Query 011146
Match_columns 492
No_of_seqs 397 out of 2871
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 08:38:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011146.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011146hhsearch_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 5.6E-27 1.2E-31 223.1 6.3 135 32-188 127-266 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.9 1.4E-24 3.1E-29 206.7 5.2 133 7-161 130-265 (279)
3 KOG1074 Transcriptional repres 99.7 2.2E-19 4.8E-24 191.4 0.1 80 104-190 605-693 (958)
4 KOG3576 Ovo and related transc 99.7 5.8E-18 1.2E-22 154.0 3.5 116 60-195 114-242 (267)
5 KOG3608 Zn finger proteins [Ge 99.7 5.2E-18 1.1E-22 165.5 0.3 153 15-189 187-345 (467)
6 KOG1074 Transcriptional repres 99.6 1.2E-16 2.7E-21 170.6 3.5 58 140-197 880-939 (958)
7 KOG3608 Zn finger proteins [Ge 99.6 2E-16 4.3E-21 154.6 0.2 169 3-193 203-380 (467)
8 KOG3576 Ovo and related transc 99.6 2.1E-16 4.6E-21 143.8 0.4 111 31-161 113-234 (267)
9 KOG3623 Homeobox transcription 99.5 1.1E-14 2.3E-19 153.4 1.5 105 64-186 211-330 (1007)
10 KOG3623 Homeobox transcription 99.5 1.5E-14 3.2E-19 152.4 1.9 81 60-160 891-971 (1007)
11 PLN03086 PRLI-interacting fact 99.2 2.2E-11 4.8E-16 129.7 8.0 103 62-190 452-565 (567)
12 PLN03086 PRLI-interacting fact 99.0 4.2E-10 9E-15 120.1 6.8 102 33-161 451-562 (567)
13 PHA00733 hypothetical protein 99.0 4.9E-10 1.1E-14 98.5 5.2 110 33-161 9-121 (128)
14 PHA00733 hypothetical protein 99.0 5.9E-10 1.3E-14 98.0 4.5 84 101-192 37-126 (128)
15 KOG3993 Transcription factor ( 98.9 1.1E-10 2.4E-15 117.1 -1.1 150 35-191 267-484 (500)
16 PHA02768 hypothetical protein; 98.5 3.5E-08 7.7E-13 72.5 2.1 44 63-128 5-48 (55)
17 PHA02768 hypothetical protein; 98.5 3.5E-08 7.6E-13 72.5 1.4 44 104-156 5-48 (55)
18 PF13465 zf-H2C2_2: Zinc-finge 98.4 1.3E-07 2.7E-12 59.4 1.3 26 126-151 1-26 (26)
19 KOG3993 Transcription factor ( 98.3 1.6E-07 3.6E-12 94.7 0.6 84 104-194 267-385 (500)
20 PF13465 zf-H2C2_2: Zinc-finge 98.0 1.1E-06 2.4E-11 55.1 0.4 26 50-75 1-26 (26)
21 PHA00616 hypothetical protein 98.0 2.8E-06 6.2E-11 59.5 1.4 34 63-109 1-34 (44)
22 PHA00732 hypothetical protein 97.9 6.7E-06 1.4E-10 66.0 3.0 48 63-135 1-48 (79)
23 PHA00616 hypothetical protein 97.8 7.2E-06 1.6E-10 57.5 0.4 35 104-145 1-35 (44)
24 PF00096 zf-C2H2: Zinc finger, 97.7 2.3E-05 5E-10 47.4 2.0 23 64-86 1-23 (23)
25 PHA00732 hypothetical protein 97.6 3.5E-05 7.6E-10 61.8 2.8 45 104-161 1-46 (79)
26 COG5189 SFP1 Putative transcri 97.5 2.8E-05 6.2E-10 76.1 0.9 69 102-186 347-419 (423)
27 COG5189 SFP1 Putative transcri 97.5 4.3E-05 9.4E-10 74.8 2.1 26 59-84 345-372 (423)
28 PF05605 zf-Di19: Drought indu 97.5 9.6E-05 2.1E-09 54.9 3.2 52 63-135 2-53 (54)
29 PF13894 zf-C2H2_4: C2H2-type 97.3 0.0002 4.2E-09 43.3 2.1 24 64-87 1-24 (24)
30 KOG2231 Predicted E3 ubiquitin 97.2 0.00052 1.1E-08 74.8 6.0 62 118-186 189-260 (669)
31 COG5048 FOG: Zn-finger [Genera 97.1 0.0004 8.7E-09 72.3 4.4 144 34-182 288-462 (467)
32 PF05605 zf-Di19: Drought indu 97.1 0.00055 1.2E-08 50.8 3.8 47 105-161 3-51 (54)
33 PF13912 zf-C2H2_6: C2H2-type 97.1 0.00029 6.3E-09 44.3 1.7 25 63-87 1-25 (27)
34 PF12756 zf-C2H2_2: C2H2 type 97.0 0.00043 9.3E-09 57.4 2.5 72 65-161 1-72 (100)
35 KOG2231 Predicted E3 ubiquitin 96.9 0.00091 2E-08 73.0 5.0 49 141-189 184-236 (669)
36 PF00096 zf-C2H2: Zinc finger, 96.9 0.00065 1.4E-08 40.9 2.1 21 167-187 1-22 (23)
37 PF12756 zf-C2H2_2: C2H2 type 96.6 0.0013 2.9E-08 54.4 2.7 73 106-189 1-74 (100)
38 PF13894 zf-C2H2_4: C2H2-type 96.5 0.0024 5.1E-08 38.3 2.3 22 167-188 1-23 (24)
39 PF13912 zf-C2H2_6: C2H2-type 96.4 0.0021 4.5E-08 40.3 1.8 24 166-189 1-25 (27)
40 smart00355 ZnF_C2H2 zinc finge 96.4 0.0021 4.6E-08 39.1 1.8 24 64-87 1-24 (26)
41 PF09237 GAGA: GAGA factor; I 96.2 0.0036 7.9E-08 45.1 2.6 36 52-87 12-48 (54)
42 KOG1146 Homeobox protein [Gene 96.0 0.0012 2.5E-08 76.0 -1.1 145 37-188 438-641 (1406)
43 PF12874 zf-met: Zinc-finger o 95.8 0.0048 1E-07 37.8 1.5 23 64-86 1-23 (25)
44 PF09237 GAGA: GAGA factor; I 95.7 0.0086 1.9E-07 43.2 2.4 31 136-166 21-52 (54)
45 COG5236 Uncharacterized conser 95.5 0.011 2.4E-07 58.9 3.4 118 63-191 151-307 (493)
46 PRK04860 hypothetical protein; 95.5 0.0054 1.2E-07 56.0 0.9 27 124-150 128-154 (160)
47 COG5048 FOG: Zn-finger [Genera 95.2 0.017 3.6E-07 60.1 3.9 111 62-192 288-415 (467)
48 PRK04860 hypothetical protein; 94.3 0.023 5E-07 51.9 1.9 39 62-124 118-156 (160)
49 PF12171 zf-C2H2_jaz: Zinc-fin 94.1 0.011 2.4E-07 37.1 -0.5 22 64-85 2-23 (27)
50 PF13909 zf-H2C2_5: C2H2-type 93.3 0.052 1.1E-06 32.9 1.5 23 64-87 1-23 (24)
51 KOG1146 Homeobox protein [Gene 93.2 0.043 9.4E-07 63.7 1.9 92 64-191 1261-1354(1406)
52 PF12874 zf-met: Zinc-finger o 93.2 0.055 1.2E-06 33.0 1.5 21 140-160 1-21 (25)
53 smart00355 ZnF_C2H2 zinc finge 93.0 0.066 1.4E-06 32.2 1.7 20 141-160 2-21 (26)
54 PF13909 zf-H2C2_5: C2H2-type 92.7 0.097 2.1E-06 31.7 2.2 22 167-189 1-23 (24)
55 KOG2785 C2H2-type Zn-finger pr 92.6 0.06 1.3E-06 54.8 1.8 48 139-186 166-241 (390)
56 PF12171 zf-C2H2_jaz: Zinc-fin 92.4 0.076 1.7E-06 33.2 1.5 22 140-161 2-23 (27)
57 KOG4173 Alpha-SNAP protein [In 92.0 0.054 1.2E-06 50.5 0.6 82 101-190 76-171 (253)
58 KOG2893 Zn finger protein [Gen 91.8 0.056 1.2E-06 51.5 0.4 49 35-87 10-59 (341)
59 COG5236 Uncharacterized conser 91.7 0.18 4E-06 50.5 3.9 78 65-163 222-306 (493)
60 smart00451 ZnF_U1 U1-like zinc 91.2 0.14 2.9E-06 33.9 1.7 23 63-85 3-25 (35)
61 KOG1883 Cofactor required for 91.0 0.16 3.5E-06 58.1 3.0 40 335-374 1430-1469(1517)
62 PF09538 FYDLN_acid: Protein o 90.8 0.14 3E-06 43.6 1.8 32 34-76 8-39 (108)
63 PF13913 zf-C2HC_2: zinc-finge 90.6 0.18 4E-06 31.1 1.7 21 64-85 3-23 (25)
64 KOG2482 Predicted C2H2-type Zn 88.6 0.42 9E-06 48.1 3.5 49 140-188 280-357 (423)
65 KOG2893 Zn finger protein [Gen 87.3 0.18 4E-06 48.1 0.1 44 64-131 11-54 (341)
66 PF13913 zf-C2HC_2: zinc-finge 86.7 0.51 1.1E-05 29.1 1.8 19 141-160 4-22 (25)
67 smart00451 ZnF_U1 U1-like zinc 85.7 0.55 1.2E-05 30.9 1.7 23 139-161 3-25 (35)
68 TIGR02300 FYDLN_acid conserved 85.1 0.57 1.2E-05 40.7 2.0 36 34-80 8-43 (129)
69 KOG2482 Predicted C2H2-type Zn 83.1 1.7 3.7E-05 43.8 4.6 26 167-192 280-306 (423)
70 KOG4407 Predicted Rho GTPase-a 82.7 0.6 1.3E-05 54.3 1.4 13 329-341 322-334 (1973)
71 KOG2186 Cell growth-regulating 82.0 0.93 2E-05 43.9 2.2 49 140-190 4-53 (276)
72 KOG4377 Zn-finger protein [Gen 81.9 1.3 2.9E-05 45.6 3.5 121 62-191 270-429 (480)
73 cd00350 rubredoxin_like Rubred 81.4 0.65 1.4E-05 30.6 0.7 25 35-71 1-25 (33)
74 KOG2071 mRNA cleavage and poly 81.1 1 2.2E-05 48.7 2.4 29 59-87 414-442 (579)
75 PF12013 DUF3505: Protein of u 81.0 2.4 5.1E-05 36.0 4.2 24 167-190 81-109 (109)
76 KOG3648 Golgi apparatus protei 80.1 0.66 1.4E-05 50.2 0.6 20 334-353 73-92 (1179)
77 TIGR00622 ssl1 transcription f 79.6 3.2 6.9E-05 35.5 4.4 80 6-87 14-105 (112)
78 PRK00464 nrdR transcriptional 78.8 0.73 1.6E-05 41.8 0.4 14 64-77 29-42 (154)
79 PF09986 DUF2225: Uncharacteri 77.8 0.86 1.9E-05 43.8 0.6 43 34-76 4-61 (214)
80 COG4049 Uncharacterized protei 77.2 1.1 2.3E-05 33.1 0.8 27 135-161 13-39 (65)
81 PRK00464 nrdR transcriptional 77.1 1.1 2.4E-05 40.7 1.0 48 8-55 1-48 (154)
82 cd00350 rubredoxin_like Rubred 75.3 1.8 3.9E-05 28.5 1.4 10 138-147 16-25 (33)
83 PF09538 FYDLN_acid: Protein o 74.8 1.8 3.8E-05 36.9 1.6 30 64-124 10-39 (108)
84 KOG4173 Alpha-SNAP protein [In 73.8 1.3 2.8E-05 41.6 0.6 78 61-161 77-168 (253)
85 PF09986 DUF2225: Uncharacteri 73.5 1 2.2E-05 43.2 -0.2 12 167-178 49-61 (214)
86 COG4049 Uncharacterized protei 73.1 1.6 3.5E-05 32.2 0.8 28 162-189 13-41 (65)
87 COG4530 Uncharacterized protei 72.3 2 4.3E-05 36.2 1.3 31 35-76 9-39 (129)
88 PF02892 zf-BED: BED zinc fing 71.8 3.3 7.1E-05 28.9 2.2 25 60-84 13-41 (45)
89 KOG4369 RTK signaling protein 69.8 5 0.00011 46.7 4.1 12 356-367 1881-1892(2131)
90 cd00729 rubredoxin_SM Rubredox 69.4 1.9 4.2E-05 28.6 0.5 25 35-71 2-26 (34)
91 KOG4407 Predicted Rho GTPase-a 68.7 2.1 4.5E-05 50.2 0.8 12 326-337 322-333 (1973)
92 COG1997 RPL43A Ribosomal prote 67.7 3 6.6E-05 33.8 1.4 13 139-151 53-65 (89)
93 TIGR00622 ssl1 transcription f 66.3 7 0.00015 33.4 3.4 80 102-189 13-105 (112)
94 KOG4124 Putative transcription 65.8 1.7 3.6E-05 44.0 -0.6 28 101-133 346-373 (442)
95 COG1198 PriA Primosomal protei 65.6 3.8 8.2E-05 46.3 2.1 10 65-74 437-446 (730)
96 PRK09678 DNA-binding transcrip 65.0 2.5 5.5E-05 33.2 0.4 41 36-78 2-44 (72)
97 PF02166 Androgen_recep: Andro 64.8 2.1 4.6E-05 43.0 0.0 11 377-387 138-148 (423)
98 PF12013 DUF3505: Protein of u 64.7 7.6 0.00016 32.9 3.4 24 140-163 81-109 (109)
99 PF13717 zinc_ribbon_4: zinc-r 62.3 5.5 0.00012 26.8 1.7 32 140-175 3-35 (36)
100 COG1327 Predicted transcriptio 62.0 4.7 0.0001 36.2 1.6 47 9-55 2-48 (156)
101 COG1592 Rubrerythrin [Energy p 60.6 5.7 0.00012 36.5 2.0 25 103-147 133-157 (166)
102 PRK04023 DNA polymerase II lar 60.5 7.9 0.00017 44.7 3.4 18 452-473 1020-1037(1121)
103 PF04959 ARS2: Arsenite-resist 60.5 3.1 6.7E-05 39.9 0.3 29 136-164 74-103 (214)
104 TIGR02098 MJ0042_CXXC MJ0042 f 60.4 5.5 0.00012 26.8 1.4 14 140-153 3-16 (38)
105 PF05443 ROS_MUCR: ROS/MUCR tr 60.3 6.8 0.00015 34.6 2.3 25 60-87 69-93 (132)
106 COG5151 SSL1 RNA polymerase II 58.8 12 0.00027 37.3 4.0 53 32-87 359-412 (421)
107 TIGR00244 transcriptional regu 58.4 6 0.00013 35.4 1.7 47 9-55 2-48 (147)
108 PHA00626 hypothetical protein 57.6 5.7 0.00012 29.4 1.1 16 62-77 22-37 (59)
109 KOG2186 Cell growth-regulating 57.3 5 0.00011 39.0 1.1 48 104-161 3-50 (276)
110 smart00614 ZnF_BED BED zinc fi 56.9 7.6 0.00016 28.0 1.7 26 62-87 17-48 (50)
111 COG1996 RPC10 DNA-directed RNA 56.3 4.8 0.0001 29.1 0.6 29 34-72 5-33 (49)
112 PRK14890 putative Zn-ribbon RN 54.5 12 0.00026 28.2 2.4 33 34-71 24-56 (59)
113 PF13719 zinc_ribbon_5: zinc-r 54.1 9 0.0002 25.9 1.6 31 141-175 4-35 (37)
114 smart00659 RPOLCX RNA polymera 53.7 6.9 0.00015 27.6 1.0 27 35-72 2-28 (44)
115 smart00531 TFIIE Transcription 52.0 8 0.00017 34.7 1.4 39 99-149 94-133 (147)
116 KOG1280 Uncharacterized conser 51.7 7.2 0.00016 39.6 1.2 36 137-172 77-116 (381)
117 TIGR00244 transcriptional regu 51.1 6.8 0.00015 35.1 0.8 44 37-80 2-45 (147)
118 PRK14873 primosome assembly pr 50.9 8.5 0.00018 43.4 1.7 11 64-74 384-394 (665)
119 KOG3648 Golgi apparatus protei 49.9 7.9 0.00017 42.3 1.2 9 473-481 294-302 (1179)
120 COG1997 RPL43A Ribosomal prote 49.9 11 0.00024 30.6 1.8 32 34-75 34-65 (89)
121 TIGR02300 FYDLN_acid conserved 49.7 12 0.00026 32.7 2.1 11 140-150 10-20 (129)
122 COG1592 Rubrerythrin [Energy p 49.2 9.1 0.0002 35.2 1.3 24 35-71 134-157 (166)
123 PF15135 UPF0515: Uncharacteri 49.0 15 0.00033 35.6 2.9 76 75-177 91-167 (278)
124 PF09416 UPF1_Zn_bind: RNA hel 48.9 23 0.0005 32.0 3.8 60 37-112 2-68 (152)
125 KOG4167 Predicted DNA-binding 48.9 5.2 0.00011 44.4 -0.3 25 63-87 792-816 (907)
126 KOG2907 RNA polymerase I trans 48.7 15 0.00033 31.2 2.5 44 32-75 71-114 (116)
127 COG1327 Predicted transcriptio 48.4 8.3 0.00018 34.6 0.9 44 37-80 2-45 (156)
128 smart00531 TFIIE Transcription 48.0 11 0.00024 33.8 1.8 40 31-74 95-134 (147)
129 smart00834 CxxC_CXXC_SSSS Puta 47.7 7 0.00015 26.5 0.3 12 35-46 5-16 (41)
130 KOG2785 C2H2-type Zn-finger pr 46.7 16 0.00034 37.8 2.7 51 104-161 166-242 (390)
131 TIGR01384 TFS_arch transcripti 46.1 16 0.00034 30.6 2.3 41 35-75 62-102 (104)
132 PF10571 UPF0547: Uncharacteri 45.7 14 0.00031 23.0 1.4 11 64-74 15-25 (26)
133 KOG4124 Putative transcription 45.1 5.6 0.00012 40.3 -0.7 25 60-84 346-372 (442)
134 PF09723 Zn-ribbon_8: Zinc rib 45.0 7.4 0.00016 27.1 0.1 30 35-71 5-34 (42)
135 smart00734 ZnF_Rad18 Rad18-lik 44.8 15 0.00033 22.7 1.5 20 64-84 2-21 (26)
136 PF06524 NOA36: NOA36 protein; 44.6 11 0.00023 36.9 1.1 19 163-181 206-225 (314)
137 COG4957 Predicted transcriptio 44.1 12 0.00026 33.0 1.2 22 63-87 76-97 (148)
138 TIGR00595 priA primosomal prot 44.0 13 0.00028 40.5 1.7 11 64-74 214-224 (505)
139 PF07282 OrfB_Zn_ribbon: Putat 43.5 18 0.00039 27.7 2.1 34 35-78 28-61 (69)
140 PF15135 UPF0515: Uncharacteri 43.2 14 0.00031 35.8 1.7 59 61-152 110-168 (278)
141 PRK04023 DNA polymerase II lar 43.1 27 0.00059 40.6 4.1 24 33-72 624-647 (1121)
142 PF04216 FdhE: Protein involve 43.1 3.1 6.8E-05 41.8 -2.9 35 139-174 211-247 (290)
143 PF15269 zf-C2H2_7: Zinc-finge 42.9 44 0.00096 23.6 3.6 22 64-85 21-42 (54)
144 PRK06266 transcription initiat 42.4 12 0.00026 34.8 1.1 33 100-148 113-145 (178)
145 COG5624 TAF61 Transcription in 42.1 9.4 0.0002 39.5 0.3 8 414-421 309-316 (505)
146 KOG2807 RNA polymerase II tran 41.3 32 0.0007 34.8 3.9 21 62-82 289-309 (378)
147 KOG2593 Transcription initiati 41.1 24 0.00051 37.1 3.1 35 137-173 126-161 (436)
148 smart00440 ZnF_C2C2 C2C2 Zinc 40.4 12 0.00025 25.8 0.5 37 36-74 1-39 (40)
149 TIGR00373 conserved hypothetic 40.3 14 0.0003 33.7 1.1 33 100-148 105-137 (158)
150 COG5624 TAF61 Transcription in 40.1 13 0.00028 38.5 1.0 9 467-475 456-464 (505)
151 COG2888 Predicted Zn-ribbon RN 40.1 11 0.00023 28.4 0.3 33 34-71 26-58 (61)
152 TIGR01562 FdhE formate dehydro 40.0 13 0.00028 37.7 0.9 12 101-112 207-218 (305)
153 PF09606 Med15: ARC105 or Med1 39.4 9.8 0.00021 43.4 0.0 10 180-189 45-54 (799)
154 TIGR00373 conserved hypothetic 38.9 21 0.00046 32.5 2.1 22 59-80 105-126 (158)
155 PRK00398 rpoP DNA-directed RNA 38.5 19 0.00041 25.4 1.4 13 63-75 3-15 (46)
156 PRK03564 formate dehydrogenase 38.5 30 0.00065 35.1 3.3 10 101-110 209-218 (309)
157 KOG1701 Focal adhesion adaptor 37.8 2.7 5.8E-05 43.8 -4.3 41 36-76 275-315 (468)
158 COG5151 SSL1 RNA polymerase II 37.4 16 0.00035 36.6 1.1 49 141-190 364-413 (421)
159 PRK03564 formate dehydrogenase 37.3 14 0.00031 37.4 0.8 38 32-72 184-221 (309)
160 PF14446 Prok-RING_1: Prokaryo 37.3 26 0.00057 25.9 1.9 31 34-76 4-34 (54)
161 PF05290 Baculo_IE-1: Baculovi 37.1 28 0.00062 30.6 2.4 13 106-125 123-135 (140)
162 PF14353 CpXC: CpXC protein 36.9 2.9 6.2E-05 36.5 -3.8 24 63-86 38-61 (128)
163 PRK05580 primosome assembly pr 36.8 19 0.00041 40.8 1.7 12 137-148 419-430 (679)
164 PF03833 PolC_DP2: DNA polymer 36.5 12 0.00025 42.7 0.0 11 62-72 654-664 (900)
165 COG3677 Transposase and inacti 36.3 17 0.00036 32.0 0.9 16 61-76 51-66 (129)
166 COG4530 Uncharacterized protei 35.6 29 0.00062 29.4 2.2 13 137-149 24-36 (129)
167 PF01096 TFIIS_C: Transcriptio 35.5 7.1 0.00015 26.7 -1.2 12 63-74 28-39 (39)
168 PRK06266 transcription initiat 34.9 15 0.00033 34.2 0.5 35 32-75 114-148 (178)
169 KOG2807 RNA polymerase II tran 34.9 24 0.00053 35.7 1.9 28 60-87 342-369 (378)
170 COG3091 SprT Zn-dependent meta 34.9 20 0.00043 32.3 1.2 32 138-174 116-149 (156)
171 COG1107 Archaea-specific RecJ- 34.6 32 0.0007 37.6 2.9 8 36-43 3-10 (715)
172 TIGR02605 CxxC_CxxC_SSSS putat 34.1 15 0.00033 26.4 0.3 10 138-147 25-34 (52)
173 PTZ00255 60S ribosomal protein 33.7 30 0.00066 28.4 2.0 14 138-151 53-66 (90)
174 COG1198 PriA Primosomal protei 33.6 23 0.00049 40.3 1.7 30 131-174 454-484 (730)
175 PF13240 zinc_ribbon_2: zinc-r 33.3 22 0.00048 21.4 0.9 7 66-72 16-22 (23)
176 PF09963 DUF2197: Uncharacteri 32.9 20 0.00042 26.8 0.7 36 63-110 2-37 (56)
177 smart00661 RPOL9 RNA polymeras 32.9 32 0.0007 24.5 1.9 14 62-75 19-32 (52)
178 KOG0320 Predicted E3 ubiquitin 32.7 29 0.00062 32.2 1.8 14 99-112 126-139 (187)
179 COG2331 Uncharacterized protei 32.6 14 0.00031 29.1 -0.1 23 58-84 7-29 (82)
180 PRK03824 hypA hydrogenase nick 32.1 17 0.00037 32.2 0.3 42 31-72 66-116 (135)
181 KOG2932 E3 ubiquitin ligase in 31.9 2E+02 0.0043 29.2 7.6 44 141-190 125-172 (389)
182 PF01780 Ribosomal_L37ae: Ribo 31.3 15 0.00033 30.2 -0.1 11 140-150 54-64 (90)
183 PRK14714 DNA polymerase II lar 31.1 42 0.00091 40.1 3.3 8 64-71 668-675 (1337)
184 TIGR00280 L37a ribosomal prote 30.8 32 0.00069 28.3 1.7 13 139-151 53-65 (91)
185 PF04959 ARS2: Arsenite-resist 30.8 17 0.00037 34.9 0.1 33 99-138 72-104 (214)
186 PF07800 DUF1644: Protein of u 30.5 86 0.0019 28.6 4.5 50 103-161 79-130 (162)
187 PF04810 zf-Sec23_Sec24: Sec23 30.3 22 0.00047 24.4 0.5 23 127-149 12-34 (40)
188 KOG3507 DNA-directed RNA polym 30.2 49 0.0011 24.8 2.4 33 30-73 15-47 (62)
189 PRK09678 DNA-binding transcrip 30.1 22 0.00047 28.0 0.6 38 140-178 2-42 (72)
190 PF01927 Mut7-C: Mut7-C RNAse 29.6 44 0.00095 29.9 2.6 49 34-82 90-143 (147)
191 PRK03976 rpl37ae 50S ribosomal 29.5 33 0.00072 28.2 1.5 13 139-151 54-66 (90)
192 KOG3362 Predicted BBOX Zn-fing 29.4 26 0.00057 31.2 1.0 41 28-85 111-151 (156)
193 COG1571 Predicted DNA-binding 29.1 31 0.00067 36.4 1.6 31 140-180 351-382 (421)
194 PF03249 TSA: Type specific an 29.0 25 0.00054 36.2 0.9 17 354-370 322-338 (503)
195 PRK14714 DNA polymerase II lar 28.9 46 0.001 39.8 3.1 12 138-149 691-702 (1337)
196 KOG1280 Uncharacterized conser 28.7 50 0.0011 33.7 3.0 26 7-45 8-33 (381)
197 COG3357 Predicted transcriptio 28.6 29 0.00062 28.5 1.0 28 62-112 57-84 (97)
198 PF11789 zf-Nse: Zinc-finger o 28.5 44 0.00096 24.9 2.0 49 32-112 8-56 (57)
199 PF05443 ROS_MUCR: ROS/MUCR tr 28.3 26 0.00057 31.0 0.8 28 101-138 69-96 (132)
200 COG1655 Uncharacterized protei 28.2 24 0.00053 34.0 0.6 40 33-72 17-71 (267)
201 PF06220 zf-U1: U1 zinc finger 27.9 32 0.0007 23.4 1.0 16 62-77 2-17 (38)
202 KOG3408 U1-like Zn-finger-cont 27.7 32 0.00069 29.8 1.2 27 60-86 54-80 (129)
203 KOG2071 mRNA cleavage and poly 27.7 31 0.00067 37.7 1.4 28 101-135 415-442 (579)
204 PF10263 SprT-like: SprT-like 26.5 35 0.00076 30.5 1.4 35 32-74 120-154 (157)
205 KOG1701 Focal adhesion adaptor 26.5 9.1 0.0002 40.0 -2.7 149 10-176 277-438 (468)
206 PF06689 zf-C4_ClpX: ClpX C4-t 26.4 15 0.00033 25.4 -0.8 33 35-72 1-33 (41)
207 COG4957 Predicted transcriptio 26.2 29 0.00063 30.6 0.7 27 103-139 75-101 (148)
208 PRK05978 hypothetical protein; 26.2 39 0.00084 30.5 1.5 33 35-76 33-65 (148)
209 KOG3002 Zn finger protein [Gen 26.0 45 0.00098 33.7 2.2 44 33-78 78-125 (299)
210 KOG4377 Zn-finger protein [Gen 25.8 24 0.00053 36.7 0.2 75 35-123 271-361 (480)
211 PF02176 zf-TRAF: TRAF-type zi 25.6 31 0.00068 25.3 0.7 26 125-150 24-53 (60)
212 PRK12380 hydrogenase nickel in 25.4 25 0.00055 30.1 0.2 29 31-71 66-94 (113)
213 PF08274 PhnA_Zn_Ribbon: PhnA 25.4 29 0.00063 22.4 0.4 25 37-72 4-28 (30)
214 KOG2593 Transcription initiati 25.3 25 0.00054 37.0 0.2 39 100-148 124-162 (436)
215 PF15269 zf-C2H2_7: Zinc-finge 25.2 47 0.001 23.5 1.5 30 28-57 13-42 (54)
216 PRK14873 primosome assembly pr 25.0 41 0.00088 38.0 1.8 28 132-174 403-431 (665)
217 PF07975 C1_4: TFIIH C1-like d 24.9 14 0.0003 27.0 -1.2 27 61-87 19-45 (51)
218 KOG4679 Uncharacterized protei 24.7 21 0.00046 37.7 -0.5 19 328-346 143-161 (572)
219 smart00132 LIM Zinc-binding do 24.7 38 0.00082 22.0 0.9 11 64-74 28-38 (39)
220 smart00731 SprT SprT homologue 24.6 44 0.00095 29.8 1.6 35 33-74 110-144 (146)
221 KOG2461 Transcription factor B 24.3 60 0.0013 34.2 2.8 23 119-141 339-361 (396)
222 PTZ00303 phosphatidylinositol 23.7 37 0.00081 38.3 1.1 73 38-130 463-535 (1374)
223 PF07754 DUF1610: Domain of un 23.5 35 0.00076 20.9 0.5 10 62-71 15-24 (24)
224 PF13878 zf-C2H2_3: zinc-finge 23.3 61 0.0013 22.4 1.8 24 64-87 14-39 (41)
225 COG1594 RPB9 DNA-directed RNA 23.2 33 0.00072 29.4 0.5 41 35-75 72-112 (113)
226 PF10013 DUF2256: Uncharacteri 23.1 60 0.0013 22.7 1.6 16 65-80 10-25 (42)
227 COG1571 Predicted DNA-binding 22.7 52 0.0011 34.8 1.9 36 32-78 347-382 (421)
228 COG3091 SprT Zn-dependent meta 22.7 43 0.00094 30.2 1.2 37 32-73 114-150 (156)
229 TIGR00595 priA primosomal prot 22.7 50 0.0011 36.0 1.9 30 131-174 232-262 (505)
230 PF13453 zf-TFIIB: Transcripti 22.6 52 0.0011 22.5 1.3 37 37-81 1-37 (41)
231 PF03604 DNA_RNApol_7kD: DNA d 22.5 60 0.0013 21.3 1.5 10 139-148 17-26 (32)
232 PHA02998 RNA polymerase subuni 22.4 44 0.00096 30.9 1.2 40 34-75 142-183 (195)
233 KOG4602 Nanos and related prot 22.3 1.4E+02 0.003 29.3 4.5 8 103-110 267-274 (318)
234 PF03833 PolC_DP2: DNA polymer 22.2 29 0.00064 39.6 0.0 11 138-148 679-689 (900)
235 TIGR01206 lysW lysine biosynth 21.4 61 0.0013 24.0 1.5 11 63-73 22-32 (54)
236 PF10263 SprT-like: SprT-like 21.1 36 0.00077 30.4 0.3 31 139-176 123-154 (157)
237 TIGR00100 hypA hydrogenase nic 20.9 34 0.00074 29.4 0.1 30 31-72 66-95 (115)
238 PF01363 FYVE: FYVE zinc finge 20.9 49 0.0011 25.2 1.0 31 34-76 8-38 (69)
239 smart00731 SprT SprT homologue 20.4 52 0.0011 29.3 1.2 31 139-175 112-143 (146)
240 PF11494 Ta0938: Ta0938; Inte 20.4 60 0.0013 26.9 1.4 41 31-77 10-51 (105)
241 COG4896 Uncharacterized protei 20.2 68 0.0015 24.3 1.6 34 64-110 3-37 (68)
242 KOG2636 Splicing factor 3a, su 20.1 59 0.0013 34.4 1.6 27 58-84 396-423 (497)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.93 E-value=5.6e-27 Score=223.14 Aligned_cols=135 Identities=21% Similarity=0.395 Sum_probs=127.2
Q ss_pred CCCCCCCCCCCCCCCChhHhhhCccccCC---CCceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCC
Q 011146 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMA---TNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICP 108 (492)
Q Consensus 32 ~~~~~~c~~cg~~~~~~~~l~~h~~~h~~---~k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~ 108 (492)
...+++|..||+.+.+...|.+|...|.. .+.+.|++|||.|...-.|+.|+|+|+ -+++|.
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 45689999999999999999999999854 678999999999999999999999996 678999
Q ss_pred CCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccccCChHHHHHhhhh-cCCCceeec-CCCccCChhHHHHHHh
Q 011146 109 EKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTLFSRKDSFITHRA 186 (492)
Q Consensus 109 ~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~-~~~kp~~C~-C~k~F~~~~~L~~H~~ 186 (492)
+| ||+|.+..-|..|+|+|+|||||.|..|+|.|+.+++|+.|+.+ .+.|.|.|. |+|+|.+++.|.+|..
T Consensus 192 iC-------GKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 192 IC-------GKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cc-------cccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 99 99999999999999999999999999999999999999999999 788999999 9999999999999986
Q ss_pred Hh
Q 011146 187 FC 188 (492)
Q Consensus 187 ~h 188 (492)
..
T Consensus 265 S~ 266 (279)
T KOG2462|consen 265 SA 266 (279)
T ss_pred hc
Confidence 54
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.90 E-value=1.4e-24 Score=206.75 Aligned_cols=133 Identities=23% Similarity=0.383 Sum_probs=126.4
Q ss_pred CCCCCCCCCCCcCCCCCCCCCCCCC---CCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHHHHH
Q 011146 7 GLSVPSTLKGFVQEPNSNPNPNPSS---NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHR 83 (492)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~ 83 (492)
-|.|+.|+|.+....+|..|...|. .++-+.|+.|||.|.+.-.|+.|.++|+ -+++|.+|||.|.+.-.|+-|+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccc
Confidence 4999999999999999999987664 4778999999999999999999999998 6799999999999999999999
Q ss_pred HhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccccCChHHHHHhhhh
Q 011146 84 RGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 84 r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~ 161 (492)
|+|+ |||||.|..| +|+|.++++|+.||.+|.+.|+|.|..|+|.|..++.|.+|...
T Consensus 208 RTHT-------------GEKPF~C~hC-------~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 208 RTHT-------------GEKPFSCPHC-------GKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cccc-------------CCCCccCCcc-------cchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 9998 9999999999 99999999999999999999999999999999999999999876
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.74 E-value=2.2e-19 Score=191.36 Aligned_cols=80 Identities=20% Similarity=0.478 Sum_probs=71.7
Q ss_pred cccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccccCChHHHHHhhhhcCCC-----ceeec----CCCc
Q 011146 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTR-----EYRCD----CGTL 174 (492)
Q Consensus 104 ~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~k-----p~~C~----C~k~ 174 (492)
|-.|-+| .|.+..++.|+.|+|+|+|||||+|.+||+.|.++.+|+.|+-+|..+ +|.|. |-+.
T Consensus 605 PNqCiiC-------~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~k 677 (958)
T KOG1074|consen 605 PNQCIIC-------LRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKK 677 (958)
T ss_pred ccceeee-------eecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccc
Confidence 3467777 999999999999999999999999999999999999999999886554 38884 8899
Q ss_pred cCChhHHHHHHhHhcC
Q 011146 175 FSRKDSFITHRAFCDA 190 (492)
Q Consensus 175 F~~~~~L~~H~~~h~~ 190 (492)
|...-.|..|++.|.+
T Consensus 678 ftn~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 678 FTNAVTLPQHIRIHLG 693 (958)
T ss_pred ccccccccceEEeecC
Confidence 9999999999999974
No 4
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.70 E-value=5.8e-18 Score=153.98 Aligned_cols=116 Identities=23% Similarity=0.524 Sum_probs=106.4
Q ss_pred CCCceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcc
Q 011146 60 ATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKK 139 (492)
Q Consensus 60 ~~k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp 139 (492)
+...|.|.+|+|.|.-...|.+|++-|. .-|.|.|..| |+.|.+.-.|++|+|+|+|.+|
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~-------------~vkr~lct~c-------gkgfndtfdlkrh~rthtgvrp 173 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHS-------------DVKRHLCTFC-------GKGFNDTFDLKRHTRTHTGVRP 173 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhcc-------------HHHHHHHhhc-------cCcccchhhhhhhhccccCccc
Confidence 3467999999999999999999999998 8899999999 9999999999999999999999
Q ss_pred cccCcCccccCChHHHHHhhhh-cC-----------CCceeec-CCCccCChhHHHHHHhHhcCccccc
Q 011146 140 WKCEKCSKKYAVQSDWKAHSKI-CG-----------TREYRCD-CGTLFSRKDSFITHRAFCDALAEES 195 (492)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~-~~-----------~kp~~C~-C~k~F~~~~~L~~H~~~h~~~~~~~ 195 (492)
|+|..|+|.|..+-.|..|++. || +|.|.|+ ||.+-.+...+..|++.|+...+..
T Consensus 174 ykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spal 242 (267)
T KOG3576|consen 174 YKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPAL 242 (267)
T ss_pred cchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCHHH
Confidence 9999999999999999999987 65 4679999 9999999999999999998755443
No 5
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.68 E-value=5.2e-18 Score=165.51 Aligned_cols=153 Identities=19% Similarity=0.290 Sum_probs=90.7
Q ss_pred CCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHhhhCccccC--CCCceecccccccccChhhHHHHHHhcCCCccc
Q 011146 15 KGFVQEPNSNPNPNPSSNQLKRKRNLPGTPDPDAEVIALSPKSLM--ATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKL 92 (492)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~c~~cg~~~~~~~~l~~h~~~h~--~~k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~ 92 (492)
+.+.....++.|...+.+++..-|..||.-|+.+..|-.|.+.-+ ...+|.|..|.|.|.++..|+.|++.|.
T Consensus 187 ~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv----- 261 (467)
T KOG3608|consen 187 KHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV----- 261 (467)
T ss_pred hhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh-----
Confidence 334444455555555555666666666666666665555554432 2445666666666666666666666554
Q ss_pred ccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcc-cCCCcccccCcCccccCChHHHHHhhhhcCCCceeec-
Q 011146 93 KQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSR-KHGEKKWKCEKCSKKYAVQSDWKAHSKICGTREYRCD- 170 (492)
Q Consensus 93 ~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~-H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~- 170 (492)
..|+|+.| ..+....+.|..|++. |..+|||+|+.|++.|.+.++|.+|..+|.+..|.|+
T Consensus 262 ----------n~ykCplC-------dmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h 324 (467)
T KOG3608|consen 262 ----------NCYKCPLC-------DMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEH 324 (467)
T ss_pred ----------hccccccc-------ccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCC
Confidence 34666666 6666666666666665 5556666666666666666666666666555566663
Q ss_pred --CCCccCChhHHHHHHhHhc
Q 011146 171 --CGTLFSRKDSFITHRAFCD 189 (492)
Q Consensus 171 --C~k~F~~~~~L~~H~~~h~ 189 (492)
|...|+++..+++|++.++
T Consensus 325 ~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 325 PDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred CCCcHHHHHHHHHHHHHHHhc
Confidence 6666666666666665555
No 6
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.62 E-value=1.2e-16 Score=170.59 Aligned_cols=58 Identities=19% Similarity=0.475 Sum_probs=54.9
Q ss_pred cccCcCccccCChHHHHHhhhh-cCCCceeec-CCCccCChhHHHHHHhHhcCccccccc
Q 011146 140 WKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTLFSRKDSFITHRAFCDALAEESAR 197 (492)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~-~~~kp~~C~-C~k~F~~~~~L~~H~~~h~~~~~~~~~ 197 (492)
..|.+|++.|...+.|..|+|+ +++|||.|. |++.|..+..|+.||.+|++....+.+
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 6899999999999999999999 899999999 999999999999999999998777666
No 7
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.58 E-value=2e-16 Score=154.57 Aligned_cols=169 Identities=15% Similarity=0.219 Sum_probs=146.4
Q ss_pred CCCCCCCCCCCCCCCcCCCCCCCCCCCC--CCCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHH
Q 011146 3 SQDHGLSVPSTLKGFVQEPNSNPNPNPS--SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQ 80 (492)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~ 80 (492)
++|+..-||.|+.-|....-+..|-.+. -....|.|..|-|.|.++..|..|+..|..- |+|+.|+.+-...+.|.
T Consensus 203 s~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~--ykCplCdmtc~~~ssL~ 280 (467)
T KOG3608|consen 203 SNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNC--YKCPLCDMTCSSASSLT 280 (467)
T ss_pred CCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhc--ccccccccCCCChHHHH
Confidence 4677788999999998777666664322 2344899999999999999999999998765 99999999999999999
Q ss_pred HHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCc--CccccCChHHHHHh
Q 011146 81 LHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEK--CSKKYAVQSDWKAH 158 (492)
Q Consensus 81 ~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~--C~k~F~~~~~L~~H 158 (492)
.|+|.-+ .++|||+|+.| .+.|.+.+.|.+|...|. +-.|.|+. |...|.....+++|
T Consensus 281 ~H~r~rH------------s~dkpfKCd~C-------d~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H 340 (467)
T KOG3608|consen 281 THIRYRH------------SKDKPFKCDEC-------DTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRH 340 (467)
T ss_pred HHHHhhh------------ccCCCccccch-------hhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHH
Confidence 9988644 38999999999 999999999999999988 77899988 99999999999999
Q ss_pred hhh-c-C--CCceeec-CCCccCChhHHHHHHhHhcCccc
Q 011146 159 SKI-C-G--TREYRCD-CGTLFSRKDSFITHRAFCDALAE 193 (492)
Q Consensus 159 ~~~-~-~--~kp~~C~-C~k~F~~~~~L~~H~~~h~~~~~ 193 (492)
++. + | +-+|.|. |++.|.+-.+|..|+++-|+..-
T Consensus 341 ~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~ 380 (467)
T KOG3608|consen 341 FLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRL 380 (467)
T ss_pred HHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccC
Confidence 988 4 3 3579999 99999999999999988776543
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.58 E-value=2.1e-16 Score=143.81 Aligned_cols=111 Identities=24% Similarity=0.408 Sum_probs=104.0
Q ss_pred CCCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCC
Q 011146 31 SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEK 110 (492)
Q Consensus 31 ~~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C 110 (492)
.....+.|.+|||.|.-.-.|.+|++-|...|+|.|..|||.|..-..|++|+|+|+ +-+||+|..|
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rtht-------------gvrpykc~~c 179 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHT-------------GVRPYKCSLC 179 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcccc-------------Cccccchhhh
Confidence 345689999999999999999999999999999999999999999999999999998 9999999999
Q ss_pred CCCCCCCCCcccChhhHHhhhcccCC-----------CcccccCcCccccCChHHHHHhhhh
Q 011146 111 SCVHHDPSRALGDLTGIKKHFSRKHG-----------EKKWKCEKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 111 ~C~~~~c~k~f~~~s~L~~H~~~H~~-----------ekp~~C~~C~k~F~~~~~L~~H~~~ 161 (492)
+++|..+..|..|++.-+| +|.|.|+.||.+-.+...+..|++.
T Consensus 180 -------~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~ 234 (267)
T KOG3576|consen 180 -------EKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKL 234 (267)
T ss_pred -------hHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHh
Confidence 9999999999999988655 5789999999999999999999987
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.46 E-value=1.1e-14 Score=153.41 Aligned_cols=105 Identities=25% Similarity=0.575 Sum_probs=95.1
Q ss_pred eecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCC-------
Q 011146 64 FLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHG------- 136 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~------- 136 (492)
..|.+|.+.+++...|+.|++.-+ +..+.-|.|..| .++|..+..|.+||.+|..
T Consensus 211 ltcpycdrgykrltslkeHikyrh-----------ekne~nfsC~lC-------sytFAyRtQLErhm~~hkpg~dqa~s 272 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRH-----------EKNEPNFSCMLC-------SYTFAYRTQLERHMQLHKPGGDQAIS 272 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHH-----------hhCCCCCcchhh-------hhhhhhHHHHHHHHHhhcCCCccccc
Confidence 579999999999999999976543 135677999999 9999999999999999852
Q ss_pred ------CcccccCcCccccCChHHHHHhhhh-cCCCceeec-CCCccCChhHHHHHHh
Q 011146 137 ------EKKWKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTLFSRKDSFITHRA 186 (492)
Q Consensus 137 ------ekp~~C~~C~k~F~~~~~L~~H~~~-~~~kp~~C~-C~k~F~~~~~L~~H~~ 186 (492)
.|+|+|..|+|.|+.+.+|+.|+|+ .|||||.|+ |+|+|+...++..||-
T Consensus 273 ltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 273 LTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred ccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 4789999999999999999999999 899999999 9999999999999985
No 10
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.46 E-value=1.5e-14 Score=152.38 Aligned_cols=81 Identities=25% Similarity=0.596 Sum_probs=74.8
Q ss_pred CCCceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcc
Q 011146 60 ATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKK 139 (492)
Q Consensus 60 ~~k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp 139 (492)
.+-.|.|+.|+|.|...+.|.+|.-.|+ |.+||.|.+| .|+|..+.+|..|+|.|.||||
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHs-------------GqRPyqC~iC-------kKAFKHKHHLtEHkRLHSGEKP 950 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHS-------------GQRPYQCIIC-------KKAFKHKHHLTEHKRLHSGEKP 950 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhc-------------CCCCcccchh-------hHhhhhhhhhhhhhhhccCCCc
Confidence 3457999999999999999999999998 9999999999 9999999999999999999999
Q ss_pred cccCcCccccCChHHHHHhhh
Q 011146 140 WKCEKCSKKYAVQSDWKAHSK 160 (492)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~ 160 (492)
|.|++|+|+|.....+..||.
T Consensus 951 fQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 951 FQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred chhhhhhhhcccccchHhhhc
Confidence 999999999999999998885
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.21 E-value=2.2e-11 Score=129.73 Aligned_cols=103 Identities=23% Similarity=0.460 Sum_probs=88.0
Q ss_pred CceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccc
Q 011146 62 NRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWK 141 (492)
Q Consensus 62 k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~ 141 (492)
+.+.|++|++.|. ...|..|++.|+ ++|.|+ | ++.+ .+..|..|+++|.++|++.
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H---------------kpv~Cp-C-------g~~~-~R~~L~~H~~thCp~Kpi~ 506 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH---------------EPLQCP-C-------GVVL-EKEQMVQHQASTCPLRLIT 506 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC---------------CCccCC-C-------CCCc-chhHHHhhhhccCCCCcee
Confidence 3468999999996 678999999885 689998 7 8755 6789999999999999999
Q ss_pred cCcCccccC----------ChHHHHHhhhhcCCCceeec-CCCccCChhHHHHHHhHhcC
Q 011146 142 CEKCSKKYA----------VQSDWKAHSKICGTREYRCD-CGTLFSRKDSFITHRAFCDA 190 (492)
Q Consensus 142 C~~C~k~F~----------~~~~L~~H~~~~~~kp~~C~-C~k~F~~~~~L~~H~~~h~~ 190 (492)
|.+|++.|. ....|..|+.++|.+++.|. |++.|..+ .|..|+..+|.
T Consensus 507 C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 507 CRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred CCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeeeh-hHHHHHHHhhc
Confidence 999999985 24589999999999999999 99988765 56788877664
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.01 E-value=4.2e-10 Score=120.12 Aligned_cols=102 Identities=14% Similarity=0.255 Sum_probs=87.1
Q ss_pred CCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCC
Q 011146 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSC 112 (492)
Q Consensus 33 ~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C 112 (492)
+..+.|..||+.|. ...|..|.+.++ ++|.|+ ||+.| .+..|..|++.|. .++++.|++|
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thC-------------p~Kpi~C~fC-- 510 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTC-------------PLRLITCRFC-- 510 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccC-------------CCCceeCCCC--
Confidence 34579999999996 678999999985 789999 99866 5689999999998 8999999999
Q ss_pred CCCCCCCccc----------ChhhHHhhhcccCCCcccccCcCccccCChHHHHHhhhh
Q 011146 113 VHHDPSRALG----------DLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 113 ~~~~c~k~f~----------~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~ 161 (492)
++.|. ....|..|...+ |.+++.|..|++.|..+ ++..|+..
T Consensus 511 -----~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 511 -----GDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIA 562 (567)
T ss_pred -----CCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHH
Confidence 88874 246899999996 99999999999988765 77888766
No 13
>PHA00733 hypothetical protein
Probab=98.99 E-value=4.9e-10 Score=98.52 Aligned_cols=110 Identities=15% Similarity=0.114 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCCC-CChhHhhhCccccCCCCceecccccccccChhhHHHH--HHhcCCCcccccccccccCcccccCCC
Q 011146 33 QLKRKRNLPGTPD-PDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLH--RRGHNLPWKLKQRTNKEVRKKVYICPE 109 (492)
Q Consensus 33 ~~~~~c~~cg~~~-~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~~H--~r~H~~~~~~~~~~~~~~~~k~y~C~~ 109 (492)
.++|..+-.|--| .+.+.|.++-..--..+++.|.+|.+.|.....|..| ++.|. ...++++|.|+.
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~----------~~~~~kPy~C~~ 78 (128)
T PHA00733 9 SKKYLSNHKGIFIHVTLEELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLL----------TSKAVSPYVCPL 78 (128)
T ss_pred hHhhcccCCCeEEecCHHHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhc----------ccCCCCCccCCC
Confidence 3444433334222 3345555554433445677777777777776666655 22221 001355666666
Q ss_pred CCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccccCChHHHHHhhhh
Q 011146 110 KSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 110 C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~ 161 (492)
| ++.|.....|..|++.| +++|.|.+|++.|.....|..|+..
T Consensus 79 C-------gk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~ 121 (128)
T PHA00733 79 C-------LMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCK 121 (128)
T ss_pred C-------CCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHH
Confidence 6 66666666666666654 3456666666666666666666554
No 14
>PHA00733 hypothetical protein
Probab=98.95 E-value=5.9e-10 Score=97.96 Aligned_cols=84 Identities=15% Similarity=0.273 Sum_probs=69.7
Q ss_pred CcccccCCCCCCCCCCCCCcccChhhHHhh--h---cccCCCcccccCcCccccCChHHHHHhhhhcCCCceeec-CCCc
Q 011146 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKH--F---SRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTL 174 (492)
Q Consensus 101 ~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H--~---~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~ 174 (492)
..+++.|.+| .+.|.....|..| + ..+++++||.|+.|++.|.....|..|++.+ +.+|.|. |++.
T Consensus 37 ~~~~~~~~~~-------~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~ 108 (128)
T PHA00733 37 EQKRLIRAVV-------KTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKE 108 (128)
T ss_pred hhhhHHHHHH-------hhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCc
Confidence 5788999998 7777766665554 1 2334589999999999999999999999874 5689999 9999
Q ss_pred cCChhHHHHHHhHhcCcc
Q 011146 175 FSRKDSFITHRAFCDALA 192 (492)
Q Consensus 175 F~~~~~L~~H~~~h~~~~ 192 (492)
|.....|.+|+...|++.
T Consensus 109 F~~~~sL~~H~~~~h~~~ 126 (128)
T PHA00733 109 FRNTDSTLDHVCKKHNIC 126 (128)
T ss_pred cCCHHHHHHHHHHhcCcc
Confidence 999999999999888753
No 15
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.93 E-value=1.1e-10 Score=117.12 Aligned_cols=150 Identities=17% Similarity=0.222 Sum_probs=113.2
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHHHHHHhcCC-Cccc---------cc----------
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNL-PWKL---------KQ---------- 94 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~r~H~~-~~~~---------~~---------- 94 (492)
.|.|.+|...|.|...|..|.-.-..-.-|+|++|+|.|....+|--|+|+|.- +... ..
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 589999999999999999997665555569999999999999999999999971 1100 00
Q ss_pred ccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCC---c---------------------------------
Q 011146 95 RTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGE---K--------------------------------- 138 (492)
Q Consensus 95 ~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~e---k--------------------------------- 138 (492)
+.-....+.-|.|.+| ++.|.+...|++|..+|+.. +
T Consensus 347 rsg~dss~gi~~C~~C-------~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~ 419 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTC-------GKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGD 419 (500)
T ss_pred ccCCcccCceeecHHh-------hhhhHHHHHHHHhHHhhhccccchhcccCcchhhccccccccccccccccccccccc
Confidence 0111133457999999 99999999999998887521 0
Q ss_pred ----------ccccCcCccccCChHHHHHhhhh-cCCCceeec-CCCccCChhHHHHHHhHhcCc
Q 011146 139 ----------KWKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTLFSRKDSFITHRAFCDAL 191 (492)
Q Consensus 139 ----------p~~C~~C~k~F~~~~~L~~H~~~-~~~kp~~C~-C~k~F~~~~~L~~H~~~h~~~ 191 (492)
...|++|+..+..+..--.|.+. +-+.-|.|+ |.-.|.....|.+|+..+|..
T Consensus 420 ~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hps 484 (500)
T KOG3993|consen 420 EVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPS 484 (500)
T ss_pred ceeeeeccccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChH
Confidence 12456666666665555555554 555669999 999999999999999988853
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.54 E-value=3.5e-08 Score=72.49 Aligned_cols=44 Identities=18% Similarity=0.257 Sum_probs=39.2
Q ss_pred ceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHH
Q 011146 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIK 128 (492)
Q Consensus 63 ~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~ 128 (492)
-|+|++|||.|.+..+|..|+|+|+ ++|+|..| ++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~---------------k~~kc~~C-------~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN---------------TNLKLSNC-------KRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC---------------CcccCCcc-------cceecccceeE
Confidence 4899999999999999999999995 68999998 99998777664
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.51 E-value=3.5e-08 Score=72.51 Aligned_cols=44 Identities=14% Similarity=0.286 Sum_probs=34.9
Q ss_pred cccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccccCChHHHH
Q 011146 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWK 156 (492)
Q Consensus 104 ~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~ 156 (492)
-|.|++| |+.|...+.|..|+++|+ ++|+|..|++.|.+.+.|.
T Consensus 5 ~y~C~~C-------GK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPIC-------GEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchh-------CCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3778887 888888888888888887 6788888888888766653
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.38 E-value=1.3e-07 Score=59.37 Aligned_cols=26 Identities=31% Similarity=0.824 Sum_probs=23.5
Q ss_pred hHHhhhcccCCCcccccCcCccccCC
Q 011146 126 GIKKHFSRKHGEKKWKCEKCSKKYAV 151 (492)
Q Consensus 126 ~L~~H~~~H~~ekp~~C~~C~k~F~~ 151 (492)
+|.+|+++|+++|||.|++|++.|..
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 48899999999999999999999863
No 19
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.29 E-value=1.6e-07 Score=94.73 Aligned_cols=84 Identities=18% Similarity=0.414 Sum_probs=69.7
Q ss_pred cccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccccCChHHHHHhhhhcCC-------------------
Q 011146 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGT------------------- 164 (492)
Q Consensus 104 ~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~------------------- 164 (492)
.|+|..| ...|.+.-.|..|.-.-.-.--|+|..|+|.|.-..+|..|.|+|.-
T Consensus 267 dyiCqLC-------K~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~r 339 (500)
T KOG3993|consen 267 DYICQLC-------KEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETR 339 (500)
T ss_pred HHHHHHH-------HHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhh
Confidence 5999999 99999999999996443333449999999999999999999987421
Q ss_pred ---------------Cceeec-CCCccCChhHHHHHHhHhcCcccc
Q 011146 165 ---------------REYRCD-CGTLFSRKDSFITHRAFCDALAEE 194 (492)
Q Consensus 165 ---------------kp~~C~-C~k~F~~~~~L~~H~~~h~~~~~~ 194 (492)
..|.|. |+|.|++...|++|...|+.....
T Consensus 340 ae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~ 385 (500)
T KOG3993|consen 340 AEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLA 385 (500)
T ss_pred hhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccc
Confidence 129999 999999999999999999865443
No 20
>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=98.05 E-value=1.1e-06 Score=55.08 Aligned_cols=26 Identities=15% Similarity=0.430 Sum_probs=23.9
Q ss_pred HhhhCccccCCCCceecccccccccC
Q 011146 50 VIALSPKSLMATNRFLCEICNKGFQR 75 (492)
Q Consensus 50 ~l~~h~~~h~~~k~~~C~~Cgk~F~~ 75 (492)
.|..|++.|+++|+|.|++|++.|.+
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 47899999999999999999999974
No 21
>PHA00616 hypothetical protein
Probab=97.97 E-value=2.8e-06 Score=59.52 Aligned_cols=34 Identities=12% Similarity=0.245 Sum_probs=31.6
Q ss_pred ceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCC
Q 011146 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPE 109 (492)
Q Consensus 63 ~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~ 109 (492)
+|.|..||+.|..+..|..|++.|+ +++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~h-------------g~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVH-------------KQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhc-------------CCCccceeE
Confidence 6899999999999999999999998 889998875
No 22
>PHA00732 hypothetical protein
Probab=97.93 E-value=6.7e-06 Score=65.97 Aligned_cols=48 Identities=23% Similarity=0.420 Sum_probs=29.5
Q ss_pred ceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccC
Q 011146 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKH 135 (492)
Q Consensus 63 ~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~ 135 (492)
+|.|++|++.|.+...|+.|++.++ . ++.|++| ++.|. .|..|++++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H-------------~--~~~C~~C-------gKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNH-------------T--LTKCPVC-------NKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhccc-------------C--CCccCCC-------CCEeC---ChhhhhcccC
Confidence 4667777777777777777766422 1 2456666 66665 3666665554
No 23
>PHA00616 hypothetical protein
Probab=97.75 E-value=7.2e-06 Score=57.52 Aligned_cols=35 Identities=17% Similarity=0.259 Sum_probs=27.9
Q ss_pred cccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcC
Q 011146 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKC 145 (492)
Q Consensus 104 ~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C 145 (492)
||.|..| |+.|..+..|.+|++.|++++++.|+.-
T Consensus 1 pYqC~~C-------G~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 1 MYQCLRC-------GGIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred CCccchh-------hHHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 5778887 8888888888888888888888887654
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.69 E-value=2.3e-05 Score=47.37 Aligned_cols=23 Identities=43% Similarity=0.902 Sum_probs=21.7
Q ss_pred eecccccccccChhhHHHHHHhc
Q 011146 64 FLCEICNKGFQRDQNLQLHRRGH 86 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~H 86 (492)
|+|++|++.|.++..|+.|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 79999999999999999999875
No 25
>PHA00732 hypothetical protein
Probab=97.64 E-value=3.5e-05 Score=61.81 Aligned_cols=45 Identities=27% Similarity=0.434 Sum_probs=38.5
Q ss_pred cccCCCCCCCCCCCCCcccChhhHHhhhcc-cCCCcccccCcCccccCChHHHHHhhhh
Q 011146 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSR-KHGEKKWKCEKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 104 ~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~-H~~ekp~~C~~C~k~F~~~~~L~~H~~~ 161 (492)
||.|++| ++.|.....|+.|++. |. ++.|+.|++.|. .|..|.++
T Consensus 1 py~C~~C-------gk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPIC-------GFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCC-------CCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhcc
Confidence 5889998 9999999999999985 65 368999999998 58888866
No 26
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.52 E-value=2.8e-05 Score=76.11 Aligned_cols=69 Identities=22% Similarity=0.534 Sum_probs=39.0
Q ss_pred cccccCCCCCCCCCCCCCcccChhhHHhhhcc-cCCCcccccC--cCccccCChHHHHHhhhhcCCCceeec-CCCccCC
Q 011146 102 KKVYICPEKSCVHHDPSRALGDLTGIKKHFSR-KHGEKKWKCE--KCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFSR 177 (492)
Q Consensus 102 ~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~-H~~ekp~~C~--~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~F~~ 177 (492)
+|||+|++-+| .|+|....+|+-|+.. |-..+...-+ +--..| ....|||+|+ |+|+|+.
T Consensus 347 ~KpykCpV~gC-----~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F-----------~~~~KPYrCevC~KRYKN 410 (423)
T COG5189 347 GKPYKCPVEGC-----NKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIF-----------SAKDKPYRCEVCDKRYKN 410 (423)
T ss_pred CceecCCCCCc-----hhhhccccchhhhhhccccCcccCCCCCccccccc-----------cccCCceeccccchhhcc
Confidence 47777777666 7777777777777655 3211111100 000011 1245777777 7777777
Q ss_pred hhHHHHHHh
Q 011146 178 KDSFITHRA 186 (492)
Q Consensus 178 ~~~L~~H~~ 186 (492)
...|+.|+.
T Consensus 411 lNGLKYHr~ 419 (423)
T COG5189 411 LNGLKYHRK 419 (423)
T ss_pred Cccceeccc
Confidence 777777754
No 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.51 E-value=4.3e-05 Score=74.85 Aligned_cols=26 Identities=23% Similarity=0.617 Sum_probs=23.2
Q ss_pred CCCCceeccc--ccccccChhhHHHHHH
Q 011146 59 MATNRFLCEI--CNKGFQRDQNLQLHRR 84 (492)
Q Consensus 59 ~~~k~~~C~~--Cgk~F~~~~~L~~H~r 84 (492)
.++|||+|++ |.|+|+...-|+.|+.
T Consensus 345 ~d~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 345 KDGKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred ecCceecCCCCCchhhhccccchhhhhh
Confidence 3469999987 9999999999999975
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=97.49 E-value=9.6e-05 Score=54.87 Aligned_cols=52 Identities=25% Similarity=0.514 Sum_probs=32.4
Q ss_pred ceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccC
Q 011146 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKH 135 (492)
Q Consensus 63 ~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~ 135 (492)
.|.|++|++. .+...|..|....+. ...+.+.|++| ...+. ..|..|+..++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~-----------~~~~~v~CPiC-------~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHR-----------SESKNVVCPIC-------SSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCc-----------CCCCCccCCCc-------hhhhh--hHHHHHHHHhc
Confidence 4788888884 445678888554331 13456788887 55433 36777776654
No 29
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.26 E-value=0.0002 Score=43.26 Aligned_cols=24 Identities=42% Similarity=0.899 Sum_probs=20.3
Q ss_pred eecccccccccChhhHHHHHHhcC
Q 011146 64 FLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
|.|++|++.|.+...|+.|++.|+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999998874
No 30
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.19 E-value=0.00052 Score=74.84 Aligned_cols=62 Identities=18% Similarity=0.303 Sum_probs=39.0
Q ss_pred CCcccChhhHHhhhcccCCCcccccCcCc------cccCChHHHHHhhhhcCCCceeec---CC-CccCChhHHHHHHh
Q 011146 118 SRALGDLTGIKKHFSRKHGEKKWKCEKCS------KKYAVQSDWKAHSKICGTREYRCD---CG-TLFSRKDSFITHRA 186 (492)
Q Consensus 118 ~k~f~~~s~L~~H~~~H~~ekp~~C~~C~------k~F~~~~~L~~H~~~~~~kp~~C~---C~-k~F~~~~~L~~H~~ 186 (492)
...|.+...|.+|++.++ |.|.+|. .-|..-.+|..|.+. .-|.|+ |. +.|.....+..|++
T Consensus 189 ~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~---~HflCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 189 HERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRK---GHFLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred hhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhh---cCccccccccccceeeehhHHHHHHH
Confidence 788888888888888765 5566663 345666778888765 235663 53 34444444554544
No 31
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=97.13 E-value=0.0004 Score=72.29 Aligned_cols=144 Identities=19% Similarity=0.218 Sum_probs=97.8
Q ss_pred CCCCCCCCCCCCCChhHhhhCcc--ccCCC--Cceecc--cccccccChhhHHHHHHhcCCC--ccccc--ccc------
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPK--SLMAT--NRFLCE--ICNKGFQRDQNLQLHRRGHNLP--WKLKQ--RTN------ 97 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~--~h~~~--k~~~C~--~Cgk~F~~~~~L~~H~r~H~~~--~~~~~--~~~------ 97 (492)
.++.|..|...|.....+..|.+ .|..+ +++.|+ .|++.|.+...|..|...|... ..+.. ...
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 57999999999999999999999 89999 999999 7999999999999999999721 11110 000
Q ss_pred ------------cccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCc--ccccCcCccccCChHHHHHhhhh-c
Q 011146 98 ------------KEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEK--KWKCEKCSKKYAVQSDWKAHSKI-C 162 (492)
Q Consensus 98 ------------~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ek--p~~C~~C~k~F~~~~~L~~H~~~-~ 162 (492)
.....+.+.|..-.| .+.+.....+..|...|...+ .+.|..|.+.|.....+..|++. .
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 442 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSC-----IRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHT 442 (467)
T ss_pred CCCCccchhhccCccCCccccccccch-----hhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccc
Confidence 011223333333222 666677777777777776655 45567788888888888887777 3
Q ss_pred CCCceeecCCCccCChhHHH
Q 011146 163 GTREYRCDCGTLFSRKDSFI 182 (492)
Q Consensus 163 ~~kp~~C~C~k~F~~~~~L~ 182 (492)
...++.|.+-+.|.....+.
T Consensus 443 ~~~~~~~~~~~~~~~~~~~~ 462 (467)
T COG5048 443 NHAPLLCSILKSFRRDLDLS 462 (467)
T ss_pred cCCceeeccccccchhhhhh
Confidence 33444444444444444433
No 32
>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=97.13 E-value=0.00055 Score=50.79 Aligned_cols=47 Identities=19% Similarity=0.360 Sum_probs=25.8
Q ss_pred ccCCCCCCCCCCCCCcccChhhHHhhhcc-cCCC-cccccCcCccccCChHHHHHhhhh
Q 011146 105 YICPEKSCVHHDPSRALGDLTGIKKHFSR-KHGE-KKWKCEKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 105 y~C~~C~C~~~~c~k~f~~~s~L~~H~~~-H~~e-kp~~C~~C~k~F~~~~~L~~H~~~ 161 (492)
|.|++| ++ ..+...|..|... |..+ +.+.|++|...+. .+|..|+..
T Consensus 3 f~CP~C-------~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYC-------GK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred cCCCCC-------CC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 566666 66 3445566666555 3332 4566666665433 255556554
No 33
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.08 E-value=0.00029 Score=44.26 Aligned_cols=25 Identities=36% Similarity=0.699 Sum_probs=23.5
Q ss_pred ceecccccccccChhhHHHHHHhcC
Q 011146 63 RFLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 63 ~~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
+|+|++|++.|.+...|..|++.|.
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 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.00 E-value=0.00043 Score=57.39 Aligned_cols=72 Identities=18% Similarity=0.452 Sum_probs=15.3
Q ss_pred ecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCc
Q 011146 65 LCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEK 144 (492)
Q Consensus 65 ~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~ 144 (492)
+|.+|+..|.....|..|+...+ +-. ... ...+.....+..+++... ...|.|.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H-------------~~~---~~~--------~~~l~~~~~~~~~~~~~~-~~~~~C~~ 55 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKH-------------GFD---IPD--------QKYLVDPNRLLNYLRKKV-KESFRCPY 55 (100)
T ss_dssp -------------------------------------------------------------------------SSEEBSS
T ss_pred Ccccccccccccccccccccccc-------------ccc---ccc--------cccccccccccccccccc-CCCCCCCc
Confidence 47788888888888888875443 110 000 111222233333333221 12566777
Q ss_pred CccccCChHHHHHhhhh
Q 011146 145 CSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 145 C~k~F~~~~~L~~H~~~ 161 (492)
|++.|.....|..|++.
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 77777777777777665
No 35
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.94 E-value=0.00091 Score=72.99 Aligned_cols=49 Identities=12% Similarity=0.207 Sum_probs=22.2
Q ss_pred ccCcCccccCChHHHHHhhhhcCCCceee---c-CCCccCChhHHHHHHhHhc
Q 011146 141 KCEKCSKKYAVQSDWKAHSKICGTREYRC---D-CGTLFSRKDSFITHRAFCD 189 (492)
Q Consensus 141 ~C~~C~k~F~~~~~L~~H~~~~~~kp~~C---~-C~k~F~~~~~L~~H~~~h~ 189 (492)
.|..|...|.....|.+|++...+.-..| + +..-|...+.|..|-+..|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhcC
Confidence 35555555555555555554421212222 1 2344445555555555444
No 36
>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=96.91 E-value=0.00065 Score=40.88 Aligned_cols=21 Identities=38% Similarity=0.812 Sum_probs=10.8
Q ss_pred eeec-CCCccCChhHHHHHHhH
Q 011146 167 YRCD-CGTLFSRKDSFITHRAF 187 (492)
Q Consensus 167 ~~C~-C~k~F~~~~~L~~H~~~ 187 (492)
|.|+ |++.|.++..|..|++.
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 4454 55555555555555544
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.63 E-value=0.0013 Score=54.38 Aligned_cols=73 Identities=15% Similarity=0.238 Sum_probs=21.5
Q ss_pred cCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccccCChHHHHHhhhhcCCCceeec-CCCccCChhHHHHH
Q 011146 106 ICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFSRKDSFITH 184 (492)
Q Consensus 106 ~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~F~~~~~L~~H 184 (492)
.|.+| +..|.....|..|+...++...- ....+.....+..+.+..-...+.|. |++.|.....|..|
T Consensus 1 ~C~~C-------~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~H 69 (100)
T PF12756_consen 1 QCLFC-------DESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEH 69 (100)
T ss_dssp -----------------------------------------------------------SSEEBSSSS-EESSHHHHHHH
T ss_pred Ccccc-------ccccccccccccccccccccccc----cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHH
Confidence 37777 99999999999999886654321 11122234444444444333479999 99999999999999
Q ss_pred HhHhc
Q 011146 185 RAFCD 189 (492)
Q Consensus 185 ~~~h~ 189 (492)
++.+.
T Consensus 70 m~~~~ 74 (100)
T PF12756_consen 70 MRSKH 74 (100)
T ss_dssp HHHTT
T ss_pred HcCcc
Confidence 99753
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=96.46 E-value=0.0024 Score=38.34 Aligned_cols=22 Identities=27% Similarity=0.664 Sum_probs=10.4
Q ss_pred eeec-CCCccCChhHHHHHHhHh
Q 011146 167 YRCD-CGTLFSRKDSFITHRAFC 188 (492)
Q Consensus 167 ~~C~-C~k~F~~~~~L~~H~~~h 188 (492)
|.|+ |++.|..+..|+.|++.|
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 4455 555555555555555544
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=96.38 E-value=0.0021 Score=40.27 Aligned_cols=24 Identities=29% Similarity=0.652 Sum_probs=14.0
Q ss_pred ceeec-CCCccCChhHHHHHHhHhc
Q 011146 166 EYRCD-CGTLFSRKDSFITHRAFCD 189 (492)
Q Consensus 166 p~~C~-C~k~F~~~~~L~~H~~~h~ 189 (492)
||.|. |++.|.....|..|++.|+
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 35565 6666666666666665554
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.37 E-value=0.0021 Score=39.14 Aligned_cols=24 Identities=33% Similarity=0.667 Sum_probs=22.2
Q ss_pred eecccccccccChhhHHHHHHhcC
Q 011146 64 FLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
|+|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999999874
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=96.25 E-value=0.0036 Score=45.05 Aligned_cols=36 Identities=25% Similarity=0.400 Sum_probs=22.8
Q ss_pred hhCccccC-CCCceecccccccccChhhHHHHHHhcC
Q 011146 52 ALSPKSLM-ATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 52 ~~h~~~h~-~~k~~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
..+.+.+. .+.|..|++|+..+....+|++|+..++
T Consensus 12 ~~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp ----CCCCTTS--EE-TTT--EESSHHHHHHHHHHHT
T ss_pred hhHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHh
Confidence 44555554 4678999999999999999999997766
No 42
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.05 E-value=0.0012 Score=76.00 Aligned_cols=145 Identities=14% Similarity=0.138 Sum_probs=100.1
Q ss_pred CCCCCCCCCCChhHhhhCccc-cCCCCceecccccccccChhhHHHHHHhcC-CC--ccccc--------c-cccccCcc
Q 011146 37 KRNLPGTPDPDAEVIALSPKS-LMATNRFLCEICNKGFQRDQNLQLHRRGHN-LP--WKLKQ--------R-TNKEVRKK 103 (492)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~-h~~~k~~~C~~Cgk~F~~~~~L~~H~r~H~-~~--~~~~~--------~-~~~~~~~k 103 (492)
.|..|+..+..+..+.-|... +.-.|.|+|+.|+..|+....|..|+|.-+ .. ..|.. + .....+.+
T Consensus 438 e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~ 517 (1406)
T KOG1146|consen 438 ELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGK 517 (1406)
T ss_pred cccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCC
Confidence 344455555555555555554 345688999999999999999999998733 11 11111 1 11224567
Q ss_pred cccCCCCCCCCCCCCCcccChhhHHhhhcc--cCC-----------------------------------------Cccc
Q 011146 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSR--KHG-----------------------------------------EKKW 140 (492)
Q Consensus 104 ~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~--H~~-----------------------------------------ekp~ 140 (492)
+|.|..| ...+..+..|.+|+.. |.. +-+|
T Consensus 518 p~~C~~C-------~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~ 590 (1406)
T KOG1146|consen 518 PYPCRAC-------NYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSW 590 (1406)
T ss_pred cccceee-------eeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCc
Confidence 8899988 9999999999999864 210 1248
Q ss_pred ccCcCccccCChHHHHHhhhh-cCC-Cceeec-CCCccCChhHHHHHHhHh
Q 011146 141 KCEKCSKKYAVQSDWKAHSKI-CGT-REYRCD-CGTLFSRKDSFITHRAFC 188 (492)
Q Consensus 141 ~C~~C~k~F~~~~~L~~H~~~-~~~-kp~~C~-C~k~F~~~~~L~~H~~~h 188 (492)
.|.+|++.-.....|+.|+.. +.. .|..|. |.-.+.....+..|.+.+
T Consensus 591 ~C~vc~yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~~~~~~~~~lp 641 (1406)
T KOG1146|consen 591 RCEVCSYETNIARNLRIHMTASPSSSPPSLVLQQNITSSLASLLGGQGRLP 641 (1406)
T ss_pred chhhhcchhhhhhccccccccCCCCCChHHHhhhcchhhccccccCcCCCC
Confidence 999999988888899999887 333 347777 877777777666666555
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.84 E-value=0.0048 Score=37.83 Aligned_cols=23 Identities=43% Similarity=0.996 Sum_probs=21.2
Q ss_pred eecccccccccChhhHHHHHHhc
Q 011146 64 FLCEICNKGFQRDQNLQLHRRGH 86 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~H 86 (492)
|.|++|++.|.....|+.|++.+
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 78999999999999999999765
No 44
>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=95.69 E-value=0.0086 Score=43.17 Aligned_cols=31 Identities=16% Similarity=0.279 Sum_probs=19.0
Q ss_pred CCcccccCcCccccCChHHHHHhhhh-cCCCc
Q 011146 136 GEKKWKCEKCSKKYAVQSDWKAHSKI-CGTRE 166 (492)
Q Consensus 136 ~ekp~~C~~C~k~F~~~~~L~~H~~~-~~~kp 166 (492)
.+.|-.|++|+..+....+|++|+.+ |+.||
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 46777888888888888888888877 76665
No 45
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.51 E-value=0.011 Score=58.92 Aligned_cols=118 Identities=17% Similarity=0.286 Sum_probs=65.0
Q ss_pred ceeccc--ccccccChhhHHHHHHhcCCCccccccc------------------ccc----c---C-cccccCCCCCCCC
Q 011146 63 RFLCEI--CNKGFQRDQNLQLHRRGHNLPWKLKQRT------------------NKE----V---R-KKVYICPEKSCVH 114 (492)
Q Consensus 63 ~~~C~~--Cgk~F~~~~~L~~H~r~H~~~~~~~~~~------------------~~~----~---~-~k~y~C~~C~C~~ 114 (492)
.|.|+. |..+-.....|+.|.+..+...-|..+. ..| . | +..-.|.+|
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC---- 226 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFC---- 226 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhc----
Confidence 477874 6655555677999977655333332110 011 0 1 112256666
Q ss_pred CCCCCcccChhhHHhhhcccCCCcccccCcCcc----ccCChHHHHHhhhhcCCCceeec---CC----CccCChhHHHH
Q 011146 115 HDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSK----KYAVQSDWKAHSKICGTREYRCD---CG----TLFSRKDSFIT 183 (492)
Q Consensus 115 ~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k----~F~~~~~L~~H~~~~~~kp~~C~---C~----k~F~~~~~L~~ 183 (492)
...|-+-..|.+|+|..| |+-|.|+.-+. -|..-..|.+|.+. ..|.|. |. ..|.....|..
T Consensus 227 ---~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~---~hy~ct~qtc~~~k~~vf~~~~el~~ 299 (493)
T COG5236 227 ---KIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRN---AHYCCTFQTCRVGKCYVFPYHTELLE 299 (493)
T ss_pred ---cceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhc---CceEEEEEEEecCcEEEeccHHHHHH
Confidence 777777777888877644 33333333221 25566667666654 236663 53 45777777888
Q ss_pred HHhHhcCc
Q 011146 184 HRAFCDAL 191 (492)
Q Consensus 184 H~~~h~~~ 191 (492)
|+..-|+.
T Consensus 300 h~~~~h~~ 307 (493)
T COG5236 300 HLTRFHKV 307 (493)
T ss_pred HHHHHhhc
Confidence 87655543
No 46
>PRK04860 hypothetical protein; Provisional
Probab=95.45 E-value=0.0054 Score=56.02 Aligned_cols=27 Identities=19% Similarity=0.580 Sum_probs=13.0
Q ss_pred hhhHHhhhcccCCCcccccCcCccccC
Q 011146 124 LTGIKKHFSRKHGEKKWKCEKCSKKYA 150 (492)
Q Consensus 124 ~s~L~~H~~~H~~ekp~~C~~C~k~F~ 150 (492)
...+++|.++|+++++|.|..|+..|.
T Consensus 128 ~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 128 QLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred eCHHHHHHHHhcCCccEECCCCCceeE
Confidence 334445555555555555555544443
No 47
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.22 E-value=0.017 Score=60.08 Aligned_cols=111 Identities=18% Similarity=0.214 Sum_probs=81.4
Q ss_pred CceecccccccccChhhHHHHHH--hcCCCcccccccccccCc--ccccCC--CCCCCCCCCCCcccChhhHHhhhcccC
Q 011146 62 NRFLCEICNKGFQRDQNLQLHRR--GHNLPWKLKQRTNKEVRK--KVYICP--EKSCVHHDPSRALGDLTGIKKHFSRKH 135 (492)
Q Consensus 62 k~~~C~~Cgk~F~~~~~L~~H~r--~H~~~~~~~~~~~~~~~~--k~y~C~--~C~C~~~~c~k~f~~~s~L~~H~~~H~ 135 (492)
.++.|..|.+.|.+...|..|.+ .|. ++ +++.|+ .| ++.|.+...+..|..+|+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~-------------~~~~~~~~~p~~~~-------~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHS-------------GESLKPFSCPYSLC-------GKLFSRNDALKRHILLHT 347 (467)
T ss_pred cCCCCccccCCccccccccccccccccc-------------cccCCceeeeccCC-------CccccccccccCCccccc
Confidence 47999999999999999999999 787 77 999999 67 999999999999999999
Q ss_pred CCcccccCc--CccccCChHHH----HHhhh-h-cCCCceeec---CCCccCChhHHHHHHhHhcCcc
Q 011146 136 GEKKWKCEK--CSKKYAVQSDW----KAHSK-I-CGTREYRCD---CGTLFSRKDSFITHRAFCDALA 192 (492)
Q Consensus 136 ~ekp~~C~~--C~k~F~~~~~L----~~H~~-~-~~~kp~~C~---C~k~F~~~~~L~~H~~~h~~~~ 192 (492)
+.+++.|.. |.+.+.....- ..+.. . ...+.+.|. |.+.+.+...+..|...|....
T Consensus 348 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 415 (467)
T COG5048 348 SISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFR 415 (467)
T ss_pred CCCccccccccCccccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccC
Confidence 988877744 55555444331 11111 1 344556663 6677777777777766665444
No 48
>PRK04860 hypothetical protein; Provisional
Probab=94.35 E-value=0.023 Score=51.93 Aligned_cols=39 Identities=21% Similarity=0.384 Sum_probs=33.3
Q ss_pred CceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccCh
Q 011146 62 NRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDL 124 (492)
Q Consensus 62 k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~ 124 (492)
-+|.|. |++ ....+.+|.++|. ++++|.|..| +..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~-------------g~~~YrC~~C-------~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVR-------------GEAVYRCRRC-------GETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhc-------------CCccEECCCC-------CceeEEe
Confidence 479998 998 7778999999998 8999999999 7776543
No 49
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.13 E-value=0.011 Score=37.10 Aligned_cols=22 Identities=32% Similarity=0.844 Sum_probs=19.1
Q ss_pred eecccccccccChhhHHHHHHh
Q 011146 64 FLCEICNKGFQRDQNLQLHRRG 85 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~ 85 (492)
|.|++|++.|.+...|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 7899999999999999888764
No 50
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.29 E-value=0.052 Score=32.89 Aligned_cols=23 Identities=26% Similarity=0.595 Sum_probs=18.7
Q ss_pred eecccccccccChhhHHHHHHhcC
Q 011146 64 FLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
|+|+.|+.... +..|..|++.|+
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 79999999888 889999998864
No 51
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=93.20 E-value=0.043 Score=63.66 Aligned_cols=92 Identities=12% Similarity=0.101 Sum_probs=50.0
Q ss_pred eecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccC
Q 011146 64 FLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCE 143 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~ 143 (492)
+.|.+|++.|.....+. |+- -..+|.|+.| ...|.....|..|. .
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~----------------~~~~~~~~~~-------~~~~~~~~~l~~~~-----------~ 1305 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLD----------------VTHRYLCRQC-------KMAFDGEAPLTAHQ-----------R 1305 (1406)
T ss_pred chhhhccccccCcccee-ecc----------------cchhHHHHHH-------HhhhcchhHHHHHH-----------H
Confidence 66666666666655554 331 2345666666 66666666666665 1
Q ss_pred cCccccCChHHHHHhhhhcCC-Cceeec-CCCccCChhHHHHHHhHhcCc
Q 011146 144 KCSKKYAVQSDWKAHSKICGT-REYRCD-CGTLFSRKDSFITHRAFCDAL 191 (492)
Q Consensus 144 ~C~k~F~~~~~L~~H~~~~~~-kp~~C~-C~k~F~~~~~L~~H~~~h~~~ 191 (492)
.|-+.|.....+.-|.-.+-. +.| |. |...|+....|..||+..+..
T Consensus 1306 k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1306 KFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAHR 1354 (1406)
T ss_pred HHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhhc
Confidence 222334444444444333222 334 76 777777777777777655443
No 52
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.16 E-value=0.055 Score=32.99 Aligned_cols=21 Identities=19% Similarity=0.730 Sum_probs=12.5
Q ss_pred cccCcCccccCChHHHHHhhh
Q 011146 140 WKCEKCSKKYAVQSDWKAHSK 160 (492)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~ 160 (492)
|.|++|++.|.....|+.|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 456666666666666666654
No 53
>smart00355 ZnF_C2H2 zinc finger.
Probab=93.01 E-value=0.066 Score=32.23 Aligned_cols=20 Identities=30% Similarity=0.753 Sum_probs=9.8
Q ss_pred ccCcCccccCChHHHHHhhh
Q 011146 141 KCEKCSKKYAVQSDWKAHSK 160 (492)
Q Consensus 141 ~C~~C~k~F~~~~~L~~H~~ 160 (492)
+|..|++.|.....|..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 44445555555545544444
No 54
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=92.73 E-value=0.097 Score=31.66 Aligned_cols=22 Identities=27% Similarity=0.498 Sum_probs=11.2
Q ss_pred eeec-CCCccCChhHHHHHHhHhc
Q 011146 167 YRCD-CGTLFSRKDSFITHRAFCD 189 (492)
Q Consensus 167 ~~C~-C~k~F~~~~~L~~H~~~h~ 189 (492)
|+|. |+.... +..|.+|++.+|
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 655555 555666655544
No 55
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=92.63 E-value=0.06 Score=54.82 Aligned_cols=48 Identities=23% Similarity=0.304 Sum_probs=38.3
Q ss_pred ccccCcCccccCChHHHHHhhhh-cCC-----------------------Cceeec-CC---CccCChhHHHHHHh
Q 011146 139 KWKCEKCSKKYAVQSDWKAHSKI-CGT-----------------------REYRCD-CG---TLFSRKDSFITHRA 186 (492)
Q Consensus 139 p~~C~~C~k~F~~~~~L~~H~~~-~~~-----------------------kp~~C~-C~---k~F~~~~~L~~H~~ 186 (492)
|-.|-.|++.|..-..-..||.. ||- +-|.|- |. +.|.+-...+.||.
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 56788888888888888888876 542 238898 98 99999999999986
No 56
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=92.44 E-value=0.076 Score=33.22 Aligned_cols=22 Identities=27% Similarity=0.688 Sum_probs=16.5
Q ss_pred cccCcCccccCChHHHHHhhhh
Q 011146 140 WKCEKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~ 161 (492)
|.|..|++.|.....|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6677777778777777777764
No 57
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.04 E-value=0.054 Score=50.46 Aligned_cols=82 Identities=21% Similarity=0.483 Sum_probs=66.8
Q ss_pred CcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccccCChHHHHHhhhh-c----------CCCceee
Q 011146 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI-C----------GTREYRC 169 (492)
Q Consensus 101 ~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~-~----------~~kp~~C 169 (492)
+.+.|.|.+-+| -+.|.....+..|..+-++. .|.+|.+.|.+...|..|+.. | |.-.|.|
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-----CQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQC 147 (253)
T ss_pred ccccccccccch-----HHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHH
Confidence 446688998877 89999999999998774443 699999999999999999754 3 4456999
Q ss_pred --c-CCCccCChhHHHHHHhHhcC
Q 011146 170 --D-CGTLFSRKDSFITHRAFCDA 190 (492)
Q Consensus 170 --~-C~k~F~~~~~L~~H~~~h~~ 190 (492)
+ |+..|.+...-+.|+-..|.
T Consensus 148 lvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 148 LVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHhhhhhhhhhhhhhhHHHHhcc
Confidence 5 99999999999999866554
No 58
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=91.82 E-value=0.056 Score=51.46 Aligned_cols=49 Identities=22% Similarity=0.345 Sum_probs=42.2
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHHHH-HHhcC
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLH-RRGHN 87 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~~H-~r~H~ 87 (492)
+-=|=.|.+.|.++..|..|.|. |-|+|.||.|...+---|.+| |.+|.
T Consensus 10 kpwcwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 10 KPWCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred Cceeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhhh
Confidence 44588999999999999999865 679999999998888889999 67774
No 59
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.73 E-value=0.18 Score=50.55 Aligned_cols=78 Identities=21% Similarity=0.373 Sum_probs=58.5
Q ss_pred ecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCc
Q 011146 65 LCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEK 144 (492)
Q Consensus 65 ~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~ 144 (492)
.|..|.+.|.....|.+|+|.-+ ++-|+|+.-+- .-..-|.+...|..|++.-+ |.|.+
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H--------------E~ChICD~v~p---~~~QYFK~Y~~Le~HF~~~h----y~ct~ 280 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH--------------EACHICDMVGP---IRYQYFKSYEDLEAHFRNAH----YCCTF 280 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh--------------hhhhhhhccCc---cchhhhhCHHHHHHHhhcCc----eEEEE
Confidence 59999999999999999998764 67777776421 11345888899999998744 77744
Q ss_pred --Cc----cccCChHHHHHhhhh-cC
Q 011146 145 --CS----KKYAVQSDWKAHSKI-CG 163 (492)
Q Consensus 145 --C~----k~F~~~~~L~~H~~~-~~ 163 (492)
|- ..|.....|..|+.. |+
T Consensus 281 qtc~~~k~~vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 281 QTCRVGKCYVFPYHTELLEHLTRFHK 306 (493)
T ss_pred EEEecCcEEEeccHHHHHHHHHHHhh
Confidence 32 368888899999866 54
No 60
>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=91.25 E-value=0.14 Score=33.92 Aligned_cols=23 Identities=30% Similarity=0.837 Sum_probs=20.7
Q ss_pred ceecccccccccChhhHHHHHHh
Q 011146 63 RFLCEICNKGFQRDQNLQLHRRG 85 (492)
Q Consensus 63 ~~~C~~Cgk~F~~~~~L~~H~r~ 85 (492)
+|.|++|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58999999999999999999754
No 61
>KOG1883 consensus Cofactor required for Sp1 transcriptional activation, subunit 3 [Transcription]
Probab=91.04 E-value=0.16 Score=58.05 Aligned_cols=40 Identities=20% Similarity=0.169 Sum_probs=25.9
Q ss_pred hhHHHHHHHHhhhhhhhccHHHHHHHHHHhcCCcCCCCCC
Q 011146 335 GQQQQQQQQQQQQGLAHMSATALLQKAAQMGSTRSNANNS 374 (492)
Q Consensus 335 QQQQQQQQQQQQQq~q~qq~~al~Qq~~Qmg~t~~~~~~~ 374 (492)
|+|+++|+|++||+..++.++++++|..+||...+++.+-
T Consensus 1430 q~q~t~q~q~~Qqq~~~~~qqqlqhq~~n~~~vQt~s~p~ 1469 (1517)
T KOG1883|consen 1430 QMQDTSQHQTIQQQSNHPTQQQLQHQIPNMSMVQTMSPPY 1469 (1517)
T ss_pred hhhhhhHHHHHHHHhcchHHHHHHHhccccceeeecCCCC
Confidence 3344444444444455666678889999999888877444
No 62
>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=90.83 E-value=0.14 Score=43.61 Aligned_cols=32 Identities=22% Similarity=0.392 Sum_probs=27.4
Q ss_pred CCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccCh
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~ 76 (492)
.||.|..||+.|.+ .++.|..|+.||..|.-.
T Consensus 8 tKR~Cp~CG~kFYD-----------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYD-----------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhcc-----------CCCCCccCCCCCCccCcc
Confidence 38999999999997 244789999999999876
No 63
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=90.62 E-value=0.18 Score=31.07 Aligned_cols=21 Identities=29% Similarity=0.672 Sum_probs=17.0
Q ss_pred eecccccccccChhhHHHHHHh
Q 011146 64 FLCEICNKGFQRDQNLQLHRRG 85 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~ 85 (492)
..|++||+.| ....|..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 5799999999 66778888753
No 64
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=88.64 E-value=0.42 Score=48.06 Aligned_cols=49 Identities=22% Similarity=0.356 Sum_probs=35.9
Q ss_pred cccCcCccccCChHHHHHhhhh-cC---------------------------CCceeec-CCCccCChhHHHHHHhHh
Q 011146 140 WKCEKCSKKYAVQSDWKAHSKI-CG---------------------------TREYRCD-CGTLFSRKDSFITHRAFC 188 (492)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~-~~---------------------------~kp~~C~-C~k~F~~~~~L~~H~~~h 188 (492)
.+|-.|...+.....|..||++ |. .+.-.|- |...|-....|..||.-+
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 4788888777777888888776 42 0113555 889999999999998643
No 65
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=87.28 E-value=0.18 Score=48.05 Aligned_cols=44 Identities=25% Similarity=0.442 Sum_probs=31.4
Q ss_pred eecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhh
Q 011146 64 FLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHF 131 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~ 131 (492)
-.|=+|++.|....-|..|.+. |.|+|.+| .|.+.+--.|..|-
T Consensus 11 pwcwycnrefddekiliqhqka-----------------khfkchic-------hkkl~sgpglsihc 54 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKA-----------------KHFKCHIC-------HKKLFSGPGLSIHC 54 (341)
T ss_pred ceeeecccccchhhhhhhhhhh-----------------ccceeeee-------hhhhccCCCceeeh
Confidence 3688888888888888888754 34788887 66666666666663
No 66
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=86.67 E-value=0.51 Score=29.08 Aligned_cols=19 Identities=26% Similarity=0.676 Sum_probs=10.0
Q ss_pred ccCcCccccCChHHHHHhhh
Q 011146 141 KCEKCSKKYAVQSDWKAHSK 160 (492)
Q Consensus 141 ~C~~C~k~F~~~~~L~~H~~ 160 (492)
.|++|++.| ..+.|.+|++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 455555555 3445555544
No 67
>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=85.71 E-value=0.55 Score=30.92 Aligned_cols=23 Identities=22% Similarity=0.416 Sum_probs=16.4
Q ss_pred ccccCcCccccCChHHHHHhhhh
Q 011146 139 KWKCEKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 139 p~~C~~C~k~F~~~~~L~~H~~~ 161 (492)
+|.|++|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46677777777777777777654
No 68
>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=85.07 E-value=0.57 Score=40.68 Aligned_cols=36 Identities=17% Similarity=0.176 Sum_probs=28.7
Q ss_pred CCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHH
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQ 80 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~ 80 (492)
.||.|..||+.|.+ .++.|..|+.||..|.....++
T Consensus 8 tKr~Cp~cg~kFYD-----------Lnk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 8 TKRICPNTGSKFYD-----------LNRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred ccccCCCcCccccc-----------cCCCCccCCCcCCccCcchhhc
Confidence 38999999999997 3447899999999987664433
No 69
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=83.12 E-value=1.7 Score=43.81 Aligned_cols=26 Identities=12% Similarity=0.341 Sum_probs=21.3
Q ss_pred eeec-CCCccCChhHHHHHHhHhcCcc
Q 011146 167 YRCD-CGTLFSRKDSFITHRAFCDALA 192 (492)
Q Consensus 167 ~~C~-C~k~F~~~~~L~~H~~~h~~~~ 192 (492)
..|- |...+-....|.+||+..|...
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~D 306 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFD 306 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhh
Confidence 4898 9988888899999999877543
No 70
>KOG4407 consensus Predicted Rho GTPase-activating protein [General function prediction only]
Probab=82.70 E-value=0.6 Score=54.33 Aligned_cols=13 Identities=69% Similarity=0.882 Sum_probs=5.1
Q ss_pred CCCcchhhHHHHH
Q 011146 329 YPSNQSGQQQQQQ 341 (492)
Q Consensus 329 ~qqQQQQQQQQQQ 341 (492)
|++||||||||||
T Consensus 322 ~~~~~Q~q~qqq~ 334 (1973)
T KOG4407|consen 322 YPQQQQQQQQQQQ 334 (1973)
T ss_pred chhhhhhhhhhhc
Confidence 3344444333333
No 71
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=82.00 E-value=0.93 Score=43.88 Aligned_cols=49 Identities=22% Similarity=0.556 Sum_probs=35.6
Q ss_pred cccCcCccccCChHHHHHhhhhcCCCceeec-CCCccCChhHHHHHHhHhcC
Q 011146 140 WKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFSRKDSFITHRAFCDA 190 (492)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~F~~~~~L~~H~~~h~~ 190 (492)
|.|.+||....- ..+.+|+..+...-|.|- |++.|-+ ..+..|...-..
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCITE 53 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCITE 53 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccCCeeEEeeccccccc-chhhhhhhhcch
Confidence 678888876553 466678877555788886 9988877 777888765543
No 72
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=81.94 E-value=1.3 Score=45.58 Aligned_cols=121 Identities=14% Similarity=0.288 Sum_probs=69.2
Q ss_pred Cceec--ccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCC--
Q 011146 62 NRFLC--EICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGE-- 137 (492)
Q Consensus 62 k~~~C--~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~e-- 137 (492)
.-|.| +.|+..|-.+....+|..+|.+...... ..++.-...|.|-.-+| .+ +-+....|-..|+..
T Consensus 270 Ehyhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~-dgf~rfs~syhC~~~~C-----~k---sTsdV~~h~nFht~~~n 340 (480)
T KOG4377|consen 270 EHYHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLI-DGFHRFSNSYHCTGQIC-----EK---STSDVLLHDNFHTDKRN 340 (480)
T ss_pred hhhcccCccccccccchhhhHHHHHHHhhcccccc-cchhhcCccchhhhccc-----Cc---ccccccccCcccccccc
Confidence 34778 4699988889999999999862111100 00011112245544333 66 334455566656431
Q ss_pred -----cccccCcCc--cccCChHHHHHhhhh-cC------------------------CCceeec---CCCccCChhHHH
Q 011146 138 -----KKWKCEKCS--KKYAVQSDWKAHSKI-CG------------------------TREYRCD---CGTLFSRKDSFI 182 (492)
Q Consensus 138 -----kp~~C~~C~--k~F~~~~~L~~H~~~-~~------------------------~kp~~C~---C~k~F~~~~~L~ 182 (492)
.-|.|.-|+ ..|.....-..|.+- .+ -..|.|. |+.+|...+.+.
T Consensus 341 ~GfrrthfhC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~ 420 (480)
T KOG4377|consen 341 NGFRRTHFHCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMA 420 (480)
T ss_pred CceecceeEEeccCCccccccccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhh
Confidence 236676655 445433333333221 00 0127884 999999999999
Q ss_pred HHHhHhcCc
Q 011146 183 THRAFCDAL 191 (492)
Q Consensus 183 ~H~~~h~~~ 191 (492)
.|.|+|.+.
T Consensus 421 shkrkheRq 429 (480)
T KOG4377|consen 421 SHKRKHERQ 429 (480)
T ss_pred hhhhhhhhh
Confidence 999999865
No 73
>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=81.44 E-value=0.65 Score=30.61 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=17.7
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccc
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk 71 (492)
.|+|.+||-.+.... .++.|++||.
T Consensus 1 ~~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCc------------CCCcCcCCCC
Confidence 377888887654422 6788888876
No 74
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=81.14 E-value=1 Score=48.75 Aligned_cols=29 Identities=17% Similarity=0.331 Sum_probs=24.9
Q ss_pred CCCCceecccccccccChhhHHHHHHhcC
Q 011146 59 MATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 59 ~~~k~~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
-..++-.|..||++|.+......||-.|.
T Consensus 414 y~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 414 YKDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred ccCCcchhcccccccccchhhhhHhhhhh
Confidence 45667899999999999999888888885
No 75
>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=80.96 E-value=2.4 Score=36.02 Aligned_cols=24 Identities=29% Similarity=0.592 Sum_probs=22.2
Q ss_pred eee----c-CCCccCChhHHHHHHhHhcC
Q 011146 167 YRC----D-CGTLFSRKDSFITHRAFCDA 190 (492)
Q Consensus 167 ~~C----~-C~k~F~~~~~L~~H~~~h~~ 190 (492)
|.| . |++.+.+...+.+|.+.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 8 99999999999999998874
No 76
>KOG3648 consensus Golgi apparatus protein (cysteine-rich fibroblast growth factor receptor) [Intracellular trafficking, secretion, and vesicular transport]
Probab=80.07 E-value=0.66 Score=50.23 Aligned_cols=20 Identities=55% Similarity=0.283 Sum_probs=8.4
Q ss_pred hhhHHHHHHHHhhhhhhhcc
Q 011146 334 SGQQQQQQQQQQQQGLAHMS 353 (492)
Q Consensus 334 QQQQQQQQQQQQQQq~q~qq 353 (492)
|||||||||||+-+|.+..+
T Consensus 73 ~~~~~~~~~~~~~~P~~~~~ 92 (1179)
T KOG3648|consen 73 QQQQQQQQQQQQLQPPQPPF 92 (1179)
T ss_pred HHHHHHHHHHHhhCCCCCCc
Confidence 44444444444444444433
No 77
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=79.56 E-value=3.2 Score=35.48 Aligned_cols=80 Identities=16% Similarity=0.165 Sum_probs=52.1
Q ss_pred CCCCCCCCCCCCcCCCCCC---------CCCCCC---CCCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccc
Q 011146 6 HGLSVPSTLKGFVQEPNSN---------PNPNPS---SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGF 73 (492)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~---------~~~~~~---~~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F 73 (492)
-|..|+.|+-..+....+. +..... .....+.|--|.+.|.+..... ........+|+|+.|...|
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~--~~~~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSP--FDELKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccc--ccccccccceeCCCCCCcc
Confidence 3678888887766543321 111111 1222356999999998653211 1113445689999999999
Q ss_pred cChhhHHHHHHhcC
Q 011146 74 QRDQNLQLHRRGHN 87 (492)
Q Consensus 74 ~~~~~L~~H~r~H~ 87 (492)
--.-+...|...|.
T Consensus 92 C~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 92 CVDCDVFVHESLHC 105 (112)
T ss_pred ccccchhhhhhccC
Confidence 99999999988885
No 78
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=78.76 E-value=0.73 Score=41.83 Aligned_cols=14 Identities=29% Similarity=0.477 Sum_probs=7.4
Q ss_pred eecccccccccChh
Q 011146 64 FLCEICNKGFQRDQ 77 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~ 77 (492)
|.|..||++|.+..
T Consensus 29 ~~c~~c~~~f~~~e 42 (154)
T PRK00464 29 RECLACGKRFTTFE 42 (154)
T ss_pred eeccccCCcceEeE
Confidence 55555555555443
No 79
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=77.83 E-value=0.86 Score=43.76 Aligned_cols=43 Identities=14% Similarity=0.162 Sum_probs=27.0
Q ss_pred CCCCCCCCCCCCCChhHhhhCcccc----------CCCCc-----eecccccccccCh
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPKSL----------MATNR-----FLCEICNKGFQRD 76 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~~h----------~~~k~-----~~C~~Cgk~F~~~ 76 (492)
++.+|++|++.|..+.+.....+.- .+..| ..|+.||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 4566777777777666555554431 12222 4699999988765
No 80
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=77.18 E-value=1.1 Score=33.07 Aligned_cols=27 Identities=22% Similarity=0.580 Sum_probs=15.8
Q ss_pred CCCcccccCcCccccCChHHHHHhhhh
Q 011146 135 HGEKKWKCEKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 135 ~~ekp~~C~~C~k~F~~~~~L~~H~~~ 161 (492)
.||.-++|+-|+..|....++.+|...
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 455556666666666666666666554
No 81
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=77.15 E-value=1.1 Score=40.70 Aligned_cols=48 Identities=17% Similarity=0.128 Sum_probs=32.5
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHhhhCc
Q 011146 8 LSVPSTLKGFVQEPNSNPNPNPSSNQLKRKRNLPGTPDPDAEVIALSP 55 (492)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~cg~~~~~~~~l~~h~ 55 (492)
+.||.|+..+.........+....-++.|+|..||+.|...+.+..=+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 479999987765544443333333445599999999998876655443
No 82
>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=75.30 E-value=1.8 Score=28.50 Aligned_cols=10 Identities=30% Similarity=1.076 Sum_probs=7.7
Q ss_pred cccccCcCcc
Q 011146 138 KKWKCEKCSK 147 (492)
Q Consensus 138 kp~~C~~C~k 147 (492)
.++.|++|+.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 6788888875
No 83
>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=74.77 E-value=1.8 Score=36.94 Aligned_cols=30 Identities=20% Similarity=0.393 Sum_probs=22.7
Q ss_pred eecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccCh
Q 011146 64 FLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDL 124 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~ 124 (492)
..|+.||++|+.. ++.|.+|+.| |..|.-.
T Consensus 10 R~Cp~CG~kFYDL------------------------nk~PivCP~C-------G~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL------------------------NKDPIVCPKC-------GTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC------------------------CCCCccCCCC-------CCccCcc
Confidence 5899999999863 4578888888 7776544
No 84
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=73.80 E-value=1.3 Score=41.57 Aligned_cols=78 Identities=22% Similarity=0.435 Sum_probs=61.0
Q ss_pred CCceeccc--ccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcc-cC--
Q 011146 61 TNRFLCEI--CNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSR-KH-- 135 (492)
Q Consensus 61 ~k~~~C~~--Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~-H~-- 135 (492)
.+.|.|.+ |-..|........|..+-+ + -.|.+| .|.|.+..-|..|+.- |.
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY~~~h-------------~---~sCs~C-------~r~~Pt~hLLd~HI~E~HDs~ 133 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHYHTLH-------------G---NSCSFC-------KRAFPTGHLLDAHILEWHDSL 133 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhhhhcc-------------c---chhHHH-------HHhCCchhhhhHHHHHHHHHH
Confidence 45688987 8888888887777754332 1 378888 9999999999999865 42
Q ss_pred -------CCccccc--CcCccccCChHHHHHhhhh
Q 011146 136 -------GEKKWKC--EKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 136 -------~ekp~~C--~~C~k~F~~~~~L~~H~~~ 161 (492)
|..-|.| ..|+..|.+....+.|+..
T Consensus 134 Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 134 FQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred HHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 4456999 4599999999999999877
No 85
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=73.52 E-value=1 Score=43.25 Aligned_cols=12 Identities=25% Similarity=0.678 Sum_probs=8.0
Q ss_pred eeec-CCCccCCh
Q 011146 167 YRCD-CGTLFSRK 178 (492)
Q Consensus 167 ~~C~-C~k~F~~~ 178 (492)
..|+ ||.+|...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5777 87776544
No 86
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=73.12 E-value=1.6 Score=32.17 Aligned_cols=28 Identities=32% Similarity=0.714 Sum_probs=19.0
Q ss_pred cCCCceeec-CCCccCChhHHHHHHhHhc
Q 011146 162 CGTREYRCD-CGTLFSRKDSFITHRAFCD 189 (492)
Q Consensus 162 ~~~kp~~C~-C~k~F~~~~~L~~H~~~h~ 189 (492)
-||.-++|+ |+..|.+...+.+|....|
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 456667777 7777777777777765544
No 87
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.32 E-value=2 Score=36.22 Aligned_cols=31 Identities=19% Similarity=0.260 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccCh
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~ 76 (492)
|+.|..||+.|.+ ....|..|++|||.|.+.
T Consensus 9 KridPetg~KFYD-----------LNrdPiVsPytG~s~P~s 39 (129)
T COG4530 9 KRIDPETGKKFYD-----------LNRDPIVSPYTGKSYPRS 39 (129)
T ss_pred cccCccccchhhc-----------cCCCccccCcccccchHH
Confidence 7889999999986 245689999999999543
No 88
>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=71.83 E-value=3.3 Score=28.95 Aligned_cols=25 Identities=24% Similarity=0.503 Sum_probs=17.0
Q ss_pred CCCceecccccccccCh----hhHHHHHH
Q 011146 60 ATNRFLCEICNKGFQRD----QNLQLHRR 84 (492)
Q Consensus 60 ~~k~~~C~~Cgk~F~~~----~~L~~H~r 84 (492)
+....+|.+|++.+... ..|..|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 45678999999998875 78999984
No 89
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=69.79 E-value=5 Score=46.71 Aligned_cols=12 Identities=25% Similarity=0.130 Sum_probs=5.3
Q ss_pred HHHHHHHHhcCC
Q 011146 356 ALLQKAAQMGST 367 (492)
Q Consensus 356 al~Qq~~Qmg~t 367 (492)
+++|+.+|-.+-
T Consensus 1881 q~~~~~~q~~sq 1892 (2131)
T KOG4369|consen 1881 QFQQQYQQHQSQ 1892 (2131)
T ss_pred HHHHHHhcccCC
Confidence 444444444433
No 90
>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=69.44 E-value=1.9 Score=28.61 Aligned_cols=25 Identities=16% Similarity=0.161 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccc
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk 71 (492)
.|+|.+||..+... +.|..|++||.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 57888888764432 24568888886
No 91
>KOG4407 consensus Predicted Rho GTPase-activating protein [General function prediction only]
Probab=68.68 E-value=2.1 Score=50.20 Aligned_cols=12 Identities=25% Similarity=0.091 Sum_probs=5.2
Q ss_pred cccCCCcchhhH
Q 011146 326 TSLYPSNQSGQQ 337 (492)
Q Consensus 326 ~~~~qqQQQQQQ 337 (492)
-++++|||||||
T Consensus 322 ~~~~~Q~q~qqq 333 (1973)
T KOG4407|consen 322 YPQQQQQQQQQQ 333 (1973)
T ss_pred chhhhhhhhhhh
Confidence 344444444433
No 92
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=67.73 E-value=3 Score=33.78 Aligned_cols=13 Identities=54% Similarity=1.262 Sum_probs=9.1
Q ss_pred ccccCcCccccCC
Q 011146 139 KWKCEKCSKKYAV 151 (492)
Q Consensus 139 p~~C~~C~k~F~~ 151 (492)
-|.|..|++.|.-
T Consensus 53 IW~C~kCg~~fAG 65 (89)
T COG1997 53 IWKCRKCGAKFAG 65 (89)
T ss_pred eEEcCCCCCeecc
Confidence 3777777777754
No 93
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=66.34 E-value=7 Score=33.43 Aligned_cols=80 Identities=15% Similarity=0.236 Sum_probs=52.7
Q ss_pred cccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcc------------cccCcCccccCChHHHHHhhhhcCCCceee
Q 011146 102 KKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKK------------WKCEKCSKKYAVQSDWKAHSKICGTREYRC 169 (492)
Q Consensus 102 ~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp------------~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C 169 (492)
+-|..|++| +-......+|.+-...--..++ ..|--|.+.|........- .......|.|
T Consensus 13 ~LP~~CpiC-------gLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~-~~~~~~~y~C 84 (112)
T TIGR00622 13 ELPVECPIC-------GLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD-ELKDSHRYVC 84 (112)
T ss_pred CCCCcCCcC-------CCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccccc-ccccccceeC
Confidence 467889888 8888888877764321111222 2499999999765321110 0133457999
Q ss_pred c-CCCccCChhHHHHHHhHhc
Q 011146 170 D-CGTLFSRKDSFITHRAFCD 189 (492)
Q Consensus 170 ~-C~k~F~~~~~L~~H~~~h~ 189 (492)
+ |...|-..=..-.|..+|.
T Consensus 85 ~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 85 AVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred CCCCCccccccchhhhhhccC
Confidence 9 9999998888888887774
No 94
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=65.77 E-value=1.7 Score=44.02 Aligned_cols=28 Identities=32% Similarity=0.618 Sum_probs=22.0
Q ss_pred CcccccCCCCCCCCCCCCCcccChhhHHhhhcc
Q 011146 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSR 133 (492)
Q Consensus 101 ~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~ 133 (492)
-.++|+|.+.+| .+.+....+|+.|...
T Consensus 346 ~~~~~~~~vp~~-----~~~~~n~ng~~~~~~~ 373 (442)
T KOG4124|consen 346 VDKPYKCPVPNC-----DKAYKNQNGLKYHKLH 373 (442)
T ss_pred ecCCCCCCCCcc-----hhhcccCcceeecccc
Confidence 457889988766 8888888888887655
No 95
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=65.58 E-value=3.8 Score=46.33 Aligned_cols=10 Identities=30% Similarity=0.561 Sum_probs=6.2
Q ss_pred eccccccccc
Q 011146 65 LCEICNKGFQ 74 (492)
Q Consensus 65 ~C~~Cgk~F~ 74 (492)
.|..||..|.
T Consensus 437 ~C~~Cg~v~~ 446 (730)
T COG1198 437 LCRDCGYIAE 446 (730)
T ss_pred ecccCCCccc
Confidence 4777766544
No 96
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=65.01 E-value=2.5 Score=33.22 Aligned_cols=41 Identities=10% Similarity=0.096 Sum_probs=26.9
Q ss_pred CCCCCCCCCCCChhHhhhCccccCCCCceecc--cccccccChhh
Q 011146 36 RKRNLPGTPDPDAEVIALSPKSLMATNRFLCE--ICNKGFQRDQN 78 (492)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~--~Cgk~F~~~~~ 78 (492)
.+|..||....-+..-..+.. ..++.|.|. .||.+|.....
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~--~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT--TKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcChh--hheeeeecCCCCCCCEEEEEEE
Confidence 468888887644333333322 556778898 89999987654
No 97
>PF02166 Androgen_recep: Androgen receptor; InterPro: IPR001103 Steroid or nuclear hormone receptors (NRs) constitute an important super-family of transcription regulators that are involved in diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members include the steroid hormone receptors and receptors for thyroid hormone, retinoids and 1,25-dihydroxy-vitamin D3. The proteins function as dimeric molecules in the nucleus to regulate the transcription of target genes in a ligand-responsive manner [, ]. NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes and hormone resistance syndromes. Many do not yet have a defined ligand and are accordingly termed "orphan" receptors. More than 300 NRs have been described to date and a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members. The androgen receptor (AR) consists of 3 functional and structural domains: an N-terminal (modulatory) domain; a DNA binding domain (IPR001628 from INTERPRO) that mediates specific binding to target DNA sequences (ligand-responsive elements); and a hormone binding domain. The N-terminal domain (NTD) is unique to the androgen receptors and spans approximately the first 530 residues; the highly-conserved DNA-binding domain is smaller (around 65 residues) and occupies the central portion of the protein; and the hormone ligand binding domain (LBD) lies at the receptor C terminus. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity. The LBDs of steroid hormone receptors fold into 12 helices that form a ligand-binding pocket. When an agonist is bound, helix 12 folds over the pocket to enclose the ligand []. When an antagonist is unbound, helix 12 is positioned away from the pocket in a way that interferes with the binding of coactivators to a groove in the hormone-binding domain formed after ligand binding. In AR, ligand binding that induces folding of helix 12 to overlie the pocket discloses a groove that binds a region of the NTD. Coactivator molecules can also bind to this groove, but the predominant site for coactivator binding to AR is in the NTD. AR ligand resides in a pocket and primarily contacts helices 4, 5, and 10. The DNA-binding region includes eight cysteine residues that form two coordination complexes, each composed of four cysteines and a Zn2+ ion. These two zinc fingers form the structure that binds to the major groove of DNA. The second zinc finger stabilises the binding complex by hydrophobic interactions with the first finger and contributes to specificity of receptor DNA binding. It is also necessary for receptor dimerisation that occurs during DNA binding Defects in the androgen receptor cause testicular feminisation syndrome, androgen insensibility syndrome (AIS) [, ]. AIS may be complete (CAIS), where external genitalia are phenotypically female; partial (PAIS), where genitalia are substantively ambiguous; or mild (MAIS), where external genitalia are normal male, or nearly so. Defects in the receptor also cause X-linked spinal and bulbar muscular atrophy (also known as Kennedy's disease).; GO: 0003677 DNA binding, 0004882 androgen receptor activity, 0005496 steroid binding, 0006355 regulation of transcription, DNA-dependent, 0030521 androgen receptor signaling pathway, 0005634 nucleus; PDB: 1XOW_B 2Q7K_B 2Q7I_B.
Probab=64.77 E-value=2.1 Score=43.02 Aligned_cols=11 Identities=18% Similarity=0.597 Sum_probs=0.0
Q ss_pred cccccccccCC
Q 011146 377 FGLMSTSFNSF 387 (492)
Q Consensus 377 ~~~~~~~~~~~ 387 (492)
+.|+-.+|..+
T Consensus 138 lSllGptfp~l 148 (423)
T PF02166_consen 138 LSLLGPTFPGL 148 (423)
T ss_dssp -----------
T ss_pred ccccccccccc
Confidence 44554444443
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=64.74 E-value=7.6 Score=32.86 Aligned_cols=24 Identities=17% Similarity=0.474 Sum_probs=21.8
Q ss_pred ccc----CcCccccCChHHHHHhhhh-cC
Q 011146 140 WKC----EKCSKKYAVQSDWKAHSKI-CG 163 (492)
Q Consensus 140 ~~C----~~C~k~F~~~~~L~~H~~~-~~ 163 (492)
|.| ..|++.+.+...+.+|.+. ||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999987 54
No 99
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=62.34 E-value=5.5 Score=26.79 Aligned_cols=32 Identities=31% Similarity=0.803 Sum_probs=17.8
Q ss_pred cccCcCccccCChHHHHHhhhhcCCCceeec-CCCcc
Q 011146 140 WKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLF 175 (492)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~F 175 (492)
..|+.|++.|...+.... -..+..+|. |+..|
T Consensus 3 i~Cp~C~~~y~i~d~~ip----~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP----PKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCC----CCCcEEECCCCCCEe
Confidence 356667766666554321 233456666 76655
No 100
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=61.98 E-value=4.7 Score=36.19 Aligned_cols=47 Identities=17% Similarity=0.075 Sum_probs=36.8
Q ss_pred CCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHhhhCc
Q 011146 9 SVPSTLKGFVQEPNSNPNPNPSSNQLKRKRNLPGTPDPDAEVIALSP 55 (492)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~cg~~~~~~~~l~~h~ 55 (492)
.||.|.......-...+...-..-.+++.|..||+.|.+-+.+..-+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 58999888777766666666667788999999999999877766653
No 101
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=60.59 E-value=5.7 Score=36.47 Aligned_cols=25 Identities=32% Similarity=0.694 Sum_probs=19.8
Q ss_pred ccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCcc
Q 011146 103 KVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSK 147 (492)
Q Consensus 103 k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k 147 (492)
+.|+|++| |+. |-|+-|.+|++||.
T Consensus 133 ~~~vC~vC-------Gy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVC-------GYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCC-------CCc-------------ccCCCCCcCCCCCC
Confidence 37999999 654 45688999999984
No 102
>PRK04023 DNA polymerase II large subunit; Validated
Probab=60.52 E-value=7.9 Score=44.75 Aligned_cols=18 Identities=33% Similarity=0.538 Sum_probs=9.3
Q ss_pred hccccccccccCCCCCCCcHHH
Q 011146 452 RRLTRDFLGVGVESSRPLSQQE 473 (492)
Q Consensus 452 ~~~t~df~g~~~~~~~~~~~~~ 473 (492)
..|-+|-+|= -|-|+-||
T Consensus 1020 sHFlPDl~GN----LRaFsrQ~ 1037 (1121)
T PRK04023 1020 SHFLPDLIGN----LRAFSRQE 1037 (1121)
T ss_pred hccchhhhhh----hhhhcccc
Confidence 4566666552 24555554
No 103
>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=60.50 E-value=3.1 Score=39.86 Aligned_cols=29 Identities=24% Similarity=0.437 Sum_probs=19.1
Q ss_pred CCcccccCcCccccCChHHHHHhhhh-cCC
Q 011146 136 GEKKWKCEKCSKKYAVQSDWKAHSKI-CGT 164 (492)
Q Consensus 136 ~ekp~~C~~C~k~F~~~~~L~~H~~~-~~~ 164 (492)
.+..|.|..|+|.|.-...++.|+.. |.+
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 45568888888888888888888776 543
No 104
>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=60.43 E-value=5.5 Score=26.79 Aligned_cols=14 Identities=21% Similarity=0.719 Sum_probs=7.3
Q ss_pred cccCcCccccCChH
Q 011146 140 WKCEKCSKKYAVQS 153 (492)
Q Consensus 140 ~~C~~C~k~F~~~~ 153 (492)
+.|+.|+..|....
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 34555555555443
No 105
>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=60.31 E-value=6.8 Score=34.63 Aligned_cols=25 Identities=32% Similarity=0.681 Sum_probs=17.2
Q ss_pred CCCceecccccccccChhhHHHHHHhcC
Q 011146 60 ATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 60 ~~k~~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
.+....|-+|||.|+. |++|++.|+
T Consensus 69 ~~d~i~clecGk~~k~---LkrHL~~~~ 93 (132)
T PF05443_consen 69 TPDYIICLECGKKFKT---LKRHLRTHH 93 (132)
T ss_dssp -SS-EE-TBT--EESB---HHHHHHHTT
T ss_pred ccCeeEEccCCcccch---HHHHHHHcc
Confidence 4455899999999986 699999996
No 106
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=58.81 E-value=12 Score=37.34 Aligned_cols=53 Identities=25% Similarity=0.424 Sum_probs=39.9
Q ss_pred CCCCCCCCCCCCCCCChhHhhhCccc-cCCCCceecccccccccChhhHHHHHHhcC
Q 011146 32 NQLKRKRNLPGTPDPDAEVIALSPKS-LMATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 32 ~~~~~~c~~cg~~~~~~~~l~~h~~~-h~~~k~~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
+.+.--|-.|-.+|+.. ..|+-. .+..-+|.|+.|...|....+...|...|.
T Consensus 359 ~~ks~~Cf~CQ~~fp~~---~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 359 NPKSTHCFVCQGPFPKP---PVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred CCCCccceeccCCCCCC---CCCcccccccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 34566799999999863 333322 234557999999999999999999988884
No 107
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=58.44 E-value=6 Score=35.43 Aligned_cols=47 Identities=15% Similarity=-0.041 Sum_probs=32.7
Q ss_pred CCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHhhhCc
Q 011146 9 SVPSTLKGFVQEPNSNPNPNPSSNQLKRKRNLPGTPDPDAEVIALSP 55 (492)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~cg~~~~~~~~l~~h~ 55 (492)
.||.|+..........+...-..-.+++.|..||+.|.+.+.+..-+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 58888776665555555555555567888999998888877666543
No 108
>PHA00626 hypothetical protein
Probab=57.61 E-value=5.7 Score=29.42 Aligned_cols=16 Identities=19% Similarity=0.555 Sum_probs=12.2
Q ss_pred CceecccccccccChh
Q 011146 62 NRFLCEICNKGFQRDQ 77 (492)
Q Consensus 62 k~~~C~~Cgk~F~~~~ 77 (492)
.+|+|+.||..|....
T Consensus 22 nrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 22 DDYVCCDCGYNDSKDA 37 (59)
T ss_pred cceEcCCCCCeechhh
Confidence 4689999998887543
No 109
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=57.34 E-value=5 Score=38.97 Aligned_cols=48 Identities=23% Similarity=0.523 Sum_probs=38.8
Q ss_pred cccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccccCChHHHHHhhhh
Q 011146 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 104 ~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~ 161 (492)
-|.|..| |.... +..+.+|+..-++ .-|.|-.|++.|.+ .+++.|..-
T Consensus 3 ~FtCnvC-------gEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 3 FFTCNVC-------GESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred EEehhhh-------hhhcc-ccchHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 3789988 77654 4568889988777 67999999999998 788899764
No 110
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=56.87 E-value=7.6 Score=27.99 Aligned_cols=26 Identities=38% Similarity=0.695 Sum_probs=20.4
Q ss_pred CceecccccccccCh-----hhHHHHHH-hcC
Q 011146 62 NRFLCEICNKGFQRD-----QNLQLHRR-GHN 87 (492)
Q Consensus 62 k~~~C~~Cgk~F~~~-----~~L~~H~r-~H~ 87 (492)
..-.|.+|++.+... ++|.+|++ .|.
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 346899999998776 58999988 553
No 111
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=56.34 E-value=4.8 Score=29.13 Aligned_cols=29 Identities=17% Similarity=0.173 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCCCChhHhhhCccccCCCCceeccccccc
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~ 72 (492)
..|+|..||+.+. ........+|+.||-.
T Consensus 5 ~~Y~C~~Cg~~~~----------~~~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVE----------LDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeee----------hhhccCceeCCCCCcE
Confidence 4688888888872 1234456788888864
No 112
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=54.52 E-value=12 Score=28.16 Aligned_cols=33 Identities=21% Similarity=0.161 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCCCChhHhhhCccccCCCCceecccccc
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk 71 (492)
.++.|..||+.. +.+-.+--.-..+|+|+.||.
T Consensus 24 ~~F~CPnCG~~~-----I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVI-----IYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCee-----EeechhHHhcCCceECCCCCC
Confidence 467788887641 112222222335789988885
No 113
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=54.11 E-value=9 Score=25.86 Aligned_cols=31 Identities=35% Similarity=0.934 Sum_probs=15.3
Q ss_pred ccCcCccccCChHHHHHhhhhcCCCceeec-CCCcc
Q 011146 141 KCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLF 175 (492)
Q Consensus 141 ~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~F 175 (492)
.|+.|+..|....+... .+.+..+|. |+..|
T Consensus 4 ~CP~C~~~f~v~~~~l~----~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLP----AGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcc----cCCcEEECCCCCcEe
Confidence 46666666655443211 233455665 65555
No 114
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=53.74 E-value=6.9 Score=27.64 Aligned_cols=27 Identities=11% Similarity=0.089 Sum_probs=18.3
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceeccccccc
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~ 72 (492)
.|.|..||..+... ...+.+|+.||-.
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCce
Confidence 47788888876532 2345788888764
No 115
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=51.98 E-value=8 Score=34.74 Aligned_cols=39 Identities=18% Similarity=0.459 Sum_probs=23.6
Q ss_pred ccCcccccCCCCCCCCCCCCCcccChhhHHh-hhcccCCCcccccCcCcccc
Q 011146 99 EVRKKVYICPEKSCVHHDPSRALGDLTGIKK-HFSRKHGEKKWKCEKCSKKY 149 (492)
Q Consensus 99 ~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~-H~~~H~~ekp~~C~~C~k~F 149 (492)
.....-|.|+.| ++.|.....+.. + . +..|.|+.||...
T Consensus 94 e~~~~~Y~Cp~C-------~~~y~~~ea~~~~d----~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 94 ETNNAYYKCPNC-------QSKYTFLEANQLLD----M-DGTFTCPRCGEEL 133 (147)
T ss_pred ccCCcEEECcCC-------CCEeeHHHHHHhcC----C-CCcEECCCCCCEE
Confidence 345567888877 777765544332 2 1 3338888887654
No 116
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=51.67 E-value=7.2 Score=39.62 Aligned_cols=36 Identities=14% Similarity=0.349 Sum_probs=25.6
Q ss_pred CcccccCcCccccCChHHHHHhhhh-cCCCce--eec-CC
Q 011146 137 EKKWKCEKCSKKYAVQSDWKAHSKI-CGTREY--RCD-CG 172 (492)
Q Consensus 137 ekp~~C~~C~k~F~~~~~L~~H~~~-~~~kp~--~C~-C~ 172 (492)
+.-|.|++|+++-.+...|..|... |.+.++ .|. |.
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 4468888888888888888888876 665543 344 54
No 117
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=51.06 E-value=6.8 Score=35.10 Aligned_cols=44 Identities=11% Similarity=0.079 Sum_probs=25.6
Q ss_pred CCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHH
Q 011146 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQ 80 (492)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~ 80 (492)
+|+.||......-.-......-.=.++=+|..||+.|.+.....
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve 45 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAE 45 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecc
Confidence 69999986553211111111111124578999999999876544
No 118
>PRK14873 primosome assembly protein PriA; Provisional
Probab=50.86 E-value=8.5 Score=43.36 Aligned_cols=11 Identities=18% Similarity=0.588 Sum_probs=7.2
Q ss_pred eeccccccccc
Q 011146 64 FLCEICNKGFQ 74 (492)
Q Consensus 64 ~~C~~Cgk~F~ 74 (492)
..|..||..+.
T Consensus 384 l~C~~Cg~~~~ 394 (665)
T PRK14873 384 LACARCRTPAR 394 (665)
T ss_pred eEhhhCcCeeE
Confidence 36877777544
No 119
>KOG3648 consensus Golgi apparatus protein (cysteine-rich fibroblast growth factor receptor) [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.90 E-value=7.9 Score=42.34 Aligned_cols=9 Identities=22% Similarity=0.401 Sum_probs=3.8
Q ss_pred HHHHhhccc
Q 011146 473 ELAKFMNLS 481 (492)
Q Consensus 473 ~~~~~~~~~ 481 (492)
|+.+.|.|+
T Consensus 294 ~iLR~AEm~ 302 (1179)
T KOG3648|consen 294 AILRVAELS 302 (1179)
T ss_pred HHHHHHHcc
Confidence 334444443
No 120
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=49.86 E-value=11 Score=30.57 Aligned_cols=32 Identities=22% Similarity=0.345 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccC
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~ 75 (492)
.+|.|+.|++. . +.+. +..-+.|..||..|.-
T Consensus 34 ~~~~Cp~C~~~-~-------VkR~--a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT-T-------VKRI--ATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc-c-------eeee--ccCeEEcCCCCCeecc
Confidence 47888888875 1 1222 3445888888888763
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=49.75 E-value=12 Score=32.65 Aligned_cols=11 Identities=18% Similarity=0.432 Sum_probs=5.3
Q ss_pred cccCcCccccC
Q 011146 140 WKCEKCSKKYA 150 (492)
Q Consensus 140 ~~C~~C~k~F~ 150 (492)
+.|..||++|.
T Consensus 10 r~Cp~cg~kFY 20 (129)
T TIGR02300 10 RICPNTGSKFY 20 (129)
T ss_pred ccCCCcCcccc
Confidence 34555555443
No 122
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=49.22 E-value=9.1 Score=35.18 Aligned_cols=24 Identities=17% Similarity=0.243 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccc
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk 71 (492)
.|.|.+||-.+ -++-|-+|++||-
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCCC
Confidence 79999999863 3577899999984
No 123
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=49.00 E-value=15 Score=35.61 Aligned_cols=76 Identities=18% Similarity=0.382 Sum_probs=42.7
Q ss_pred ChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccccCChHH
Q 011146 75 RDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKKYAVQSD 154 (492)
Q Consensus 75 ~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~F~~~~~ 154 (492)
+..+|+.+-+.+.. .....++-|.|..| .... ..+.-.....-.|..|.+.|.--..
T Consensus 91 Te~Nlrm~d~a~~~--------~ip~~drqFaC~~C-------d~~W--------wRrvp~rKeVSRCr~C~~rYDPVP~ 147 (278)
T PF15135_consen 91 TEENLRMFDDAQEN--------LIPSVDRQFACSSC-------DHMW--------WRRVPQRKEVSRCRKCRKRYDPVPC 147 (278)
T ss_pred hHHHHHHhhhhhhc--------cccccceeeecccc-------chHH--------HhccCcccccccccccccccCCCcc
Confidence 44567666655531 01124578999998 3210 1122222344678888888764321
Q ss_pred HHHhhhhcCCCceeec-CCCccCC
Q 011146 155 WKAHSKICGTREYRCD-CGTLFSR 177 (492)
Q Consensus 155 L~~H~~~~~~kp~~C~-C~k~F~~ 177 (492)
- +..|...|.|. |+..|+-
T Consensus 148 d----kmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 148 D----KMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred c----cccceeeeecccccccchh
Confidence 1 11566779998 9988863
No 124
>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=48.92 E-value=23 Score=32.01 Aligned_cols=60 Identities=22% Similarity=0.330 Sum_probs=26.4
Q ss_pred CCCCCCCCCCChhHhhhCccccCCCCceecccccccccC------hhhHHHHH-HhcCCCcccccccccccCcccccCCC
Q 011146 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR------DQNLQLHR-RGHNLPWKLKQRTNKEVRKKVYICPE 109 (492)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~------~~~L~~H~-r~H~~~~~~~~~~~~~~~~k~y~C~~ 109 (492)
.|..||-..+ .-..+|..|+|.|-. .+++..|+ +.+++...+ +.....++..++|-.
T Consensus 2 aC~YCG~~~p--------------~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~L--H~~s~lgdt~leCy~ 65 (152)
T PF09416_consen 2 ACAYCGIHDP--------------SCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSL--HPDSPLGDTVLECYN 65 (152)
T ss_dssp S-TTT----C--------------CCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE---TTSTT-S-B---TT
T ss_pred CccccCCCCc--------------ccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceee--CCCCCCCCcEEEEEe
Confidence 5777775433 345799999999975 35677774 333321111 112224667778887
Q ss_pred CCC
Q 011146 110 KSC 112 (492)
Q Consensus 110 C~C 112 (492)
|++
T Consensus 66 Cg~ 68 (152)
T PF09416_consen 66 CGS 68 (152)
T ss_dssp T--
T ss_pred cCC
Confidence 754
No 125
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=48.92 E-value=5.2 Score=44.38 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=23.6
Q ss_pred ceecccccccccChhhHHHHHHhcC
Q 011146 63 RFLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 63 ~~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
-|.|.+|+|.|.....+..||+.|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 5999999999999999999999996
No 126
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=48.73 E-value=15 Score=31.24 Aligned_cols=44 Identities=18% Similarity=0.238 Sum_probs=29.8
Q ss_pred CCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccC
Q 011146 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (492)
Q Consensus 32 ~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~ 75 (492)
...+++|+.||..-.....+..--..-...--|.|..|++.|..
T Consensus 71 a~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred cchhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeeec
Confidence 45689999999875554444333333333456999999999875
No 127
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=48.44 E-value=8.3 Score=34.63 Aligned_cols=44 Identities=16% Similarity=0.148 Sum_probs=25.9
Q ss_pred CCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHH
Q 011146 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQ 80 (492)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~ 80 (492)
+|+.|+......-.-..-.....=.++-.|+.|++.|.+-....
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~E 45 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAE 45 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheee
Confidence 68899887654211111111112235678999999999876433
No 128
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=48.04 E-value=11 Score=33.77 Aligned_cols=40 Identities=20% Similarity=0.194 Sum_probs=28.0
Q ss_pred CCCCCCCCCCCCCCCCChhHhhhCccccCCCCceeccccccccc
Q 011146 31 SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (492)
Q Consensus 31 ~~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~ 74 (492)
....-|.|+.|+..|...+.+..-- . +..|.|+.||....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~d---~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLLD---M-DGTFTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhcC---C-CCcEECCCCCCEEE
Confidence 3455799999999888766655411 1 34499999998754
No 129
>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=47.66 E-value=7 Score=26.55 Aligned_cols=12 Identities=8% Similarity=-0.133 Sum_probs=7.0
Q ss_pred CCCCCCCCCCCC
Q 011146 35 KRKRNLPGTPDP 46 (492)
Q Consensus 35 ~~~c~~cg~~~~ 46 (492)
.|+|..||+.|.
T Consensus 5 ~y~C~~Cg~~fe 16 (41)
T smart00834 5 EYRCEDCGHTFE 16 (41)
T ss_pred EEEcCCCCCEEE
Confidence 356666666554
No 130
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=46.68 E-value=16 Score=37.78 Aligned_cols=51 Identities=20% Similarity=0.274 Sum_probs=43.8
Q ss_pred cccCCCCCCCCCCCCCcccChhhHHhhhcccCCC-----------------------cccccCcCc---cccCChHHHHH
Q 011146 104 VYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGE-----------------------KKWKCEKCS---KKYAVQSDWKA 157 (492)
Q Consensus 104 ~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~e-----------------------kp~~C~~C~---k~F~~~~~L~~ 157 (492)
|-.|-.| ++.+.+...-.+||..+||- .-|.|-.|+ +.|.+....+.
T Consensus 166 Pt~CLfC-------~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~ 238 (390)
T KOG2785|consen 166 PTDCLFC-------DKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRA 238 (390)
T ss_pred Ccceeec-------CCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHH
Confidence 4567777 99999999999999999862 247899999 99999999999
Q ss_pred hhhh
Q 011146 158 HSKI 161 (492)
Q Consensus 158 H~~~ 161 (492)
||..
T Consensus 239 HM~~ 242 (390)
T KOG2785|consen 239 HMRD 242 (390)
T ss_pred HHhh
Confidence 9986
No 131
>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=46.08 E-value=16 Score=30.58 Aligned_cols=41 Identities=10% Similarity=0.114 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccC
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~ 75 (492)
..+|..||.....-..+......-.-..-|.|..|+..|+.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 67899898654322211111111112345899999987753
No 132
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=45.66 E-value=14 Score=22.97 Aligned_cols=11 Identities=27% Similarity=0.791 Sum_probs=7.9
Q ss_pred eeccccccccc
Q 011146 64 FLCEICNKGFQ 74 (492)
Q Consensus 64 ~~C~~Cgk~F~ 74 (492)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 36888887774
No 133
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=45.06 E-value=5.6 Score=40.33 Aligned_cols=25 Identities=20% Similarity=0.739 Sum_probs=20.7
Q ss_pred CCCceeccc--ccccccChhhHHHHHH
Q 011146 60 ATNRFLCEI--CNKGFQRDQNLQLHRR 84 (492)
Q Consensus 60 ~~k~~~C~~--Cgk~F~~~~~L~~H~r 84 (492)
-.++|+|.+ |.|.+.....|+.|..
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~ 372 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKL 372 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccc
Confidence 467899975 9999999989998854
No 134
>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=45.04 E-value=7.4 Score=27.07 Aligned_cols=30 Identities=10% Similarity=0.109 Sum_probs=15.0
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccc
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk 71 (492)
.|+|..||..|.... .. .....-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~------~~-~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ------SI-SEDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEE------Ec-CCCCCCcCCCCCC
Confidence 356666666555311 11 1134456666665
No 135
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=44.85 E-value=15 Score=22.74 Aligned_cols=20 Identities=15% Similarity=0.458 Sum_probs=15.3
Q ss_pred eecccccccccChhhHHHHHH
Q 011146 64 FLCEICNKGFQRDQNLQLHRR 84 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r 84 (492)
..|++|++.+ ....+..|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 4699999998 5567777764
No 136
>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=44.61 E-value=11 Score=36.90 Aligned_cols=19 Identities=16% Similarity=0.424 Sum_probs=10.8
Q ss_pred CCCceeec-CCCccCChhHH
Q 011146 163 GTREYRCD-CGTLFSRKDSF 181 (492)
Q Consensus 163 ~~kp~~C~-C~k~F~~~~~L 181 (492)
..+++.|+ |+.....-..|
T Consensus 206 k~k~~PCPKCg~et~eTkdL 225 (314)
T PF06524_consen 206 KGKPIPCPKCGYETQETKDL 225 (314)
T ss_pred cCCCCCCCCCCCcccccccc
Confidence 34677777 77554443333
No 137
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=44.14 E-value=12 Score=32.95 Aligned_cols=22 Identities=27% Similarity=0.412 Sum_probs=19.5
Q ss_pred ceecccccccccChhhHHHHHHhcC
Q 011146 63 RFLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 63 ~~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
-..|-+|||.|+ .|++|+++|.
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred eEEEeccCcchH---HHHHHHhccc
Confidence 368999999997 5999999987
No 138
>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=43.98 E-value=13 Score=40.54 Aligned_cols=11 Identities=27% Similarity=0.637 Sum_probs=7.3
Q ss_pred eeccccccccc
Q 011146 64 FLCEICNKGFQ 74 (492)
Q Consensus 64 ~~C~~Cgk~F~ 74 (492)
..|..||..+.
T Consensus 214 ~~C~~Cg~~~~ 224 (505)
T TIGR00595 214 LLCRSCGYILC 224 (505)
T ss_pred eEhhhCcCccC
Confidence 36888877644
No 139
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=43.52 E-value=18 Score=27.68 Aligned_cols=34 Identities=21% Similarity=0.306 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhh
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQN 78 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~ 78 (492)
-..|..||..... ....+.|.|+.||..+.+..+
T Consensus 28 Sq~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~rD~n 61 (69)
T PF07282_consen 28 SQTCPRCGHRNKK----------RRSGRVFTCPNCGFEMDRDVN 61 (69)
T ss_pred ccCccCccccccc----------ccccceEEcCCCCCEECcHHH
Confidence 5679999987554 334567999999998776543
No 140
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=43.24 E-value=14 Score=35.82 Aligned_cols=59 Identities=22% Similarity=0.509 Sum_probs=36.7
Q ss_pred CCceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCccc
Q 011146 61 TNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKW 140 (492)
Q Consensus 61 ~k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~ 140 (492)
.+.|.|..|+....+ |+-. .+.+-.|..| .+.|.--- ...-.|.-.|
T Consensus 110 drqFaC~~Cd~~WwR--------rvp~-------------rKeVSRCr~C-------~~rYDPVP-----~dkmwG~aef 156 (278)
T PF15135_consen 110 DRQFACSSCDHMWWR--------RVPQ-------------RKEVSRCRKC-------RKRYDPVP-----CDKMWGIAEF 156 (278)
T ss_pred ceeeeccccchHHHh--------ccCc-------------cccccccccc-------ccccCCCc-----cccccceeee
Confidence 477999999775443 2222 5566788887 66654321 0112244558
Q ss_pred ccCcCccccCCh
Q 011146 141 KCEKCSKKYAVQ 152 (492)
Q Consensus 141 ~C~~C~k~F~~~ 152 (492)
.|..|+..|.--
T Consensus 157 ~C~~C~h~F~G~ 168 (278)
T PF15135_consen 157 HCPKCRHNFRGF 168 (278)
T ss_pred ecccccccchhh
Confidence 999999988743
No 141
>PRK04023 DNA polymerase II large subunit; Validated
Probab=43.15 E-value=27 Score=40.58 Aligned_cols=24 Identities=21% Similarity=0.203 Sum_probs=16.5
Q ss_pred CCCCCCCCCCCCCCChhHhhhCccccCCCCceeccccccc
Q 011146 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (492)
Q Consensus 33 ~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~ 72 (492)
.-.+.|..||... -.+.|+.||..
T Consensus 624 Vg~RfCpsCG~~t----------------~~frCP~CG~~ 647 (1121)
T PRK04023 624 IGRRKCPSCGKET----------------FYRRCPFCGTH 647 (1121)
T ss_pred ccCccCCCCCCcC----------------CcccCCCCCCC
Confidence 3367888888862 23678888775
No 142
>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=43.08 E-value=3.1 Score=41.78 Aligned_cols=35 Identities=20% Similarity=0.448 Sum_probs=14.4
Q ss_pred ccccCcCccccCChHHHHHhhhh-cCCCceeec-CCCc
Q 011146 139 KWKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTL 174 (492)
Q Consensus 139 p~~C~~C~k~F~~~~~L~~H~~~-~~~kp~~C~-C~k~ 174 (492)
..+|..||..-...-.+.. ... -+.+.+.|+ |+.-
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~-~e~~~~~rve~C~~C~~Y 247 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFT-VEGEPAYRVEVCESCGSY 247 (290)
T ss_dssp TTS-TTT---SS-EEE---------SEEEEEETTTTEE
T ss_pred CCCCcCCCCCCCcceeeEe-cCCCCcEEEEECCcccch
Confidence 3579999876433221110 111 345678898 9743
No 143
>PF15269 zf-C2H2_7: Zinc-finger
Probab=42.93 E-value=44 Score=23.64 Aligned_cols=22 Identities=18% Similarity=0.282 Sum_probs=13.9
Q ss_pred eecccccccccChhhHHHHHHh
Q 011146 64 FLCEICNKGFQRDQNLQLHRRG 85 (492)
Q Consensus 64 ~~C~~Cgk~F~~~~~L~~H~r~ 85 (492)
|+|-.|..+-..++.|..||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5666666666666666666654
No 144
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=42.43 E-value=12 Score=34.85 Aligned_cols=33 Identities=12% Similarity=0.423 Sum_probs=19.3
Q ss_pred cCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccc
Q 011146 100 VRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKK 148 (492)
Q Consensus 100 ~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~ 148 (492)
....-|.|+.| ++.|.....+. .-|.|+.||..
T Consensus 113 ~~~~~Y~Cp~C-------~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 113 ENNMFFFCPNC-------HIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred cCCCEEECCCC-------CcEEeHHHHhh---------cCCcCCCCCCC
Confidence 34456677766 66665555542 24777777654
No 145
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=42.15 E-value=9.4 Score=39.52 Aligned_cols=8 Identities=25% Similarity=0.215 Sum_probs=3.3
Q ss_pred hHhhhccC
Q 011146 414 NELIMNSF 421 (492)
Q Consensus 414 ~~~~~~~~ 421 (492)
|.|+.|..
T Consensus 309 ~gmanN~~ 316 (505)
T COG5624 309 NGMANNAQ 316 (505)
T ss_pred hhhhhhhh
Confidence 44444433
No 146
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=41.32 E-value=32 Score=34.82 Aligned_cols=21 Identities=19% Similarity=0.346 Sum_probs=16.1
Q ss_pred CceecccccccccChhhHHHH
Q 011146 62 NRFLCEICNKGFQRDQNLQLH 82 (492)
Q Consensus 62 k~~~C~~Cgk~F~~~~~L~~H 82 (492)
-|.+|++|+-+....-+|-+-
T Consensus 289 LP~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARS 309 (378)
T ss_pred CCccCCccceeEecchHHHHH
Confidence 367899999988877777643
No 147
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=41.15 E-value=24 Score=37.12 Aligned_cols=35 Identities=29% Similarity=0.647 Sum_probs=22.3
Q ss_pred CcccccCcCccccCChHHHHHhhhhcCCCceeec-CCC
Q 011146 137 EKKWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGT 173 (492)
Q Consensus 137 ekp~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k 173 (492)
..-|.|+.|.+.|.....+..= .-.+..|.|. |+-
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~--~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLL--DNETGEFHCENCGG 161 (436)
T ss_pred cccccCCccccchhhhHHHHhh--cccCceEEEecCCC
Confidence 4568888888888766554321 1334568887 873
No 148
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=40.39 E-value=12 Score=25.85 Aligned_cols=37 Identities=16% Similarity=0.315 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCChhHhhhCccccC--CCCceeccccccccc
Q 011146 36 RKRNLPGTPDPDAEVIALSPKSLM--ATNRFLCEICNKGFQ 74 (492)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~--~~k~~~C~~Cgk~F~ 74 (492)
++|+.||..... .+....++-. -..-|+|..|+..|.
T Consensus 1 ~~Cp~C~~~~a~--~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREAT--FFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEE--EEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 357777744322 2222222211 123488988988765
No 149
>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=40.30 E-value=14 Score=33.73 Aligned_cols=33 Identities=15% Similarity=0.493 Sum_probs=22.7
Q ss_pred cCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccc
Q 011146 100 VRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKK 148 (492)
Q Consensus 100 ~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~ 148 (492)
....-|.|+.| +..|.....+. .-|.|+.||..
T Consensus 105 ~~~~~Y~Cp~c-------~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 105 TNNMFFICPNM-------CVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred cCCCeEECCCC-------CcEeeHHHHHH---------cCCcCCCCCCE
Confidence 45566788877 77777666664 24788888765
No 150
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=40.14 E-value=13 Score=38.54 Aligned_cols=9 Identities=0% Similarity=-0.012 Sum_probs=4.1
Q ss_pred CCCcHHHHH
Q 011146 467 RPLSQQELA 475 (492)
Q Consensus 467 ~~~~~~~~~ 475 (492)
+.|...||.
T Consensus 456 pGf~~d~I~ 464 (505)
T COG5624 456 PGFVDDIIH 464 (505)
T ss_pred CcchHHHHH
Confidence 444444444
No 151
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=40.14 E-value=11 Score=28.41 Aligned_cols=33 Identities=18% Similarity=0.138 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCCCChhHhhhCccccCCCCceecccccc
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk 71 (492)
.++.|..||+.-- .+-.+--.-..+|+|+.||.
T Consensus 26 v~F~CPnCGe~~I-----~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEI-----YRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceee-----ehhhhHHHcCCceECCCcCc
Confidence 4778888885422 22222222345788888874
No 152
>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=39.98 E-value=13 Score=37.71 Aligned_cols=12 Identities=8% Similarity=0.102 Sum_probs=9.6
Q ss_pred CcccccCCCCCC
Q 011146 101 RKKVYICPEKSC 112 (492)
Q Consensus 101 ~~k~y~C~~C~C 112 (492)
|.|...|..|++
T Consensus 207 G~RyL~CslC~t 218 (305)
T TIGR01562 207 GLRYLSCSLCAT 218 (305)
T ss_pred CceEEEcCCCCC
Confidence 778889999944
No 153
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=39.45 E-value=9.8 Score=43.41 Aligned_cols=10 Identities=20% Similarity=0.089 Sum_probs=5.2
Q ss_pred HHHHHHhHhc
Q 011146 180 SFITHRAFCD 189 (492)
Q Consensus 180 ~L~~H~~~h~ 189 (492)
.|+.|+|..+
T Consensus 45 rli~h~r~~~ 54 (799)
T PF09606_consen 45 RLILHIRDMS 54 (799)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHhh
Confidence 3555655443
No 154
>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=38.89 E-value=21 Score=32.50 Aligned_cols=22 Identities=14% Similarity=0.285 Sum_probs=16.7
Q ss_pred CCCCceecccccccccChhhHH
Q 011146 59 MATNRFLCEICNKGFQRDQNLQ 80 (492)
Q Consensus 59 ~~~k~~~C~~Cgk~F~~~~~L~ 80 (492)
....-|.|+.|+..|.....+.
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~ 126 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME 126 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH
Confidence 4455689999999888877764
No 155
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=38.54 E-value=19 Score=25.39 Aligned_cols=13 Identities=15% Similarity=0.664 Sum_probs=9.5
Q ss_pred ceecccccccccC
Q 011146 63 RFLCEICNKGFQR 75 (492)
Q Consensus 63 ~~~C~~Cgk~F~~ 75 (492)
.|+|+.||..|.-
T Consensus 3 ~y~C~~CG~~~~~ 15 (46)
T PRK00398 3 EYKCARCGREVEL 15 (46)
T ss_pred EEECCCCCCEEEE
Confidence 5788888887664
No 156
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=38.53 E-value=30 Score=35.12 Aligned_cols=10 Identities=10% Similarity=0.046 Sum_probs=5.9
Q ss_pred CcccccCCCC
Q 011146 101 RKKVYICPEK 110 (492)
Q Consensus 101 ~~k~y~C~~C 110 (492)
|.|...|..|
T Consensus 209 G~RyL~CslC 218 (309)
T PRK03564 209 GLRYLHCNLC 218 (309)
T ss_pred CceEEEcCCC
Confidence 4555566666
No 157
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=37.77 E-value=2.7 Score=43.76 Aligned_cols=41 Identities=10% Similarity=0.180 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCChhHhhhCccccCCCCceecccccccccCh
Q 011146 36 RKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (492)
Q Consensus 36 ~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~ 76 (492)
-.|-.|+|...-...--.-|...--..=|.|..|++...-+
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq 315 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQ 315 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccc
Confidence 37888888765544444444443333348888887654433
No 158
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=37.37 E-value=16 Score=36.59 Aligned_cols=49 Identities=14% Similarity=0.381 Sum_probs=33.1
Q ss_pred ccCcCccccCChHHHHHhhhhcCCCceeec-CCCccCChhHHHHHHhHhcC
Q 011146 141 KCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFSRKDSFITHRAFCDA 190 (492)
Q Consensus 141 ~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~F~~~~~L~~H~~~h~~ 190 (492)
.|-.|.-.|.....-..-.. +....|.|+ |...|...-..-.|...|.-
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~~-~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~C 413 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDES-TSSGRYQCELCKSTFCSDCDVFIHETLHFC 413 (421)
T ss_pred cceeccCCCCCCCCCccccc-ccccceechhhhhhhhhhhHHHHHHHHhhC
Confidence 38888877765432211111 345679999 99999988888888877753
No 159
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=37.33 E-value=14 Score=37.44 Aligned_cols=38 Identities=13% Similarity=0.314 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCCCCCChhHhhhCccccCCCCceeccccccc
Q 011146 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (492)
Q Consensus 32 ~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~ 72 (492)
...+..|.+||.. +....+ +.....+.|-..|..|+-.
T Consensus 184 ~~~~~~CPvCGs~-P~~s~v--~~~~~~G~RyL~CslC~te 221 (309)
T PRK03564 184 GEQRQFCPVCGSM-PVSSVV--QIGTTQGLRYLHCNLCESE 221 (309)
T ss_pred ccCCCCCCCCCCc-chhhee--eccCCCCceEEEcCCCCCc
Confidence 3456778888863 322222 2223445666678888653
No 160
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=37.31 E-value=26 Score=25.92 Aligned_cols=31 Identities=23% Similarity=0.372 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccCh
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~ 76 (492)
...+|..||+.|.+ ++....|+.|+..+-+.
T Consensus 4 ~~~~C~~Cg~~~~~------------~dDiVvCp~CgapyHR~ 34 (54)
T PF14446_consen 4 EGCKCPVCGKKFKD------------GDDIVVCPECGAPYHRD 34 (54)
T ss_pred cCccChhhCCcccC------------CCCEEECCCCCCcccHH
Confidence 45789999988764 33457888888875443
No 161
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=37.08 E-value=28 Score=30.63 Aligned_cols=13 Identities=15% Similarity=0.496 Sum_probs=9.5
Q ss_pred cCCCCCCCCCCCCCcccChh
Q 011146 106 ICPEKSCVHHDPSRALGDLT 125 (492)
Q Consensus 106 ~C~~C~C~~~~c~k~f~~~s 125 (492)
+|+.| ..+|.+..
T Consensus 123 vCPvC-------kTSFKss~ 135 (140)
T PF05290_consen 123 VCPVC-------KTSFKSSS 135 (140)
T ss_pred CCCcc-------cccccccc
Confidence 78888 77776643
No 162
>PF14353 CpXC: CpXC protein
Probab=36.89 E-value=2.9 Score=36.53 Aligned_cols=24 Identities=25% Similarity=0.549 Sum_probs=15.7
Q ss_pred ceecccccccccChhhHHHHHHhc
Q 011146 63 RFLCEICNKGFQRDQNLQLHRRGH 86 (492)
Q Consensus 63 ~~~C~~Cgk~F~~~~~L~~H~r~H 86 (492)
.|.|+.||+.|.-...+..|-..+
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCCC
Confidence 477888887777666666554433
No 163
>PRK05580 primosome assembly protein PriA; Validated
Probab=36.78 E-value=19 Score=40.76 Aligned_cols=12 Identities=17% Similarity=0.479 Sum_probs=7.5
Q ss_pred CcccccCcCccc
Q 011146 137 EKKWKCEKCSKK 148 (492)
Q Consensus 137 ekp~~C~~C~k~ 148 (492)
..|+.|+.|+..
T Consensus 419 ~~~~~Cp~Cg~~ 430 (679)
T PRK05580 419 PIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCcCC
Confidence 445677777654
No 164
>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=36.49 E-value=12 Score=42.66 Aligned_cols=11 Identities=36% Similarity=0.694 Sum_probs=0.0
Q ss_pred Cceeccccccc
Q 011146 62 NRFLCEICNKG 72 (492)
Q Consensus 62 k~~~C~~Cgk~ 72 (492)
-.++|+.||+.
T Consensus 654 ~~r~Cp~Cg~~ 664 (900)
T PF03833_consen 654 GRRRCPKCGKE 664 (900)
T ss_dssp -----------
T ss_pred ecccCcccCCc
Confidence 34678888773
No 165
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.33 E-value=17 Score=32.05 Aligned_cols=16 Identities=25% Similarity=0.783 Sum_probs=10.1
Q ss_pred CCceecccccccccCh
Q 011146 61 TNRFLCEICNKGFQRD 76 (492)
Q Consensus 61 ~k~~~C~~Cgk~F~~~ 76 (492)
.-+|+|..|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4456777777766643
No 166
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.64 E-value=29 Score=29.45 Aligned_cols=13 Identities=15% Similarity=0.138 Sum_probs=9.1
Q ss_pred CcccccCcCcccc
Q 011146 137 EKKWKCEKCSKKY 149 (492)
Q Consensus 137 ekp~~C~~C~k~F 149 (492)
..|..|++||+.|
T Consensus 24 rdPiVsPytG~s~ 36 (129)
T COG4530 24 RDPIVSPYTGKSY 36 (129)
T ss_pred CCccccCcccccc
Confidence 4567777777777
No 167
>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=35.50 E-value=7.1 Score=26.75 Aligned_cols=12 Identities=17% Similarity=0.722 Sum_probs=9.4
Q ss_pred ceeccccccccc
Q 011146 63 RFLCEICNKGFQ 74 (492)
Q Consensus 63 ~~~C~~Cgk~F~ 74 (492)
-|.|..|++.|+
T Consensus 28 fy~C~~C~~~wr 39 (39)
T PF01096_consen 28 FYVCCNCGHRWR 39 (39)
T ss_dssp EEEESSSTEEEE
T ss_pred EEEeCCCCCeeC
Confidence 488999988763
No 168
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=34.93 E-value=15 Score=34.19 Aligned_cols=35 Identities=14% Similarity=0.074 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccC
Q 011146 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (492)
Q Consensus 32 ~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~ 75 (492)
...-|.|+.|+..|..-+.+. .-|.|+.||.....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 345688988998887766653 25899999886543
No 169
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=34.89 E-value=24 Score=35.65 Aligned_cols=28 Identities=32% Similarity=0.646 Sum_probs=24.2
Q ss_pred CCCceecccccccccChhhHHHHHHhcC
Q 011146 60 ATNRFLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 60 ~~k~~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
....|+|+.|...|.-..+...|...|.
T Consensus 342 ~~~~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 342 SSGRYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred CCCcEEchhccceeeccchHHHHhhhhc
Confidence 3446999999999999999999988885
No 170
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=34.87 E-value=20 Score=32.31 Aligned_cols=32 Identities=31% Similarity=0.910 Sum_probs=20.8
Q ss_pred cccccCcCccccCChHHHHHhhhh-cCCCceeec-CCCc
Q 011146 138 KKWKCEKCSKKYAVQSDWKAHSKI-CGTREYRCD-CGTL 174 (492)
Q Consensus 138 kp~~C~~C~k~F~~~~~L~~H~~~-~~~kp~~C~-C~k~ 174 (492)
.+|.|. |+..|.+. ++|-.+ -|+ .|.|. |+-.
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 468888 88776654 344444 455 78887 8644
No 171
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=34.56 E-value=32 Score=37.60 Aligned_cols=8 Identities=25% Similarity=0.102 Sum_probs=4.6
Q ss_pred CCCCCCCC
Q 011146 36 RKRNLPGT 43 (492)
Q Consensus 36 ~~c~~cg~ 43 (492)
.+|+.|+-
T Consensus 3 ~~C~~C~g 10 (715)
T COG1107 3 KKCPECGG 10 (715)
T ss_pred ccccccCC
Confidence 35666664
No 172
>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=34.13 E-value=15 Score=26.42 Aligned_cols=10 Identities=20% Similarity=0.561 Sum_probs=5.9
Q ss_pred cccccCcCcc
Q 011146 138 KKWKCEKCSK 147 (492)
Q Consensus 138 kp~~C~~C~k 147 (492)
.+-.|+.|+.
T Consensus 25 ~~~~CP~Cg~ 34 (52)
T TIGR02605 25 PLATCPECGG 34 (52)
T ss_pred CCCCCCCCCC
Confidence 4455777764
No 173
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=33.72 E-value=30 Score=28.40 Aligned_cols=14 Identities=36% Similarity=0.909 Sum_probs=8.7
Q ss_pred cccccCcCccccCC
Q 011146 138 KKWKCEKCSKKYAV 151 (492)
Q Consensus 138 kp~~C~~C~k~F~~ 151 (492)
-.|.|..|++.|.-
T Consensus 53 GIW~C~~C~~~~AG 66 (90)
T PTZ00255 53 GIWRCKGCKKTVAG 66 (90)
T ss_pred EEEEcCCCCCEEeC
Confidence 34677777766653
No 174
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=33.59 E-value=23 Score=40.27 Aligned_cols=30 Identities=17% Similarity=0.540 Sum_probs=20.4
Q ss_pred hcccCCCcccccCcCccccCChHHHHHhhhhcCCCceeec-CCCc
Q 011146 131 FSRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTL 174 (492)
Q Consensus 131 ~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~ 174 (492)
+..|...+...|.+||+. ...|..|. ||-.
T Consensus 454 lt~H~~~~~L~CH~Cg~~--------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 454 LTLHKATGQLRCHYCGYQ--------------EPIPQSCPECGSE 484 (730)
T ss_pred eEEecCCCeeEeCCCCCC--------------CCCCCCCCCCCCC
Confidence 344555566888888863 35688898 9854
No 175
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=33.33 E-value=22 Score=21.35 Aligned_cols=7 Identities=29% Similarity=0.885 Sum_probs=4.5
Q ss_pred ccccccc
Q 011146 66 CEICNKG 72 (492)
Q Consensus 66 C~~Cgk~ 72 (492)
|+.||..
T Consensus 16 C~~CG~~ 22 (23)
T PF13240_consen 16 CPNCGTP 22 (23)
T ss_pred hhhhCCc
Confidence 7777654
No 176
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=32.95 E-value=20 Score=26.78 Aligned_cols=36 Identities=28% Similarity=0.498 Sum_probs=21.3
Q ss_pred ceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCC
Q 011146 63 RFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEK 110 (492)
Q Consensus 63 ~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C 110 (492)
..+|-+|++.+.-......-.|.-.. ....|.|++|
T Consensus 2 ~vkC~lCdk~~~Id~~~~~aKrLrnr------------Pi~tYmC~eC 37 (56)
T PF09963_consen 2 RVKCILCDKKEEIDEDTPEAKRLRNR------------PIHTYMCDEC 37 (56)
T ss_pred eeEEEecCCEEEeccCCHHHHHhhcC------------CCcceeChhH
Confidence 35799999987654432222222221 4567999998
No 177
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.91 E-value=32 Score=24.54 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=9.7
Q ss_pred CceecccccccccC
Q 011146 62 NRFLCEICNKGFQR 75 (492)
Q Consensus 62 k~~~C~~Cgk~F~~ 75 (492)
..|.|+.||..+.-
T Consensus 19 ~~~vC~~Cg~~~~~ 32 (52)
T smart00661 19 RRFVCRKCGYEEPI 32 (52)
T ss_pred CEEECCcCCCeEEC
Confidence 36888888876543
No 178
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.70 E-value=29 Score=32.19 Aligned_cols=14 Identities=21% Similarity=0.287 Sum_probs=10.0
Q ss_pred ccCcccccCCCCCC
Q 011146 99 EVRKKVYICPEKSC 112 (492)
Q Consensus 99 ~~~~k~y~C~~C~C 112 (492)
+..+-.|.|++|-|
T Consensus 126 ~~~~~~~~CPiCl~ 139 (187)
T KOG0320|consen 126 LRKEGTYKCPICLD 139 (187)
T ss_pred cccccccCCCceec
Confidence 34566799999944
No 179
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.60 E-value=14 Score=29.11 Aligned_cols=23 Identities=26% Similarity=0.524 Sum_probs=15.4
Q ss_pred cCCCCceecccccccccChhhHHHHHH
Q 011146 58 LMATNRFLCEICNKGFQRDQNLQLHRR 84 (492)
Q Consensus 58 h~~~k~~~C~~Cgk~F~~~~~L~~H~r 84 (492)
.+..-.|+|..|+..|. +..|++
T Consensus 7 lMPtY~Y~c~~cg~~~d----vvq~~~ 29 (82)
T COG2331 7 LMPTYSYECTECGNRFD----VVQAMT 29 (82)
T ss_pred cccceEEeecccchHHH----HHHhcc
Confidence 34455699999998765 555553
No 180
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.08 E-value=17 Score=32.21 Aligned_cols=42 Identities=14% Similarity=0.082 Sum_probs=23.5
Q ss_pred CCCCCCCCCCCCCCCCChh---Hh------hhCccccCCCCceeccccccc
Q 011146 31 SNQLKRKRNLPGTPDPDAE---VI------ALSPKSLMATNRFLCEICNKG 72 (492)
Q Consensus 31 ~~~~~~~c~~cg~~~~~~~---~l------~~h~~~h~~~k~~~C~~Cgk~ 72 (492)
..+..++|..||..|.... .| ..|.-.-.....+.|+.||..
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 3456899999998776531 11 111111111345779999864
No 181
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=31.89 E-value=2e+02 Score=29.17 Aligned_cols=44 Identities=14% Similarity=0.309 Sum_probs=30.3
Q ss_pred ccCcCccccCChHHHHHhhhhcCCCceeec----CCCccCChhHHHHHHhHhcC
Q 011146 141 KCEKCSKKYAVQSDWKAHSKICGTREYRCD----CGTLFSRKDSFITHRAFCDA 190 (492)
Q Consensus 141 ~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~----C~k~F~~~~~L~~H~~~h~~ 190 (492)
.|..|+....+-. .+.-+..|.|. |.++|..+..|..|+.--|.
T Consensus 125 ~Cp~C~d~VqrIe------q~~~g~iFmC~~~~GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 125 ICPLCDDRVQRIE------QIMMGGIFMCAAPHGCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred cCcCcccHHHHHH------HhcccceEEeecchhHHHHHhhHHHHHHHhhhhhc
Confidence 5777765432211 11455689993 99999999999999875554
No 182
>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=31.31 E-value=15 Score=30.16 Aligned_cols=11 Identities=73% Similarity=1.787 Sum_probs=6.7
Q ss_pred cccCcCccccC
Q 011146 140 WKCEKCSKKYA 150 (492)
Q Consensus 140 ~~C~~C~k~F~ 150 (492)
|.|..|++.|.
T Consensus 54 W~C~~C~~~~A 64 (90)
T PF01780_consen 54 WKCKKCGKKFA 64 (90)
T ss_dssp EEETTTTEEEE
T ss_pred eecCCCCCEEe
Confidence 66666666554
No 183
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.09 E-value=42 Score=40.10 Aligned_cols=8 Identities=25% Similarity=0.658 Sum_probs=4.6
Q ss_pred eecccccc
Q 011146 64 FLCEICNK 71 (492)
Q Consensus 64 ~~C~~Cgk 71 (492)
++|+.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 55666655
No 184
>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=30.82 E-value=32 Score=28.33 Aligned_cols=13 Identities=46% Similarity=1.183 Sum_probs=8.3
Q ss_pred ccccCcCccccCC
Q 011146 139 KWKCEKCSKKYAV 151 (492)
Q Consensus 139 p~~C~~C~k~F~~ 151 (492)
.|.|..|++.|.-
T Consensus 53 IW~C~~C~~~~AG 65 (91)
T TIGR00280 53 IWTCRKCGAKFAG 65 (91)
T ss_pred EEEcCCCCCEEeC
Confidence 4677777766653
No 185
>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=30.77 E-value=17 Score=34.88 Aligned_cols=33 Identities=27% Similarity=0.403 Sum_probs=25.6
Q ss_pred ccCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCc
Q 011146 99 EVRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEK 138 (492)
Q Consensus 99 ~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ek 138 (492)
...+..|.|.+| +|.|.-..-.++|+...|.|+
T Consensus 72 e~~~~K~~C~lc-------~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 72 EEDEDKWRCPLC-------GKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSSSEEEEE-SS-------S-EESSHHHHHHHHHHH-HHH
T ss_pred HHcCCEECCCCC-------CcccCChHHHHHHHhhcCHHH
Confidence 356677999999 999999999999999977664
No 186
>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=30.46 E-value=86 Score=28.56 Aligned_cols=50 Identities=22% Similarity=0.320 Sum_probs=32.5
Q ss_pred ccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCc--CccccCChHHHHHhhhh
Q 011146 103 KVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEK--CSKKYAVQSDWKAHSKI 161 (492)
Q Consensus 103 k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~--C~k~F~~~~~L~~H~~~ 161 (492)
....|++| . |..+... ...--|.+...|+-.|.. |.+. .+-..|++|.+.
T Consensus 79 ~~L~CPLC-R-----G~V~GWt--vve~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~ 130 (162)
T PF07800_consen 79 PELACPLC-R-----GEVKGWT--VVEPARRFLNAKKRSCSQESCSFS-GTYSELRKHARS 130 (162)
T ss_pred ccccCccc-c-----CceeceE--EchHHHHHhccCCccCcccccccc-cCHHHHHHHHHh
Confidence 45789988 2 6655543 234456677778877744 6543 345689999887
No 187
>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=30.34 E-value=22 Score=24.44 Aligned_cols=23 Identities=26% Similarity=0.639 Sum_probs=12.8
Q ss_pred HHhhhcccCCCcccccCcCcccc
Q 011146 127 IKKHFSRKHGEKKWKCEKCSKKY 149 (492)
Q Consensus 127 L~~H~~~H~~ekp~~C~~C~k~F 149 (492)
|.-+.....+.+.|.|.+|+..-
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 33445555566778888887643
No 188
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=30.15 E-value=49 Score=24.84 Aligned_cols=33 Identities=12% Similarity=0.166 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccc
Q 011146 30 SSNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGF 73 (492)
Q Consensus 30 ~~~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F 73 (492)
.+....|.|..||.... ......++|..||..-
T Consensus 15 r~~~miYiCgdC~~en~-----------lk~~D~irCReCG~RI 47 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENT-----------LKRGDVIRCRECGYRI 47 (62)
T ss_pred CcccEEEEecccccccc-----------ccCCCcEehhhcchHH
Confidence 45677999999998533 3345679999999763
No 189
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=30.09 E-value=22 Score=27.99 Aligned_cols=38 Identities=16% Similarity=0.418 Sum_probs=18.8
Q ss_pred cccCcCccccCChHHHHHhhhhcCCCceeec---CCCccCCh
Q 011146 140 WKCEKCSKKYAVQSDWKAHSKICGTREYRCD---CGTLFSRK 178 (492)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~---C~k~F~~~ 178 (492)
+.|+.|+..-........+.. ..++-+.|. ||.+|...
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~-~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT-TKERYHQCQNVNCSATFITY 42 (72)
T ss_pred ccCCCCCCccEEEEChhcChh-hheeeeecCCCCCCCEEEEE
Confidence 456667654422222111111 345567773 88777654
No 190
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=29.58 E-value=44 Score=29.92 Aligned_cols=49 Identities=10% Similarity=0.086 Sum_probs=30.3
Q ss_pred CCCCCCCCCCCCCChhHhhhC----cccc-CCCCceecccccccccChhhHHHH
Q 011146 34 LKRKRNLPGTPDPDAEVIALS----PKSL-MATNRFLCEICNKGFQRDQNLQLH 82 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h----~~~h-~~~k~~~C~~Cgk~F~~~~~L~~H 82 (492)
.--+|..|+........-... ..+. ..++-+.|+.|||.|-.-++.+.-
T Consensus 90 ~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 90 IFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred CCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHHH
Confidence 357899999876543322221 1111 223468999999999877665543
No 191
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=29.52 E-value=33 Score=28.20 Aligned_cols=13 Identities=46% Similarity=1.211 Sum_probs=8.3
Q ss_pred ccccCcCccccCC
Q 011146 139 KWKCEKCSKKYAV 151 (492)
Q Consensus 139 p~~C~~C~k~F~~ 151 (492)
.|.|..|++.|.-
T Consensus 54 IW~C~~C~~~~AG 66 (90)
T PRK03976 54 IWECRKCGAKFAG 66 (90)
T ss_pred EEEcCCCCCEEeC
Confidence 4677777766653
No 192
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=29.44 E-value=26 Score=31.16 Aligned_cols=41 Identities=20% Similarity=0.382 Sum_probs=31.4
Q ss_pred CCCCCCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHHHHHHh
Q 011146 28 NPSSNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRG 85 (492)
Q Consensus 28 ~~~~~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~r~ 85 (492)
+|..++.+.-|.+|| +.+ +|-|.-||-.+....-|..|..+
T Consensus 111 ~p~~KP~r~fCaVCG--~~S---------------~ysC~~CG~kyCsv~C~~~HneT 151 (156)
T KOG3362|consen 111 KPSFKPLRKFCAVCG--YDS---------------KYSCVNCGTKYCSVRCLKTHNET 151 (156)
T ss_pred CCCCCCcchhhhhcC--CCc---------------hhHHHhcCCceeechhhhhcccc
Confidence 344556778899999 332 49999999999999998888543
No 193
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=29.11 E-value=31 Score=36.42 Aligned_cols=31 Identities=29% Similarity=0.651 Sum_probs=22.6
Q ss_pred cccCcCccccCChHHHHHhhhhcCCCceeec-CCCccCChhH
Q 011146 140 WKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFSRKDS 180 (492)
Q Consensus 140 ~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~F~~~~~ 180 (492)
-+|+.||.+. +..|.+-|+|. |++.+.....
T Consensus 351 p~Cp~Cg~~m----------~S~G~~g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 351 PVCPRCGGRM----------KSAGRNGFRCKKCGTRARETLI 382 (421)
T ss_pred CCCCccCCch----------hhcCCCCcccccccccCCcccc
Confidence 3799998763 33466689999 9998876544
No 194
>PF03249 TSA: Type specific antigen; InterPro: IPR004933 There are several antigenic variants in Rickettsia tsutsugamushi, and a type-specific antigen (TSA) of 56-kilodaltons located on the rickettsial surface is responsible for the variation [, ]. TSA proteins are probably integral membrane proteins. ; GO: 0016021 integral to membrane
Probab=29.03 E-value=25 Score=36.18 Aligned_cols=17 Identities=35% Similarity=0.286 Sum_probs=9.7
Q ss_pred HHHHHHHHHHhcCCcCC
Q 011146 354 ATALLQKAAQMGSTRSN 370 (492)
Q Consensus 354 ~~al~Qq~~Qmg~t~~~ 370 (492)
+++--|.++..++.|--
T Consensus 322 ~qataqea~aaaavr~l 338 (503)
T PF03249_consen 322 AQATAQEAAAAAAVRAL 338 (503)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 33445666666666643
No 195
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.87 E-value=46 Score=39.80 Aligned_cols=12 Identities=17% Similarity=0.645 Sum_probs=8.3
Q ss_pred cccccCcCcccc
Q 011146 138 KKWKCEKCSKKY 149 (492)
Q Consensus 138 kp~~C~~C~k~F 149 (492)
.+|.|..||...
T Consensus 691 ~vy~CPsCGaev 702 (1337)
T PRK14714 691 PVYVCPDCGAEV 702 (1337)
T ss_pred CceeCccCCCcc
Confidence 357888888754
No 196
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=28.71 E-value=50 Score=33.74 Aligned_cols=26 Identities=19% Similarity=-0.041 Sum_probs=17.6
Q ss_pred CCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 011146 7 GLSVPSTLKGFVQEPNSNPNPNPSSNQLKRKRNLPGTPD 45 (492)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~cg~~~ 45 (492)
.++|+-|+|.-- --++|||-.|-.-+
T Consensus 8 ~v~CdgC~k~~~-------------t~rrYkCL~C~DyD 33 (381)
T KOG1280|consen 8 GVSCDGCGKTAF-------------TFRRYKCLRCSDYD 33 (381)
T ss_pred Cceeccccccce-------------eeeeeEeeeecchh
Confidence 799999987622 12478888776543
No 197
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=28.65 E-value=29 Score=28.46 Aligned_cols=28 Identities=29% Similarity=0.516 Sum_probs=21.1
Q ss_pred CceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCC
Q 011146 62 NRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSC 112 (492)
Q Consensus 62 k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C 112 (492)
+|-+|..||..|.... -++|-.|+.|.-
T Consensus 57 ~Pa~CkkCGfef~~~~-----------------------ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRDDK-----------------------IKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCccccccc-----------------------cCCcccCCcchh
Confidence 5678999999998621 356889999843
No 198
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=28.54 E-value=44 Score=24.89 Aligned_cols=49 Identities=16% Similarity=0.299 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCC
Q 011146 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKS 111 (492)
Q Consensus 32 ~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~ 111 (492)
....++|.+..+.|. .|++...|+-.|.+..- ..++ . ..+...|++-|
T Consensus 8 ~~~~~~CPiT~~~~~---------------~PV~s~~C~H~fek~aI-~~~i---~-------------~~~~~~CPv~G 55 (57)
T PF11789_consen 8 GTISLKCPITLQPFE---------------DPVKSKKCGHTFEKEAI-LQYI---Q-------------RNGSKRCPVAG 55 (57)
T ss_dssp SB--SB-TTTSSB-S---------------SEEEESSS--EEEHHHH-HHHC---T-------------TTS-EE-SCCC
T ss_pred cEeccCCCCcCChhh---------------CCcCcCCCCCeecHHHH-HHHH---H-------------hcCCCCCCCCC
Confidence 345677777777655 36777888888877653 3333 2 45667888865
Q ss_pred C
Q 011146 112 C 112 (492)
Q Consensus 112 C 112 (492)
|
T Consensus 56 C 56 (57)
T PF11789_consen 56 C 56 (57)
T ss_dssp -
T ss_pred C
Confidence 5
No 199
>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=28.28 E-value=26 Score=30.95 Aligned_cols=28 Identities=25% Similarity=0.504 Sum_probs=13.3
Q ss_pred CcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCc
Q 011146 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEK 138 (492)
Q Consensus 101 ~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ek 138 (492)
.+...+|-+| |+.|.. |++|++.|+|..
T Consensus 69 ~~d~i~clec-------Gk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 69 TPDYIICLEC-------GKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp -SS-EE-TBT---------EESB---HHHHHHHTT-S-
T ss_pred ccCeeEEccC-------Ccccch---HHHHHHHccCCC
Confidence 3444566666 777655 477777776643
No 200
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.24 E-value=24 Score=33.96 Aligned_cols=40 Identities=18% Similarity=0.137 Sum_probs=28.4
Q ss_pred CCCCCCCCCCCCCCChhHhhhCccccCCCC---------------ceeccccccc
Q 011146 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATN---------------RFLCEICNKG 72 (492)
Q Consensus 33 ~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k---------------~~~C~~Cgk~ 72 (492)
++...|++|+..|..++.+.-..|...++- ...|++|..+
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yA 71 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYA 71 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHH
Confidence 456788888888888877777766654431 2469999874
No 201
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=27.85 E-value=32 Score=23.41 Aligned_cols=16 Identities=31% Similarity=0.862 Sum_probs=6.4
Q ss_pred CceecccccccccChh
Q 011146 62 NRFLCEICNKGFQRDQ 77 (492)
Q Consensus 62 k~~~C~~Cgk~F~~~~ 77 (492)
++|-|+.|.+.|....
T Consensus 2 ~ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDS 17 (38)
T ss_dssp -S-B-TTT--B-S--S
T ss_pred cCeecccccceecCCC
Confidence 4699999999995443
No 202
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=27.67 E-value=32 Score=29.76 Aligned_cols=27 Identities=22% Similarity=0.485 Sum_probs=23.0
Q ss_pred CCCceecccccccccChhhHHHHHHhc
Q 011146 60 ATNRFLCEICNKGFQRDQNLQLHRRGH 86 (492)
Q Consensus 60 ~~k~~~C~~Cgk~F~~~~~L~~H~r~H 86 (492)
+.--|-|-.|.+-|.+...|+.|.++-
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhcc
Confidence 344599999999999999999998753
No 203
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=27.67 E-value=31 Score=37.72 Aligned_cols=28 Identities=14% Similarity=0.186 Sum_probs=23.1
Q ss_pred CcccccCCCCCCCCCCCCCcccChhhHHhhhcccC
Q 011146 101 RKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKH 135 (492)
Q Consensus 101 ~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~ 135 (492)
..++-.|..| |.+|.+.....+||-.|.
T Consensus 415 ~~~pnqC~~C-------G~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSC-------GLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhccc-------ccccccchhhhhHhhhhh
Confidence 4567789998 999999988888887775
No 204
>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=26.48 E-value=35 Score=30.49 Aligned_cols=35 Identities=14% Similarity=0.222 Sum_probs=24.9
Q ss_pred CCCCCCCCCCCCCCCChhHhhhCccccCCCCceeccccccccc
Q 011146 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (492)
Q Consensus 32 ~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~ 74 (492)
..-.|.|..|+..+. +|.+. ..+.|.|..|+..|.
T Consensus 120 ~~~~~~C~~C~~~~~------r~~~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 120 KKYVYRCPSCGREYK------RHRRS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred cceEEEcCCCCCEee------eeccc--chhhEECCCCCCEEE
Confidence 445899999998753 34444 445699999997765
No 205
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=26.46 E-value=9.1 Score=39.97 Aligned_cols=149 Identities=11% Similarity=0.081 Sum_probs=71.3
Q ss_pred CCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHhhhCccccCCC----CceecccccccccChhhHHHH-HH
Q 011146 10 VPSTLKGFVQEPNSNPNPNPSSNQLKRKRNLPGTPDPDAEVIALSPKSLMAT----NRFLCEICNKGFQRDQNLQLH-RR 84 (492)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~----k~~~C~~Cgk~F~~~~~L~~H-~r 84 (492)
|.-|.|+..=....=...+.-....-++|..|++..+-..-+.+..|..-++ -.-+|..||+.-..+ -|+.- .-
T Consensus 277 C~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d~-iLrA~Gka 355 (468)
T KOG1701|consen 277 CAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMDR-ILRALGKA 355 (468)
T ss_pred hhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHHHHH-HHHhcccc
Confidence 4445554432222222233334455689999988877766666665554332 123588888753221 12211 11
Q ss_pred hcCCCcccccccccccCcccccCCCCCCCCCCCCCcccChhhHHhhh-cccCCCcccccCcCccccCChHHHHHhhhh--
Q 011146 85 GHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDPSRALGDLTGIKKHF-SRKHGEKKWKCEKCSKKYAVQSDWKAHSKI-- 161 (492)
Q Consensus 85 ~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~-~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~-- 161 (492)
.|- .-|+|-.|+- .--|..|.--..=..|- .--|..-.-+|.+|++...-..--..-.|+
T Consensus 356 yHp---------------~CF~Cv~C~r--~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvva 418 (468)
T KOG1701|consen 356 YHP---------------GCFTCVVCAR--CLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVA 418 (468)
T ss_pred cCC---------------CceEEEEecc--ccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEE
Confidence 222 3355555510 01123333222222221 111222234788888876554443333333
Q ss_pred ----cCCCceeec-CCCccC
Q 011146 162 ----CGTREYRCD-CGTLFS 176 (492)
Q Consensus 162 ----~~~kp~~C~-C~k~F~ 176 (492)
....-|+|+ |+...+
T Consensus 419 mdr~fHv~CY~CEDCg~~LS 438 (468)
T KOG1701|consen 419 MDRDFHVNCYKCEDCGLLLS 438 (468)
T ss_pred ccccccccceehhhcCcccc
Confidence 234568998 998776
No 206
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=26.37 E-value=15 Score=25.38 Aligned_cols=33 Identities=15% Similarity=0.590 Sum_probs=17.5
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceeccccccc
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~ 72 (492)
+.+|..||++......|..-. ...|.|+.|=..
T Consensus 1 ~~~CSFCgr~~~~v~~li~g~-----~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 1 EKRCSFCGRPESEVGRLISGP-----NGAYICDECVEQ 33 (41)
T ss_dssp --B-TTT--BTTTSSSEEEES------SEEEEHHHHHH
T ss_pred CCCccCCCCCHHHHhceecCC-----CCcEECHHHHHH
Confidence 468999999877654443221 137999988543
No 207
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=26.18 E-value=29 Score=30.57 Aligned_cols=27 Identities=22% Similarity=0.492 Sum_probs=21.0
Q ss_pred ccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcc
Q 011146 103 KVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKK 139 (492)
Q Consensus 103 k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp 139 (492)
.-.+|-+| |+.|.+ |++|+.+|.+--|
T Consensus 75 D~IicLED-------GkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 75 DYIICLED-------GKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred CeEEEecc-------CcchHH---HHHHHhcccCCCH
Confidence 34578888 999865 8999999987543
No 208
>PRK05978 hypothetical protein; Provisional
Probab=26.17 E-value=39 Score=30.51 Aligned_cols=33 Identities=12% Similarity=0.201 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccCh
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~ 76 (492)
+-+|..||+..--+..|+.+ -.|+.||..|...
T Consensus 33 ~grCP~CG~G~LF~g~Lkv~---------~~C~~CG~~~~~~ 65 (148)
T PRK05978 33 RGRCPACGEGKLFRAFLKPV---------DHCAACGEDFTHH 65 (148)
T ss_pred cCcCCCCCCCcccccccccC---------CCccccCCccccC
Confidence 67999999875544444333 3799999987654
No 209
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=25.99 E-value=45 Score=33.71 Aligned_cols=44 Identities=14% Similarity=0.190 Sum_probs=26.1
Q ss_pred CCCCCCCCCCCCCCChhHhhhCccccCCCCceeccc----ccccccChhh
Q 011146 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEI----CNKGFQRDQN 78 (492)
Q Consensus 33 ~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~----Cgk~F~~~~~ 78 (492)
++..+|..|..++.+. ..+++....+...+.|.. |.+.|.....
T Consensus 78 ~~~~~CP~Cr~~~g~~--R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~~ 125 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNI--RCRAMEKVAEAVLVPCKNAKLGCTKSFPYGEK 125 (299)
T ss_pred hhcccCCccccccccH--HHHHHHHHHHhceecccccccCCceeeccccc
Confidence 5567777777776643 444444445555666663 6666665554
No 210
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=25.81 E-value=24 Score=36.73 Aligned_cols=75 Identities=16% Similarity=0.321 Sum_probs=43.9
Q ss_pred CCCC--CCCCCCCCChhHhhhCccccCCCC------------ceecc--cccccccChhhHHHHHHhcCCCccccccccc
Q 011146 35 KRKR--NLPGTPDPDAEVIALSPKSLMATN------------RFLCE--ICNKGFQRDQNLQLHRRGHNLPWKLKQRTNK 98 (492)
Q Consensus 35 ~~~c--~~cg~~~~~~~~l~~h~~~h~~~k------------~~~C~--~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~ 98 (492)
.|.| +.|+-.+..+..+.+|.+.|...+ -|-|. +|.| .-++...|-..|+ .....
T Consensus 271 hyhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht------~~~n~ 341 (480)
T KOG4377|consen 271 HYHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHT------DKRNN 341 (480)
T ss_pred hhcccCccccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCcccc------ccccC
Confidence 3444 357665666888888887774422 25664 6888 3445666766665 11111
Q ss_pred ccCcccccCCCCCCCCCCCCCcccC
Q 011146 99 EVRKKVYICPEKSCVHHDPSRALGD 123 (492)
Q Consensus 99 ~~~~k~y~C~~C~C~~~~c~k~f~~ 123 (492)
..+..-|.|..|+| -..|..
T Consensus 342 GfrrthfhC~r~gC-----TdtfK~ 361 (480)
T KOG4377|consen 342 GFRRTHFHCQRIGC-----TDTFKD 361 (480)
T ss_pred ceecceeEEeccCC-----cccccc
Confidence 23345688888866 555553
No 211
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=25.63 E-value=31 Score=25.35 Aligned_cols=26 Identities=12% Similarity=0.432 Sum_probs=12.5
Q ss_pred hhHHhhhcccCCCcccccCc----CccccC
Q 011146 125 TGIKKHFSRKHGEKKWKCEK----CSKKYA 150 (492)
Q Consensus 125 s~L~~H~~~H~~ekp~~C~~----C~k~F~ 150 (492)
..|..|+...=..++..|.+ |+..+.
T Consensus 24 ~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 24 KELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp CCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred HHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 45566665444455556666 655544
No 212
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.43 E-value=25 Score=30.10 Aligned_cols=29 Identities=7% Similarity=-0.112 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccc
Q 011146 31 SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNK 71 (492)
Q Consensus 31 ~~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk 71 (492)
.-+...+|..||..|... ...|.|+.||.
T Consensus 66 ~vp~~~~C~~Cg~~~~~~------------~~~~~CP~Cgs 94 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIH------------QHDAQCPHCHG 94 (113)
T ss_pred eeCcEEEcccCCCEEecC------------CcCccCcCCCC
Confidence 345678999999776642 24467999985
No 213
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=25.40 E-value=29 Score=22.41 Aligned_cols=25 Identities=20% Similarity=0.297 Sum_probs=12.3
Q ss_pred CCCCCCCCCCChhHhhhCccccCCCCceeccccccc
Q 011146 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (492)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~ 72 (492)
+|..|+..+.. .....|.|+.|+..
T Consensus 4 ~Cp~C~se~~y-----------~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E-----------E-SSSEEETTTTEE
T ss_pred CCCCCCCccee-----------ccCCEEeCCccccc
Confidence 68888876653 34456999999864
No 214
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=25.27 E-value=25 Score=36.97 Aligned_cols=39 Identities=18% Similarity=0.533 Sum_probs=28.3
Q ss_pred cCcccccCCCCCCCCCCCCCcccChhhHHhhhcccCCCcccccCcCccc
Q 011146 100 VRKKVYICPEKSCVHHDPSRALGDLTGIKKHFSRKHGEKKWKCEKCSKK 148 (492)
Q Consensus 100 ~~~k~y~C~~C~C~~~~c~k~f~~~s~L~~H~~~H~~ekp~~C~~C~k~ 148 (492)
....-|.|+.| .+.|.....+. ..-...-.|.|..|+-.
T Consensus 124 t~~~~Y~Cp~C-------~kkyt~Lea~~---L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNC-------QKKYTSLEALQ---LLDNETGEFHCENCGGE 162 (436)
T ss_pred cccccccCCcc-------ccchhhhHHHH---hhcccCceEEEecCCCc
Confidence 45678999999 99998877655 23333456999999854
No 215
>PF15269 zf-C2H2_7: Zinc-finger
Probab=25.16 E-value=47 Score=23.49 Aligned_cols=30 Identities=13% Similarity=-0.055 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCCCCCCCCCChhHhhhCccc
Q 011146 28 NPSSNQLKRKRNLPGTPDPDAEVIALSPKS 57 (492)
Q Consensus 28 ~~~~~~~~~~c~~cg~~~~~~~~l~~h~~~ 57 (492)
.|..++-+|+|-.|......++.|-.|++-
T Consensus 13 rp~gkp~~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 13 RPPGKPFKYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred CCCCCCccceeecCCcccchHHHHHHHHHH
Confidence 444556699999999999999999988864
No 216
>PRK14873 primosome assembly protein PriA; Provisional
Probab=24.95 E-value=41 Score=38.01 Aligned_cols=28 Identities=21% Similarity=0.643 Sum_probs=18.7
Q ss_pred cccCCCcccccCcCccccCChHHHHHhhhhcCCCceeec-CCCc
Q 011146 132 SRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTL 174 (492)
Q Consensus 132 ~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~ 174 (492)
..|...+...|.+||+. ..++.|. |+..
T Consensus 403 ~~h~~~~~l~Ch~CG~~---------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 403 GLPSAGGTPRCRWCGRA---------------APDWRCPRCGSD 431 (665)
T ss_pred eEecCCCeeECCCCcCC---------------CcCccCCCCcCC
Confidence 34455567888888853 1467898 9864
No 217
>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=24.93 E-value=14 Score=27.01 Aligned_cols=27 Identities=30% Similarity=0.629 Sum_probs=17.2
Q ss_pred CCceecccccccccChhhHHHHHHhcC
Q 011146 61 TNRFLCEICNKGFQRDQNLQLHRRGHN 87 (492)
Q Consensus 61 ~k~~~C~~Cgk~F~~~~~L~~H~r~H~ 87 (492)
..+|+|+.|...|--.-.+-.|...|.
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 467999999999999999888877775
No 218
>KOG4679 consensus Uncharacterized protein PSP1 (suppressor of DNA polymerase alpha mutations in yeast) [General function prediction only]
Probab=24.70 E-value=21 Score=37.70 Aligned_cols=19 Identities=42% Similarity=0.475 Sum_probs=7.8
Q ss_pred cCCCcchhhHHHHHHHHhh
Q 011146 328 LYPSNQSGQQQQQQQQQQQ 346 (492)
Q Consensus 328 ~~qqQQQQQQQQQQQQQQQ 346 (492)
-+++.|++|||+++++||+
T Consensus 143 ~~p~~q~~QQqp~~~~qq~ 161 (572)
T KOG4679|consen 143 RFPRPQVGQQQPLSSAQQF 161 (572)
T ss_pred cCCchhhcccCchhhcCCC
Confidence 3444444444443333333
No 219
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=24.68 E-value=38 Score=21.96 Aligned_cols=11 Identities=36% Similarity=0.878 Sum_probs=8.0
Q ss_pred eeccccccccc
Q 011146 64 FLCEICNKGFQ 74 (492)
Q Consensus 64 ~~C~~Cgk~F~ 74 (492)
|.|..|++.+.
T Consensus 28 f~C~~C~~~L~ 38 (39)
T smart00132 28 FKCSKCGKPLG 38 (39)
T ss_pred CCCcccCCcCc
Confidence 77888887653
No 220
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=24.57 E-value=44 Score=29.81 Aligned_cols=35 Identities=11% Similarity=0.161 Sum_probs=24.1
Q ss_pred CCCCCCCCCCCCCCChhHhhhCccccCCCCceeccccccccc
Q 011146 33 QLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQ 74 (492)
Q Consensus 33 ~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~ 74 (492)
.-.|+|..|+..+.. + +.+.....|.|..|+-.|.
T Consensus 110 ~~~y~C~~C~~~~~~------~-rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 110 KYPYRCTGCGQRYLR------V-RRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred eEEEECCCCCCCCce------E-ccccCcceEEcCCCCCEEE
Confidence 348999999987642 2 2333336799999997764
No 221
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=24.31 E-value=60 Score=34.20 Aligned_cols=23 Identities=13% Similarity=-0.091 Sum_probs=9.5
Q ss_pred CcccChhhHHhhhcccCCCcccc
Q 011146 119 RALGDLTGIKKHFSRKHGEKKWK 141 (492)
Q Consensus 119 k~f~~~s~L~~H~~~H~~ekp~~ 141 (492)
+.+.....+..|...+.++.++.
T Consensus 339 ~~~~~~~~~~~~~~~~~~~~~~~ 361 (396)
T KOG2461|consen 339 RTPAGQLIYTQSHSMEVAEPTDM 361 (396)
T ss_pred cccccccchhhhhhcccCCCCcc
Confidence 33333344444444444444333
No 222
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=23.70 E-value=37 Score=38.28 Aligned_cols=73 Identities=12% Similarity=0.099 Sum_probs=0.0
Q ss_pred CCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHHHHHHhcCCCcccccccccccCcccccCCCCCCCCCCC
Q 011146 38 RNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEKSCVHHDP 117 (492)
Q Consensus 38 c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C~C~~~~c 117 (492)
|..|++.|... ......+++-|..||+.|.....=+ +.+..-.++............-.|+.|
T Consensus 463 C~~C~kkFfSl-------sK~L~~RKHHCRkCGrVFC~~CSSn---Rs~yp~aKLpKPgsseE~ppRRVCD~C------- 525 (1374)
T PTZ00303 463 CPSCGRAFISL-------SRPLGTRAHHCRSCGIRLCVFCITK---RAHYSFAKLAKPGSSDEAEERLVCDTC------- 525 (1374)
T ss_pred ccCcCCccccc-------ccccccccccccCCccccCccccCC---cccCcccccCCCCCcccccccchhHHH-------
Q ss_pred CCcccChhhHHhh
Q 011146 118 SRALGDLTGIKKH 130 (492)
Q Consensus 118 ~k~f~~~s~L~~H 130 (492)
|.....+..|
T Consensus 526 ---Ydq~EnLlQm 535 (1374)
T PTZ00303 526 ---YKEYETVSQL 535 (1374)
T ss_pred ---HHHHHhHHhh
No 223
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=23.47 E-value=35 Score=20.90 Aligned_cols=10 Identities=30% Similarity=0.614 Sum_probs=7.5
Q ss_pred Cceecccccc
Q 011146 62 NRFLCEICNK 71 (492)
Q Consensus 62 k~~~C~~Cgk 71 (492)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4588888875
No 224
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=23.28 E-value=61 Score=22.40 Aligned_cols=24 Identities=21% Similarity=0.541 Sum_probs=17.3
Q ss_pred eecccccccccC--hhhHHHHHHhcC
Q 011146 64 FLCEICNKGFQR--DQNLQLHRRGHN 87 (492)
Q Consensus 64 ~~C~~Cgk~F~~--~~~L~~H~r~H~ 87 (492)
-.|..||..|.. ...-+.|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 578888888764 456677877774
No 225
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=23.17 E-value=33 Score=29.41 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=23.5
Q ss_pred CCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccC
Q 011146 35 KRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQR 75 (492)
Q Consensus 35 ~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~ 75 (492)
..+|..||..-..-..+..-...-..+.-|+|..||..|+.
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeec
Confidence 45688888653332222222222233455999999998863
No 226
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.09 E-value=60 Score=22.72 Aligned_cols=16 Identities=19% Similarity=0.758 Sum_probs=10.5
Q ss_pred ecccccccccChhhHH
Q 011146 65 LCEICNKGFQRDQNLQ 80 (492)
Q Consensus 65 ~C~~Cgk~F~~~~~L~ 80 (492)
.|.+|++.|.-.....
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 5777777777655443
No 227
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.74 E-value=52 Score=34.78 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhh
Q 011146 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQN 78 (492)
Q Consensus 32 ~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~ 78 (492)
...+-+|+.||..-. +- +.+-|+|..||+.+.....
T Consensus 347 ~~~~p~Cp~Cg~~m~----------S~-G~~g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 347 ERVNPVCPRCGGRMK----------SA-GRNGFRCKKCGTRARETLI 382 (421)
T ss_pred EEcCCCCCccCCchh----------hc-CCCCcccccccccCCcccc
Confidence 345678999998643 32 2337999999999887654
No 228
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=22.71 E-value=43 Score=30.21 Aligned_cols=37 Identities=8% Similarity=0.053 Sum_probs=27.9
Q ss_pred CCCCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccc
Q 011146 32 NQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGF 73 (492)
Q Consensus 32 ~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F 73 (492)
..-.|.|. |+..+.. ..+|-+...++ .|.|..|+-..
T Consensus 114 ~~~~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 114 TTYPYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred cceeEEee-cCCccch---hhhcccccccc-eEEeccCCceE
Confidence 45589999 9998764 45666666666 89999998754
No 229
>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=22.65 E-value=50 Score=35.96 Aligned_cols=30 Identities=23% Similarity=0.561 Sum_probs=19.5
Q ss_pred hcccCCCcccccCcCccccCChHHHHHhhhhcCCCceeec-CCCc
Q 011146 131 FSRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTL 174 (492)
Q Consensus 131 ~~~H~~ekp~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~ 174 (492)
+..|..+....|.+||+.. ..|..|. |+..
T Consensus 232 l~~h~~~~~l~Ch~Cg~~~--------------~~~~~Cp~C~s~ 262 (505)
T TIGR00595 232 LTYHKKEGKLRCHYCGYQE--------------PIPKTCPQCGSE 262 (505)
T ss_pred eEEecCCCeEEcCCCcCcC--------------CCCCCCCCCCCC
Confidence 4445556677888888642 3466788 8753
No 230
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=22.59 E-value=52 Score=22.52 Aligned_cols=37 Identities=19% Similarity=0.124 Sum_probs=23.6
Q ss_pred CCCCCCCCCCChhHhhhCccccCCCCceecccccccccChhhHHH
Q 011146 37 KRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQL 81 (492)
Q Consensus 37 ~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~~~L~~ 81 (492)
+|+.|+...... ...+...+.|+.|+-.|-....|..
T Consensus 1 ~CP~C~~~l~~~--------~~~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELEPV--------RLGDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccceE--------EECCEEEEECCCCCeEEccHHHHHH
Confidence 477777643321 1134456789999888887777764
No 231
>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=22.45 E-value=60 Score=21.29 Aligned_cols=10 Identities=20% Similarity=0.923 Sum_probs=5.4
Q ss_pred ccccCcCccc
Q 011146 139 KWKCEKCSKK 148 (492)
Q Consensus 139 p~~C~~C~k~ 148 (492)
+.+|..||.+
T Consensus 17 ~irC~~CG~R 26 (32)
T PF03604_consen 17 PIRCPECGHR 26 (32)
T ss_dssp TSSBSSSS-S
T ss_pred cEECCcCCCe
Confidence 4566666654
No 232
>PHA02998 RNA polymerase subunit; Provisional
Probab=22.36 E-value=44 Score=30.92 Aligned_cols=40 Identities=13% Similarity=0.220 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCCCChhHhhhCcccc--CCCCceecccccccccC
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPKSL--MATNRFLCEICNKGFQR 75 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~~h--~~~k~~~C~~Cgk~F~~ 75 (492)
...+|..|+..-.. ......|+- ....-|+|..||+.|.-
T Consensus 142 t~v~CPkCg~~~A~--f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTT--PMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceE--EEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 56889999865332 222222221 12345899999998764
No 233
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=22.27 E-value=1.4e+02 Score=29.29 Aligned_cols=8 Identities=38% Similarity=1.090 Sum_probs=6.2
Q ss_pred ccccCCCC
Q 011146 103 KVYICPEK 110 (492)
Q Consensus 103 k~y~C~~C 110 (492)
+.|+|++|
T Consensus 267 R~YVCPiC 274 (318)
T KOG4602|consen 267 RSYVCPIC 274 (318)
T ss_pred hhhcCccc
Confidence 56888888
No 234
>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=22.24 E-value=29 Score=39.60 Aligned_cols=11 Identities=18% Similarity=0.685 Sum_probs=0.0
Q ss_pred cccccCcCccc
Q 011146 138 KKWKCEKCSKK 148 (492)
Q Consensus 138 kp~~C~~C~k~ 148 (492)
..|.|+.|+..
T Consensus 679 ~~~~Cp~C~~~ 689 (900)
T PF03833_consen 679 PVYVCPDCGIE 689 (900)
T ss_dssp -----------
T ss_pred cceeccccccc
Confidence 34667666654
No 235
>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=21.41 E-value=61 Score=23.98 Aligned_cols=11 Identities=18% Similarity=0.754 Sum_probs=6.1
Q ss_pred ceecccccccc
Q 011146 63 RFLCEICNKGF 73 (492)
Q Consensus 63 ~~~C~~Cgk~F 73 (492)
...|+.||..|
T Consensus 22 iV~Cp~CGael 32 (54)
T TIGR01206 22 LVICDECGAEL 32 (54)
T ss_pred EEeCCCCCCEE
Confidence 34666666554
No 236
>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=21.12 E-value=36 Score=30.43 Aligned_cols=31 Identities=29% Similarity=0.921 Sum_probs=19.4
Q ss_pred ccccCcCccccCChHHHHHhhhhcCCCceeec-CCCccC
Q 011146 139 KWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLFS 176 (492)
Q Consensus 139 p~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~F~ 176 (492)
.|.|..|+..+.+ |.+. ..+.|.|. |+..|.
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 5788888877633 3333 33458887 876654
No 237
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=20.87 E-value=34 Score=29.39 Aligned_cols=30 Identities=7% Similarity=0.087 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCCCCCCChhHhhhCccccCCCCceeccccccc
Q 011146 31 SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKG 72 (492)
Q Consensus 31 ~~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~ 72 (492)
.-+...+|+.||..|.... ..+.|+.||..
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~------------~~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEI------------DLYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecCC------------cCccCcCCcCC
Confidence 3455789999998776421 14779999864
No 238
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=20.86 E-value=49 Score=25.16 Aligned_cols=31 Identities=13% Similarity=0.105 Sum_probs=14.0
Q ss_pred CCCCCCCCCCCCCChhHhhhCccccCCCCceecccccccccCh
Q 011146 34 LKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRD 76 (492)
Q Consensus 34 ~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~~~C~~Cgk~F~~~ 76 (492)
....|.+|++.|.- -.+++.|..||+.|-..
T Consensus 8 ~~~~C~~C~~~F~~------------~~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 8 EASNCMICGKKFSL------------FRRRHHCRNCGRVVCSS 38 (69)
T ss_dssp G-SB-TTT--B-BS------------SS-EEE-TTT--EEECC
T ss_pred CCCcCcCcCCcCCC------------ceeeEccCCCCCEECCc
Confidence 45677888887742 24567788888777644
No 239
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=20.43 E-value=52 Score=29.34 Aligned_cols=31 Identities=26% Similarity=0.829 Sum_probs=18.0
Q ss_pred ccccCcCccccCChHHHHHhhhhcCCCceeec-CCCcc
Q 011146 139 KWKCEKCSKKYAVQSDWKAHSKICGTREYRCD-CGTLF 175 (492)
Q Consensus 139 p~~C~~C~k~F~~~~~L~~H~~~~~~kp~~C~-C~k~F 175 (492)
.|.|..|+..+. +|.+......|.|. |+..+
T Consensus 112 ~y~C~~C~~~~~------~~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYL------RVRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCc------eEccccCcceEEcCCCCCEE
Confidence 577877877654 22232222567777 77654
No 240
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=20.39 E-value=60 Score=26.92 Aligned_cols=41 Identities=20% Similarity=0.235 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCCCCCCChhHhhhCccccCCCCc-eecccccccccChh
Q 011146 31 SNQLKRKRNLPGTPDPDAEVIALSPKSLMATNR-FLCEICNKGFQRDQ 77 (492)
Q Consensus 31 ~~~~~~~c~~cg~~~~~~~~l~~h~~~h~~~k~-~~C~~Cgk~F~~~~ 77 (492)
.+.+...|.+||++..+. +.. ..++|. |=|++|-+.|.+.-
T Consensus 10 ag~ke~~CalCG~tWg~~-----y~E-v~G~rLfFCCd~ca~EF~nmi 51 (105)
T PF11494_consen 10 AGTKEMGCALCGATWGDY-----YEE-VDGERLFFCCDDCAKEFKNMI 51 (105)
T ss_dssp --SGGGS-SS---S---S-----S-B--TT--BSSS--SSSS-TTS-T
T ss_pred cccccccccccCCcHHHH-----HHh-hcCCEEEEEcHHHHHHHHHHH
Confidence 356678999999997752 222 334454 56899999999764
No 241
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.21 E-value=68 Score=24.30 Aligned_cols=34 Identities=24% Similarity=0.571 Sum_probs=20.4
Q ss_pred eeccccccc-ccChhhHHHHHHhcCCCcccccccccccCcccccCCCC
Q 011146 64 FLCEICNKG-FQRDQNLQLHRRGHNLPWKLKQRTNKEVRKKVYICPEK 110 (492)
Q Consensus 64 ~~C~~Cgk~-F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~k~y~C~~C 110 (492)
.+|-+|++. |.....++.-+..-. .-+.|.|++|
T Consensus 3 vkCiiCd~v~~iD~rt~~tKrLrN~-------------PIrtymC~eC 37 (68)
T COG4896 3 VKCIICDRVDEIDNRTFKTKRLRNK-------------PIRTYMCPEC 37 (68)
T ss_pred ceEEEecceeeecchhHHHHHhhCC-------------CceeEechhh
Confidence 578888874 444445544432221 3467899998
No 242
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=20.09 E-value=59 Score=34.41 Aligned_cols=27 Identities=19% Similarity=0.359 Sum_probs=21.4
Q ss_pred cCCCCceeccccc-ccccChhhHHHHHH
Q 011146 58 LMATNRFLCEICN-KGFQRDQNLQLHRR 84 (492)
Q Consensus 58 h~~~k~~~C~~Cg-k~F~~~~~L~~H~r 84 (492)
|.=.+-|.|+||| +++.=...+.+|..
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 4456779999999 78888888888853
Done!