999999999999999999999998 88999999996 9999999999999999999
Q ss_pred ccccccccCCcccChhHHHHHHHH-hC-----------CcceecC-CCCccCChHHHHHHHHHhhhcc
Q 007898 167 KKWKCDKCSKRYAVQSDWKAHSKT-CG-----------TREYRCD-CGTLFSRRDSFITHRAFCDALA 221 (585)
Q Consensus 167 kpy~C~~CgK~F~~~s~L~~H~r~-hg-----------ekpy~C~-Cgk~F~~~s~L~~H~~~h~~~~ 221 (585)
+||+|..|+|.|..+..|..|.+. || +|.|.|+ ||.+-.+...+..|++.||...
T Consensus 172 rpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 172 RPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred cccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 999999999999999999999887 86 3679999 9999999999999998887654
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.63 E-value=9.6e-17 Score=177.26 Aligned_cols=66 Identities=20% Similarity=0.402 Sum_probs=58.6
Q ss_pred cccCCCCCCCCcccccCCCCCCCCCCchhhccCcccccccCcccccccCcccccccccchhccccc
Q 007898 51 YFATPPTQAQPPAKKKRNLPGNPDPDAEVIALSPKTLMATNRFVCEICNKGFQRDQNLQLHRRGHN 116 (585)
Q Consensus 51 ~~~~~~~~~~~p~k~k~~~~~~~~~~~~~~~~~~k~~~~~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 116 (585)
+........++-.+.+|..|.+-+.....+..|.++|++++||+|++||..|.++.+|+.|...|+
T Consensus 340 ~~~v~~~~~~~~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 340 YFSVEGPSEKPFFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred ccccccCCccccccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeecc
Confidence 444455566778889999999999999999999999999999999999999999999999988886
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.62 E-value=1.5e-16 Score=175.85 Aligned_cols=82 Identities=17% Similarity=0.381 Sum_probs=70.3
Q ss_pred ccccccCCcccChhHHHHHHHH-hCCcceecC-CCCccCChHHHHHHHHHhhhccccccccccCCCCccCC---CCCCCC
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRRDSFITHRAFCDALAEESTRAITGTNPILSS---SSHHQP 243 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F~~~s~L~~H~~~h~~~~~~~~r~ht~ekp~~cs---~c~~sf 243 (585)
..|-+|.++..-++.|+.|.|+ +|||||+|+ ||+.|.+|.+|+.|+-+|... +.-.-.++|. +|.+.|
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~-------p~~R~q~ScP~~~ic~~kf 678 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAK-------PPARVQFSCPSTFICQKKF 678 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccC-------ccccccccCCchhhhcccc
Confidence 4799999999999999999999 799999999 999999999999999777532 2333568899 999999
Q ss_pred CcCCCccccccccc
Q 007898 244 GIVAGASSHVNLQI 257 (585)
Q Consensus 244 ~~~s~l~sH~~~~~ 257 (585)
...-.+..|+++|.
T Consensus 679 tn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 679 TNAVTLPQHIRIHL 692 (958)
T ss_pred cccccccceEEeec
Confidence 99999999999876
No 6
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.61 E-value=1.8e-16 Score=160.42 Aligned_cols=193 Identities=16% Similarity=0.227 Sum_probs=152.0
Q ss_pred CCCCCCCCCchhhccCcccccccCcccccccCcccccccccchhccccc----Ccccccc---------chhhhc--ccc
Q 007898 68 NLPGNPDPDAEVIALSPKTLMATNRFVCEICNKGFQRDQNLQLHRRGHN----LPWKLKQ---------RTSKEI--RKK 132 (585)
Q Consensus 68 ~~~~~~~~~~~~~~~~~k~~~~~kpy~C~~Cgk~F~~~~~L~~H~r~H~----~~~~~~~---------~~~~~~--~~k 132 (585)
..|.....+...+..|.++|+++|...|+.||.-|.++..|..|.+.-+ .++.|+. ....|+ .-.
T Consensus 183 ~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn 262 (467)
T KOG3608|consen 183 AMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN 262 (467)
T ss_pred hhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 4444555566778899999999999999999999999999999987654 3344332 111222 235
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhc-cccCCccccccccCCcccChhHHHHHHHHhCCcceecC---CCCccCChH
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFC-RKHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD---CGTLFSRRD 208 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r-~Htgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~---Cgk~F~~~s 208 (585)
.|+|+.|. -.....+.|.+|++ .|..+|||+|+.|++.|.+.++|.+|..+|.+..|.|+ |...|+.+.
T Consensus 263 ~ykCplCd-------mtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~ 335 (467)
T KOG3608|consen 263 CYKCPLCD-------MTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYT 335 (467)
T ss_pred cccccccc-------cCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHH
Confidence 78999994 88888899999988 57788999999999999999999999999888889997 999999999
Q ss_pred HHHHHHHHhhhccccccccccCCCCccCCCCCCCCCcCCCcccccccccCCCCCCcccccccchhhh
Q 007898 209 SFITHRAFCDALAEESTRAITGTNPILSSSSHHQPGIVAGASSHVNLQIPQFNPQDFSAFSLKKEQQ 275 (585)
Q Consensus 209 ~L~~H~~~h~~~~~~~~r~ht~ekp~~cs~c~~sf~~~s~l~sH~~~~~~~~~~~~~~~~~~k~eqq 275 (585)
.|++|++-++... .+.+|.|..|.+.|.+..+|..|+...+...-+.....|.+|..+.
T Consensus 336 q~~~H~~evhEg~--------np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh~RFtYk~~ed 394 (467)
T KOG3608|consen 336 QMRRHFLEVHEGN--------NPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGHKRFTYKVDED 394 (467)
T ss_pred HHHHHHHHhccCC--------CCCceeeecchhhhccchhHHHHHHHhhcccCCCCCCceeeeeccC
Confidence 9999986554222 3567999999999999999999987666544466666777776555
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.55 E-value=1.2e-15 Score=165.95 Aligned_cols=169 Identities=18% Similarity=0.348 Sum_probs=128.4
Q ss_pred CcccccccCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccC-----
Q 007898 91 NRFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHG----- 165 (585)
Q Consensus 91 kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htg----- 165 (585)
....|.+|.+.|++...|+.|++.-+ +..+..|.|..| .+.|..+..|.+||.+|..
T Consensus 209 qlltcpycdrgykrltslkeHikyrh-----------ekne~nfsC~lC-------sytFAyRtQLErhm~~hkpg~dqa 270 (1007)
T KOG3623|consen 209 QLLTCPYCDRGYKRLTSLKEHIKYRH-----------EKNEPNFSCMLC-------SYTFAYRTQLERHMQLHKPGGDQA 270 (1007)
T ss_pred hhhcchhHHHHHHHHHHHHHHHHHHH-----------hhCCCCCcchhh-------hhhhhhHHHHHHHHHhhcCCCccc
Confidence 35689999999999999999987643 125667999999 5999999999999998852
Q ss_pred --------CccccccccCCcccChhHHHHHHHH-hCCcceecC-CCCccCChHHHHHHHH--HhhhccccccccccCCCC
Q 007898 166 --------EKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRRDSFITHRA--FCDALAEESTRAITGTNP 233 (585)
Q Consensus 166 --------ekpy~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F~~~s~L~~H~~--~h~~~~~~~~r~ht~ekp 233 (585)
.|.|+|.+|||.|+.+.+|+.|+|+ .|||||.|+ |+|+|....++..|+. .|-.+.....|..++-|.
T Consensus 271 ~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSSKKCIsli~vngr~R~~lKt 350 (1007)
T KOG3623|consen 271 ISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSSKKCISLILVNGRNRALLKT 350 (1007)
T ss_pred ccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccccchhhhhcccCcchhhhhh
Confidence 4779999999999999999999999 699999999 9999999999999984 455555555666666666
Q ss_pred ccCCCCCCCCCcCCCcccccccccCCCCCCcccccccchhhhhc
Q 007898 234 ILSSSSHHQPGIVAGASSHVNLQIPQFNPQDFSAFSLKKEQQSY 277 (585)
Q Consensus 234 ~~cs~c~~sf~~~s~l~sH~~~~~~~~~~~~~~~~~~k~eqq~~ 277 (585)
..|+.-..+.+.....+.+.+..........+...+|+.+...+
T Consensus 351 ~~~Sp~saSsSp~~s~~pq~r~klen~~slql~~~qistepsda 394 (1007)
T KOG3623|consen 351 LEKSPGSASSSPRRSPSPQGRGKLENQPSLQLLPHQISTEPSDA 394 (1007)
T ss_pred cccCCcccCCCCCCCCChhHhhhccCchhhccCCcccccccchh
Confidence 66666555555555555555543333222334445566666544
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.50 E-value=2e-15 Score=142.90 Aligned_cols=122 Identities=19% Similarity=0.334 Sum_probs=110.9
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHH-hCCcceecC-CCCccCCh
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRR 207 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F~~~ 207 (585)
+...|.|.+|+ |.|....-|.+|++.|...|.|-|..|||.|...-+|++|+|+ +|.+||+|. |+|.|..+
T Consensus 114 d~d~ftCrvCg-------K~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqr 186 (267)
T KOG3576|consen 114 DQDSFTCRVCG-------KKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQR 186 (267)
T ss_pred CCCeeeeehhh-------hhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhh
Confidence 56789999996 9999999999999999999999999999999999999999999 799999999 99999999
Q ss_pred HHHHHHHHHhhhccccccccccCCCCccCCCCCCCCCcCCCcccccccccC
Q 007898 208 DSFITHRAFCDALAEESTRAITGTNPILSSSSHHQPGIVAGASSHVNLQIP 258 (585)
Q Consensus 208 s~L~~H~~~h~~~~~~~~r~ht~ekp~~cs~c~~sf~~~s~l~sH~~~~~~ 258 (585)
-+|..|.+..|+.....+-....+|.|.|+.|+..-.....+-.|++.+++
T Consensus 187 csleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 187 CSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred ccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 999999988887776666555668999999999998888888888887764
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.37 E-value=1.6e-13 Score=149.61 Aligned_cols=104 Identities=25% Similarity=0.518 Sum_probs=93.5
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhcccc--CCccccccccCCcccChhHHHHHHHHhC--------------Ccce
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFCRKH--GEKKWKCDKCSKRYAVQSDWKAHSKTCG--------------TREY 196 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Ht--gekpy~C~~CgK~F~~~s~L~~H~r~hg--------------ekpy 196 (585)
...|++|. +.+.+...|+.|++.-+ .+..|.|..|..+|..+..|.+|+.+|. -|.|
T Consensus 210 lltcpycd-------rgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKF 282 (1007)
T KOG3623|consen 210 LLTCPYCD-------RGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKF 282 (1007)
T ss_pred hhcchhHH-------HHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccc
Confidence 46899995 99999999999987533 3456999999999999999999999852 2679
Q ss_pred ecC-CCCccCChHHHHHHHHHhhhccccccccccCCCCccCCCCCCCCCcCCCcccccc
Q 007898 197 RCD-CGTLFSRRDSFITHRAFCDALAEESTRAITGTNPILSSSSHHQPGIVAGASSHVN 254 (585)
Q Consensus 197 ~C~-Cgk~F~~~s~L~~H~~~h~~~~~~~~r~ht~ekp~~cs~c~~sf~~~s~l~sH~~ 254 (585)
+|. |+|.|+++..|+.|+ |+|+|||||.|..|.+.|+...++++||.
T Consensus 283 KCtECgKAFKfKHHLKEHl-----------RIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 283 KCTECGKAFKFKHHLKEHL-----------RIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred cccccchhhhhHHHHHhhh-----------eeecCCCCcCCcccccccccCCccccccc
Confidence 999 999999999999999 89999999999999999999999999974
No 10
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.28 E-value=4.9e-13 Score=135.77 Aligned_cols=138 Identities=20% Similarity=0.342 Sum_probs=75.0
Q ss_pred ccc--cccCcccccccccchhcccccCccccccchhhhccccccccCCCCccc-----------------------CCCC
Q 007898 93 FVC--EICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVH-----------------------HDPS 147 (585)
Q Consensus 93 y~C--~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~-----------------------~~~~ 147 (585)
+.| ..|-+.|..++.|++|+|.|+ ++|...|+.||..| ..|.
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~Hs-------------~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~ 244 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRTHS-------------NEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCF 244 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHhcC-------------CCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHH
Confidence 445 569999999999999999998 55555555553000 0002
Q ss_pred CccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHH-h-CCcceecC-CCCccCChHHHHHHHHHhhhccccc
Q 007898 148 RALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT-C-GTREYRCD-CGTLFSRRDSFITHRAFCDALAEES 224 (585)
Q Consensus 148 k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~-h-gekpy~C~-Cgk~F~~~s~L~~H~~~h~~~~~~~ 224 (585)
|.|.....|+.|++.|. .-|+|+.|+......+.|.+|++. | ..|||+|+ |.+.|.+.+.|.+|..
T Consensus 245 KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~--------- 313 (467)
T KOG3608|consen 245 KRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ--------- 313 (467)
T ss_pred HHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH---------
Confidence 44444444444444442 235555555555555555555555 3 34555555 5555555555555552
Q ss_pred cccccCCCCccCCC--CCCCCCcCCCccccccccc
Q 007898 225 TRAITGTNPILSSS--SHHQPGIVAGASSHVNLQI 257 (585)
Q Consensus 225 ~r~ht~ekp~~cs~--c~~sf~~~s~l~sH~~~~~ 257 (585)
+|+ +..|.|.. |..++.....+++|++-++
T Consensus 314 --~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 314 --VHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred --hcc-ccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 222 33455544 5555555555555554444
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.10 E-value=8.5e-11 Score=129.70 Aligned_cols=103 Identities=21% Similarity=0.446 Sum_probs=55.8
Q ss_pred cCcccccccCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccCCccc
Q 007898 90 TNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKW 169 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy 169 (585)
++.+.|+.|++.|. ...|..|+++|+ ++|.|+ || +.+ .+..|..|+++|..+|++
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H---------------kpv~Cp-Cg-------~~~-~R~~L~~H~~thCp~Kpi 505 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH---------------EPLQCP-CG-------VVL-EKEQMVQHQASTCPLRLI 505 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC---------------CCccCC-CC-------CCc-chhHHHhhhhccCCCCce
Confidence 34455666666553 344555555542 455665 53 333 345566666666666666
Q ss_pred cccccCCcccC----------hhHHHHHHHHhCCcceecC-CCCccCChHHHHHHHHHhh
Q 007898 170 KCDKCSKRYAV----------QSDWKAHSKTCGTREYRCD-CGTLFSRRDSFITHRAFCD 218 (585)
Q Consensus 170 ~C~~CgK~F~~----------~s~L~~H~r~hgekpy~C~-Cgk~F~~~s~L~~H~~~h~ 218 (585)
.|.+|++.|.. ...|..|..++|.+++.|. |++.|..+ .|..|+..+|
T Consensus 506 ~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 506 TCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred eCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeeeh-hHHHHHHHhh
Confidence 66666665531 2355666555666666666 66655444 3455554444
No 12
>PHA00733 hypothetical protein
Probab=98.83 E-value=2.9e-09 Score=97.17 Aligned_cols=83 Identities=14% Similarity=0.267 Sum_probs=67.1
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhh--h---ccccCCccccccccCCcccChhHHHHHHHHhCCcceecC-CCCc
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKH--F---CRKHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTL 203 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H--~---r~Htgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~ 203 (585)
..|.+.|.+|. +.|.....|..| + ..++++++|.|+.|++.|.....|..|++++ +++|.|. |++.
T Consensus 37 ~~~~~~~~~~~-------~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~ 108 (128)
T PHA00733 37 EQKRLIRAVVK-------TLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKE 108 (128)
T ss_pred hhhhHHHHHHh-------hhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCc
Confidence 56889999994 566665555444 1 2334589999999999999999999999876 5689999 9999
Q ss_pred cCChHHHHHHHHHhhhc
Q 007898 204 FSRRDSFITHRAFCDAL 220 (585)
Q Consensus 204 F~~~s~L~~H~~~h~~~ 220 (585)
|.....|.+|+...|++
T Consensus 109 F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 109 FRNTDSTLDHVCKKHNI 125 (128)
T ss_pred cCCHHHHHHHHHHhcCc
Confidence 99999999999776654
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.81 E-value=5.1e-09 Score=115.80 Aligned_cols=129 Identities=18% Similarity=0.303 Sum_probs=96.7
Q ss_pred cccccccCcccccccccchhcccccC-----c-cccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccC
Q 007898 92 RFVCEICNKGFQRDQNLQLHRRGHNL-----P-WKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHG 165 (585)
Q Consensus 92 py~C~~Cgk~F~~~~~L~~H~r~H~~-----~-~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htg 165 (585)
.-.|..|.+.... .+|..|...... + ..|.........++.+.|+.|+ +.|. ...|..|+++|+
T Consensus 407 ~V~C~NC~~~i~l-~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cg-------k~f~-~s~LekH~~~~H- 476 (567)
T PLN03086 407 TVECRNCKHYIPS-RSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCG-------QAFQ-QGEMEKHMKVFH- 476 (567)
T ss_pred eEECCCCCCccch-hHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCC-------Cccc-hHHHHHHHHhcC-
Confidence 3468889876654 556677654321 1 1244444444567788999996 7885 678999999986
Q ss_pred CccccccccCCcccChhHHHHHHHH-hCCcceecC-CCCccCC----------hHHHHHHHHHhhhccccccccccCCCC
Q 007898 166 EKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSR----------RDSFITHRAFCDALAEESTRAITGTNP 233 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F~~----------~s~L~~H~~~h~~~~~~~~r~ht~ekp 233 (585)
++|.|. ||+.| .+..|..|+++ +.+|++.|. |++.|.. ...|..|... ++.++
T Consensus 477 -kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~------------CG~rt 541 (567)
T PLN03086 477 -EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI------------CGSRT 541 (567)
T ss_pred -CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh------------cCCcc
Confidence 889999 99865 67999999998 899999999 9999952 3478888733 47899
Q ss_pred ccCCCCCCCCCc
Q 007898 234 ILSSSSHHQPGI 245 (585)
Q Consensus 234 ~~cs~c~~sf~~ 245 (585)
+.|..|++.+..
T Consensus 542 ~~C~~Cgk~Vrl 553 (567)
T PLN03086 542 APCDSCGRSVML 553 (567)
T ss_pred eEccccCCeeee
Confidence 999999986543
No 14
>PHA00733 hypothetical protein
Probab=98.77 E-value=5.2e-09 Score=95.49 Aligned_cols=87 Identities=16% Similarity=0.168 Sum_probs=71.6
Q ss_pred ccccCcccccccCcccccccccchh--cccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhcccc
Q 007898 87 LMATNRFVCEICNKGFQRDQNLQLH--RRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKH 164 (585)
Q Consensus 87 ~~~~kpy~C~~Cgk~F~~~~~L~~H--~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Ht 164 (585)
....++++|.+|.+.|.....|..| ++.|. .+...++|.|+.|| +.|.....|..|++.|
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~----------~~~~~kPy~C~~Cg-------k~Fss~s~L~~H~r~h- 96 (128)
T PHA00733 35 TPEQKRLIRAVVKTLIYNPQLLDESSYLYKLL----------TSKAVSPYVCPLCL-------MPFSSSVSLKQHIRYT- 96 (128)
T ss_pred ChhhhhHHHHHHhhhccChhhhcchHHHHhhc----------ccCCCCCccCCCCC-------CcCCCHHHHHHHHhcC-
Confidence 3447899999999999988777766 22221 11167899999996 9999999999999987
Q ss_pred CCccccccccCCcccChhHHHHHHHH-hC
Q 007898 165 GEKKWKCDKCSKRYAVQSDWKAHSKT-CG 192 (585)
Q Consensus 165 gekpy~C~~CgK~F~~~s~L~~H~r~-hg 192 (585)
+++|.|.+|++.|.....|.+|+.. |+
T Consensus 97 -~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 97 -EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred -CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 4679999999999999999999988 75
No 15
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.59 E-value=7.7e-09 Score=107.90 Aligned_cols=147 Identities=18% Similarity=0.243 Sum_probs=97.3
Q ss_pred cccccccCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccCC-----
Q 007898 92 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGE----- 166 (585)
Q Consensus 92 py~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htge----- 166 (585)
-|.|..|...|.+...|-.|.-.-. -..-|+|++|+ |.|....+|..|.|+|.-.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RI-------------V~vEYrCPEC~-------KVFsCPANLASHRRWHKPR~eaa~ 326 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRI-------------VHVEYRCPECD-------KVFSCPANLASHRRWHKPRPEAAK 326 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCee-------------EEeeecCCccc-------ccccCchhhhhhhcccCCchhhhh
Confidence 5999999999999999999964322 34579999995 9999999999999998521
Q ss_pred ----------------------------ccccccccCCcccChhHHHHHHHHhCCc------------------ceecC-
Q 007898 167 ----------------------------KKWKCDKCSKRYAVQSDWKAHSKTCGTR------------------EYRCD- 199 (585)
Q Consensus 167 ----------------------------kpy~C~~CgK~F~~~s~L~~H~r~hgek------------------py~C~- 199 (585)
-.|.|.+|+|.|.+...|+.|+.+|... -+-|.
T Consensus 327 a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~ 406 (500)
T KOG3993|consen 327 AGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQA 406 (500)
T ss_pred cCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccc
Confidence 1277888888888888888887663111 02233
Q ss_pred CCCccCChHHHHHHHHHhhhcc------------------ccccccccCCCCccCCCCCCCCCcCCCcccccccccC
Q 007898 200 CGTLFSRRDSFITHRAFCDALA------------------EESTRAITGTNPILSSSSHHQPGIVAGASSHVNLQIP 258 (585)
Q Consensus 200 Cgk~F~~~s~L~~H~~~h~~~~------------------~~~~r~ht~ekp~~cs~c~~sf~~~s~l~sH~~~~~~ 258 (585)
|.-.|...+.--.|...+-+.. ....|.-..+.-|.|.+|...|...-++.+|++..++
T Consensus 407 ~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hp 483 (500)
T KOG3993|consen 407 VATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHP 483 (500)
T ss_pred cccccccccccccceeeeeccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcCh
Confidence 4333333222222221111000 1112222335568999999999999999999987764
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.54 E-value=2.7e-08 Score=76.34 Aligned_cols=42 Identities=17% Similarity=0.475 Sum_probs=25.7
Q ss_pred ccccccCCcccChhHHHHHHHHhCCcceecC-CCCccCChHHHH
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFSRRDSFI 211 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~~~s~L~ 211 (585)
|+|++|||.|...++|..|+++|. ++|+|. |+|.|.+.+.|+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceecccceeE
Confidence 566666666666666666666644 566666 666666555543
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.34 E-value=1.4e-07 Score=72.43 Aligned_cols=44 Identities=14% Similarity=0.275 Sum_probs=40.1
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHH
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWK 185 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~ 185 (585)
-|+|++|| +.|....+|..|+++|+ ++|+|..|+|.|...+.|.
T Consensus 5 ~y~C~~CG-------K~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICG-------EIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhC-------CeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 48999996 99999999999999998 7999999999999877664
No 18
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.27 E-value=9.2e-08 Score=100.03 Aligned_cols=138 Identities=17% Similarity=0.238 Sum_probs=97.0
Q ss_pred CchhhccCcccccccCcccccccCcccccccccchhcccccCccccc--------c------------chhhhccccccc
Q 007898 76 DAEVIALSPKTLMATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLK--------Q------------RTSKEIRKKVYV 135 (585)
Q Consensus 76 ~~~~~~~~~k~~~~~kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~--------~------------~~~~~~~~k~y~ 135 (585)
+...+..|.-...-..-|+|++|+|+|....+|-.|+|.|.-..... . +......+..|.
T Consensus 279 D~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~ 358 (500)
T KOG3993|consen 279 DAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFS 358 (500)
T ss_pred hHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceee
Confidence 33334444333333456999999999999999999999996111100 0 000112345799
Q ss_pred cCCCCcccCCCCCccCChhhhhhhhccccCC----------------------------------------------ccc
Q 007898 136 CPEPNCVHHDPSRALGDLTGIKKHFCRKHGE----------------------------------------------KKW 169 (585)
Q Consensus 136 C~~CgC~~~~~~k~F~~~~~L~~H~r~Htge----------------------------------------------kpy 169 (585)
|.+|+ |.|.+...|++|..+|... ...
T Consensus 359 C~~C~-------KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~ 431 (500)
T KOG3993|consen 359 CHTCG-------KKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELE 431 (500)
T ss_pred cHHhh-------hhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeecccccc
Confidence 99996 9999999999998777531 013
Q ss_pred cccccCCcccChhHHHHHHHH-hCCcceecC-CCCccCChHHHHHHHHHhhhc
Q 007898 170 KCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRRDSFITHRAFCDAL 220 (585)
Q Consensus 170 ~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F~~~s~L~~H~~~h~~~ 220 (585)
.|++|+-.+..+..--.|.+. +.+.-|.|+ |.-+|-....|.+|...+|..
T Consensus 432 ~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hps 484 (500)
T KOG3993|consen 432 LPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPS 484 (500)
T ss_pred CCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChH
Confidence 467777777766666666666 667789999 999999999999999777643
No 19
>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=5.1e-07 Score=59.14 Aligned_cols=26 Identities=31% Similarity=0.792 Sum_probs=21.3
Q ss_pred hhhhhhccccCCccccccccCCcccC
Q 007898 155 GIKKHFCRKHGEKKWKCDKCSKRYAV 180 (585)
Q Consensus 155 ~L~~H~r~Htgekpy~C~~CgK~F~~ 180 (585)
+|.+|+++|+++|+|+|++|+|.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47788888888888888888888863
No 20
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=97.74 E-value=1.7e-05 Score=57.64 Aligned_cols=26 Identities=31% Similarity=0.302 Sum_probs=19.9
Q ss_pred cccChHHHHHHHHHHHHhhccccccC
Q 007898 4 GLIFHQQQQQQQQVLEENMSNLTSQS 29 (585)
Q Consensus 4 q~ld~qQqQlyqqVmlEn~~nL~S~~ 29 (585)
++|++.||.+|++||+|||++++|++
T Consensus 16 ~~L~~~Qk~ly~dvm~Eny~~l~slG 41 (41)
T PF01352_consen 16 ELLDPAQKNLYRDVMLENYRNLVSLG 41 (41)
T ss_dssp HTS-HHHHHHHHHHHHHTTTS---S-
T ss_pred ccccceecccchhHHHHhhcccEecC
Confidence 47999999999999999999999983
No 21
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.67 E-value=1e-05 Score=82.15 Aligned_cols=49 Identities=31% Similarity=0.670 Sum_probs=27.7
Q ss_pred Cccccccc--cCCcccChhHHHHHHHH-h-------------------CCcceecC-CCCccCChHHHHHHH
Q 007898 166 EKKWKCDK--CSKRYAVQSDWKAHSKT-C-------------------GTREYRCD-CGTLFSRRDSFITHR 214 (585)
Q Consensus 166 ekpy~C~~--CgK~F~~~s~L~~H~r~-h-------------------gekpy~C~-Cgk~F~~~s~L~~H~ 214 (585)
+|||+|++ |.|.|+....|+.|+.- | ..|||+|+ |+|+|+...-|+.|+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 36666655 66666666666666554 3 12555555 555555555555554
No 22
>PHA00616 hypothetical protein
Probab=97.65 E-value=2e-05 Score=57.80 Aligned_cols=31 Identities=10% Similarity=0.324 Sum_probs=14.4
Q ss_pred ccccccCCcccChhHHHHHHHH-hCCcceecC
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD 199 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~ 199 (585)
|+|..||+.|..++.|..|++. |+++++.|+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 4444444444444444444444 444444443
No 23
>PHA00732 hypothetical protein
Probab=97.63 E-value=2.9e-05 Score=64.87 Aligned_cols=45 Identities=27% Similarity=0.423 Sum_probs=30.9
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhcc-ccCCccccccccCCcccChhHHHHHHHH
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFCR-KHGEKKWKCDKCSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~-Htgekpy~C~~CgK~F~~~s~L~~H~r~ 190 (585)
+|.|+.|+ +.|.....|+.|++. |.+ +.|++|++.|. .|..|.++
T Consensus 1 py~C~~Cg-------k~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICG-------FTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCC-------CccCCHHHHHHHhhcccCC---CccCCCCCEeC---Chhhhhcc
Confidence 46777774 777777777777764 442 46777777776 46677655
No 24
>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=97.62 E-value=3.3e-05 Score=50.54 Aligned_cols=24 Identities=38% Similarity=0.951 Sum_probs=20.0
Q ss_pred HHHHHHHH-hCCcceecC-CCCccCC
Q 007898 183 DWKAHSKT-CGTREYRCD-CGTLFSR 206 (585)
Q Consensus 183 ~L~~H~r~-hgekpy~C~-Cgk~F~~ 206 (585)
+|.+|+++ +++|||.|+ |++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47889988 688999999 9988863
No 25
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.58 E-value=1.5e-05 Score=80.83 Aligned_cols=56 Identities=32% Similarity=0.697 Sum_probs=48.4
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhcccc-------------------CCccccccccCCcccChhHHHHHHHH
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKH-------------------GEKKWKCDKCSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Ht-------------------gekpy~C~~CgK~F~~~s~L~~H~r~ 190 (585)
++|||+|++-|| .|.|+....|+.|+..-+ .+|||+|++|+|+|+....|+.|+.-
T Consensus 346 d~KpykCpV~gC-----~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 346 DGKPYKCPVEGC-----NKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred cCceecCCCCCc-----hhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccc
Confidence 569999999987 799999999999986422 35899999999999999999999654
No 26
>PHA00616 hypothetical protein
Probab=97.46 E-value=3.1e-05 Score=56.80 Aligned_cols=40 Identities=13% Similarity=0.214 Sum_probs=34.9
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCccc
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYA 179 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~ 179 (585)
+|+|+.|| +.|..+..|.+|++.|+|++++.|+.--..|.
T Consensus 1 pYqC~~CG-------~~F~~~s~l~~H~r~~hg~~~~~~~~~y~~f~ 40 (44)
T PHA00616 1 MYQCLRCG-------GIFRKKKEVIEHLLSVHKQNKLTLEYFYIYFR 40 (44)
T ss_pred CCccchhh-------HHHhhHHHHHHHHHHhcCCCccceeEEEEEEE
Confidence 68999996 99999999999999999999999987544443
No 27
>PHA00732 hypothetical protein
Probab=97.37 E-value=0.0001 Score=61.60 Aligned_cols=44 Identities=18% Similarity=0.349 Sum_probs=38.1
Q ss_pred cccccccCCcccChhHHHHHHHH-hCCcceecC-CCCccCChHHHHHHHHH
Q 007898 168 KWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRRDSFITHRAF 216 (585)
Q Consensus 168 py~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F~~~s~L~~H~~~ 216 (585)
||.|+.|++.|.....|..|++. |. ++.|+ |++.|. .|..|.+.
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 58999999999999999999986 64 46899 999998 47889844
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.22 E-value=0.00042 Score=53.55 Aligned_cols=47 Identities=21% Similarity=0.447 Sum_probs=24.4
Q ss_pred ccccccCCcccChhHHHHHHHH-hC--CcceecC-CCCccCChHHHHHHHHHhh
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKT-CG--TREYRCD-CGTLFSRRDSFITHRAFCD 218 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~-hg--ekpy~C~-Cgk~F~~~s~L~~H~~~h~ 218 (585)
|.|++|++ ......|..|... |. .+.+.|+ |...+. ..|..|+..+|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 55666666 3334556666555 42 2445666 655443 25666655443
No 29
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.11 E-value=0.00083 Score=79.78 Aligned_cols=25 Identities=28% Similarity=0.527 Sum_probs=20.6
Q ss_pred cCcccccccCcccccccccchhccc
Q 007898 90 TNRFVCEICNKGFQRDQNLQLHRRG 114 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~~~~L~~H~r~ 114 (585)
.|.|+|+.|+..|+....|..|+|.
T Consensus 463 ~kt~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 463 FKTLKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred cccccCCccchhhhhHHHhhhcccc
Confidence 4778888888888888888888876
No 30
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=96.92 E-value=0.0008 Score=51.96 Aligned_cols=50 Identities=22% Similarity=0.371 Sum_probs=38.9
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhcccc-CC-ccccccccCCcccChhHHHHHHHH-hC
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFCRKH-GE-KKWKCDKCSKRYAVQSDWKAHSKT-CG 192 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Ht-ge-kpy~C~~CgK~F~~~s~L~~H~r~-hg 192 (585)
.|.|++|+ + ..+...|..|....+ .+ +.+.|++|...+. .+|..|++. |+
T Consensus 2 ~f~CP~C~-------~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCG-------K-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCC-------C-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 58999996 6 455688999987644 33 5799999998755 499999987 63
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=96.89 E-value=0.00068 Score=42.61 Aligned_cols=21 Identities=33% Similarity=0.804 Sum_probs=12.4
Q ss_pred eecC-CCCccCChHHHHHHHHH
Q 007898 196 YRCD-CGTLFSRRDSFITHRAF 216 (585)
Q Consensus 196 y~C~-Cgk~F~~~s~L~~H~~~ 216 (585)
|.|+ |++.|..+..|.+|++.
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 4565 66666666666666544
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.83 E-value=0.00073 Score=57.85 Aligned_cols=72 Identities=18% Similarity=0.454 Sum_probs=16.2
Q ss_pred cccccCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccc
Q 007898 94 VCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDK 173 (585)
Q Consensus 94 ~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~ 173 (585)
+|..|+..|.....|..|+...+ +-. .+.. ..+.....+..+++... ...|.|.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H-------------~~~---~~~~--------~~l~~~~~~~~~~~~~~-~~~~~C~~ 55 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKH-------------GFD---IPDQ--------KYLVDPNRLLNYLRKKV-KESFRCPY 55 (100)
T ss_dssp -------------------------------------------------------------------------SSEEBSS
T ss_pred Ccccccccccccccccccccccc-------------ccc---cccc--------ccccccccccccccccc-CCCCCCCc
Confidence 47778888888888888875443 110 0000 11222223333332211 22577777
Q ss_pred cCCcccChhHHHHHHHH
Q 007898 174 CSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 174 CgK~F~~~s~L~~H~r~ 190 (585)
|++.|.....|..|++.
T Consensus 56 C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 56 CNKTFRSREALQEHMRS 72 (100)
T ss_dssp SS-EESSHHHHHHHHHH
T ss_pred cCCCCcCHHHHHHHHcC
Confidence 77777777777777776
No 33
>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=96.70 E-value=0.00086 Score=42.14 Aligned_cols=22 Identities=32% Similarity=0.773 Sum_probs=16.2
Q ss_pred ccccccCCcccChhHHHHHHHH
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~ 190 (585)
|+|++|++.|..+..|..|++.
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 5677777777777777777764
No 34
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.40 E-value=0.0023 Score=68.30 Aligned_cols=137 Identities=15% Similarity=0.156 Sum_probs=100.1
Q ss_pred CcccccccCcccccccccchhcc--cccCccccccchhhhccc--cccccC--CCCcccCCCCCccCChhhhhhhhcccc
Q 007898 91 NRFVCEICNKGFQRDQNLQLHRR--GHNLPWKLKQRTSKEIRK--KVYVCP--EPNCVHHDPSRALGDLTGIKKHFCRKH 164 (585)
Q Consensus 91 kpy~C~~Cgk~F~~~~~L~~H~r--~H~~~~~~~~~~~~~~~~--k~y~C~--~CgC~~~~~~k~F~~~~~L~~H~r~Ht 164 (585)
.++.|..|.+.|.....|.+|.+ .|. .+ +++.|+ .|+ +.|.+...+..|...|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~-------------~~~~~~~~~p~~~~~-------~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHS-------------GESLKPFSCPYSLCG-------KLFSRNDALKRHILLHT 347 (467)
T ss_pred cCCCCccccCCccccccccccccccccc-------------cccCCceeeeccCCC-------ccccccccccCCccccc
Confidence 57999999999999999999999 677 77 899999 685 99999999999999999
Q ss_pred CCccccccc--cCCcccChhHH----HHHHH-H-hCCcceecC---CCCccCChHHHHHHHHHhhhccccccccccCCCC
Q 007898 165 GEKKWKCDK--CSKRYAVQSDW----KAHSK-T-CGTREYRCD---CGTLFSRRDSFITHRAFCDALAEESTRAITGTNP 233 (585)
Q Consensus 165 gekpy~C~~--CgK~F~~~s~L----~~H~r-~-hgekpy~C~---Cgk~F~~~s~L~~H~~~h~~~~~~~~r~ht~ekp 233 (585)
+.++++|.. |.+.+.....- ..+.+ . +..+.+.|. |-+.+.....+..|...|-. -....
T Consensus 348 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~ 418 (467)
T COG5048 348 SISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLS---------FRPYN 418 (467)
T ss_pred CCCccccccccCccccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccc---------cCCcC
Confidence 988888755 55655544431 11112 2 455667775 77888887777777632211 12335
Q ss_pred ccCCCCCCCCCcCCCcccccccc
Q 007898 234 ILSSSSHHQPGIVAGASSHVNLQ 256 (585)
Q Consensus 234 ~~cs~c~~sf~~~s~l~sH~~~~ 256 (585)
+.+..|...+.....+..|.+.+
T Consensus 419 ~~~~~~~~~~~~~~~~~~~~~~~ 441 (467)
T COG5048 419 CKNPPCSKSFNRHYNLIPHKKIH 441 (467)
T ss_pred CCCCcchhhccCccccccccccc
Confidence 66778888888888777776654
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=96.39 E-value=0.0027 Score=39.71 Aligned_cols=22 Identities=23% Similarity=0.656 Sum_probs=11.0
Q ss_pred eecC-CCCccCChHHHHHHHHHh
Q 007898 196 YRCD-CGTLFSRRDSFITHRAFC 217 (585)
Q Consensus 196 y~C~-Cgk~F~~~s~L~~H~~~h 217 (585)
|.|+ |++.|..+..|+.|++.|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 4555 555555555555555444
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.35 E-value=0.0024 Score=54.60 Aligned_cols=73 Identities=16% Similarity=0.253 Sum_probs=21.2
Q ss_pred ccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHHhCCcceecC-CCCccCChHHHHHH
Q 007898 135 VCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFSRRDSFITH 213 (585)
Q Consensus 135 ~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~~~s~L~~H 213 (585)
+|.+|+ ..|.....|..|+...++-..- ..+.+.....+..+.+..-...+.|. |++.|.....|..|
T Consensus 1 ~C~~C~-------~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~H 69 (100)
T PF12756_consen 1 QCLFCD-------ESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEH 69 (100)
T ss_dssp -----------------------------------------------------------SSEEBSSSS-EESSHHHHHHH
T ss_pred Cccccc-------cccccccccccccccccccccc----cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHH
Confidence 488885 8899999999999876653221 11222244444444444233479999 99999999999999
Q ss_pred HHHhh
Q 007898 214 RAFCD 218 (585)
Q Consensus 214 ~~~h~ 218 (585)
++.+.
T Consensus 70 m~~~~ 74 (100)
T PF12756_consen 70 MRSKH 74 (100)
T ss_dssp HHHTT
T ss_pred HcCcc
Confidence 98643
No 37
>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=96.20 E-value=0.0021 Score=42.01 Aligned_cols=23 Identities=30% Similarity=0.725 Sum_probs=14.2
Q ss_pred ceecC-CCCccCChHHHHHHHHHh
Q 007898 195 EYRCD-CGTLFSRRDSFITHRAFC 217 (585)
Q Consensus 195 py~C~-Cgk~F~~~s~L~~H~~~h 217 (585)
+|.|+ |++.|.....|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 45666 666666666666666444
No 38
>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=96.02 E-value=0.0041 Score=38.84 Aligned_cols=22 Identities=27% Similarity=0.761 Sum_probs=15.1
Q ss_pred ccccccCCcccChhHHHHHHHH
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~ 190 (585)
|.|++|++.|.....|..|+++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 5677777777777777777765
No 39
>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=95.91 E-value=0.0021 Score=42.03 Aligned_cols=25 Identities=36% Similarity=0.711 Sum_probs=23.5
Q ss_pred cccccccCcccccccccchhccccc
Q 007898 92 RFVCEICNKGFQRDQNLQLHRRGHN 116 (585)
Q Consensus 92 py~C~~Cgk~F~~~~~L~~H~r~H~ 116 (585)
+|+|.+|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 6899999999999999999999885
No 40
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.83 E-value=0.0058 Score=69.22 Aligned_cols=22 Identities=36% Similarity=0.806 Sum_probs=15.2
Q ss_pred cccccccCcccc---------------cccccchhcc
Q 007898 92 RFVCEICNKGFQ---------------RDQNLQLHRR 113 (585)
Q Consensus 92 py~C~~Cgk~F~---------------~~~~L~~H~r 113 (585)
.+.|.+|++.|. ....|+.|++
T Consensus 99 ~~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~ 135 (669)
T KOG2231|consen 99 HHSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMR 135 (669)
T ss_pred hhhcCccccchhhhcccCCCccccchhHHHHHHHHHH
Confidence 467888887773 5566777763
No 41
>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=95.39 E-value=0.013 Score=44.28 Aligned_cols=31 Identities=13% Similarity=0.224 Sum_probs=20.5
Q ss_pred CCccccccccCCcccChhHHHHHHHH-hCCcc
Q 007898 165 GEKKWKCDKCSKRYAVQSDWKAHSKT-CGTRE 195 (585)
Q Consensus 165 gekpy~C~~CgK~F~~~s~L~~H~r~-hgekp 195 (585)
.+.|-.|++|+..+....+|++|+.+ |+.||
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 46778888888888888888888887 77765
No 42
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.29 E-value=0.016 Score=61.92 Aligned_cols=132 Identities=19% Similarity=0.251 Sum_probs=77.5
Q ss_pred ccCCCCCCCCCCchhhccCcc--ccccc--Cccccc--ccCcccccccccchhcccccCccccccchhhhccccccccCC
Q 007898 65 KKRNLPGNPDPDAEVIALSPK--TLMAT--NRFVCE--ICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPE 138 (585)
Q Consensus 65 ~k~~~~~~~~~~~~~~~~~~k--~~~~~--kpy~C~--~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~ 138 (585)
..+..+.........+..+.+ .|.++ +++.|. .|++.|.+...+..|...|. ..+.+.|..
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~ 356 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHT-------------SISPAKEKL 356 (467)
T ss_pred CCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccccc-------------CCCcccccc
Confidence 444555555556666677777 79999 999999 79999999999999999997 444455544
Q ss_pred CCcccCCCCCccCChhh-----hhhhhccccCCccccccc--cCCcccChhHHHHHHHHh-CCc--ceecC-CCCccCCh
Q 007898 139 PNCVHHDPSRALGDLTG-----IKKHFCRKHGEKKWKCDK--CSKRYAVQSDWKAHSKTC-GTR--EYRCD-CGTLFSRR 207 (585)
Q Consensus 139 CgC~~~~~~k~F~~~~~-----L~~H~r~Htgekpy~C~~--CgK~F~~~s~L~~H~r~h-gek--py~C~-Cgk~F~~~ 207 (585)
..| .+.+..... ...........+.+.|.. |-+.+.....+..|...+ ..+ .+.|. |.+.|...
T Consensus 357 ~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 431 (467)
T COG5048 357 LNS-----SSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRH 431 (467)
T ss_pred ccC-----ccccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCc
Confidence 432 122222211 111111122233444433 555566666666555542 222 23334 66667666
Q ss_pred HHHHHHH
Q 007898 208 DSFITHR 214 (585)
Q Consensus 208 s~L~~H~ 214 (585)
..+..|+
T Consensus 432 ~~~~~~~ 438 (467)
T COG5048 432 YNLIPHK 438 (467)
T ss_pred ccccccc
Confidence 6666666
No 43
>PRK04860 hypothetical protein; Provisional
Probab=94.88 E-value=0.0093 Score=56.58 Aligned_cols=36 Identities=28% Similarity=0.755 Sum_probs=25.4
Q ss_pred cccccccCCcccChhHHHHHHHH-hCCcceecC-CCCccCCh
Q 007898 168 KWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRR 207 (585)
Q Consensus 168 py~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F~~~ 207 (585)
+|.|. |++ ....+.+|.++ .++++|+|. |++.|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 57776 776 55667777777 577777777 77777654
No 44
>PRK04860 hypothetical protein; Provisional
Probab=94.76 E-value=0.014 Score=55.35 Aligned_cols=39 Identities=18% Similarity=0.475 Sum_probs=31.0
Q ss_pred cccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccCh
Q 007898 132 KVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQ 181 (585)
Q Consensus 132 k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~ 181 (585)
-+|.|. |+ + ....+++|.++|+++++|+|..|++.|...
T Consensus 118 ~~Y~C~-C~-------~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQ-------E---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CC-------C---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 478887 84 4 566788899999998899999998887654
No 45
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.69 E-value=0.025 Score=35.58 Aligned_cols=22 Identities=32% Similarity=0.825 Sum_probs=15.4
Q ss_pred eecC-CCCccCChHHHHHHHHHh
Q 007898 196 YRCD-CGTLFSRRDSFITHRAFC 217 (585)
Q Consensus 196 y~C~-Cgk~F~~~s~L~~H~~~h 217 (585)
|.|. |++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 4677 777777777777777544
No 46
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.52 E-value=0.033 Score=35.04 Aligned_cols=23 Identities=30% Similarity=0.725 Sum_probs=17.5
Q ss_pred ccccccCCcccChhHHHHHHHHh
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKTC 191 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~h 191 (585)
|+|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 56778888888888888887754
No 47
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=94.27 E-value=0.019 Score=68.80 Aligned_cols=139 Identities=14% Similarity=0.123 Sum_probs=80.5
Q ss_pred ccccCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccCCcccccccc
Q 007898 95 CEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKC 174 (585)
Q Consensus 95 C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~C 174 (585)
|..|+..|.++..+.-|+..-. ...|.|+|+.|+ ..|+....|..|+|..+-+-.- .+|
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~------------S~~kt~~cpkc~-------~~yk~a~~L~vhmRskhp~~~~--~~c 497 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLH------------SFFKTLKCPKCN-------WHYKLAQTLGVHMRSKHPESQS--AYC 497 (1406)
T ss_pred ccchhhhhhhhcccccceeeee------------cccccccCCccc-------hhhhhHHHhhhcccccccccch--hHh
Confidence 4445555555555555533221 155889999995 8889999999999874432111 223
Q ss_pred CCcccChhHHHHHHHH-hCCcceecC-CCCccCChHHHHHHHHHhhhccc--cc---c----c-----------------
Q 007898 175 SKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRRDSFITHRAFCDALAE--ES---T----R----------------- 226 (585)
Q Consensus 175 gK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F~~~s~L~~H~~~h~~~~~--~~---~----r----------------- 226 (585)
. .+.....+.+=... .+.++|.|. |...|..+..|.+|++......+ +. . +
T Consensus 498 ~-~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~ 576 (1406)
T KOG1146|consen 498 K-AGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLG 576 (1406)
T ss_pred H-hccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCC
Confidence 1 11111111111111 456788888 88888888888888764322211 00 0 0
Q ss_pred -----cccC-CCCccCCCCCCCCCcCCCccccccc
Q 007898 227 -----AITG-TNPILSSSSHHQPGIVAGASSHVNL 255 (585)
Q Consensus 227 -----~ht~-ekp~~cs~c~~sf~~~s~l~sH~~~ 255 (585)
.-.. +-++.|.+|..-.+...+++.|+..
T Consensus 577 ~~ags~~pktkP~~~C~vc~yetniarnlrihmts 611 (1406)
T KOG1146|consen 577 PSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTA 611 (1406)
T ss_pred CCCCCCCCCCCCCcchhhhcchhhhhhcccccccc
Confidence 0011 2347899999999999999888764
No 48
>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=94.17 E-value=0.028 Score=42.47 Aligned_cols=32 Identities=16% Similarity=0.320 Sum_probs=24.2
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCcc
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKK 168 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekp 168 (585)
.+.|..|++|+ ..+....+|++|+.++++.||
T Consensus 21 S~~PatCP~C~-------a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICG-------AVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT---------EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcch-------hhccchhhHHHHHHHHhcccC
Confidence 67899999996 999999999999999988876
No 49
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=92.47 E-value=0.03 Score=35.77 Aligned_cols=23 Identities=43% Similarity=0.980 Sum_probs=21.2
Q ss_pred ccccccCcccccccccchhcccc
Q 007898 93 FVCEICNKGFQRDQNLQLHRRGH 115 (585)
Q Consensus 93 y~C~~Cgk~F~~~~~L~~H~r~H 115 (585)
|.|++|++.|.....|+.|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 68999999999999999998865
No 50
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=91.96 E-value=0.074 Score=33.88 Aligned_cols=20 Identities=25% Similarity=0.735 Sum_probs=9.2
Q ss_pred cccccCCcccChhHHHHHHH
Q 007898 170 KCDKCSKRYAVQSDWKAHSK 189 (585)
Q Consensus 170 ~C~~CgK~F~~~s~L~~H~r 189 (585)
.|++|++.|.....|..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 34444444444444444443
No 51
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=91.72 E-value=0.16 Score=32.15 Aligned_cols=22 Identities=23% Similarity=0.490 Sum_probs=11.0
Q ss_pred eecC-CCCccCChHHHHHHHHHhh
Q 007898 196 YRCD-CGTLFSRRDSFITHRAFCD 218 (585)
Q Consensus 196 y~C~-Cgk~F~~~s~L~~H~~~h~ 218 (585)
|+|. |..... +..|.+|++.+|
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 4555 555555 555666655544
No 52
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=91.57 E-value=0.077 Score=52.51 Aligned_cols=44 Identities=20% Similarity=0.609 Sum_probs=23.3
Q ss_pred CccccccccCCcccChhHHHHHHHHhCCcceecC-CCCccCChHHHHHH
Q 007898 166 EKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFSRRDSFITH 213 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~~~s~L~~H 213 (585)
+|+| |-+|.+.|.....|..|++. |.|+|- |-|..-.---|..|
T Consensus 9 ~kpw-cwycnrefddekiliqhqka---khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKA---KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhh---ccceeeeehhhhccCCCceee
Confidence 3444 55666666666666666553 446666 65443333334444
No 53
>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=91.56 E-value=0.061 Score=35.22 Aligned_cols=24 Identities=29% Similarity=0.787 Sum_probs=21.1
Q ss_pred cccccccCcccccccccchhcccc
Q 007898 92 RFVCEICNKGFQRDQNLQLHRRGH 115 (585)
Q Consensus 92 py~C~~Cgk~F~~~~~L~~H~r~H 115 (585)
.|.|..|++.|.+...|..|++..
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCCcccCCCCcCCHHHHHHHHccC
Confidence 378999999999999999998763
No 54
>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=90.52 E-value=0.073 Score=34.85 Aligned_cols=21 Identities=33% Similarity=0.786 Sum_probs=10.4
Q ss_pred ccccccCCcccChhHHHHHHH
Q 007898 169 WKCDKCSKRYAVQSDWKAHSK 189 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r 189 (585)
|.|..|++.|.+...|..|++
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 345555555555555554443
No 55
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.75 E-value=0.2 Score=52.22 Aligned_cols=65 Identities=22% Similarity=0.407 Sum_probs=30.4
Q ss_pred CccCChhhhhhhhccccCCccccccccC----CcccChhHHHHHHHHhCCcceecC---CC----CccCChHHHHHHHHH
Q 007898 148 RALGDLTGIKKHFCRKHGEKKWKCDKCS----KRYAVQSDWKAHSKTCGTREYRCD---CG----TLFSRRDSFITHRAF 216 (585)
Q Consensus 148 k~F~~~~~L~~H~r~Htgekpy~C~~Cg----K~F~~~s~L~~H~r~hgekpy~C~---Cg----k~F~~~s~L~~H~~~ 216 (585)
+.|-+-..|.+|+|..+ |+-|.|+.-+ .-|..-..|.+|.+. ..|.|. |. ..|.+...|..|+..
T Consensus 228 ~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~---~hy~ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 228 IYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRN---AHYCCTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred ceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhc---CceEEEEEEEecCcEEEeccHHHHHHHHHH
Confidence 55555556666655433 2222222211 124455555555443 125553 42 256666666666543
No 56
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=89.69 E-value=0.25 Score=31.22 Aligned_cols=21 Identities=38% Similarity=0.699 Sum_probs=11.4
Q ss_pred ccccccCCcccChhHHHHHHHH
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~ 190 (585)
|+|..|..... +..|.+|+++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 45666665555 5566666655
No 57
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=89.59 E-value=0.26 Score=51.31 Aligned_cols=118 Identities=16% Similarity=0.232 Sum_probs=82.5
Q ss_pred ccccccCCCCcccCCCCCccCChhhhhhhhccccCC----------------------ccccccccCCcccChhHHHHHH
Q 007898 131 KKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGE----------------------KKWKCDKCSKRYAVQSDWKAHS 188 (585)
Q Consensus 131 ~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htge----------------------kpy~C~~CgK~F~~~s~L~~H~ 188 (585)
.+..+|-.|. ......++.+..|+-..++- ..+.|-+|.|.|..+..|+.||
T Consensus 142 ~fslqClFCn------~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHM 215 (423)
T KOG2482|consen 142 IFSLQCLFCN------NEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHM 215 (423)
T ss_pred eeeeEEEEec------chhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHH
Confidence 3456799996 35555667777776543321 2378999999999999999999
Q ss_pred HH--hCC-----c------------------------------------------------c--eecC-CCCccCChHHH
Q 007898 189 KT--CGT-----R------------------------------------------------E--YRCD-CGTLFSRRDSF 210 (585)
Q Consensus 189 r~--hge-----k------------------------------------------------p--y~C~-Cgk~F~~~s~L 210 (585)
|. |.+ + + .+|- |....-....|
T Consensus 216 rkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l 295 (423)
T KOG2482|consen 216 RKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFL 295 (423)
T ss_pred HhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHH
Confidence 87 531 0 1 2788 99988889999
Q ss_pred HHHHHHhhhcccccccc----------------ccCCCCccCCCCCCCCCcCCCcccccc
Q 007898 211 ITHRAFCDALAEESTRA----------------ITGTNPILSSSSHHQPGIVAGASSHVN 254 (585)
Q Consensus 211 ~~H~~~h~~~~~~~~r~----------------ht~ekp~~cs~c~~sf~~~s~l~sH~~ 254 (585)
..||+..|...-..... ....+-..|-.|.-+|-....+..|+-
T Consensus 296 ~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~ 355 (423)
T KOG2482|consen 296 FEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMV 355 (423)
T ss_pred HHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcc
Confidence 99999877544222111 112334567888889999999988874
No 58
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=89.17 E-value=4.4 Score=42.05 Aligned_cols=115 Identities=12% Similarity=0.101 Sum_probs=55.9
Q ss_pred CcccccccCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhh-hccccCCccc
Q 007898 91 NRFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKH-FCRKHGEKKW 169 (585)
Q Consensus 91 kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H-~r~Htgekpy 169 (585)
..|.|.. +..|+....+--|...-. .......+.++.+.+-|+.|+.--...+|....+..+-.- -+.|. .-
T Consensus 52 ~~~~~~~-~p~f~~~~r~pphl~w~~---~V~~~gek~l~p~VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~---dK 124 (389)
T KOG2932|consen 52 DHLVLAD-LPVFKGIGRVPPHLTWIK---PVGRRGEKQLGPRVHFCDRCDFPIAIYGRMIPCKHVFCLECARSDS---DK 124 (389)
T ss_pred hhhhhcC-CchhcccccCCCceeeee---ecccccccccCcceEeecccCCcceeeecccccchhhhhhhhhcCc---cc
Confidence 3444433 455666655555544322 1112223344677788999962100111111111111000 01111 12
Q ss_pred cccccCCcccChhHHHHHHHHhCCcceecC----CCCccCChHHHHHHHHHhh
Q 007898 170 KCDKCSKRYAVQSDWKAHSKTCGTREYRCD----CGTLFSRRDSFITHRAFCD 218 (585)
Q Consensus 170 ~C~~CgK~F~~~s~L~~H~r~hgekpy~C~----Cgk~F~~~s~L~~H~~~h~ 218 (585)
.|..|..... +=..+.-+..|.|. |.++|..+..|..|+..-|
T Consensus 125 ~Cp~C~d~Vq------rIeq~~~g~iFmC~~~~GC~RTyLsqrDlqAHInhrH 171 (389)
T KOG2932|consen 125 ICPLCDDRVQ------RIEQIMMGGIFMCAAPHGCLRTYLSQRDLQAHINHRH 171 (389)
T ss_pred cCcCcccHHH------HHHHhcccceEEeecchhHHHHHhhHHHHHHHhhhhh
Confidence 4666654321 11112446789995 9999999999999985444
No 59
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.02 E-value=0.23 Score=48.24 Aligned_cols=83 Identities=20% Similarity=0.444 Sum_probs=64.4
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHH-h----------CCcceec
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT-C----------GTREYRC 198 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~-h----------gekpy~C 198 (585)
+...|.|++-|| -+.|.....+..|.-+-++ -.|.+|.+.|.+..-|..|+.- | |..-|.|
T Consensus 76 ~~~~~~cqvagc-----~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~C 147 (253)
T KOG4173|consen 76 RVPAFACQVAGC-----CQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQC 147 (253)
T ss_pred ccccccccccch-----HHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHH
Confidence 445688999887 5788877777777655444 4799999999999999999865 5 3446999
Q ss_pred C---CCCccCChHHHHHHHHHhhhc
Q 007898 199 D---CGTLFSRRDSFITHRAFCDAL 220 (585)
Q Consensus 199 ~---Cgk~F~~~s~L~~H~~~h~~~ 220 (585)
- |+..|.+...-+.|+-..|..
T Consensus 148 lvEgCt~KFkT~r~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 148 LVEGCTEKFKTSRDRKDHMIRMHKY 172 (253)
T ss_pred HHHhhhhhhhhhhhhhhHHHHhccC
Confidence 4 999999999989998555543
No 60
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=87.29 E-value=0.37 Score=50.26 Aligned_cols=48 Identities=21% Similarity=0.325 Sum_probs=38.4
Q ss_pred ccccccCCcccChhHHHHHHHH-hCC---------------------------cceecC-CCCccCChHHHHHHHHH
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKT-CGT---------------------------REYRCD-CGTLFSRRDSFITHRAF 216 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~-hge---------------------------kpy~C~-Cgk~F~~~s~L~~H~~~ 216 (585)
.+|-.|.+...+...|..||++ |.- +.-.|- |.-.|-....|..|+.-
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e 356 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhccc
Confidence 4899999999889999999998 731 112555 99999999999999843
No 61
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=86.17 E-value=0.59 Score=30.20 Aligned_cols=19 Identities=32% Similarity=0.754 Sum_probs=9.9
Q ss_pred ecC-CCCccCChHHHHHHHHH
Q 007898 197 RCD-CGTLFSRRDSFITHRAF 216 (585)
Q Consensus 197 ~C~-Cgk~F~~~s~L~~H~~~ 216 (585)
.|. ||+.| ..+.|.+|++.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 455 55555 44455555543
No 62
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.01 E-value=0.67 Score=53.03 Aligned_cols=72 Identities=17% Similarity=0.260 Sum_probs=49.6
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhccccCCcccccccc------CCcccChhHHHHHHHHhCCcceecC---CC-C
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKC------SKRYAVQSDWKAHSKTCGTREYRCD---CG-T 202 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~C------gK~F~~~s~L~~H~r~hgekpy~C~---Cg-k 202 (585)
.-.|..| ...|-....|.+|++.++ |.|.+| +..|....+|..|-|. .-|.|+ |. +
T Consensus 182 hp~C~~C-------~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~---~HflCE~~~C~~~ 247 (669)
T KOG2231|consen 182 HPLCKFC-------HERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRK---GHFLCEEEFCRTK 247 (669)
T ss_pred Cccchhh-------hhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhh---cCccccccccccc
Confidence 3568888 488999999999998765 667776 4567888899999887 236775 53 4
Q ss_pred ccCChHHHHHHHHHhh
Q 007898 203 LFSRRDSFITHRAFCD 218 (585)
Q Consensus 203 ~F~~~s~L~~H~~~h~ 218 (585)
.|.....+..|++.|.
T Consensus 248 ~f~~~~~~ei~lk~~~ 263 (669)
T KOG2231|consen 248 KFYVAFELEIELKAHN 263 (669)
T ss_pred eeeehhHHHHHHHhhc
Confidence 4444444555554433
No 63
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=83.86 E-value=0.26 Score=48.83 Aligned_cols=41 Identities=27% Similarity=0.403 Sum_probs=34.1
Q ss_pred cCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHH
Q 007898 136 CPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAH 187 (585)
Q Consensus 136 C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H 187 (585)
|.+|+ +.|.+..-|..|.+. |.|+|.+|.|....--.|..|
T Consensus 13 cwycn-------refddekiliqhqka----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCN-------REFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecc-------cccchhhhhhhhhhh----ccceeeeehhhhccCCCceee
Confidence 88885 999999999988775 459999999987777777766
No 64
>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=83.49 E-value=0.79 Score=31.44 Aligned_cols=23 Identities=22% Similarity=0.450 Sum_probs=14.4
Q ss_pred cccccccCCcccChhHHHHHHHH
Q 007898 168 KWKCDKCSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 168 py~C~~CgK~F~~~s~L~~H~r~ 190 (585)
+|.|++|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 35566666666666666666554
No 65
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=82.57 E-value=0.79 Score=46.10 Aligned_cols=44 Identities=25% Similarity=0.684 Sum_probs=26.3
Q ss_pred ccccccCCcccChhHHHHHHHHhCCcceecC-CCCccCChHHHHHHH
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFSRRDSFITHR 214 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~~~s~L~~H~ 214 (585)
|.|.+||.... +..+.+|+..+...-|.|- |++.|-+ .+++.|.
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccCCeeEEeeccccccc-chhhhhh
Confidence 55666666544 3455666666333666776 7777766 5556664
No 66
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=82.56 E-value=1.1 Score=29.03 Aligned_cols=21 Identities=19% Similarity=0.550 Sum_probs=15.5
Q ss_pred ccccccCCcccChhHHHHHHHH
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~ 190 (585)
..|..||+.| ....|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4688888888 56777888764
No 67
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.05 E-value=3.3 Score=36.92 Aligned_cols=78 Identities=10% Similarity=0.143 Sum_probs=48.3
Q ss_pred CccccccccCCcccChhHHHHHHHH-hCCcc------------eecC-CCCccCChHHHHHHHHHhhhccccccccccCC
Q 007898 166 EKKWKCDKCSKRYAVQSDWKAHSKT-CGTRE------------YRCD-CGTLFSRRDSFITHRAFCDALAEESTRAITGT 231 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~s~L~~H~r~-hgekp------------y~C~-Cgk~F~~~s~L~~H~~~h~~~~~~~~r~ht~e 231 (585)
+=|-.|++||-......+|.+--.. -.-++ ..|. |.+.|....... ...-...
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~-------------~~~~~~~ 79 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSP-------------FDELKDS 79 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccc-------------ccccccc
Confidence 3467888888888888877763211 11111 2488 888887653111 0012234
Q ss_pred CCccCCCCCCCCCcCCCcccccccc
Q 007898 232 NPILSSSSHHQPGIVAGASSHVNLQ 256 (585)
Q Consensus 232 kp~~cs~c~~sf~~~s~l~sH~~~~ 256 (585)
..|.|..|.+.|-..=..-.|..++
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cceeCCCCCCccccccchhhhhhcc
Confidence 5688999999888777777776554
No 68
>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=79.78 E-value=1.6 Score=29.86 Aligned_cols=22 Identities=23% Similarity=0.430 Sum_probs=19.6
Q ss_pred ceecC-CCCccCChHHHHHHHHH
Q 007898 195 EYRCD-CGTLFSRRDSFITHRAF 216 (585)
Q Consensus 195 py~C~-Cgk~F~~~s~L~~H~~~ 216 (585)
+|.|+ |++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 68999 99999999999999843
No 69
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=79.36 E-value=0.41 Score=50.76 Aligned_cols=154 Identities=14% Similarity=0.198 Sum_probs=96.6
Q ss_pred cccccccCcccccccccchhccc--ccCccccccc------------------------hhhhccccccccCCCCcccCC
Q 007898 92 RFVCEICNKGFQRDQNLQLHRRG--HNLPWKLKQR------------------------TSKEIRKKVYVCPEPNCVHHD 145 (585)
Q Consensus 92 py~C~~Cgk~F~~~~~L~~H~r~--H~~~~~~~~~------------------------~~~~~~~k~y~C~~CgC~~~~ 145 (585)
-|.|.-|...|.....-+.|.++ |. |.++++ ......+-++.|.+|.
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHR--YNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~----- 75 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHR--YNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACN----- 75 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHH--hhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhh-----
Confidence 48999999999998888888774 33 222211 0113356688999995
Q ss_pred CCCccCChhhhhhhhccccC-----------------Ccccc-------------ccccCCcccChhHHHHHH------H
Q 007898 146 PSRALGDLTGIKKHFCRKHG-----------------EKKWK-------------CDKCSKRYAVQSDWKAHS------K 189 (585)
Q Consensus 146 ~~k~F~~~~~L~~H~r~Htg-----------------ekpy~-------------C~~CgK~F~~~s~L~~H~------r 189 (585)
|.|....+...|+..... .+.+. |..|-..+........+. .
T Consensus 76 --k~~~s~~a~~~hl~Sk~h~~~~~~~~r~~e~d~a~~~q~~~~~p~~l~~~~e~e~~~~E~~~~~d~~~e~~~dd~~Ed 153 (390)
T KOG2785|consen 76 --KSFASPKAHENHLKSKKHVENLSNHQRSEEGDSAKISQLPSRRPSNLQNKGESELKWYEVDSDEDSSEEEEEDDEEED 153 (390)
T ss_pred --ccccChhhHHHHHHHhhcchhhhhhhccccccchhhhhccccCccccccCCCcccchhhcccccccchhhccCcchhh
Confidence 999888887777653210 01122 333333333322222221 1
Q ss_pred H-h-C-----CcceecC-CCCccCChHHHHHHHHHhhhccccccccccC------------CCCccCCCCC---CCCCcC
Q 007898 190 T-C-G-----TREYRCD-CGTLFSRRDSFITHRAFCDALAEESTRAITG------------TNPILSSSSH---HQPGIV 246 (585)
Q Consensus 190 ~-h-g-----ekpy~C~-Cgk~F~~~s~L~~H~~~h~~~~~~~~r~ht~------------ekp~~cs~c~---~sf~~~ 246 (585)
+ . + .-|-.|- |++.|..-..-..||..+|+...+-...-+. ..-+.|-.|+ +.|.+.
T Consensus 154 i~~d~~~e~e~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sl 233 (390)
T KOG2785|consen 154 IEEDGDDEDELIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSL 233 (390)
T ss_pred hhhccchhcccCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCccccc
Confidence 2 1 1 2356788 9999999999999999998876443221111 2347788888 889888
Q ss_pred CCcccccc
Q 007898 247 AGASSHVN 254 (585)
Q Consensus 247 s~l~sH~~ 254 (585)
...+.||.
T Consensus 234 eavr~HM~ 241 (390)
T KOG2785|consen 234 EAVRAHMR 241 (390)
T ss_pred HHHHHHHh
Confidence 88888875
No 70
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=77.83 E-value=1 Score=34.72 Aligned_cols=30 Identities=23% Similarity=0.629 Sum_probs=19.8
Q ss_pred ccCCccccccccCCcccChhHHHHHHHH-hC
Q 007898 163 KHGEKKWKCDKCSKRYAVQSDWKAHSKT-CG 192 (585)
Q Consensus 163 Htgekpy~C~~CgK~F~~~s~L~~H~r~-hg 192 (585)
-.||..++|+-||+.|....++.+|... |+
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3456667777777777777777777655 53
No 71
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=74.49 E-value=5.9 Score=41.75 Aligned_cols=25 Identities=20% Similarity=0.744 Sum_probs=20.9
Q ss_pred ccCcccccc--cCcccccccccchhcc
Q 007898 89 ATNRFVCEI--CNKGFQRDQNLQLHRR 113 (585)
Q Consensus 89 ~~kpy~C~~--Cgk~F~~~~~L~~H~r 113 (585)
-.++|+|.+ |.|.++....|+.|..
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~ 372 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKL 372 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccc
Confidence 368999976 9999999988888854
No 72
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=74.21 E-value=1.6 Score=36.94 Aligned_cols=34 Identities=29% Similarity=0.567 Sum_probs=21.9
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccC
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAV 180 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~ 180 (585)
....|.|+.|+ +. .+.|+- ...|.|..||..|.-
T Consensus 32 ~~~~~~Cp~C~-------~~--------~VkR~a--~GIW~C~kCg~~fAG 65 (89)
T COG1997 32 QRAKHVCPFCG-------RT--------TVKRIA--TGIWKCRKCGAKFAG 65 (89)
T ss_pred HhcCCcCCCCC-------Cc--------ceeeec--cCeEEcCCCCCeecc
Confidence 34578899996 21 233333 345899999988864
No 73
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=73.69 E-value=1.8 Score=33.51 Aligned_cols=29 Identities=34% Similarity=0.718 Sum_probs=24.7
Q ss_pred hCCcceecC-CCCccCChHHHHHHHHHhhh
Q 007898 191 CGTREYRCD-CGTLFSRRDSFITHRAFCDA 219 (585)
Q Consensus 191 hgekpy~C~-Cgk~F~~~s~L~~H~~~h~~ 219 (585)
.||.-++|+ |++.|.+..++.+|...-|.
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 478889999 99999999999999865443
No 74
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=72.98 E-value=1.9 Score=42.89 Aligned_cols=25 Identities=20% Similarity=0.457 Sum_probs=19.8
Q ss_pred cCcccccccCcccccccccchhccc
Q 007898 90 TNRFVCEICNKGFQRDQNLQLHRRG 114 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~~~~L~~H~r~ 114 (585)
+|.+.|++|++.|..+.-+....+.
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 4678999999999998776666554
No 75
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=72.36 E-value=4.7 Score=42.33 Aligned_cols=112 Identities=16% Similarity=0.220 Sum_probs=74.5
Q ss_pred cccccc--cCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccCCccc
Q 007898 92 RFVCEI--CNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKW 169 (585)
Q Consensus 92 py~C~~--Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy 169 (585)
.|.|+. |..+...-..|+.|.+.-+...-|.... ..++.|.|.+ ..| .+..|+.|...-..+.-|
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~---~nKk~F~~E~---------~lF-~~~~Lr~H~~~G~~e~GF 217 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECI---GNKKDFWNEI---------RLF-RSSTLRDHKNGGLEEEGF 217 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhh---cCcccCccce---------eee-ecccccccccCCccccCc
Confidence 577865 6655555667888877654333232221 1566777764 344 455688887654333233
Q ss_pred ----cccccCCcccChhHHHHHHHHhCCcceecC-CC----CccCChHHHHHHHHH
Q 007898 170 ----KCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CG----TLFSRRDSFITHRAF 216 (585)
Q Consensus 170 ----~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cg----k~F~~~s~L~~H~~~ 216 (585)
.|.+|.+.|-.-..|.+|+|.-.|+-|.|+ -+ .-|+....|..|-+.
T Consensus 218 KGHP~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~ 273 (493)
T COG5236 218 KGHPLCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRN 273 (493)
T ss_pred CCCchhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhc
Confidence 599999999999999999999446777776 33 348888999999753
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=71.79 E-value=2.4 Score=29.22 Aligned_cols=10 Identities=30% Similarity=1.069 Sum_probs=7.8
Q ss_pred ccccccccCC
Q 007898 167 KKWKCDKCSK 176 (585)
Q Consensus 167 kpy~C~~CgK 176 (585)
.++.|++||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 6788888875
No 77
>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=71.05 E-value=4 Score=41.30 Aligned_cols=89 Identities=18% Similarity=0.392 Sum_probs=51.4
Q ss_pred cccCCccccccccCCcccChhHHHHHHHH---hCCcceecC-CCCccCChHHHHHHHHHhhhccccccccccCCCCccCC
Q 007898 162 RKHGEKKWKCDKCSKRYAVQSDWKAHSKT---CGTREYRCD-CGTLFSRRDSFITHRAFCDALAEESTRAITGTNPILSS 237 (585)
Q Consensus 162 ~Htgekpy~C~~CgK~F~~~s~L~~H~r~---hgekpy~C~-Cgk~F~~~s~L~~H~~~h~~~~~~~~r~ht~ekp~~cs 237 (585)
..+|.+.|+|.+|.. |.-..+--.|+.. -....|+|. |.+. ...+-|+--.-++..-+....-.....+++.|+
T Consensus 136 w~hGGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNrl-Gq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCP 213 (314)
T PF06524_consen 136 WDHGGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNRL-GQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCP 213 (314)
T ss_pred ccCCCeEEEeecCCC-eeeccchhhhhhhhhhhhcccccccccccc-cchhhhheeeeehhhhhhhcccccccCCCCCCC
Confidence 356788999999986 4445555567766 244568887 8653 233344432223322222222333456899999
Q ss_pred CCCCCCCcCCCcccc
Q 007898 238 SSHHQPGIVAGASSH 252 (585)
Q Consensus 238 ~c~~sf~~~s~l~sH 252 (585)
.|+.-......|+-.
T Consensus 214 KCg~et~eTkdLSmS 228 (314)
T PF06524_consen 214 KCGYETQETKDLSMS 228 (314)
T ss_pred CCCCcccccccceee
Confidence 999765555444433
No 78
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=70.31 E-value=2.5 Score=47.50 Aligned_cols=28 Identities=18% Similarity=0.347 Sum_probs=24.5
Q ss_pred ccCcccccccCcccccccccchhccccc
Q 007898 89 ATNRFVCEICNKGFQRDQNLQLHRRGHN 116 (585)
Q Consensus 89 ~~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 116 (585)
...+..|..||.+|.+......|+..|-
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3567899999999999999998888885
No 79
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=67.08 E-value=3.2 Score=39.69 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=20.1
Q ss_pred ccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCC
Q 007898 131 KKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSK 176 (585)
Q Consensus 131 ~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK 176 (585)
.+.|+|++|| . +|.|+-|.+|++||-
T Consensus 132 ~~~~vC~vCG-------y-------------~~~ge~P~~CPiCga 157 (166)
T COG1592 132 GKVWVCPVCG-------Y-------------THEGEAPEVCPICGA 157 (166)
T ss_pred CCEEEcCCCC-------C-------------cccCCCCCcCCCCCC
Confidence 3479999997 2 455788999999984
No 80
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=66.05 E-value=2.8 Score=41.78 Aligned_cols=44 Identities=16% Similarity=0.304 Sum_probs=26.8
Q ss_pred ccccccCCCCcccCCCCCccCChhhhhhhhccc----------cCCcc-----ccccccCCcccCh
Q 007898 131 KKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRK----------HGEKK-----WKCDKCSKRYAVQ 181 (585)
Q Consensus 131 ~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~H----------tgekp-----y~C~~CgK~F~~~ 181 (585)
+|.++|++|+ +.|..+.-.....+.- .+..| +.|+.||.+|...
T Consensus 3 ~k~~~CPvC~-------~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCG-------KEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCC-------CeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 4678899995 7777765444444331 12222 5688888777644
No 81
>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=65.99 E-value=2.3 Score=42.38 Aligned_cols=29 Identities=24% Similarity=0.471 Sum_probs=17.8
Q ss_pred CCccccccccCCcccChhHHHHHHHH-hCC
Q 007898 165 GEKKWKCDKCSKRYAVQSDWKAHSKT-CGT 193 (585)
Q Consensus 165 gekpy~C~~CgK~F~~~s~L~~H~r~-hge 193 (585)
.+..|.|..|+|.|.-...++.|+.. |.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 34457777777777777777777766 644
No 82
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=65.67 E-value=1.5 Score=42.79 Aligned_cols=80 Identities=19% Similarity=0.372 Sum_probs=61.0
Q ss_pred cCcccccc--cCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccc----
Q 007898 90 TNRFVCEI--CNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRK---- 163 (585)
Q Consensus 90 ~kpy~C~~--Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~H---- 163 (585)
.+.|.|.+ |-..|.....+..|..+-+ --.|.+| .+.|....-|..|+..-
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY~~~h----------------~~sCs~C-------~r~~Pt~hLLd~HI~E~HDs~ 133 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHYHTLH----------------GNSCSFC-------KRAFPTGHLLDAHILEWHDSL 133 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhhhhcc----------------cchhHHH-------HHhCCchhhhhHHHHHHHHHH
Confidence 46788987 7788888777777754332 2468888 59999999999997542
Q ss_pred ------cCCccccccc--cCCcccChhHHHHHHHH-hC
Q 007898 164 ------HGEKKWKCDK--CSKRYAVQSDWKAHSKT-CG 192 (585)
Q Consensus 164 ------tgekpy~C~~--CgK~F~~~s~L~~H~r~-hg 192 (585)
.|..-|.|-+ |+..|.+...-+.|+.. |.
T Consensus 134 Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 134 FQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 3556799955 99999999999999887 63
No 83
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=64.86 E-value=3 Score=39.44 Aligned_cols=16 Identities=25% Similarity=0.671 Sum_probs=11.6
Q ss_pred cccccccCCcccChhH
Q 007898 168 KWKCDKCSKRYAVQSD 183 (585)
Q Consensus 168 py~C~~CgK~F~~~s~ 183 (585)
.|+|..||++|..-..
T Consensus 28 ~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 28 RRECLACGKRFTTFER 43 (154)
T ss_pred eeeccccCCcceEeEe
Confidence 3788888888876443
No 84
>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=64.30 E-value=4.6 Score=28.11 Aligned_cols=10 Identities=30% Similarity=0.604 Sum_probs=7.2
Q ss_pred ccccccccCC
Q 007898 167 KKWKCDKCSK 176 (585)
Q Consensus 167 kpy~C~~CgK 176 (585)
.|..|++||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 4667888875
No 85
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=63.63 E-value=4.5 Score=47.34 Aligned_cols=11 Identities=18% Similarity=0.377 Sum_probs=6.4
Q ss_pred cccccCccccc
Q 007898 94 VCEICNKGFQR 104 (585)
Q Consensus 94 ~C~~Cgk~F~~ 104 (585)
.|..||..+..
T Consensus 437 ~C~~Cg~v~~C 447 (730)
T COG1198 437 LCRDCGYIAEC 447 (730)
T ss_pred ecccCCCcccC
Confidence 46666665544
No 86
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=63.19 E-value=3.6 Score=41.55 Aligned_cols=48 Identities=21% Similarity=0.516 Sum_probs=37.3
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHH
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~ 190 (585)
.|.|.+|| ... .+..+.+|+.+-++ ..|.|--|++.|.+ .+++.|..=
T Consensus 3 ~FtCnvCg-------Esv-KKp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 3 FFTCNVCG-------ESV-KKPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred EEehhhhh-------hhc-cccchHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 48899997 333 35567889887777 67999999999998 777888654
No 87
>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=62.18 E-value=4.7 Score=35.78 Aligned_cols=15 Identities=20% Similarity=0.625 Sum_probs=7.8
Q ss_pred ccccccccCCcccCh
Q 007898 167 KKWKCDKCSKRYAVQ 181 (585)
Q Consensus 167 kpy~C~~CgK~F~~~ 181 (585)
.|..|++||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 455555555555443
No 88
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=61.30 E-value=2.1 Score=44.94 Aligned_cols=26 Identities=8% Similarity=-0.146 Sum_probs=21.2
Q ss_pred cccccCcccccccCcccccccccchhc
Q 007898 86 TLMATNRFVCEICNKGFQRDQNLQLHR 112 (585)
Q Consensus 86 ~~~~~kpy~C~~Cgk~F~~~~~L~~H~ 112 (585)
..+-.++|+| .|++.+.++..|+.|-
T Consensus 207 ~~t~~~p~k~-~~~~~~~T~~~l~~HS 232 (442)
T KOG4124|consen 207 AETTGTPKKM-PESLVMDTSSPLSDHS 232 (442)
T ss_pred cccccCCccC-cccccccccchhhhcc
Confidence 3455689999 4999999999998884
No 89
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=61.21 E-value=2.7 Score=43.76 Aligned_cols=33 Identities=21% Similarity=0.440 Sum_probs=13.0
Q ss_pred ccccccCCcccChhHHHHHHHHhCCcceecC-CC
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CG 201 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cg 201 (585)
.+|..||..-..+-.+..-...-+.+.+.|+ |+
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCG 245 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTT
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCccc
Confidence 5788888764433322211111345678888 87
No 90
>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=58.65 E-value=5.4 Score=29.03 Aligned_cols=29 Identities=28% Similarity=0.616 Sum_probs=21.1
Q ss_pred cccccccCcccccccccchhcccccCccccccchhhhccccccccCCCC
Q 007898 92 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPN 140 (585)
Q Consensus 92 py~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~Cg 140 (585)
.|+|..||..|.....+. ....-.|+.||
T Consensus 5 ey~C~~Cg~~fe~~~~~~--------------------~~~~~~CP~Cg 33 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSIS--------------------EDDPVPCPECG 33 (42)
T ss_pred EEEeCCCCCEEEEEEEcC--------------------CCCCCcCCCCC
Confidence 489999999987654432 23466799997
No 91
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=57.97 E-value=9.1 Score=42.04 Aligned_cols=15 Identities=20% Similarity=0.470 Sum_probs=9.9
Q ss_pred cCcccccccCccccc
Q 007898 90 TNRFVCEICNKGFQR 104 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~ 104 (585)
++--.|-.|...|..
T Consensus 899 ~~a~~cmacq~pf~a 913 (990)
T KOG1819|consen 899 EDAEQCMACQMPFNA 913 (990)
T ss_pred CcchhhhhccCcHHH
Confidence 455567778777653
No 92
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=57.92 E-value=7.8 Score=36.44 Aligned_cols=26 Identities=23% Similarity=0.346 Sum_probs=14.8
Q ss_pred CCccccccccCCccc------ChhHHHHHHHH
Q 007898 165 GEKKWKCDKCSKRYA------VQSDWKAHSKT 190 (585)
Q Consensus 165 gekpy~C~~CgK~F~------~~s~L~~H~r~ 190 (585)
..-..+|..|+|-|- ..+++..|+..
T Consensus 11 p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~ 42 (152)
T PF09416_consen 11 PSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVR 42 (152)
T ss_dssp CCCEEEETTTTEEEES--TTSSS-HHHHHHHH
T ss_pred cccEeEcCCCCcEeecCCCCCcccHHHHHHHH
Confidence 344567777777773 34556666544
No 93
>PRK04023 DNA polymerase II large subunit; Validated
Probab=56.59 E-value=9.3 Score=45.74 Aligned_cols=13 Identities=31% Similarity=0.593 Sum_probs=9.2
Q ss_pred ccCcccccccCcc
Q 007898 89 ATNRFVCEICNKG 101 (585)
Q Consensus 89 ~~kpy~C~~Cgk~ 101 (585)
......|+.||+.
T Consensus 623 EVg~RfCpsCG~~ 635 (1121)
T PRK04023 623 EIGRRKCPSCGKE 635 (1121)
T ss_pred cccCccCCCCCCc
Confidence 3456778888876
No 94
>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=56.25 E-value=5.5 Score=35.35 Aligned_cols=29 Identities=24% Similarity=0.627 Sum_probs=20.8
Q ss_pred ccccccCCcccChhHHHHHHHHhCCcceecC-CCCccCCh
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFSRR 207 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~~~ 207 (585)
..|..||++|-.- +..|..|+ ||..|.-.
T Consensus 10 R~Cp~CG~kFYDL----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC----------CCCCccCCCCCCccCcc
Confidence 5788888887542 23678888 88888665
No 95
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=56.19 E-value=5.6 Score=36.39 Aligned_cols=15 Identities=20% Similarity=0.596 Sum_probs=13.0
Q ss_pred cccccccCccccccc
Q 007898 92 RFVCEICNKGFQRDQ 106 (585)
Q Consensus 92 py~C~~Cgk~F~~~~ 106 (585)
||+|..||+.|.+..
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 689999999998755
No 96
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=55.72 E-value=6.4 Score=29.70 Aligned_cols=14 Identities=21% Similarity=0.674 Sum_probs=11.6
Q ss_pred cccccccCcccccc
Q 007898 92 RFVCEICNKGFQRD 105 (585)
Q Consensus 92 py~C~~Cgk~F~~~ 105 (585)
.|+|..||..|...
T Consensus 5 ey~C~~Cg~~fe~~ 18 (52)
T TIGR02605 5 EYRCTACGHRFEVL 18 (52)
T ss_pred EEEeCCCCCEeEEE
Confidence 48999999999743
No 97
>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=55.12 E-value=6.9 Score=27.75 Aligned_cols=15 Identities=33% Similarity=0.702 Sum_probs=12.0
Q ss_pred cccccccCccccccc
Q 007898 92 RFVCEICNKGFQRDQ 106 (585)
Q Consensus 92 py~C~~Cgk~F~~~~ 106 (585)
.|+|..||+.|....
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 589999999987543
No 98
>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=54.63 E-value=21 Score=31.40 Aligned_cols=24 Identities=25% Similarity=0.585 Sum_probs=21.1
Q ss_pred eec----C-CCCccCChHHHHHHHHHhhh
Q 007898 196 YRC----D-CGTLFSRRDSFITHRAFCDA 219 (585)
Q Consensus 196 y~C----~-Cgk~F~~~s~L~~H~~~h~~ 219 (585)
|.| . |+..+.....+++|.+.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 7 99999999999999977653
No 99
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=54.27 E-value=7 Score=37.37 Aligned_cols=24 Identities=25% Similarity=0.592 Sum_probs=19.4
Q ss_pred CcccccccCcccccccccchhcccccCccccccchhhhccccccccCCCC
Q 007898 91 NRFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPN 140 (585)
Q Consensus 91 kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~Cg 140 (585)
+.|+|++||..+. ++-|-+||+||
T Consensus 133 ~~~vC~vCGy~~~--------------------------ge~P~~CPiCg 156 (166)
T COG1592 133 KVWVCPVCGYTHE--------------------------GEAPEVCPICG 156 (166)
T ss_pred CEEEcCCCCCccc--------------------------CCCCCcCCCCC
Confidence 3799999987532 67799999997
No 100
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=53.96 E-value=14 Score=29.03 Aligned_cols=30 Identities=23% Similarity=0.672 Sum_probs=16.0
Q ss_pred cccccccCCcccCh-hHHHHHHHHhCCcceecC-CCC
Q 007898 168 KWKCDKCSKRYAVQ-SDWKAHSKTCGTREYRCD-CGT 202 (585)
Q Consensus 168 py~C~~CgK~F~~~-s~L~~H~r~hgekpy~C~-Cgk 202 (585)
.|.|+.||+....+ ..-+ --..+|+|+ ||.
T Consensus 25 ~F~CPnCG~~~I~RC~~CR-----k~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRCEKCR-----KQSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeechhHH-----hcCCceECCCCCC
Confidence 47777777762222 1111 123678887 874
No 101
>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=53.07 E-value=9.1 Score=27.81 Aligned_cols=24 Identities=42% Similarity=0.578 Sum_probs=10.9
Q ss_pred CccccccccCCcccCh----hHHHHHHH
Q 007898 166 EKKWKCDKCSKRYAVQ----SDWKAHSK 189 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~----s~L~~H~r 189 (585)
++..+|.+|++.+... +.|.+|++
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 4445666666665543 45555553
No 102
>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=52.97 E-value=14 Score=32.40 Aligned_cols=24 Identities=17% Similarity=0.498 Sum_probs=22.2
Q ss_pred ccc----cccCCcccChhHHHHHHHH-hC
Q 007898 169 WKC----DKCSKRYAVQSDWKAHSKT-CG 192 (585)
Q Consensus 169 y~C----~~CgK~F~~~s~L~~H~r~-hg 192 (585)
|.| ..|+..+.....+.+|.+. ||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999988 65
No 103
>PHA00626 hypothetical protein
Probab=52.94 E-value=7.5 Score=30.18 Aligned_cols=11 Identities=18% Similarity=0.594 Sum_probs=5.4
Q ss_pred ccccccCCccc
Q 007898 169 WKCDKCSKRYA 179 (585)
Q Consensus 169 y~C~~CgK~F~ 179 (585)
|+|+.||..|.
T Consensus 24 YkCkdCGY~ft 34 (59)
T PHA00626 24 YVCCDCGYNDS 34 (59)
T ss_pred eEcCCCCCeec
Confidence 55555554443
No 104
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=51.56 E-value=9 Score=28.30 Aligned_cols=15 Identities=20% Similarity=0.682 Sum_probs=11.8
Q ss_pred CcccccccCcccccc
Q 007898 91 NRFVCEICNKGFQRD 105 (585)
Q Consensus 91 kpy~C~~Cgk~F~~~ 105 (585)
..|+|..||..|...
T Consensus 2 ~~y~C~~CG~~~~~~ 16 (46)
T PRK00398 2 AEYKCARCGREVELD 16 (46)
T ss_pred CEEECCCCCCEEEEC
Confidence 368999999987653
No 105
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=51.43 E-value=6.9 Score=33.52 Aligned_cols=14 Identities=36% Similarity=0.885 Sum_probs=10.4
Q ss_pred ccccccccCCcccC
Q 007898 167 KKWKCDKCSKRYAV 180 (585)
Q Consensus 167 kpy~C~~CgK~F~~ 180 (585)
-.|.|..|++.|.-
T Consensus 53 GIW~C~~C~~~~AG 66 (90)
T PTZ00255 53 GIWRCKGCKKTVAG 66 (90)
T ss_pred EEEEcCCCCCEEeC
Confidence 46888888887754
No 106
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=49.36 E-value=8.5 Score=30.27 Aligned_cols=8 Identities=63% Similarity=1.713 Sum_probs=4.7
Q ss_pred cceecC-CC
Q 007898 194 REYRCD-CG 201 (585)
Q Consensus 194 kpy~C~-Cg 201 (585)
.+|+|+ ||
T Consensus 49 ~~Y~Cp~CG 57 (61)
T COG2888 49 NPYRCPKCG 57 (61)
T ss_pred CceECCCcC
Confidence 456665 65
No 107
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=48.94 E-value=13 Score=39.24 Aligned_cols=32 Identities=9% Similarity=0.207 Sum_probs=24.3
Q ss_pred CccccccccCCcccChhHHHHHHHH-hCCccee
Q 007898 166 EKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYR 197 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~s~L~~H~r~-hgekpy~ 197 (585)
+..|.|++|++.=.+...|..|... |.+-.+.
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~ 109 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTS 109 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcc
Confidence 3468888998888888888888877 7665543
No 108
>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=48.03 E-value=7.4 Score=33.38 Aligned_cols=14 Identities=36% Similarity=1.044 Sum_probs=10.4
Q ss_pred ccccccccCCcccC
Q 007898 167 KKWKCDKCSKRYAV 180 (585)
Q Consensus 167 kpy~C~~CgK~F~~ 180 (585)
-.|+|..|++.|.-
T Consensus 52 GIW~C~~C~~~~AG 65 (91)
T TIGR00280 52 GIWTCRKCGAKFAG 65 (91)
T ss_pred EEEEcCCCCCEEeC
Confidence 35888888887754
No 109
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.93 E-value=11 Score=44.01 Aligned_cols=10 Identities=20% Similarity=0.634 Sum_probs=4.7
Q ss_pred ccccccccCC
Q 007898 167 KKWKCDKCSK 176 (585)
Q Consensus 167 kpy~C~~CgK 176 (585)
+..+|.+||.
T Consensus 409 ~~l~Ch~CG~ 418 (665)
T PRK14873 409 GTPRCRWCGR 418 (665)
T ss_pred CeeECCCCcC
Confidence 3444555553
No 110
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=47.89 E-value=19 Score=33.62 Aligned_cols=12 Identities=33% Similarity=1.101 Sum_probs=6.1
Q ss_pred cccccccCCccc
Q 007898 168 KWKCDKCSKRYA 179 (585)
Q Consensus 168 py~C~~CgK~F~ 179 (585)
.|.|+.|++.|.
T Consensus 99 ~Y~Cp~C~~~y~ 110 (147)
T smart00531 99 YYKCPNCQSKYT 110 (147)
T ss_pred EEECcCCCCEee
Confidence 355555555544
No 111
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=47.72 E-value=8.6 Score=29.17 Aligned_cols=13 Identities=15% Similarity=0.616 Sum_probs=11.2
Q ss_pred cCcccccccCccc
Q 007898 90 TNRFVCEICNKGF 102 (585)
Q Consensus 90 ~kpy~C~~Cgk~F 102 (585)
...|+|-.||+.|
T Consensus 4 ~~~Y~C~~Cg~~~ 16 (49)
T COG1996 4 MMEYKCARCGREV 16 (49)
T ss_pred eEEEEhhhcCCee
Confidence 3569999999998
No 112
>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=47.03 E-value=6.4 Score=46.25 Aligned_cols=9 Identities=44% Similarity=0.870 Sum_probs=0.0
Q ss_pred cccccccCc
Q 007898 92 RFVCEICNK 100 (585)
Q Consensus 92 py~C~~Cgk 100 (585)
.++|+.||+
T Consensus 655 ~r~Cp~Cg~ 663 (900)
T PF03833_consen 655 RRRCPKCGK 663 (900)
T ss_dssp ---------
T ss_pred cccCcccCC
Confidence 455666655
No 113
>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=46.59 E-value=13 Score=33.89 Aligned_cols=14 Identities=21% Similarity=0.257 Sum_probs=7.3
Q ss_pred cceecC-CCCccCCh
Q 007898 194 REYRCD-CGTLFSRR 207 (585)
Q Consensus 194 kpy~C~-Cgk~F~~~ 207 (585)
.|..|. ||..|...
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 455555 55555443
No 114
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=46.11 E-value=31 Score=30.86 Aligned_cols=90 Identities=18% Similarity=0.228 Sum_probs=41.9
Q ss_pred cCcccccccCcccccccccchhcccccC-ccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccCCcc
Q 007898 90 TNRFVCEICNKGFQRDQNLQLHRRGHNL-PWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKK 168 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~~~~L~~H~r~H~~-~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekp 168 (585)
+-|-+|++||-..-...+|.+- .|++ |...-.............|--|. +.|........- .-.....
T Consensus 13 ~LP~~CpiCgLtLVss~HLARS--yHHLfPl~~f~ev~~~~~~~~~~C~~C~-------~~f~~~~~~~~~--~~~~~~~ 81 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARS--YHHLFPLKAFQEIPLEEYNGSRFCFGCQ-------GPFPKPPVSPFD--ELKDSHR 81 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHh--hhccCCCcccccccccccCCCCcccCcC-------CCCCCccccccc--ccccccc
Confidence 3467888998887776666554 3431 10000000000011112355553 555433211100 0112335
Q ss_pred ccccccCCcccChhHHHHHHHH
Q 007898 169 WKCDKCSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 169 y~C~~CgK~F~~~s~L~~H~r~ 190 (585)
|+|..|.+.|-..-+.-.|...
T Consensus 82 y~C~~C~~~FC~dCD~fiHe~L 103 (112)
T TIGR00622 82 YVCAVCKNVFCVDCDVFVHESL 103 (112)
T ss_pred eeCCCCCCccccccchhhhhhc
Confidence 7777777777776666666443
No 115
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=45.58 E-value=6.3 Score=33.76 Aligned_cols=33 Identities=33% Similarity=0.781 Sum_probs=19.9
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCccc
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYA 179 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~ 179 (585)
....|.|++|| ...+ .|.-.| .|.|..|++.|.
T Consensus 32 q~~ky~Cp~Cg------k~~v---------kR~a~G--IW~C~~C~~~~A 64 (90)
T PF01780_consen 32 QHAKYTCPFCG------KTSV---------KRVATG--IWKCKKCGKKFA 64 (90)
T ss_dssp HHS-BEESSSS------SSEE---------EEEETT--EEEETTTTEEEE
T ss_pred HhCCCcCCCCC------Ccee---------EEeeeE--EeecCCCCCEEe
Confidence 45678999997 1211 122223 489999988875
No 116
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=43.85 E-value=12 Score=35.01 Aligned_cols=41 Identities=17% Similarity=0.446 Sum_probs=27.1
Q ss_pred hccccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCccc
Q 007898 128 EIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYA 179 (585)
Q Consensus 128 ~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~ 179 (585)
.....-|.|+.|+ +.|.....+.. . .. +..|.|+.||....
T Consensus 94 e~~~~~Y~Cp~C~-------~~y~~~ea~~~-~--d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 94 ETNNAYYKCPNCQ-------SKYTFLEANQL-L--DM-DGTFTCPRCGEELE 134 (147)
T ss_pred ccCCcEEECcCCC-------CEeeHHHHHHh-c--CC-CCcEECCCCCCEEE
Confidence 3356789999996 77776544332 0 11 33499999998764
No 117
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=43.60 E-value=11 Score=31.03 Aligned_cols=13 Identities=31% Similarity=0.767 Sum_probs=6.4
Q ss_pred cceecC---CCCccCC
Q 007898 194 REYRCD---CGTLFSR 206 (585)
Q Consensus 194 kpy~C~---Cgk~F~~ 206 (585)
+-|.|. ||.+|..
T Consensus 26 ~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 26 RYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeecCCCCCCCEEEE
Confidence 344553 5555544
No 118
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=43.29 E-value=17 Score=25.57 Aligned_cols=10 Identities=30% Similarity=1.029 Sum_probs=4.9
Q ss_pred ccccccCCcc
Q 007898 169 WKCDKCSKRY 178 (585)
Q Consensus 169 y~C~~CgK~F 178 (585)
.+|..|+..|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 4455555444
No 119
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=43.05 E-value=17 Score=41.19 Aligned_cols=25 Identities=16% Similarity=0.459 Sum_probs=18.7
Q ss_pred CccccccccCCcccChhHHHHHHHH
Q 007898 166 EKKWKCDKCSKRYAVQSDWKAHSKT 190 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~s~L~~H~r~ 190 (585)
.++..|..||++|........||.+
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~ 440 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDI 440 (579)
T ss_pred CCcchhcccccccccchhhhhHhhh
Confidence 4568899999999887766665544
No 120
>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=42.68 E-value=16 Score=41.23 Aligned_cols=14 Identities=29% Similarity=0.674 Sum_probs=7.3
Q ss_pred cCCccccccccCCc
Q 007898 164 HGEKKWKCDKCSKR 177 (585)
Q Consensus 164 tgekpy~C~~CgK~ 177 (585)
..+....|..||..
T Consensus 236 ~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 236 KKEGKLRCHYCGYQ 249 (505)
T ss_pred cCCCeEEcCCCcCc
Confidence 33445556666653
No 121
>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=42.54 E-value=13 Score=33.89 Aligned_cols=34 Identities=12% Similarity=0.286 Sum_probs=24.1
Q ss_pred cccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhH
Q 007898 132 KVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSD 183 (585)
Q Consensus 132 k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~ 183 (585)
....|+.|| ++|... +..|..|++||..|.....
T Consensus 8 tKr~Cp~cg-------~kFYDL-----------nk~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 8 TKRICPNTG-------SKFYDL-----------NRRPAVSPYTGEQFPPEEA 41 (129)
T ss_pred ccccCCCcC-------cccccc-----------CCCCccCCCcCCccCcchh
Confidence 457899996 666543 2468899999998866533
No 122
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=42.50 E-value=10 Score=32.51 Aligned_cols=14 Identities=36% Similarity=1.070 Sum_probs=10.4
Q ss_pred ccccccccCCcccC
Q 007898 167 KKWKCDKCSKRYAV 180 (585)
Q Consensus 167 kpy~C~~CgK~F~~ 180 (585)
-.|.|..|++.|.-
T Consensus 53 GIW~C~~C~~~~AG 66 (90)
T PRK03976 53 GIWECRKCGAKFAG 66 (90)
T ss_pred EEEEcCCCCCEEeC
Confidence 35888888887754
No 123
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=41.91 E-value=11 Score=36.35 Aligned_cols=33 Identities=12% Similarity=0.439 Sum_probs=18.2
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcc
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRY 178 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F 178 (585)
...-|.|+.|+ +.|.....+. .-|.|+.||...
T Consensus 114 ~~~~Y~Cp~C~-------~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNCH-------IRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCCC-------cEEeHHHHhh---------cCCcCCCCCCCC
Confidence 34556676664 5555554432 246666666544
No 124
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=41.19 E-value=21 Score=43.94 Aligned_cols=10 Identities=30% Similarity=0.664 Sum_probs=7.3
Q ss_pred cccccccCcc
Q 007898 92 RFVCEICNKG 101 (585)
Q Consensus 92 py~C~~Cgk~ 101 (585)
.++|+.||..
T Consensus 667 ~rkCPkCG~~ 676 (1337)
T PRK14714 667 RRRCPSCGTE 676 (1337)
T ss_pred EEECCCCCCc
Confidence 4788888763
No 125
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=40.97 E-value=22 Score=38.79 Aligned_cols=34 Identities=26% Similarity=0.681 Sum_probs=20.0
Q ss_pred CccccccccCCcccChhHHHHHHHH-hCCcceecC-CCC
Q 007898 166 EKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGT 202 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk 202 (585)
..-|.|+.|.+.|..-..+ ..+ ..+..|.|. |+-
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~---~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEAL---QLLDNETGEFHCENCGG 161 (436)
T ss_pred cccccCCccccchhhhHHH---HhhcccCceEEEecCCC
Confidence 3457788888777654333 223 334567777 763
No 126
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=40.86 E-value=13 Score=40.19 Aligned_cols=28 Identities=18% Similarity=0.354 Sum_probs=21.6
Q ss_pred ccCcccc--cccCcccccccccchhccccc
Q 007898 89 ATNRFVC--EICNKGFQRDQNLQLHRRGHN 116 (585)
Q Consensus 89 ~~kpy~C--~~Cgk~F~~~~~L~~H~r~H~ 116 (585)
+..-|.| +.|+..+-.+..+.+|..+|.
T Consensus 268 ~rEhyhcl~e~C~ykr~~k~DvirH~~~hk 297 (480)
T KOG4377|consen 268 GREHYHCLNEYCFYKRGQKNDVIRHVEIHK 297 (480)
T ss_pred cchhhcccCccccccccchhhhHHHHHHHh
Confidence 3456777 458877777889999998885
No 127
>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=40.34 E-value=13 Score=35.18 Aligned_cols=33 Identities=12% Similarity=0.449 Sum_probs=18.9
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcc
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRY 178 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F 178 (585)
...-|.|+.|+ ..|....++. .-|.|+.||...
T Consensus 106 ~~~~Y~Cp~c~-------~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 106 NNMFFICPNMC-------VRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CCCeEECCCCC-------cEeeHHHHHH---------cCCcCCCCCCEe
Confidence 44556677664 5555555543 246677776543
No 128
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=40.10 E-value=17 Score=32.51 Aligned_cols=17 Identities=18% Similarity=0.483 Sum_probs=13.4
Q ss_pred cCcccccccCccccccc
Q 007898 90 TNRFVCEICNKGFQRDQ 106 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~~~ 106 (585)
...+.|..||..+....
T Consensus 20 ~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 20 GGKLVCRKCGYEEEASN 36 (113)
T ss_pred CcEEECCCCCcchhccc
Confidence 44899999998877664
No 129
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=39.90 E-value=20 Score=25.27 Aligned_cols=12 Identities=33% Similarity=0.988 Sum_probs=6.4
Q ss_pred ccccccccCCcc
Q 007898 167 KKWKCDKCSKRY 178 (585)
Q Consensus 167 kpy~C~~CgK~F 178 (585)
+..+|..|+..|
T Consensus 24 ~~vrC~~C~~~f 35 (37)
T PF13719_consen 24 RKVRCPKCGHVF 35 (37)
T ss_pred cEEECCCCCcEe
Confidence 345555555554
No 130
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=39.75 E-value=11 Score=32.93 Aligned_cols=15 Identities=20% Similarity=0.538 Sum_probs=12.8
Q ss_pred cccccccCccccccc
Q 007898 92 RFVCEICNKGFQRDQ 106 (585)
Q Consensus 92 py~C~~Cgk~F~~~~ 106 (585)
++.|..||+.|.+-.
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 689999999998753
No 131
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=39.52 E-value=19 Score=27.01 Aligned_cols=21 Identities=29% Similarity=0.619 Sum_probs=12.2
Q ss_pred ccccccCCcccCh-----hHHHHHHH
Q 007898 169 WKCDKCSKRYAVQ-----SDWKAHSK 189 (585)
Q Consensus 169 y~C~~CgK~F~~~-----s~L~~H~r 189 (585)
-.|.+|++.+... +.|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4566777666544 35555555
No 132
>PF14353 CpXC: CpXC protein
Probab=39.41 E-value=27 Score=31.52 Aligned_cols=13 Identities=15% Similarity=0.968 Sum_probs=6.5
Q ss_pred ccccccCCcccCh
Q 007898 169 WKCDKCSKRYAVQ 181 (585)
Q Consensus 169 y~C~~CgK~F~~~ 181 (585)
|.|+.||+.|.-.
T Consensus 39 ~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 39 FTCPSCGHKFRLE 51 (128)
T ss_pred EECCCCCCceecC
Confidence 4555555555443
No 133
>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=39.10 E-value=16 Score=25.61 Aligned_cols=15 Identities=20% Similarity=0.576 Sum_probs=11.9
Q ss_pred ccccccCcccccccc
Q 007898 93 FVCEICNKGFQRDQN 107 (585)
Q Consensus 93 y~C~~Cgk~F~~~~~ 107 (585)
+.|+.|+..|.-...
T Consensus 3 ~~CP~C~~~~~v~~~ 17 (38)
T TIGR02098 3 IQCPNCKTSFRVVDS 17 (38)
T ss_pred EECCCCCCEEEeCHH
Confidence 679999999876654
No 134
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.84 E-value=20 Score=42.16 Aligned_cols=28 Identities=18% Similarity=0.536 Sum_probs=18.9
Q ss_pred cccCCccccccccCCcccChhHHHHHHHHhCCcceecC-CCCc
Q 007898 162 RKHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTL 203 (585)
Q Consensus 162 ~Htgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~ 203 (585)
.|...+..+|.+||+. ...|..|+ ||-.
T Consensus 456 ~H~~~~~L~CH~Cg~~--------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 456 LHKATGQLRCHYCGYQ--------------EPIPQSCPECGSE 484 (730)
T ss_pred EecCCCeeEeCCCCCC--------------CCCCCCCCCCCCC
Confidence 3444566888888864 23678888 8854
No 135
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=38.16 E-value=17 Score=36.84 Aligned_cols=59 Identities=22% Similarity=0.433 Sum_probs=35.5
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHHhCCcceecC-CCCccCCh
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFSRR 207 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~~~ 207 (585)
..+.|.|..|. .. .-.++-...+.-+|..|.+.|.---. -+.-|.-.|.|. |+..|+-.
T Consensus 109 ~drqFaC~~Cd-------~~--------WwRrvp~rKeVSRCr~C~~rYDPVP~----dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 109 VDRQFACSSCD-------HM--------WWRRVPQRKEVSRCRKCRKRYDPVPC----DKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred cceeeeccccc-------hH--------HHhccCcccccccccccccccCCCcc----ccccceeeeecccccccchhh
Confidence 45789999994 11 11123333445678889888754321 112355678998 99988643
No 136
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=38.11 E-value=5.4 Score=44.48 Aligned_cols=72 Identities=15% Similarity=0.349 Sum_probs=45.0
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHHhCCcceecC-CCCccCChH
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFSRRD 208 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~~~s 208 (585)
.+-.|.|+-- |.+.+-.-.....|.+|..+|....-=+|..|||.|..+-.+.. + ..-...|. |...|..+.
T Consensus 218 eKiNfrCKpt---FRe~gsr~~rE~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~Fhs--K--EivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 218 EKINFRCKPT---FREYGSRKTRESGFVRHHWVHRRRQEGKCNTCGKGFQQKFFFHS--K--EIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred HHhccccccc---hhhccccCcccccchHHhHhhHhhhccccchhhhhhhhheeecc--c--cEEEEEehHHHHHhhcch
Confidence 3445666532 22222333345688888888877666789999999986543321 1 11336799 998887765
No 137
>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=37.34 E-value=23 Score=35.39 Aligned_cols=30 Identities=23% Similarity=0.429 Sum_probs=22.5
Q ss_pred CCcceecC-CCCccCChHHHHHHHHHhhhcc
Q 007898 192 GTREYRCD-CGTLFSRRDSFITHRAFCDALA 221 (585)
Q Consensus 192 gekpy~C~-Cgk~F~~~s~L~~H~~~h~~~~ 221 (585)
.+..|.|. |+|.|+-....++|+..-|...
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 45679999 9999999999999987766544
No 138
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=37.18 E-value=8.4 Score=44.46 Aligned_cols=55 Identities=16% Similarity=0.402 Sum_probs=31.9
Q ss_pred ccCCCCcccCCCCCccCChhhhhhhhccccCCccc-cccccCCcccChhHHHHHHHHhCCcceecC-CCC
Q 007898 135 VCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKW-KCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGT 202 (585)
Q Consensus 135 ~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy-~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk 202 (585)
.|..|| -+|+-...|-.-. .++.-+.| .|+.|.+.|....+-+-| ..|..|+ ||-
T Consensus 125 ~CT~CG-------PRfTIi~alPYDR-~nTsM~~F~lC~~C~~EY~dP~nRRfH-----AQp~aCp~CGP 181 (750)
T COG0068 125 NCTNCG-------PRFTIIEALPYDR-ENTSMADFPLCPFCDKEYKDPLNRRFH-----AQPIACPKCGP 181 (750)
T ss_pred ccCCCC-------cceeeeccCCCCc-ccCccccCcCCHHHHHHhcCccccccc-----cccccCcccCC
Confidence 477775 5565544443322 22223333 488888887777665444 4567788 874
No 139
>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=37.09 E-value=21 Score=25.21 Aligned_cols=27 Identities=22% Similarity=0.390 Sum_probs=18.4
Q ss_pred ccccccCcccccccccchhcccccCccccccchhhhccccccccCCCC
Q 007898 93 FVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPN 140 (585)
Q Consensus 93 y~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~Cg 140 (585)
+.|+.||+.|.....- ....-+|+.||
T Consensus 2 r~C~~Cg~~Yh~~~~p---------------------P~~~~~Cd~cg 28 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNP---------------------PKVEGVCDNCG 28 (36)
T ss_dssp EEETTTTEEEETTTB-----------------------SSTTBCTTTT
T ss_pred cCcCCCCCccccccCC---------------------CCCCCccCCCC
Confidence 5799999988643221 45667899997
No 140
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=36.69 E-value=12 Score=30.79 Aligned_cols=15 Identities=27% Similarity=0.789 Sum_probs=7.7
Q ss_pred Ccccccc--ccCCcccC
Q 007898 166 EKKWKCD--KCSKRYAV 180 (585)
Q Consensus 166 ekpy~C~--~CgK~F~~ 180 (585)
++-+.|. .||.+|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 4445555 55555543
No 141
>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=36.54 E-value=21 Score=33.79 Aligned_cols=34 Identities=15% Similarity=0.555 Sum_probs=22.7
Q ss_pred cCCccccccccCCcccChhHHHHHHHHhCCcceecC-CCCccC
Q 007898 164 HGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFS 205 (585)
Q Consensus 164 tgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~ 205 (585)
....-|.|+.|+..|..-..+. .-|.|+ ||....
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME--------LNFTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH--------cCCcCCCCCCEee
Confidence 3445688888888777666553 358888 886543
No 142
>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=34.77 E-value=20 Score=33.02 Aligned_cols=25 Identities=28% Similarity=0.527 Sum_probs=10.8
Q ss_pred cccccccCCcccChhHHHHHHHH-hCCcc
Q 007898 168 KWKCDKCSKRYAVQSDWKAHSKT-CGTRE 195 (585)
Q Consensus 168 py~C~~CgK~F~~~s~L~~H~r~-hgekp 195 (585)
...|-+|||.|.. |++|++. ||-.|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCCcccch---HHHHHHHccCCCH
Confidence 3556666666654 3666666 35544
No 143
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.14 E-value=28 Score=30.81 Aligned_cols=13 Identities=15% Similarity=0.125 Sum_probs=8.0
Q ss_pred CccccccccCCcc
Q 007898 166 EKKWKCDKCSKRY 178 (585)
Q Consensus 166 ekpy~C~~CgK~F 178 (585)
..|..|++|||.|
T Consensus 24 rdPiVsPytG~s~ 36 (129)
T COG4530 24 RDPIVSPYTGKSY 36 (129)
T ss_pred CCccccCcccccc
Confidence 3456666666666
No 144
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=33.97 E-value=24 Score=34.14 Aligned_cols=33 Identities=21% Similarity=0.709 Sum_probs=21.5
Q ss_pred CccccccccCCcccChhHHHHHHHHhCCcceecC-CCCccCC
Q 007898 166 EKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFSR 206 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~~ 206 (585)
..-|.|+.|++.|..-..+. .-|.|+ ||.....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCee
Confidence 34578888888777655442 357888 8765543
No 145
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=33.70 E-value=24 Score=33.36 Aligned_cols=21 Identities=29% Similarity=0.532 Sum_probs=16.4
Q ss_pred cCcccccccCcccccccccch
Q 007898 90 TNRFVCEICNKGFQRDQNLQL 110 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~~~~L~~ 110 (585)
.+.|.|+.||+.|.....+..
T Consensus 26 ~~~~~c~~c~~~f~~~e~~~~ 46 (154)
T PRK00464 26 RRRRECLACGKRFTTFERVEL 46 (154)
T ss_pred eeeeeccccCCcceEeEeccC
Confidence 345999999999998766543
No 146
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=33.67 E-value=31 Score=32.90 Aligned_cols=24 Identities=33% Similarity=0.754 Sum_probs=16.8
Q ss_pred CccccccccCCcccChhHHHHHHH
Q 007898 166 EKKWKCDKCSKRYAVQSDWKAHSK 189 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~s~L~~H~r 189 (585)
+..|.|+.|||.|-.-+++.+=.+
T Consensus 128 ~~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 128 EEFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred cceeECCCCcccccCchHHHHHHH
Confidence 345778888888877777765444
No 147
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=33.43 E-value=19 Score=33.78 Aligned_cols=34 Identities=29% Similarity=0.837 Sum_probs=21.9
Q ss_pred CccccccccCCcccChhHHHHHHHH-hCCcceecC-CCCcc
Q 007898 166 EKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLF 204 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-Cgk~F 204 (585)
..+|.|. |+..|.+. .+|-.+ -|+ .|.|. |+-..
T Consensus 115 ~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 115 TYPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred ceeEEee-cCCccchh---hhcccccccc-eEEeccCCceE
Confidence 3468888 88876653 445445 455 78888 87543
No 148
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=32.92 E-value=31 Score=36.27 Aligned_cols=60 Identities=15% Similarity=0.274 Sum_probs=41.5
Q ss_pred CccccccccCCcccChhHHHHHHHH-hCCcceecC-----CCCccCChHHHHHHHHHhhhccccccccccCCCCccCCCC
Q 007898 166 EKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-----CGTLFSRRDSFITHRAFCDALAEESTRAITGTNPILSSSS 239 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~-----Cgk~F~~~s~L~~H~~~h~~~~~~~~r~ht~ekp~~cs~c 239 (585)
++..+|+.|...+... ..++|.. -....+.|+ |.+.|.+... ..|.+.|. -+|+.|+.-
T Consensus 78 ~~~~~CP~Cr~~~g~~--R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~------------f~~~~CP~p 142 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNI--RCRAMEKVAEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCE------------FRPCSCPVP 142 (299)
T ss_pred hhcccCCccccccccH--HHHHHHHHHHhceecccccccCCceeeccccc-cccccccc------------cCCcCCCCC
Confidence 5678999999988854 4445544 555667785 9999998877 56764432 367777654
Q ss_pred C
Q 007898 240 H 240 (585)
Q Consensus 240 ~ 240 (585)
+
T Consensus 143 ~ 143 (299)
T KOG3002|consen 143 G 143 (299)
T ss_pred c
Confidence 3
No 149
>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=32.72 E-value=31 Score=23.75 Aligned_cols=11 Identities=18% Similarity=0.869 Sum_probs=8.5
Q ss_pred ccccccCcccc
Q 007898 93 FVCEICNKGFQ 103 (585)
Q Consensus 93 y~C~~Cgk~F~ 103 (585)
|.|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 78999998876
No 150
>PRK05580 primosome assembly protein PriA; Validated
Probab=32.38 E-value=30 Score=40.59 Aligned_cols=11 Identities=18% Similarity=0.945 Sum_probs=5.4
Q ss_pred ccccccccCCc
Q 007898 167 KKWKCDKCSKR 177 (585)
Q Consensus 167 kpy~C~~CgK~ 177 (585)
+...|..||+.
T Consensus 407 ~~l~Ch~Cg~~ 417 (679)
T PRK05580 407 RRLRCHHCGYQ 417 (679)
T ss_pred CeEECCCCcCC
Confidence 34455555543
No 151
>cd07765 KRAB_A-box KRAB (Kruppel-associated box) domain -A box. The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through
Probab=32.33 E-value=49 Score=19.88 Aligned_cols=23 Identities=35% Similarity=0.378 Sum_probs=18.9
Q ss_pred ccChHHHHHHHHHHHHhhccccc
Q 007898 5 LIFHQQQQQQQQVLEENMSNLTS 27 (585)
Q Consensus 5 ~ld~qQqQlyqqVmlEn~~nL~S 27 (585)
.++..|+.+|.+++++++.++..
T Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~ 39 (40)
T cd07765 17 LLDPAQRDLYRDVMLENYENLVS 39 (40)
T ss_pred cCCHHHHHHHHHHHHHhhccccC
Confidence 46789999999999999877643
No 152
>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=31.61 E-value=27 Score=32.14 Aligned_cols=29 Identities=21% Similarity=0.443 Sum_probs=13.3
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCcc
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKK 168 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekp 168 (585)
.+....|-+|| |.|+. |++|++.|+|-.+
T Consensus 69 ~~d~i~clecG-------k~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 69 TPDYIICLECG-------KKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -SS-EE-TBT---------EESB---HHHHHHHTT-S-H
T ss_pred ccCeeEEccCC-------cccch---HHHHHHHccCCCH
Confidence 44555666665 65544 3677777766543
No 153
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.46 E-value=27 Score=32.23 Aligned_cols=16 Identities=13% Similarity=0.439 Sum_probs=13.2
Q ss_pred cCcccccccCcccccc
Q 007898 90 TNRFVCEICNKGFQRD 105 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~~ 105 (585)
...|.|..||..|...
T Consensus 68 p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK 83 (135)
T ss_pred ceEEECCCCCCEEecc
Confidence 4679999999988764
No 154
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=31.21 E-value=27 Score=29.87 Aligned_cols=15 Identities=20% Similarity=0.483 Sum_probs=13.0
Q ss_pred cCcccccccCccccc
Q 007898 90 TNRFVCEICNKGFQR 104 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~ 104 (585)
.+|-.|..||..|..
T Consensus 56 v~Pa~CkkCGfef~~ 70 (97)
T COG3357 56 VRPARCKKCGFEFRD 70 (97)
T ss_pred ecChhhcccCccccc
Confidence 468899999999976
No 155
>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=31.18 E-value=49 Score=24.88 Aligned_cols=16 Identities=13% Similarity=0.762 Sum_probs=12.4
Q ss_pred cccccccCcccccccc
Q 007898 92 RFVCEICNKGFQRDQN 107 (585)
Q Consensus 92 py~C~~Cgk~F~~~~~ 107 (585)
+|+|.+|+..|.-...
T Consensus 1 ky~C~~CgyvYd~~~G 16 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKG 16 (47)
T ss_dssp EEEETTTSBEEETTTB
T ss_pred CcCCCCCCEEEcCCcC
Confidence 4899999988876544
No 156
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=31.07 E-value=14 Score=39.10 Aligned_cols=60 Identities=15% Similarity=0.220 Sum_probs=37.4
Q ss_pred CcceecC-CCCccCChHHHHHHHHHhhhccc-cccccccCCCCccCCCCCCCCCcCCCcccc
Q 007898 193 TREYRCD-CGTLFSRRDSFITHRAFCDALAE-ESTRAITGTNPILSSSSHHQPGIVAGASSH 252 (585)
Q Consensus 193 ekpy~C~-Cgk~F~~~s~L~~H~~~h~~~~~-~~~r~ht~ekp~~cs~c~~sf~~~s~l~sH 252 (585)
..-|.|. |++.=.....|..|....|.... .......+..++.|..|.+--........|
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~~qp~~~~~~~~~~~~~~~ 138 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPEMQPIHSKETENLSVHWTE 138 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcccCchhhhhhhhhhhhhhh
Confidence 3579999 99987788889999866554433 223344456666666666644433333333
No 157
>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=30.88 E-value=25 Score=35.82 Aligned_cols=73 Identities=14% Similarity=0.240 Sum_probs=36.8
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhcc--ccCCccccccccCCcccChhH-------HHHHHHH-----hCCcc
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCR--KHGEKKWKCDKCSKRYAVQSD-------WKAHSKT-----CGTRE 195 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~--Htgekpy~C~~CgK~F~~~s~-------L~~H~r~-----hgekp 195 (585)
+.+.|+|.+|. .|.....--.|+.. ......|+|.-|.+.= ..+- -..|.|. -..++
T Consensus 139 GGrif~CsfC~--------~flCEDDQFEHQAsCQvLe~E~~KC~SCNrlG-q~sCLRCK~cfCddHvrrKg~ky~k~k~ 209 (314)
T PF06524_consen 139 GGRIFKCSFCD--------NFLCEDDQFEHQASCQVLESETFKCQSCNRLG-QYSCLRCKICFCDDHVRRKGFKYEKGKP 209 (314)
T ss_pred CCeEEEeecCC--------Ceeeccchhhhhhhhhhhhccccccccccccc-chhhhheeeeehhhhhhhcccccccCCC
Confidence 77788888884 33333333333321 1122345555554421 1111 1245443 24478
Q ss_pred eecC-CCCccCChHHHH
Q 007898 196 YRCD-CGTLFSRRDSFI 211 (585)
Q Consensus 196 y~C~-Cgk~F~~~s~L~ 211 (585)
+.|+ |+........|.
T Consensus 210 ~PCPKCg~et~eTkdLS 226 (314)
T PF06524_consen 210 IPCPKCGYETQETKDLS 226 (314)
T ss_pred CCCCCCCCcccccccce
Confidence 9999 997666555553
No 158
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.51 E-value=29 Score=38.03 Aligned_cols=29 Identities=34% Similarity=0.815 Sum_probs=21.3
Q ss_pred cccccCCcccChhHHHHHHHHhCCcceecC-CCCccCChH
Q 007898 170 KCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFSRRD 208 (585)
Q Consensus 170 ~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~~~s 208 (585)
+|+.||.+ |+..|.+-|+|+ ||+++....
T Consensus 352 ~Cp~Cg~~----------m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGR----------MKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCc----------hhhcCCCCcccccccccCCccc
Confidence 69999875 334455589999 999887653
No 159
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=30.47 E-value=17 Score=42.06 Aligned_cols=27 Identities=30% Similarity=0.518 Sum_probs=24.9
Q ss_pred cCcccccccCcccccccccchhccccc
Q 007898 90 TNRFVCEICNKGFQRDQNLQLHRRGHN 116 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 116 (585)
...|.|.+|+|+|.....+..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 457999999999999999999999996
No 160
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=29.61 E-value=21 Score=37.52 Aligned_cols=10 Identities=10% Similarity=0.119 Sum_probs=4.4
Q ss_pred cccccccCCC
Q 007898 130 RKKVYVCPEP 139 (585)
Q Consensus 130 ~~k~y~C~~C 139 (585)
|.+...|..|
T Consensus 207 G~RyL~CslC 216 (305)
T TIGR01562 207 GLRYLSCSLC 216 (305)
T ss_pred CceEEEcCCC
Confidence 3344444444
No 161
>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=27.10 E-value=19 Score=25.80 Aligned_cols=10 Identities=30% Similarity=1.092 Sum_probs=7.6
Q ss_pred ccccccCCcc
Q 007898 169 WKCDKCSKRY 178 (585)
Q Consensus 169 y~C~~CgK~F 178 (585)
|.|..|++.|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 7788888765
No 162
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=26.99 E-value=38 Score=25.02 Aligned_cols=12 Identities=25% Similarity=0.697 Sum_probs=7.1
Q ss_pred ccccccccCCcc
Q 007898 167 KKWKCDKCSKRY 178 (585)
Q Consensus 167 kpy~C~~CgK~F 178 (585)
.+.+|+.||...
T Consensus 18 ~~irC~~CG~rI 29 (44)
T smart00659 18 DVVRCRECGYRI 29 (44)
T ss_pred CceECCCCCceE
Confidence 456677776543
No 163
>PRK04023 DNA polymerase II large subunit; Validated
Probab=26.93 E-value=40 Score=40.66 Aligned_cols=11 Identities=18% Similarity=0.854 Sum_probs=7.0
Q ss_pred ccccccccCCc
Q 007898 167 KKWKCDKCSKR 177 (585)
Q Consensus 167 kpy~C~~CgK~ 177 (585)
..|.|..|++.
T Consensus 650 ~i~fCP~CG~~ 660 (1121)
T PRK04023 650 PVYRCPRCGIE 660 (1121)
T ss_pred cceeCccccCc
Confidence 45677777664
No 164
>PF15269 zf-C2H2_7: Zinc-finger
Probab=26.90 E-value=47 Score=24.67 Aligned_cols=21 Identities=19% Similarity=0.633 Sum_probs=13.2
Q ss_pred eecC-CCCccCChHHHHHHHHH
Q 007898 196 YRCD-CGTLFSRRDSFITHRAF 216 (585)
Q Consensus 196 y~C~-Cgk~F~~~s~L~~H~~~ 216 (585)
|+|- |..+...++.|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 4555 66666666667777654
No 165
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.78 E-value=31 Score=40.29 Aligned_cols=6 Identities=17% Similarity=0.528 Sum_probs=3.3
Q ss_pred ccCCCC
Q 007898 135 VCPEPN 140 (585)
Q Consensus 135 ~C~~Cg 140 (585)
.|..||
T Consensus 385 ~C~~Cg 390 (665)
T PRK14873 385 ACARCR 390 (665)
T ss_pred EhhhCc
Confidence 566554
No 166
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=26.11 E-value=17 Score=41.96 Aligned_cols=26 Identities=23% Similarity=0.422 Sum_probs=22.6
Q ss_pred ceecC-CCCccCChHHHHHHHHHhhhc
Q 007898 195 EYRCD-CGTLFSRRDSFITHRAFCDAL 220 (585)
Q Consensus 195 py~C~-Cgk~F~~~s~L~~H~~~h~~~ 220 (585)
-|-|. |+|.|-.-.+++.||+.|.-.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 48999 999999999999999988643
No 167
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=25.75 E-value=15 Score=38.18 Aligned_cols=52 Identities=19% Similarity=0.407 Sum_probs=20.9
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHHhCCcceecC-CCCccCCh
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFSRR 207 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~~~ 207 (585)
.-.|++|| + ....+.|..-.. .|.|...|..|+-.+.. +...|. ||..-..+
T Consensus 172 ~g~CPvCG------s--~P~~s~l~~~~~--~G~R~L~Cs~C~t~W~~-------------~R~~Cp~Cg~~~~~~ 224 (290)
T PF04216_consen 172 RGYCPVCG------S--PPVLSVLRGGER--EGKRYLHCSLCGTEWRF-------------VRIKCPYCGNTDHEK 224 (290)
T ss_dssp -SS-TTT-----------EEEEEEE--------EEEEEETTT--EEE---------------TTS-TTT---SS-E
T ss_pred CCcCCCCC------C--cCceEEEecCCC--CccEEEEcCCCCCeeee-------------cCCCCcCCCCCCCcc
Confidence 45899998 2 222222222111 36788899999876542 345799 99765443
No 168
>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=25.75 E-value=34 Score=24.57 Aligned_cols=23 Identities=22% Similarity=0.613 Sum_probs=13.5
Q ss_pred hhhhhccccCCccccccccCCcc
Q 007898 156 IKKHFCRKHGEKKWKCDKCSKRY 178 (585)
Q Consensus 156 L~~H~r~Htgekpy~C~~CgK~F 178 (585)
|.-+.....+.+.|+|.+|+..-
T Consensus 12 lNp~~~~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 12 LNPFCQFDDGGKTWICNFCGTKN 34 (40)
T ss_dssp S-TTSEEETTTTEEEETTT--EE
T ss_pred ECCcceEcCCCCEEECcCCCCcC
Confidence 33345555567789999998743
No 169
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.62 E-value=35 Score=31.29 Aligned_cols=16 Identities=25% Similarity=0.970 Sum_probs=12.4
Q ss_pred CccccccccCCcccCh
Q 007898 166 EKKWKCDKCSKRYAVQ 181 (585)
Q Consensus 166 ekpy~C~~CgK~F~~~ 181 (585)
.-.|+|..|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4568999999988754
No 170
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=25.37 E-value=40 Score=36.93 Aligned_cols=35 Identities=23% Similarity=0.477 Sum_probs=23.6
Q ss_pred ccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhH
Q 007898 131 KKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSD 183 (585)
Q Consensus 131 ~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~ 183 (585)
...-.|+.|| ....+ .|.+-|+|+.||..+.....
T Consensus 348 ~~~p~Cp~Cg-------~~m~S-----------~G~~g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 348 RVNPVCPRCG-------GRMKS-----------AGRNGFRCKKCGTRARETLI 382 (421)
T ss_pred EcCCCCCccC-------Cchhh-----------cCCCCcccccccccCCcccc
Confidence 3445799997 43222 24458999999999876543
No 171
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=24.99 E-value=45 Score=34.84 Aligned_cols=29 Identities=28% Similarity=0.485 Sum_probs=23.9
Q ss_pred cCCccccccc---cCCcccChhHHHHHHHH-hC
Q 007898 164 HGEKKWKCDK---CSKRYAVQSDWKAHSKT-CG 192 (585)
Q Consensus 164 tgekpy~C~~---CgK~F~~~s~L~~H~r~-hg 192 (585)
..+-.|.|.. |.++|..+.+|..|+.- |+
T Consensus 140 ~~g~iFmC~~~~GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 140 MMGGIFMCAAPHGCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred cccceEEeecchhHHHHHhhHHHHHHHhhhhhc
Confidence 4566799966 99999999999999776 54
No 172
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=24.59 E-value=62 Score=34.83 Aligned_cols=73 Identities=16% Similarity=0.115 Sum_probs=43.4
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHHhCCcceecC-CC---CccCChH
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CG---TLFSRRD 208 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cg---k~F~~~s 208 (585)
|-.|-.|+ +.+.....-..||..+||-. .=+. .-......|..-+..--..-|.|- |. +.|....
T Consensus 166 Pt~CLfC~-------~~~k~~e~~~~HM~~~Hgff--IPdr--eYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sle 234 (390)
T KOG2785|consen 166 PTDCLFCD-------KKSKSLEENLKHMFKEHGFF--IPDR--EYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLE 234 (390)
T ss_pred CcceeecC-------CCcccHHHHHHHHhhccCCc--CCch--HhhhchhHHHHHHHHHhccCceEEEeccccCcccccH
Confidence 46788885 88888888889999888731 1000 001112222222222112346777 77 8888888
Q ss_pred HHHHHHHH
Q 007898 209 SFITHRAF 216 (585)
Q Consensus 209 ~L~~H~~~ 216 (585)
..+.||.-
T Consensus 235 avr~HM~~ 242 (390)
T KOG2785|consen 235 AVRAHMRD 242 (390)
T ss_pred HHHHHHhh
Confidence 88889853
No 173
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=24.57 E-value=13 Score=40.38 Aligned_cols=23 Identities=17% Similarity=0.518 Sum_probs=15.0
Q ss_pred CcccccccCcccccccccchhcc
Q 007898 91 NRFVCEICNKGFQRDQNLQLHRR 113 (585)
Q Consensus 91 kpy~C~~Cgk~F~~~~~L~~H~r 113 (585)
.=|+|..|++...-+.-+..-.+
T Consensus 301 ~CFtC~~C~r~L~Gq~FY~v~~k 323 (468)
T KOG1701|consen 301 QCFTCRTCRRQLAGQSFYQVDGK 323 (468)
T ss_pred cceehHhhhhhhccccccccCCc
Confidence 45899999887666555444433
No 174
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.48 E-value=24 Score=38.52 Aligned_cols=40 Identities=18% Similarity=0.505 Sum_probs=27.7
Q ss_pred ccccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcc
Q 007898 129 IRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRY 178 (585)
Q Consensus 129 ~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F 178 (585)
....-|.|+.|. +.|.....++- .--..-.|.|..|+-..
T Consensus 124 t~~~~Y~Cp~C~-------kkyt~Lea~~L---~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 124 TNVAGYVCPNCQ-------KKYTSLEALQL---LDNETGEFHCENCGGEL 163 (436)
T ss_pred cccccccCCccc-------cchhhhHHHHh---hcccCceEEEecCCCch
Confidence 355789999995 88887766543 22223469999997543
No 175
>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=24.24 E-value=40 Score=24.83 Aligned_cols=11 Identities=27% Similarity=1.056 Sum_probs=7.7
Q ss_pred CccccccccCC
Q 007898 166 EKKWKCDKCSK 176 (585)
Q Consensus 166 ekpy~C~~CgK 176 (585)
...|+|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 45677877765
No 176
>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=24.16 E-value=42 Score=37.84 Aligned_cols=18 Identities=22% Similarity=0.696 Sum_probs=8.2
Q ss_pred hhccccCCccccccccCC
Q 007898 159 HFCRKHGEKKWKCDKCSK 176 (585)
Q Consensus 159 H~r~Htgekpy~C~~CgK 176 (585)
|..-+....++.|+.|+.
T Consensus 244 h~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 244 HYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred CCCcCcCCCCCCCCCCCC
Confidence 333333344555555554
No 177
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=24.15 E-value=31 Score=24.82 Aligned_cols=11 Identities=36% Similarity=1.144 Sum_probs=7.6
Q ss_pred ccccccCCccc
Q 007898 169 WKCDKCSKRYA 179 (585)
Q Consensus 169 y~C~~CgK~F~ 179 (585)
|.|..|++.|.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 77777776654
No 178
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=24.14 E-value=30 Score=31.76 Aligned_cols=18 Identities=17% Similarity=0.593 Sum_probs=11.7
Q ss_pred ccCcccccccCccccccc
Q 007898 89 ATNRFVCEICNKGFQRDQ 106 (585)
Q Consensus 89 ~~kpy~C~~Cgk~F~~~~ 106 (585)
..+.|+|++|......+.
T Consensus 77 d~~lYeCnIC~etS~ee~ 94 (140)
T PF05290_consen 77 DPKLYECNICKETSAEER 94 (140)
T ss_pred CCCceeccCcccccchhh
Confidence 346788888877655443
No 179
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=23.86 E-value=1.8e+02 Score=31.92 Aligned_cols=32 Identities=6% Similarity=-0.010 Sum_probs=18.9
Q ss_pred ccccccCcccccccCcccccccccchhccccc
Q 007898 85 KTLMATNRFVCEICNKGFQRDQNLQLHRRGHN 116 (585)
Q Consensus 85 k~~~~~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 116 (585)
+.........|+.|+..+.....+..+...+.
T Consensus 203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (396)
T KOG2461|consen 203 EVLDSDSHNLADEESVSLKEQGQLLEPVEVAS 234 (396)
T ss_pred hhcccccCCccccccccccccccccccccccC
Confidence 33444556666666666666666666655554
No 180
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=23.82 E-value=45 Score=28.92 Aligned_cols=15 Identities=20% Similarity=0.594 Sum_probs=11.8
Q ss_pred CcccccccCcccccc
Q 007898 91 NRFVCEICNKGFQRD 105 (585)
Q Consensus 91 kpy~C~~Cgk~F~~~ 105 (585)
..+.|+.|+..+...
T Consensus 15 ~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 15 GVYVCPSCGYEKEKK 29 (104)
T ss_pred CeEECcCCCCccccc
Confidence 468999999887653
No 181
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.40 E-value=41 Score=30.01 Aligned_cols=15 Identities=13% Similarity=0.220 Sum_probs=11.6
Q ss_pred cCcccccccCccccc
Q 007898 90 TNRFVCEICNKGFQR 104 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~ 104 (585)
.-.++|..||..|..
T Consensus 68 p~~~~C~~Cg~~~~~ 82 (113)
T PRK12380 68 PAQAWCWDCSQVVEI 82 (113)
T ss_pred CcEEEcccCCCEEec
Confidence 456899999987754
No 182
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=23.28 E-value=26 Score=32.53 Aligned_cols=11 Identities=27% Similarity=0.760 Sum_probs=8.9
Q ss_pred cccccCccccc
Q 007898 94 VCEICNKGFQR 104 (585)
Q Consensus 94 ~C~~Cgk~F~~ 104 (585)
.|+.||+.|..
T Consensus 5 nC~~CgklF~~ 15 (137)
T TIGR03826 5 NCPKCGRLFVK 15 (137)
T ss_pred cccccchhhhh
Confidence 58899998865
No 183
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=23.12 E-value=1.5e+02 Score=28.20 Aligned_cols=50 Identities=10% Similarity=0.164 Sum_probs=25.8
Q ss_pred cccccccCCcccChhHHHHHHHH-hCCcceecC---CCCccCChHHHHHHHHHhhh
Q 007898 168 KWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD---CGTLFSRRDSFITHRAFCDA 219 (585)
Q Consensus 168 py~C~~CgK~F~~~s~L~~H~r~-hgekpy~C~---Cgk~F~~~s~L~~H~~~h~~ 219 (585)
...|+.|.-...--.-. .--|. -..|+-.|. |...= ....|++|.+.-|.
T Consensus 80 ~L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~G-tY~eLrKHar~~HP 133 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFSG-TYSELRKHARSEHP 133 (162)
T ss_pred cccCccccCceeceEEc-hHHHHHhccCCccCccccccccc-CHHHHHHHHHhhCC
Confidence 36788884222111111 11222 345676775 76433 45679999865443
No 184
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=22.15 E-value=31 Score=31.76 Aligned_cols=20 Identities=30% Similarity=0.453 Sum_probs=0.0
Q ss_pred cccccCcccccccccchhccccc
Q 007898 94 VCEICNKGFQRDQNLQLHRRGHN 116 (585)
Q Consensus 94 ~C~~Cgk~F~~~~~L~~H~r~H~ 116 (585)
.|-+|||.|+. |++|..+|.
T Consensus 78 icLEDGkkfKS---LKRHL~t~~ 97 (148)
T COG4957 78 ICLEDGKKFKS---LKRHLTTHY 97 (148)
T ss_pred EEeccCcchHH---HHHHHhccc
No 185
>PRK05978 hypothetical protein; Provisional
Probab=21.99 E-value=53 Score=30.85 Aligned_cols=33 Identities=15% Similarity=0.337 Sum_probs=20.1
Q ss_pred ccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccCh
Q 007898 133 VYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQ 181 (585)
Q Consensus 133 ~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~ 181 (585)
.-+|+.||. ++-|.... + + .-.|+.||..|...
T Consensus 33 ~grCP~CG~-----G~LF~g~L--k----v-----~~~C~~CG~~~~~~ 65 (148)
T PRK05978 33 RGRCPACGE-----GKLFRAFL--K----P-----VDHCAACGEDFTHH 65 (148)
T ss_pred cCcCCCCCC-----Cccccccc--c----c-----CCCccccCCccccC
Confidence 457999974 46664221 1 1 13688998887654
No 186
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.57 E-value=53 Score=28.90 Aligned_cols=9 Identities=33% Similarity=0.648 Sum_probs=6.6
Q ss_pred cccccCCCC
Q 007898 132 KVYVCPEPN 140 (585)
Q Consensus 132 k~y~C~~Cg 140 (585)
||-.|+.||
T Consensus 1 ~p~~CpYCg 9 (102)
T PF11672_consen 1 KPIICPYCG 9 (102)
T ss_pred CCcccCCCC
Confidence 466788887
No 187
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=21.53 E-value=38 Score=25.97 Aligned_cols=27 Identities=30% Similarity=0.631 Sum_probs=17.5
Q ss_pred cCcccccccCcccccccccchhccccc
Q 007898 90 TNRFVCEICNKGFQRDQNLQLHRRGHN 116 (585)
Q Consensus 90 ~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 116 (585)
..+|+|+.|...|=..-.+-.|...|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CCeEECCCCCCccccCcChhhhccccC
Confidence 468999999999999988888887775
No 188
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=21.43 E-value=26 Score=32.55 Aligned_cols=31 Identities=29% Similarity=0.946 Sum_probs=17.0
Q ss_pred cccccccCCcccChhHHHHHHHHhCCcceecC-CCCccC
Q 007898 168 KWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTLFS 205 (585)
Q Consensus 168 py~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~F~ 205 (585)
.|.|..|+..+.. |.++ ..+.|.|. |+..|.
T Consensus 123 ~~~C~~C~~~~~r------~~~~-~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRRS-KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeee------eccc-chhhEECCCCCCEEE
Confidence 4677777766533 2222 23447777 775553
No 189
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=21.22 E-value=68 Score=33.84 Aligned_cols=69 Identities=17% Similarity=0.453 Sum_probs=0.0
Q ss_pred ccccccCcccccccccchhcccccCccccccchhhhccccccccCCCCcccCCCCCccCChhhhhhhhccccCCcc----
Q 007898 93 FVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKK---- 168 (585)
Q Consensus 93 y~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekp---- 168 (585)
|.|+.|.... -.-|-+|++|+ -......+|.+-.+-----++
T Consensus 277 y~CP~Ckakv---------------------------CsLP~eCpiC~-------ltLVss~hLARSyhhL~PL~~F~Ei 322 (378)
T KOG2807|consen 277 YFCPQCKAKV---------------------------CSLPIECPICS-------LTLVSSPHLARSYHHLFPLKPFVEI 322 (378)
T ss_pred eeCCcccCee---------------------------ecCCccCCccc-------eeEecchHHHHHHHhhcCCcchhhc
Q ss_pred -----------------------ccccccCCcccChhHHHHHHHHhCCcceecC-C
Q 007898 169 -----------------------WKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-C 200 (585)
Q Consensus 169 -----------------------y~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-C 200 (585)
|.|..|...|-.--+.-.| |.-+.|. |
T Consensus 323 p~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iH-----esLh~CpgC 373 (378)
T KOG2807|consen 323 PETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIH-----ESLHNCPGC 373 (378)
T ss_pred cccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHH-----hhhhcCCCc
No 190
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=20.69 E-value=39 Score=26.56 Aligned_cols=14 Identities=21% Similarity=0.563 Sum_probs=9.0
Q ss_pred ccccccccCCcccC
Q 007898 167 KKWKCDKCSKRYAV 180 (585)
Q Consensus 167 kpy~C~~CgK~F~~ 180 (585)
..++|..||.....
T Consensus 36 D~irCReCG~RIly 49 (62)
T KOG3507|consen 36 DVIRCRECGYRILY 49 (62)
T ss_pred CcEehhhcchHHHH
Confidence 45778888765443
No 191
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.67 E-value=69 Score=33.76 Aligned_cols=28 Identities=18% Similarity=0.600 Sum_probs=19.9
Q ss_pred ccCCccccccccCCcccChhHHHHHHHHhCCcceecC-CCCc
Q 007898 163 KHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CGTL 203 (585)
Q Consensus 163 Htgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cgk~ 203 (585)
..|.|...|..|+-.+.. +.-+|. ||..
T Consensus 205 ~~G~RyL~CslC~teW~~-------------~R~~C~~Cg~~ 233 (305)
T TIGR01562 205 ETGLRYLSCSLCATEWHY-------------VRVKCSHCEES 233 (305)
T ss_pred CCCceEEEcCCCCCcccc-------------cCccCCCCCCC
Confidence 457788899999865432 345899 9864
No 192
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.44 E-value=73 Score=33.63 Aligned_cols=49 Identities=16% Similarity=0.421 Sum_probs=0.0
Q ss_pred cccccccCCCCcccCCCCCccCChhhhhhhhccccCCccccccccCCcccChhHHHHHHHHhCCcceecC-CC
Q 007898 130 RKKVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTREYRCD-CG 201 (585)
Q Consensus 130 ~~k~y~C~~CgC~~~~~~k~F~~~~~L~~H~r~Htgekpy~C~~CgK~F~~~s~L~~H~r~hgekpy~C~-Cg 201 (585)
++..-.|++|| .....-..+.....|.|...|..|+-.... +.-+|. ||
T Consensus 184 ~~~~~~CPvCG----------s~P~~s~v~~~~~~G~RyL~CslC~teW~~-------------~R~~C~~Cg 233 (309)
T PRK03564 184 GEQRQFCPVCG----------SMPVSSVVQIGTTQGLRYLHCNLCESEWHV-------------VRVKCSNCE 233 (309)
T ss_pred ccCCCCCCCCC----------CcchhheeeccCCCCceEEEcCCCCCcccc-------------cCccCCCCC
No 193
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=20.29 E-value=52 Score=23.60 Aligned_cols=15 Identities=20% Similarity=0.538 Sum_probs=9.8
Q ss_pred CccccccccCCcccC
Q 007898 166 EKKWKCDKCSKRYAV 180 (585)
Q Consensus 166 ekpy~C~~CgK~F~~ 180 (585)
..-|.|+.||..|..
T Consensus 30 vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 30 VPALVCPQCGEEYLD 44 (46)
T ss_pred CCccccccCCCEeeC
Confidence 344778888876643
No 194
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=20.19 E-value=34 Score=37.01 Aligned_cols=76 Identities=17% Similarity=0.329 Sum_probs=44.0
Q ss_pred cccccccC--CCCcccCCCCCccCChhhhhhhhccccCCc------------cccccc--cCCcccChhHHHHHHHHhCC
Q 007898 130 RKKVYVCP--EPNCVHHDPSRALGDLTGIKKHFCRKHGEK------------KWKCDK--CSKRYAVQSDWKAHSKTCGT 193 (585)
Q Consensus 130 ~~k~y~C~--~CgC~~~~~~k~F~~~~~L~~H~r~Htgek------------py~C~~--CgK~F~~~s~L~~H~r~hge 193 (585)
+...|.|- .|+ ..+..+.++.+|..+|...+ .|.|.. |.| .-++...|...|.+
T Consensus 268 ~rEhyhcl~e~C~-------ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~ 337 (480)
T KOG4377|consen 268 GREHYHCLNEYCF-------YKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTD 337 (480)
T ss_pred cchhhcccCcccc-------ccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCccccc
Confidence 45567774 454 44444889999998886432 267744 888 34455556544322
Q ss_pred c--------ceecC-CCCccCChHHHHHHHHHh
Q 007898 194 R--------EYRCD-CGTLFSRRDSFITHRAFC 217 (585)
Q Consensus 194 k--------py~C~-Cgk~F~~~s~L~~H~~~h 217 (585)
+ -|.|. |+-++..+ ...|+..|
T Consensus 338 ~~n~GfrrthfhC~r~gCTdtfK--~~khk~yh 368 (480)
T KOG4377|consen 338 KRNNGFRRTHFHCQRIGCTDTFK--DSKHKPYH 368 (480)
T ss_pred cccCceecceeEEeccCCccccc--cccccccc
Confidence 2 37787 66444443 34555444
No 195
>PHA02998 RNA polymerase subunit; Provisional
Probab=20.11 E-value=52 Score=31.74 Aligned_cols=11 Identities=27% Similarity=0.927 Sum_probs=5.9
Q ss_pred ccccccCCccc
Q 007898 169 WKCDKCSKRYA 179 (585)
Q Consensus 169 y~C~~CgK~F~ 179 (585)
|+|..||+.|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 55555555543
No 196
>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=20.01 E-value=65 Score=24.97 Aligned_cols=13 Identities=23% Similarity=0.641 Sum_probs=10.1
Q ss_pred cccccccCccccc
Q 007898 92 RFVCEICNKGFQR 104 (585)
Q Consensus 92 py~C~~Cgk~F~~ 104 (585)
.|+|+.||..+.-
T Consensus 2 ~~~CP~CG~~iev 14 (54)
T TIGR01206 2 QFECPDCGAEIEL 14 (54)
T ss_pred ccCCCCCCCEEec
Confidence 3789999997644
Done!