Query 015552
Match_columns 405
No_of_seqs 264 out of 1465
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 07:22:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015552.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015552hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2893 Zn finger protein [Gen 100.0 2.4E-27 5.1E-32 222.3 21.2 110 1-114 1-110 (341)
2 KOG2462 C2H2-type Zn-finger pr 99.6 1.6E-15 3.5E-20 145.9 5.8 89 14-114 164-254 (279)
3 KOG2462 C2H2-type Zn-finger pr 99.5 1E-14 2.2E-19 140.4 3.0 76 11-98 187-266 (279)
4 KOG3623 Homeobox transcription 99.3 1.3E-12 2.9E-17 138.2 1.3 74 11-96 893-971 (1007)
5 KOG3576 Ovo and related transc 99.2 1.9E-12 4.2E-17 120.0 1.0 80 9-100 115-198 (267)
6 KOG3576 Ovo and related transc 99.1 2E-11 4.3E-16 113.3 1.4 88 10-101 144-238 (267)
7 KOG3623 Homeobox transcription 98.9 2.3E-10 5E-15 121.6 2.0 74 12-97 241-331 (1007)
8 KOG1074 Transcriptional repres 98.9 4.1E-10 8.8E-15 121.4 2.2 85 12-104 606-697 (958)
9 PHA00733 hypothetical protein 98.7 8.3E-09 1.8E-13 90.6 4.6 76 12-101 41-125 (128)
10 KOG1074 Transcriptional repres 98.7 6.6E-09 1.4E-13 112.3 2.2 54 9-62 351-408 (958)
11 PHA02768 hypothetical protein; 98.4 7.4E-08 1.6E-12 72.3 1.5 42 36-91 6-47 (55)
12 KOG3608 Zn finger proteins [Ge 98.4 1.3E-07 2.7E-12 94.3 3.1 89 9-99 204-316 (467)
13 PHA00733 hypothetical protein 98.4 2.3E-07 4.9E-12 81.5 4.2 52 9-60 70-124 (128)
14 PHA02768 hypothetical protein; 98.4 1.2E-07 2.6E-12 71.2 1.9 40 13-52 7-48 (55)
15 KOG3608 Zn finger proteins [Ge 98.3 3.4E-07 7.4E-12 91.3 3.7 88 12-100 264-377 (467)
16 KOG3993 Transcription factor ( 98.3 3.9E-07 8.4E-12 92.7 2.2 93 12-105 268-386 (500)
17 PLN03086 PRLI-interacting fact 98.2 2.5E-06 5.3E-11 91.1 6.6 83 8-106 449-544 (567)
18 PHA00732 hypothetical protein 98.0 3.3E-06 7.3E-11 68.2 2.6 33 14-46 4-38 (79)
19 PHA00616 hypothetical protein 97.8 7.1E-06 1.5E-10 59.0 0.9 32 35-66 1-32 (44)
20 PHA00732 hypothetical protein 97.8 1.6E-05 3.5E-10 64.2 2.7 49 35-100 1-49 (79)
21 PLN03086 PRLI-interacting fact 97.5 9E-05 2E-09 79.4 4.9 73 11-99 477-564 (567)
22 COG5189 SFP1 Putative transcri 97.5 2.4E-05 5.2E-10 77.4 0.5 64 33-96 347-419 (423)
23 KOG3993 Transcription factor ( 97.4 4.8E-05 1E-09 77.7 1.1 52 11-62 295-383 (500)
24 PF12756 zf-C2H2_2: C2H2 type 97.3 9.6E-05 2.1E-09 60.1 1.7 72 14-98 2-73 (100)
25 PF05605 zf-Di19: Drought indu 97.3 0.00022 4.9E-09 53.2 3.5 44 13-59 4-53 (54)
26 KOG2893 Zn finger protein [Gen 97.3 0.002 4.3E-08 61.9 10.5 54 290-343 283-336 (341)
27 PF13465 zf-H2C2_2: Zinc-finge 97.3 0.00011 2.4E-09 46.9 1.1 13 51-63 2-14 (26)
28 PF13465 zf-H2C2_2: Zinc-finge 97.2 0.00011 2.3E-09 46.9 0.8 22 26-47 1-26 (26)
29 PF00096 zf-C2H2: Zinc finger, 97.2 0.00012 2.7E-09 44.7 1.0 22 36-57 1-22 (23)
30 PF13894 zf-C2H2_4: C2H2-type 97.1 0.00025 5.5E-09 43.0 1.2 24 36-59 1-24 (24)
31 PF05605 zf-Di19: Drought indu 97.0 0.00089 1.9E-08 49.9 3.9 53 35-100 2-54 (54)
32 PF13912 zf-C2H2_6: C2H2-type 96.7 0.00066 1.4E-08 43.1 1.1 25 35-59 1-25 (27)
33 COG5189 SFP1 Putative transcri 96.7 0.00051 1.1E-08 68.2 0.5 47 9-55 346-418 (423)
34 PHA00616 hypothetical protein 96.5 0.0012 2.5E-08 47.6 1.4 30 76-105 2-31 (44)
35 PF00096 zf-C2H2: Zinc finger, 96.3 0.0017 3.7E-08 39.6 0.9 23 76-98 1-23 (23)
36 smart00355 ZnF_C2H2 zinc finge 96.0 0.0049 1.1E-07 37.5 1.9 22 36-57 1-22 (26)
37 PF09237 GAGA: GAGA factor; I 95.9 0.0034 7.3E-08 46.6 1.0 31 33-63 22-52 (54)
38 PF13894 zf-C2H2_4: C2H2-type 95.6 0.0066 1.4E-07 36.6 1.4 24 76-99 1-24 (24)
39 PF12171 zf-C2H2_jaz: Zinc-fin 95.5 0.0049 1.1E-07 39.4 0.5 21 12-32 2-22 (27)
40 KOG3671 Actin regulatory prote 95.4 1.3 2.8E-05 47.0 17.9 18 331-348 541-558 (569)
41 KOG1924 RhoA GTPase effector D 95.2 0.27 5.9E-06 54.4 12.9 12 240-251 607-618 (1102)
42 PF13909 zf-H2C2_5: C2H2-type 94.5 0.018 3.9E-07 35.5 1.1 24 36-60 1-24 (24)
43 PF13912 zf-C2H2_6: C2H2-type 94.5 0.016 3.4E-07 36.7 0.8 25 76-100 2-26 (27)
44 KOG2231 Predicted E3 ubiquitin 94.5 0.036 7.8E-07 60.6 4.0 22 38-59 185-206 (669)
45 smart00355 ZnF_C2H2 zinc finge 94.4 0.037 8.1E-07 33.5 2.5 24 76-99 1-24 (26)
46 KOG1924 RhoA GTPase effector D 94.4 0.36 7.9E-06 53.5 11.3 10 243-252 599-608 (1102)
47 PF12874 zf-met: Zinc-finger o 94.4 0.019 4.1E-07 35.6 1.0 21 36-56 1-21 (25)
48 KOG2231 Predicted E3 ubiquitin 94.3 0.036 7.9E-07 60.6 3.6 69 12-96 183-260 (669)
49 KOG2482 Predicted C2H2-type Zn 94.2 0.026 5.7E-07 56.9 2.0 89 10-98 194-357 (423)
50 KOG1146 Homeobox protein [Gene 94.0 0.024 5.2E-07 65.5 1.5 84 14-97 439-540 (1406)
51 PF12171 zf-C2H2_jaz: Zinc-fin 93.3 0.038 8.3E-07 35.2 1.0 22 36-57 2-23 (27)
52 PRK04860 hypothetical protein; 93.1 0.035 7.5E-07 50.8 0.8 40 34-89 118-157 (160)
53 PF12874 zf-met: Zinc-finger o 92.9 0.062 1.3E-06 33.2 1.5 21 12-32 1-21 (25)
54 COG5048 FOG: Zn-finger [Genera 92.5 0.048 1E-06 54.2 1.0 55 12-66 290-354 (467)
55 COG5236 Uncharacterized conser 92.1 0.14 3.1E-06 51.8 3.7 72 13-100 222-306 (493)
56 smart00451 ZnF_U1 U1-like zinc 91.2 0.16 3.5E-06 33.7 2.1 21 12-32 4-24 (35)
57 PF12756 zf-C2H2_2: C2H2 type 89.4 0.22 4.9E-06 40.1 1.9 37 23-59 35-74 (100)
58 COG5236 Uncharacterized conser 88.9 0.25 5.4E-06 50.1 2.2 60 23-98 200-274 (493)
59 COG5048 FOG: Zn-finger [Genera 88.8 0.14 3E-06 50.9 0.3 59 34-104 288-352 (467)
60 KOG1146 Homeobox protein [Gene 88.0 0.18 4E-06 58.5 0.6 88 12-101 1261-1354(1406)
61 KOG4173 Alpha-SNAP protein [In 87.2 0.27 5.9E-06 46.6 1.2 84 11-97 79-168 (253)
62 PF09538 FYDLN_acid: Protein o 86.8 0.4 8.6E-06 41.1 1.9 37 8-51 6-42 (108)
63 smart00451 ZnF_U1 U1-like zinc 86.4 0.48 1E-05 31.4 1.7 23 35-57 3-25 (35)
64 PF09237 GAGA: GAGA factor; I 85.7 0.75 1.6E-05 34.3 2.5 25 8-32 20-45 (54)
65 PF13913 zf-C2HC_2: zinc-finge 85.2 0.54 1.2E-05 29.7 1.4 18 37-55 4-21 (25)
66 COG4888 Uncharacterized Zn rib 84.6 0.21 4.5E-06 42.2 -0.9 17 33-49 20-36 (104)
67 PF13909 zf-H2C2_5: C2H2-type 84.3 0.58 1.3E-05 28.6 1.3 24 76-100 1-24 (24)
68 KOG2932 E3 ubiquitin ligase in 83.1 57 0.0012 33.2 17.5 25 76-100 145-172 (389)
69 PF13913 zf-C2HC_2: zinc-finge 82.4 0.93 2E-05 28.6 1.7 19 13-32 4-22 (25)
70 TIGR02300 FYDLN_acid conserved 81.4 0.91 2E-05 40.0 1.8 38 8-52 6-43 (129)
71 KOG2186 Cell growth-regulating 80.9 0.88 1.9E-05 44.4 1.7 42 14-57 6-50 (276)
72 COG5188 PRP9 Splicing factor 3 80.4 1.4 3E-05 45.0 2.9 24 9-32 236-259 (470)
73 COG4049 Uncharacterized protei 77.9 1 2.2E-05 34.3 0.8 26 7-32 12-38 (65)
74 KOG2482 Predicted C2H2-type Zn 77.3 1.9 4E-05 44.0 2.7 74 25-98 129-218 (423)
75 PF02892 zf-BED: BED zinc fing 76.4 1.4 3E-05 31.0 1.2 26 33-58 14-43 (45)
76 COG0068 HypF Hydrogenase matur 76.1 0.87 1.9E-05 50.3 0.1 53 14-84 126-182 (750)
77 smart00614 ZnF_BED BED zinc fi 73.1 2 4.2E-05 31.3 1.3 21 37-57 20-45 (50)
78 PF06220 zf-U1: U1 zinc finger 73.1 2.4 5.2E-05 29.5 1.7 22 11-32 3-26 (38)
79 PF12013 DUF3505: Protein of u 72.1 7.4 0.00016 32.8 4.8 29 72-100 77-109 (109)
80 KOG4173 Alpha-SNAP protein [In 70.9 1.3 2.9E-05 42.0 -0.0 47 14-60 109-171 (253)
81 PF05443 ROS_MUCR: ROS/MUCR tr 69.5 1.9 4.1E-05 38.3 0.6 28 33-63 70-97 (132)
82 PF04959 ARS2: Arsenite-resist 68.8 1.7 3.7E-05 41.6 0.2 30 33-62 75-104 (214)
83 KOG3214 Uncharacterized Zn rib 68.6 2.4 5.1E-05 35.9 1.0 8 1-8 1-8 (109)
84 smart00531 TFIIE Transcription 66.7 2.1 4.6E-05 38.3 0.3 18 34-51 98-115 (147)
85 TIGR00622 ssl1 transcription f 66.0 7.5 0.00016 33.6 3.5 72 14-99 18-105 (112)
86 PF09986 DUF2225: Uncharacteri 65.2 2.1 4.6E-05 40.7 0.1 54 33-88 3-61 (214)
87 KOG3408 U1-like Zn-finger-cont 65.1 2.9 6.3E-05 36.6 0.9 23 36-58 58-80 (129)
88 KOG2071 mRNA cleavage and poly 64.2 5.1 0.00011 43.5 2.7 19 14-32 421-439 (579)
89 COG4530 Uncharacterized protei 64.2 4.9 0.00011 34.6 2.0 38 8-53 6-43 (129)
90 PF09986 DUF2225: Uncharacteri 62.9 1.9 4.1E-05 41.1 -0.8 36 13-48 7-61 (214)
91 KOG2785 C2H2-type Zn-finger pr 62.4 6.6 0.00014 40.6 3.0 45 13-57 167-242 (390)
92 PRK00464 nrdR transcriptional 61.7 2 4.4E-05 39.0 -0.7 39 13-52 2-45 (154)
93 PRK14892 putative transcriptio 61.7 3.5 7.6E-05 34.8 0.8 7 1-7 1-7 (99)
94 PRK04023 DNA polymerase II lar 59.5 8.9 0.00019 44.3 3.6 23 63-85 651-673 (1121)
95 PRK06266 transcription initiat 58.8 5.3 0.00011 37.1 1.5 33 34-87 116-148 (178)
96 COG4957 Predicted transcriptio 57.3 4.4 9.5E-05 36.1 0.6 25 36-63 77-101 (148)
97 KOG2785 C2H2-type Zn-finger pr 54.7 14 0.00031 38.2 3.9 62 36-97 167-242 (390)
98 TIGR00373 conserved hypothetic 54.3 6.2 0.00013 35.9 1.1 33 33-86 107-139 (158)
99 PF10716 NdhL: NADH dehydrogen 54.2 8.9 0.00019 31.2 1.9 19 382-400 45-63 (81)
100 PF13717 zinc_ribbon_4: zinc-r 53.7 6 0.00013 27.1 0.7 31 14-45 5-35 (36)
101 KOG1280 Uncharacterized conser 53.5 8.4 0.00018 39.4 2.0 30 72-101 76-105 (381)
102 PF01286 XPA_N: XPA protein N- 52.6 5.5 0.00012 27.3 0.4 26 12-43 4-29 (34)
103 PTZ00255 60S ribosomal protein 50.9 6.5 0.00014 32.7 0.6 12 33-44 34-45 (90)
104 KOG2593 Transcription initiati 50.5 8.3 0.00018 40.4 1.5 20 33-52 126-145 (436)
105 PF04959 ARS2: Arsenite-resist 48.9 9.6 0.00021 36.6 1.5 24 9-32 75-98 (214)
106 PTZ00303 phosphatidylinositol 48.7 7.5 0.00016 43.7 0.8 35 13-50 462-496 (1374)
107 KOG4124 Putative transcription 48.5 3.9 8.4E-05 41.8 -1.2 65 33-97 347-420 (442)
108 PF09332 Mcm10: Mcm10 replicat 48.2 4.9 0.00011 41.2 -0.6 34 14-47 255-297 (344)
109 TIGR02098 MJ0042_CXXC MJ0042 f 48.2 6.4 0.00014 26.7 0.2 32 14-46 5-36 (38)
110 COG1571 Predicted DNA-binding 47.8 9.6 0.00021 40.0 1.4 33 10-49 349-381 (421)
111 COG3677 Transposase and inacti 47.7 5.5 0.00012 35.1 -0.3 37 11-49 30-67 (129)
112 COG5112 UFD2 U1-like Zn-finger 47.6 6.9 0.00015 33.5 0.3 20 36-55 56-75 (126)
113 KOG2186 Cell growth-regulating 47.3 11 0.00023 37.1 1.6 45 36-95 4-48 (276)
114 PF12013 DUF3505: Protein of u 46.7 11 0.00024 31.7 1.4 25 36-60 81-109 (109)
115 KOG2593 Transcription initiati 46.7 11 0.00024 39.6 1.7 29 14-42 131-160 (436)
116 KOG4849 mRNA cleavage factor I 46.3 3.6E+02 0.0079 28.0 13.5 13 300-312 328-340 (498)
117 COG4049 Uncharacterized protei 45.9 7.3 0.00016 29.7 0.2 29 33-61 15-43 (65)
118 PF13719 zinc_ribbon_5: zinc-r 45.8 9.7 0.00021 26.1 0.8 31 14-45 5-35 (37)
119 COG3357 Predicted transcriptio 45.2 8.9 0.00019 32.0 0.6 15 33-47 56-70 (97)
120 PF05191 ADK_lid: Adenylate ki 45.2 6.5 0.00014 27.1 -0.2 32 13-48 3-34 (36)
121 PF14353 CpXC: CpXC protein 45.1 2.5 5.5E-05 36.6 -2.8 45 13-57 3-60 (128)
122 PF04404 ERF: ERF superfamily; 44.8 14 0.00031 33.1 1.9 67 318-395 45-116 (160)
123 PRK06266 transcription initiat 43.4 9.1 0.0002 35.5 0.4 36 10-50 115-151 (178)
124 KOG1802 RNA helicase nonsense 42.9 20 0.00043 40.1 2.9 20 36-55 75-100 (935)
125 PF09845 DUF2072: Zn-ribbon co 42.3 15 0.00033 32.6 1.6 15 35-49 1-15 (131)
126 PRK00398 rpoP DNA-directed RNA 42.1 7.2 0.00016 27.8 -0.4 27 14-46 6-32 (46)
127 PF15269 zf-C2H2_7: Zinc-finge 42.0 15 0.00032 26.9 1.2 21 36-56 21-41 (54)
128 KOG4124 Putative transcription 41.9 5 0.00011 41.1 -1.6 46 10-55 347-418 (442)
129 KOG4577 Transcription factor L 41.4 16 0.00035 36.5 1.8 42 10-51 32-81 (383)
130 PF14369 zf-RING_3: zinc-finge 41.3 12 0.00027 25.5 0.7 32 11-47 2-33 (35)
131 COG2331 Uncharacterized protei 41.3 8.4 0.00018 31.1 -0.1 28 14-45 15-43 (82)
132 COG1996 RPC10 DNA-directed RNA 41.2 12 0.00026 27.7 0.6 25 14-44 9-33 (49)
133 cd00350 rubredoxin_like Rubred 39.7 17 0.00038 24.2 1.2 9 34-42 16-24 (33)
134 COG1997 RPL43A Ribosomal prote 39.4 14 0.0003 30.6 0.8 12 33-44 33-44 (89)
135 KOG1280 Uncharacterized conser 39.0 13 0.00028 38.0 0.8 60 33-94 77-138 (381)
136 TIGR00373 conserved hypothetic 38.9 13 0.00028 33.8 0.7 36 9-49 106-142 (158)
137 PF04573 SPC22: Signal peptida 35.8 28 0.0006 32.4 2.3 36 316-352 99-138 (175)
138 PRK09678 DNA-binding transcrip 35.6 8.8 0.00019 30.6 -0.8 18 33-50 25-44 (72)
139 KOG1923 Rac1 GTPase effector F 35.6 1.4E+02 0.003 33.9 7.9 33 319-351 387-427 (830)
140 smart00659 RPOLCX RNA polymera 35.1 19 0.0004 25.9 0.9 24 14-44 5-28 (44)
141 KOG4215 Hepatocyte nuclear fac 35.0 12 0.00026 38.6 -0.2 17 38-55 39-55 (432)
142 KOG0717 Molecular chaperone (D 34.9 20 0.00044 38.1 1.4 29 9-37 290-318 (508)
143 PHA00626 hypothetical protein 34.8 12 0.00027 28.5 -0.1 15 34-48 22-36 (59)
144 PF03604 DNA_RNApol_7kD: DNA d 33.9 24 0.00053 23.7 1.2 24 14-44 3-26 (32)
145 COG2888 Predicted Zn-ribbon RN 33.8 44 0.00096 25.8 2.7 50 12-84 10-59 (61)
146 cd00065 FYVE FYVE domain; Zinc 33.5 25 0.00054 25.6 1.4 27 14-48 5-31 (57)
147 COG5222 Uncharacterized conser 33.4 88 0.0019 31.7 5.5 6 14-19 277-282 (427)
148 TIGR02605 CxxC_CxxC_SSSS putat 33.0 13 0.00028 26.9 -0.2 12 36-47 6-17 (52)
149 PF01155 HypA: Hydrogenase exp 32.9 17 0.00036 31.2 0.4 26 11-44 70-95 (113)
150 KOG4849 mRNA cleavage factor I 32.6 6E+02 0.013 26.5 17.3 9 79-87 157-165 (498)
151 KOG4167 Predicted DNA-binding 31.8 9.9 0.00021 42.4 -1.5 26 36-61 793-818 (907)
152 TIGR00143 hypF [NiFe] hydrogen 31.1 13 0.00028 41.7 -0.7 35 14-51 71-106 (711)
153 PF06524 NOA36: NOA36 protein; 30.9 25 0.00055 34.8 1.3 81 8-98 138-232 (314)
154 KOG3815 Transcription factor D 30.3 22 0.00047 36.0 0.8 43 9-52 34-79 (322)
155 smart00064 FYVE Protein presen 30.2 28 0.00062 26.4 1.2 28 13-48 12-39 (68)
156 smart00531 TFIIE Transcription 29.9 26 0.00056 31.3 1.1 37 11-48 98-136 (147)
157 KOG1813 Predicted E3 ubiquitin 29.7 30 0.00065 34.8 1.6 57 33-97 239-301 (313)
158 KOG4217 Nuclear receptors of t 29.1 32 0.00068 36.8 1.7 23 13-42 271-293 (605)
159 PRK14873 primosome assembly pr 28.9 40 0.00087 37.6 2.6 10 75-84 422-431 (665)
160 PF05443 ROS_MUCR: ROS/MUCR tr 28.8 31 0.00066 30.7 1.4 21 10-30 70-92 (132)
161 cd00729 rubredoxin_SM Rubredox 28.5 27 0.00059 23.6 0.8 22 14-43 5-26 (34)
162 COG1198 PriA Primosomal protei 28.3 22 0.00047 40.1 0.4 8 14-21 438-445 (730)
163 PF04216 FdhE: Protein involve 27.8 16 0.00034 36.3 -0.8 14 35-48 211-224 (290)
164 KOG4672 Uncharacterized conser 27.5 3.8E+02 0.0083 28.4 9.0 23 8-30 9-32 (487)
165 COG3364 Zn-ribbon containing p 27.5 34 0.00073 29.2 1.3 14 35-48 2-15 (112)
166 PRK04860 hypothetical protein; 26.9 44 0.00095 30.6 2.1 32 76-111 120-151 (160)
167 TIGR00280 L37a ribosomal prote 26.9 20 0.00044 29.9 -0.1 12 33-44 33-44 (91)
168 KOG4727 U1-like Zn-finger prot 26.9 31 0.00067 32.1 1.0 21 12-32 76-96 (193)
169 PF13878 zf-C2H2_3: zinc-finge 26.8 51 0.0011 23.2 1.9 24 76-99 14-39 (41)
170 PF10571 UPF0547: Uncharacteri 26.6 36 0.00077 21.8 1.0 10 37-46 16-25 (26)
171 PF09723 Zn-ribbon_8: Zinc rib 26.1 16 0.00035 25.7 -0.7 13 36-48 6-18 (42)
172 KOG4215 Hepatocyte nuclear fac 25.8 21 0.00046 36.9 -0.2 18 14-32 39-56 (432)
173 COG4957 Predicted transcriptio 25.7 37 0.0008 30.4 1.3 21 9-32 73-94 (148)
174 KOG4167 Predicted DNA-binding 25.5 13 0.00029 41.4 -1.8 25 76-100 793-817 (907)
175 TIGR00622 ssl1 transcription f 25.4 36 0.00078 29.5 1.1 46 13-58 57-104 (112)
176 KOG0978 E3 ubiquitin ligase in 25.1 32 0.00069 38.5 0.9 19 76-94 679-697 (698)
177 PRK12380 hydrogenase nickel in 25.1 29 0.00063 29.7 0.5 12 12-23 71-82 (113)
178 PF13240 zinc_ribbon_2: zinc-r 25.0 37 0.0008 21.0 0.8 7 14-20 2-8 (23)
179 PRK03824 hypA hydrogenase nick 24.5 29 0.00064 30.7 0.4 10 14-23 73-82 (135)
180 COG5151 SSL1 RNA polymerase II 24.5 39 0.00084 34.3 1.3 26 74-99 387-412 (421)
181 PF01363 FYVE: FYVE zinc finge 24.5 24 0.00053 26.9 -0.1 30 12-49 10-39 (69)
182 PF09416 UPF1_Zn_bind: RNA hel 24.1 48 0.001 30.2 1.7 48 36-84 15-69 (152)
183 KOG3454 U1 snRNP-specific prot 23.6 35 0.00075 31.5 0.7 9 11-19 3-11 (165)
184 KOG2807 RNA polymerase II tran 23.2 87 0.0019 32.1 3.5 65 33-99 288-369 (378)
185 KOG3408 U1-like Zn-finger-cont 23.1 46 0.00099 29.3 1.3 30 69-98 51-80 (129)
186 PRK03976 rpl37ae 50S ribosomal 22.8 26 0.00056 29.2 -0.2 12 33-44 34-45 (90)
187 PRK14890 putative Zn-ribbon RN 22.6 67 0.0014 24.7 2.0 33 11-49 7-39 (59)
188 COG0186 RpsQ Ribosomal protein 22.6 22 0.00047 29.5 -0.7 37 339-389 45-84 (87)
189 KOG1923 Rac1 GTPase effector F 22.5 3.7E+02 0.0079 30.7 8.3 8 54-61 177-184 (830)
190 KOG0132 RNA polymerase II C-te 22.5 8.6E+02 0.019 28.0 11.1 10 82-91 510-519 (894)
191 smart00132 LIM Zinc-binding do 22.2 32 0.0007 22.3 0.2 10 76-85 28-37 (39)
192 KOG1740 Predicted mitochondria 22.1 77 0.0017 27.0 2.4 37 339-389 39-78 (107)
193 PF07975 C1_4: TFIIH C1-like d 22.0 30 0.00064 25.8 -0.0 43 14-58 2-44 (51)
194 COG1066 Sms Predicted ATP-depe 21.9 45 0.00098 35.3 1.3 29 1-43 1-29 (456)
195 TIGR00244 transcriptional regu 21.9 29 0.00062 31.5 -0.1 22 33-54 26-47 (147)
196 PRK11823 DNA repair protein Ra 21.8 52 0.0011 34.8 1.8 22 12-43 8-29 (446)
197 PRK03681 hypA hydrogenase nick 21.7 31 0.00068 29.6 0.1 12 12-23 71-82 (114)
198 PF14051 Requiem_N: N-terminal 21.1 44 0.00096 26.8 0.8 22 331-352 21-42 (74)
199 CHL00142 rps17 ribosomal prote 21.1 23 0.0005 29.1 -0.8 55 318-389 21-79 (84)
200 PF15168 TRIQK: Triple QxxK/R 20.9 44 0.00096 27.0 0.7 15 391-405 61-75 (79)
201 TIGR00100 hypA hydrogenase nic 20.9 40 0.00087 28.9 0.6 11 36-46 71-81 (115)
202 PRK08572 rps17p 30S ribosomal 20.8 26 0.00056 30.1 -0.6 67 303-388 34-105 (108)
203 PF07535 zf-DBF: DBF zinc fing 20.7 45 0.00098 24.6 0.7 19 11-32 5-23 (49)
204 PF02176 zf-TRAF: TRAF-type zi 20.7 35 0.00075 25.1 0.1 33 14-47 12-54 (60)
205 PF00301 Rubredoxin: Rubredoxi 20.6 30 0.00066 25.2 -0.2 13 36-48 2-14 (47)
206 KOG0782 Predicted diacylglycer 20.6 20 0.00044 39.1 -1.6 80 315-394 453-557 (1004)
207 PF12907 zf-met2: Zinc-binding 20.5 21 0.00046 25.3 -1.0 27 36-62 2-31 (40)
208 PF00412 LIM: LIM domain; Int 20.3 22 0.00047 25.8 -1.0 36 14-49 1-40 (58)
209 cd00730 rubredoxin Rubredoxin; 20.2 39 0.00084 25.0 0.3 13 36-48 2-14 (50)
210 KOG2071 mRNA cleavage and poly 20.0 55 0.0012 35.8 1.5 26 33-58 416-441 (579)
211 PRK05610 rpsQ 30S ribosomal pr 20.0 28 0.00061 28.5 -0.5 51 321-388 28-81 (84)
No 1
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=99.96 E-value=2.4e-27 Score=222.31 Aligned_cols=110 Identities=56% Similarity=1.064 Sum_probs=96.9
Q ss_pred CCCCCCCCCCcccccccCcccCChhHHHHHhhcCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCcccccc
Q 015552 1 MGKKKKRVSSKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEI 80 (405)
Q Consensus 1 mgkKkrr~geKp~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~i 80 (405)
|||||++ ..|+||.+|++.|.++..|.+|++.|+|||++|.|++.+--.|..|..++|+|...+++++..+|+..+.+|
T Consensus 1 mgrkkkk-~~kpwcwycnrefddekiliqhqkakhfkchichkkl~sgpglsihcmqvhketid~ip~av~gr~~i~vei 79 (341)
T KOG2893|consen 1 MGRKKKK-VDKPWCWYCNREFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIHCMQVHKETIDKIPAAVHGRDNIHVEI 79 (341)
T ss_pred CCccccc-cCCceeeecccccchhhhhhhhhhhccceeeeehhhhccCCCceeehhhhhhhhhhcccccccCCcceeEEE
Confidence 8999999 789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCChHHHHHHHhhhcCCCcccccccCCCCC
Q 015552 81 YGMQGIPPDVLAAHYGEEEEEVPSKMAKVDTSFP 114 (405)
Q Consensus 81 Cgk~F~~~s~L~~H~r~h~~e~~~k~ak~~~p~~ 114 (405)
+|+..+.++..+. ..+++.++|+.+++..+.
T Consensus 80 ygmqgip~~~~r~---~~de~~~ekr~~~d~~~~ 110 (341)
T KOG2893|consen 80 YGMQGIPSGAYRG---AADEEPDEKRSRMDNGPP 110 (341)
T ss_pred eeccCCCchhhhh---hhhcCchhhhhcccCCCC
Confidence 9999999876543 344455556666665443
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.58 E-value=1.6e-15 Score=145.89 Aligned_cols=89 Identities=19% Similarity=0.276 Sum_probs=80.6
Q ss_pred ccccCcccCChhHHHHHhh--cCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCCCChHHH
Q 015552 14 CYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVL 91 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R--EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F~~~s~L 91 (405)
|.+|||+|.....|+.|+| .-+++|.+|||.|.+.-.|+.|+|+|+|||+ |.|..|+|.|.++++|
T Consensus 164 C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP------------F~C~hC~kAFADRSNL 231 (279)
T KOG2462|consen 164 CKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKP------------FSCPHCGKAFADRSNL 231 (279)
T ss_pred CCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCC------------ccCCcccchhcchHHH
Confidence 9999999999999999999 6699999999999999999999999999987 8888999999999999
Q ss_pred HHHHhhhcCCCcccccccCCCCC
Q 015552 92 AAHYGEEEEEVPSKMAKVDTSFP 114 (405)
Q Consensus 92 ~~H~r~h~~e~~~k~ak~~~p~~ 114 (405)
+.|+++|.+.+.+++.+......
T Consensus 232 RAHmQTHS~~K~~qC~~C~KsFs 254 (279)
T KOG2462|consen 232 RAHMQTHSDVKKHQCPRCGKSFA 254 (279)
T ss_pred HHHHHhhcCCccccCcchhhHHH
Confidence 99999999998888777754433
No 3
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.49 E-value=1e-14 Score=140.40 Aligned_cols=76 Identities=18% Similarity=0.291 Sum_probs=70.0
Q ss_pred cccccccCcccCChhHHHHHhh----cCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCCC
Q 015552 11 KVWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGI 86 (405)
Q Consensus 11 Kp~C~~CgK~F~~ks~Lk~H~R----EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F~ 86 (405)
...|.+|||+|++...|+.|+| ||||.|..|+|+|..++||+.|+++|.+.|. |+|..|+|.|.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~------------~qC~~C~KsFs 254 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK------------HQCPRCGKSFA 254 (279)
T ss_pred CcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc------------ccCcchhhHHH
Confidence 3449999999999999999999 9999999999999999999999999988775 99999999999
Q ss_pred ChHHHHHHHhhh
Q 015552 87 PPDVLAAHYGEE 98 (405)
Q Consensus 87 ~~s~L~~H~r~h 98 (405)
..+.|.+|...-
T Consensus 255 l~SyLnKH~ES~ 266 (279)
T KOG2462|consen 255 LKSYLNKHSESA 266 (279)
T ss_pred HHHHHHHhhhhc
Confidence 999999997543
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.25 E-value=1.3e-12 Score=138.25 Aligned_cols=74 Identities=16% Similarity=0.345 Sum_probs=70.2
Q ss_pred ccc-ccccCcccCChhHHHHHhh----cCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCC
Q 015552 11 KVW-CYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQG 85 (405)
Q Consensus 11 Kp~-C~~CgK~F~~ks~Lk~H~R----EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F 85 (405)
-.| |+.|+|+|...+.|.+|.- .|||+|.+|.|.|..+.+|..|.|.|.|||+ |+|+.|+|+|
T Consensus 893 gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP------------fQCdKClKRF 960 (1007)
T KOG3623|consen 893 GMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP------------FQCDKCLKRF 960 (1007)
T ss_pred ccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc------------chhhhhhhhc
Confidence 345 9999999999999999988 8999999999999999999999999999997 9999999999
Q ss_pred CChHHHHHHHh
Q 015552 86 IPPDVLAAHYG 96 (405)
Q Consensus 86 ~~~s~L~~H~r 96 (405)
.+.....+||.
T Consensus 961 SHSGSYSQHMN 971 (1007)
T KOG3623|consen 961 SHSGSYSQHMN 971 (1007)
T ss_pred ccccchHhhhc
Confidence 99999999985
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.23 E-value=1.9e-12 Score=119.99 Aligned_cols=80 Identities=16% Similarity=0.245 Sum_probs=67.8
Q ss_pred CCcccccccCcccCChhHHHHHhh----cCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCC
Q 015552 9 SSKVWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQ 84 (405)
Q Consensus 9 geKp~C~~CgK~F~~ks~Lk~H~R----EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~ 84 (405)
...+.|.+|+|.|.....|.+|++ .|.|.|..|||.|...-.|+||+|+|++.++ |+|..|+|.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp------------ykc~~c~ka 182 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP------------YKCSLCEKA 182 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc------------cchhhhhHH
Confidence 345569999999999999999999 7889999999999999999999999998887 777888888
Q ss_pred CCChHHHHHHHhhhcC
Q 015552 85 GIPPDVLAAHYGEEEE 100 (405)
Q Consensus 85 F~~~s~L~~H~r~h~~ 100 (405)
|.++..|+.|.+.-++
T Consensus 183 ftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 183 FTQRCSLESHLKKVHG 198 (267)
T ss_pred HHhhccHHHHHHHHcC
Confidence 8888888888776554
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.10 E-value=2e-11 Score=113.33 Aligned_cols=88 Identities=22% Similarity=0.385 Sum_probs=74.6
Q ss_pred CcccccccCcccCChhHHHHHhh----cCcccccccccCCCChhhHHHHhhhhccccc---cccCCCCCCCCccccccCC
Q 015552 10 SKVWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENV---TKVPNAKPGRESTDIEIYG 82 (405)
Q Consensus 10 eKp~C~~CgK~F~~ks~Lk~H~R----EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp---~~cp~~kpgRk~~~C~iCg 82 (405)
.|+.|..|||.|.+-.+|++|+| .|||+|..|+|.|+++..|..|++.+|+... |+.. ..+-|-|+.||
T Consensus 144 kr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yayker----r~kl~vcedcg 219 (267)
T KOG3576|consen 144 KRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKER----RAKLYVCEDCG 219 (267)
T ss_pred HHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHh----hhheeeecccC
Confidence 34559999999999999999999 8999999999999999999999999998642 2221 22349999999
Q ss_pred CCCCChHHHHHHHhhhcCC
Q 015552 83 MQGIPPDVLAAHYGEEEEE 101 (405)
Q Consensus 83 k~F~~~s~L~~H~r~h~~e 101 (405)
..-...+.+..|++.|+..
T Consensus 220 ~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 220 YTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred CCCCChhHHHHHHHhcCCC
Confidence 9999999999999988754
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.95 E-value=2.3e-10 Score=121.61 Aligned_cols=74 Identities=18% Similarity=0.269 Sum_probs=55.4
Q ss_pred ccccccCcccCChhHHHHHhh-----------------cCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCC
Q 015552 12 VWCYYCDREFDDEKILVQHQK-----------------AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRE 74 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~R-----------------EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk 74 (405)
+.|-.|..+|.++..|.+|+. -|.|||..|||.|..+.+|+.|+|+|.|||+
T Consensus 241 fsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKP----------- 309 (1007)
T KOG3623|consen 241 FSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKP----------- 309 (1007)
T ss_pred CcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCC-----------
Confidence 337778888888877777776 4668888888888888888888888877776
Q ss_pred ccccccCCCCCCChHHHHHHHhh
Q 015552 75 STDIEIYGMQGIPPDVLAAHYGE 97 (405)
Q Consensus 75 ~~~C~iCgk~F~~~s~L~~H~r~ 97 (405)
|+|..|+|+|.+...+..|+..
T Consensus 310 -feCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 310 -FECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred -cCCcccccccccCCcccccccc
Confidence 6666677777777777777643
No 8
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.91 E-value=4.1e-10 Score=121.45 Aligned_cols=85 Identities=25% Similarity=0.378 Sum_probs=74.0
Q ss_pred ccccccCcccCChhHHHHHhh----cCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccc---cCCCC
Q 015552 12 VWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIE---IYGMQ 84 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~R----EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~---iCgk~ 84 (405)
-.|-+|.|..+.++.|+.|+| ||||||++||+.|+++.||+.|+ .+|+-++ +.|-.+.|. +|.+.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~-~vHka~p-------~~R~q~ScP~~~ic~~k 677 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHM-SVHKAKP-------PARVQFSCPSTFICQKK 677 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcc-cccccCc-------cccccccCCchhhhccc
Confidence 349999999999999999999 99999999999999999999998 5666553 345558898 99999
Q ss_pred CCChHHHHHHHhhhcCCCcc
Q 015552 85 GIPPDVLAAHYGEEEEEVPS 104 (405)
Q Consensus 85 F~~~s~L~~H~r~h~~e~~~ 104 (405)
|...-.|.+|+++|.+....
T Consensus 678 ftn~V~lpQhIriH~~~~~s 697 (958)
T KOG1074|consen 678 FTNAVTLPQHIRIHLGGQIS 697 (958)
T ss_pred ccccccccceEEeecCCCCC
Confidence 99999999999999865433
No 9
>PHA00733 hypothetical protein
Probab=98.75 E-value=8.3e-09 Score=90.57 Aligned_cols=76 Identities=11% Similarity=0.143 Sum_probs=64.1
Q ss_pred ccccccCcccCChhHHHHH------hh---cCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCC
Q 015552 12 VWCYYCDREFDDEKILVQH------QK---AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYG 82 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H------~R---EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCg 82 (405)
..|.+|++.|.....|..| .. +++|+|..|++.|.+..+|.+|++.+ . .. +.|.+|+
T Consensus 41 ~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~-~~------------~~C~~Cg 106 (128)
T PHA00733 41 LIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT-E-HS------------KVCPVCG 106 (128)
T ss_pred HHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC-C-cC------------ccCCCCC
Confidence 3499999999988777766 22 78999999999999999999998654 2 22 8899999
Q ss_pred CCCCChHHHHHHHhhhcCC
Q 015552 83 MQGIPPDVLAAHYGEEEEE 101 (405)
Q Consensus 83 k~F~~~s~L~~H~r~h~~e 101 (405)
+.|...+.|.+|++..++.
T Consensus 107 K~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 107 KEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred CccCCHHHHHHHHHHhcCc
Confidence 9999999999999887753
No 10
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.68 E-value=6.6e-09 Score=112.29 Aligned_cols=54 Identities=26% Similarity=0.620 Sum_probs=48.7
Q ss_pred CCcccccccCcccCChhHHHHHhh----cCcccccccccCCCChhhHHHHhhhhcccc
Q 015552 9 SSKVWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKEN 62 (405)
Q Consensus 9 geKp~C~~CgK~F~~ks~Lk~H~R----EKPfkC~~CgKsFs~~s~L~rH~r~hH~ek 62 (405)
..|+.|.+|.|.|...+.|+.|.| ||||+|++||.+|+++.+|+.|..+|+.+.
T Consensus 351 ~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~ 408 (958)
T KOG1074|consen 351 FFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREKY 408 (958)
T ss_pred cccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeeccccC
Confidence 446679999999999999999999 999999999999999999999986666554
No 11
>PHA02768 hypothetical protein; Provisional
Probab=98.43 E-value=7.4e-08 Score=72.31 Aligned_cols=42 Identities=10% Similarity=0.226 Sum_probs=26.3
Q ss_pred ccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCCCChHHH
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVL 91 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F~~~s~L 91 (405)
|+|..|||.|++.++|.+|+|+|+ ++ ++|..|++.|.+.+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~------------~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TN------------LKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--Cc------------ccCCcccceeccccee
Confidence 566666666666666666666655 22 5566666666655544
No 12
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.42 E-value=1.3e-07 Score=94.34 Aligned_cols=89 Identities=21% Similarity=0.361 Sum_probs=61.0
Q ss_pred CCccc-ccccCcccCChhHHHHHhh------cCcccccccccCCCChhhHHHHhhhhccccccccCCCC-----------
Q 015552 9 SSKVW-CYYCDREFDDEKILVQHQK------AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAK----------- 70 (405)
Q Consensus 9 geKp~-C~~CgK~F~~ks~Lk~H~R------EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~k----------- 70 (405)
+||.. |..||+.|.++..|-.|.| ..+|.|..|.|+|.++..|+.|+++|-. .++|+.|.
T Consensus 204 ~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~ 281 (467)
T KOG3608|consen 204 NEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASSLTT 281 (467)
T ss_pred CCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCChHHHHH
Confidence 56666 7777777777777777777 4567777777777777777777655432 34555431
Q ss_pred ------CCCCccccccCCCCCCChHHHHHHHhhhc
Q 015552 71 ------PGRESTDIEIYGMQGIPPDVLAAHYGEEE 99 (405)
Q Consensus 71 ------pgRk~~~C~iCgk~F~~~s~L~~H~r~h~ 99 (405)
-..+.|+|+.|++.|.+.++|.+|...|.
T Consensus 282 H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 282 HIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 12345888888888888888888777665
No 13
>PHA00733 hypothetical protein
Probab=98.41 E-value=2.3e-07 Score=81.53 Aligned_cols=52 Identities=25% Similarity=0.441 Sum_probs=48.3
Q ss_pred CCccc-ccccCcccCChhHHHHHhh--cCcccccccccCCCChhhHHHHhhhhcc
Q 015552 9 SSKVW-CYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLSTAGGMAIHVLQVHK 60 (405)
Q Consensus 9 geKp~-C~~CgK~F~~ks~Lk~H~R--EKPfkC~~CgKsFs~~s~L~rH~r~hH~ 60 (405)
+++++ |..|++.|.....|++|++ +++|+|.+|++.|.....|.+|++..|+
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 46677 9999999999999999999 8899999999999999999999988775
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.40 E-value=1.2e-07 Score=71.16 Aligned_cols=40 Identities=18% Similarity=0.379 Sum_probs=37.4
Q ss_pred cccccCcccCChhHHHHHhh--cCcccccccccCCCChhhHH
Q 015552 13 WCYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLSTAGGMA 52 (405)
Q Consensus 13 ~C~~CgK~F~~ks~Lk~H~R--EKPfkC~~CgKsFs~~s~L~ 52 (405)
.|.+|||.|.+.++|.+|+| .|+|+|..|+|.|.+.+.|.
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred CcchhCCeeccHHHHHHHHHhcCCcccCCcccceecccceeE
Confidence 49999999999999999999 78999999999999988775
No 15
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.33 E-value=3.4e-07 Score=91.33 Aligned_cols=88 Identities=22% Similarity=0.300 Sum_probs=71.1
Q ss_pred ccccccCcccCChhHHHHHhh-----cCcccccccccCCCChhhHHHHhhhhccccccccCC--CC--------------
Q 015552 12 VWCYYCDREFDDEKILVQHQK-----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPN--AK-------------- 70 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~R-----EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~--~k-------------- 70 (405)
+.|..|+.+....+.|.+|+| +|+|||..|++.|.+.+.|.+|.. +|.+..+.|.. |.
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~-~HS~~~y~C~h~~C~~s~r~~~q~~~H~~ 342 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ-VHSKTVYQCEHPDCHYSVRTYTQMRRHFL 342 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH-hccccceecCCCCCcHHHHHHHHHHHHHH
Confidence 348888888888888888888 899999999999999999999985 66677788865 31
Q ss_pred ---C--CCCccccccCCCCCCChHHHHHHHhhhcC
Q 015552 71 ---P--GRESTDIEIYGMQGIPPDVLAAHYGEEEE 100 (405)
Q Consensus 71 ---p--gRk~~~C~iCgk~F~~~s~L~~H~r~h~~ 100 (405)
+ ..-.|.|+.|++.|..-..|.+|+...++
T Consensus 343 evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 343 EVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred HhccCCCCCceeeecchhhhccchhHHHHHHHhhc
Confidence 1 22349999999999999999999876654
No 16
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.25 E-value=3.9e-07 Score=92.68 Aligned_cols=93 Identities=22% Similarity=0.353 Sum_probs=71.9
Q ss_pred ccccccCcccCChhHHHHHhh----cCcccccccccCCCChhhHHHHhhhhcccccccc----CCC--------------
Q 015552 12 VWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKV----PNA-------------- 69 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~R----EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~c----p~~-------------- 69 (405)
+.|+.|...|.+...|.+|.. .-.|+|..|+|.|+--.||..| |+.|+-++.-- +-.
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASH-RRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASH-RRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhh-hcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 349999999999999999988 5679999999999999999999 56776543111 000
Q ss_pred CCCC----CccccccCCCCCCChHHHHHHHhhhcCCCccc
Q 015552 70 KPGR----ESTDIEIYGMQGIPPDVLAAHYGEEEEEVPSK 105 (405)
Q Consensus 70 kpgR----k~~~C~iCgk~F~~~s~L~~H~r~h~~e~~~k 105 (405)
+-|. .-|.|++|+|.|.+...|+.|..+|+.....+
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 0111 12899999999999999999999987644333
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.19 E-value=2.5e-06 Score=91.11 Aligned_cols=83 Identities=14% Similarity=0.189 Sum_probs=59.4
Q ss_pred CCCccc-ccccCcccCChhHHHHHhh--cCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCC
Q 015552 8 VSSKVW-CYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQ 84 (405)
Q Consensus 8 ~geKp~-C~~CgK~F~~ks~Lk~H~R--EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~ 84 (405)
..++++ |.+|++.|. ...|+.|++ .+++.|. |++.+ .+..|..|+++|..+++ +.|..|++.
T Consensus 449 el~~H~~C~~Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp------------i~C~fC~~~ 513 (567)
T PLN03086 449 EAKNHVHCEKCGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRL------------ITCRFCGDM 513 (567)
T ss_pred ccccCccCCCCCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCc------------eeCCCCCCc
Confidence 346677 999999996 677999999 7899999 99765 66899999877776666 666667766
Q ss_pred CCC----------hHHHHHHHhhhcCCCcccc
Q 015552 85 GIP----------PDVLAAHYGEEEEEVPSKM 106 (405)
Q Consensus 85 F~~----------~s~L~~H~r~h~~e~~~k~ 106 (405)
|.. ...|..|+... +.+...+
T Consensus 514 v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C 544 (567)
T PLN03086 514 VQAGGSAMDVRDRLRGMSEHESIC-GSRTAPC 544 (567)
T ss_pred cccCccccchhhhhhhHHHHHHhc-CCcceEc
Confidence 631 23566666553 4444433
No 18
>PHA00732 hypothetical protein
Probab=98.00 E-value=3.3e-06 Score=68.21 Aligned_cols=33 Identities=30% Similarity=0.460 Sum_probs=15.4
Q ss_pred ccccCcccCChhHHHHHhh--cCcccccccccCCC
Q 015552 14 CYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLS 46 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R--EKPfkC~~CgKsFs 46 (405)
|..|++.|.+...|++|++ ...+.|..|+++|.
T Consensus 4 C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~ 38 (79)
T PHA00732 4 CPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR 38 (79)
T ss_pred CCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC
Confidence 4444444444444444443 23344444444444
No 19
>PHA00616 hypothetical protein
Probab=97.79 E-value=7.1e-06 Score=58.96 Aligned_cols=32 Identities=25% Similarity=0.485 Sum_probs=28.7
Q ss_pred cccccccccCCCChhhHHHHhhhhcccccccc
Q 015552 35 HFKCHVCHKKLSTAGGMAIHVLQVHKENVTKV 66 (405)
Q Consensus 35 PfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~c 66 (405)
+|+|..||+.|..+++|.+|+++||+++++.|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 68999999999999999999999999987544
No 20
>PHA00732 hypothetical protein
Probab=97.76 E-value=1.6e-05 Score=64.22 Aligned_cols=49 Identities=20% Similarity=0.259 Sum_probs=41.5
Q ss_pred cccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCCCChHHHHHHHhhhcC
Q 015552 35 HFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVLAAHYGEEEE 100 (405)
Q Consensus 35 PfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F~~~s~L~~H~r~h~~ 100 (405)
+|+|..|++.|.+.++|++|++.+|.. +.|++|++.|. .|.+|.+++.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~--------------~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL--------------TKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC--------------CccCCCCCEeC---ChhhhhcccCC
Confidence 589999999999999999998755542 56999999999 47889888765
No 21
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.52 E-value=9e-05 Score=79.36 Aligned_cols=73 Identities=18% Similarity=0.323 Sum_probs=55.7
Q ss_pred ccc-ccccCcccCChhHHHHHhh----cCcccccccccCCCC----------hhhHHHHhhhhccccccccCCCCCCCCc
Q 015552 11 KVW-CYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLST----------AGGMAIHVLQVHKENVTKVPNAKPGRES 75 (405)
Q Consensus 11 Kp~-C~~CgK~F~~ks~Lk~H~R----EKPfkC~~CgKsFs~----------~s~L~rH~r~hH~ekp~~cp~~kpgRk~ 75 (405)
+.+ |. ||+.| .+..|..|++ +|++.|..|++.|.. ...|..|++. .+.+.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~-CG~rt------------ 541 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI-CGSRT------------ 541 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh-cCCcc------------
Confidence 344 99 99866 5689999987 899999999999952 3578889754 34443
Q ss_pred cccccCCCCCCChHHHHHHHhhhc
Q 015552 76 TDIEIYGMQGIPPDVLAAHYGEEE 99 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H~r~h~ 99 (405)
+.|..||+.+..++ +..|+..-+
T Consensus 542 ~~C~~Cgk~Vrlrd-m~~H~~~~h 564 (567)
T PLN03086 542 APCDSCGRSVMLKE-MDIHQIAVH 564 (567)
T ss_pred eEccccCCeeeehh-HHHHHHHhh
Confidence 89999999887765 567765543
No 22
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.52 E-value=2.4e-05 Score=77.37 Aligned_cols=64 Identities=25% Similarity=0.351 Sum_probs=46.3
Q ss_pred cCcccccc--cccCCCChhhHHHHhhhhcc-----ccccccCC--CCCCCCccccccCCCCCCChHHHHHHHh
Q 015552 33 AKHFKCHV--CHKKLSTAGGMAIHVLQVHK-----ENVTKVPN--AKPGRESTDIEIYGMQGIPPDVLAAHYG 96 (405)
Q Consensus 33 EKPfkC~~--CgKsFs~~s~L~rH~r~hH~-----ekp~~cp~--~kpgRk~~~C~iCgk~F~~~s~L~~H~r 96 (405)
+|+|+|.+ |+|++...-.|+-|++--|. +.+...+. -.-..|.|+|++|+|++.....|+-|++
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 79999998 99999999999999643341 11111111 0123455999999999999999998865
No 23
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.42 E-value=4.8e-05 Score=77.74 Aligned_cols=52 Identities=27% Similarity=0.538 Sum_probs=44.9
Q ss_pred cccccccCcccCChhHHHHHhh----------------cC---------------------cccccccccCCCChhhHHH
Q 015552 11 KVWCYYCDREFDDEKILVQHQK----------------AK---------------------HFKCHVCHKKLSTAGGMAI 53 (405)
Q Consensus 11 Kp~C~~CgK~F~~ks~Lk~H~R----------------EK---------------------PfkC~~CgKsFs~~s~L~r 53 (405)
.|.|.+|+|.|+.-.+|..|+| ++ -|.|.+|+|+|.+...|+.
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 3459999999999999999999 11 2889999999999999999
Q ss_pred Hhhhhcccc
Q 015552 54 HVLQVHKEN 62 (405)
Q Consensus 54 H~r~hH~ek 62 (405)
|+.+||...
T Consensus 375 Hqlthq~~~ 383 (500)
T KOG3993|consen 375 HQLTHQRAP 383 (500)
T ss_pred hHHhhhccc
Confidence 998887543
No 24
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.33 E-value=9.6e-05 Score=60.10 Aligned_cols=72 Identities=24% Similarity=0.229 Sum_probs=20.9
Q ss_pred ccccCcccCChhHHHHHhhcCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCCCChHHHHH
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVLAA 93 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F~~~s~L~~ 93 (405)
|.+|+..|.....|..|+++..-......+.+.....+..+.+.... ..+.|.+|++.|.....|..
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~-------------~~~~C~~C~~~f~s~~~l~~ 68 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVK-------------ESFRCPYCNKTFRSREALQE 68 (100)
T ss_dssp ------------------------------------------------------------SSEEBSSSS-EESSHHHHHH
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccC-------------CCCCCCccCCCCcCHHHHHH
Confidence 66666666666666666652221111122222333333333322111 13889999999999999999
Q ss_pred HHhhh
Q 015552 94 HYGEE 98 (405)
Q Consensus 94 H~r~h 98 (405)
|++.+
T Consensus 69 Hm~~~ 73 (100)
T PF12756_consen 69 HMRSK 73 (100)
T ss_dssp HHHHT
T ss_pred HHcCc
Confidence 99875
No 25
>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=97.32 E-value=0.00022 Score=53.16 Aligned_cols=44 Identities=27% Similarity=0.625 Sum_probs=23.3
Q ss_pred cccccCcccCChhHHHHHhh------cCcccccccccCCCChhhHHHHhhhhc
Q 015552 13 WCYYCDREFDDEKILVQHQK------AKHFKCHVCHKKLSTAGGMAIHVLQVH 59 (405)
Q Consensus 13 ~C~~CgK~F~~ks~Lk~H~R------EKPfkC~~CgKsFs~~s~L~rH~r~hH 59 (405)
.|.+|++. .+...|..|.. .+.+.|.+|.+.+. .+|.+|++.+|
T Consensus 4 ~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 4 TCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 36666663 33445665555 24455666665433 25666655544
No 26
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=97.31 E-value=0.002 Score=61.89 Aligned_cols=54 Identities=33% Similarity=0.447 Sum_probs=40.8
Q ss_pred CCCCCCCCCCCCCCCcccCCCCCCCCCCceEEEEEcccccChHHHhhccCceee
Q 015552 290 ASGPNTGGPSIGPPPVIANKAPATQPAVNEVYLVWEDEAMSMEERRMSSVKYQV 343 (405)
Q Consensus 290 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 343 (405)
++...|+.++.+.+.++...-+++--++.-.-|+-+||.+|.||||+.|+|||-
T Consensus 283 ~sttsttnsta~kpaasitskpatltttsatklihpdedisleerraqlpkyqr 336 (341)
T KOG2893|consen 283 ESTTSTTNSTAGKPAASITSKPATLTTTSATKLIHPDEDISLEERRAQLPKYQR 336 (341)
T ss_pred cccccCcccccccchhhhhcccceeccccceeeeCCcccccHHHHhhhhhhhhh
Confidence 344445555566666655555777766777799999999999999999999984
No 27
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.27 E-value=0.00011 Score=46.90 Aligned_cols=13 Identities=15% Similarity=0.115 Sum_probs=7.1
Q ss_pred HHHHhhhhccccc
Q 015552 51 MAIHVLQVHKENV 63 (405)
Q Consensus 51 L~rH~r~hH~ekp 63 (405)
|.+|++.|+++++
T Consensus 2 l~~H~~~H~~~k~ 14 (26)
T PF13465_consen 2 LRRHMRTHTGEKP 14 (26)
T ss_dssp HHHHHHHHSSSSS
T ss_pred HHHHhhhcCCCCC
Confidence 5555555555544
No 28
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.23 E-value=0.00011 Score=46.94 Aligned_cols=22 Identities=36% Similarity=0.700 Sum_probs=18.4
Q ss_pred HHHHHhh----cCcccccccccCCCC
Q 015552 26 ILVQHQK----AKHFKCHVCHKKLST 47 (405)
Q Consensus 26 ~Lk~H~R----EKPfkC~~CgKsFs~ 47 (405)
+|++|++ ||+|+|.+|+++|.+
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 3666776 999999999999974
No 29
>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=97.22 E-value=0.00012 Score=44.72 Aligned_cols=22 Identities=27% Similarity=0.730 Sum_probs=16.9
Q ss_pred ccccccccCCCChhhHHHHhhh
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQ 57 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~ 57 (405)
|+|.+|++.|.++..|.+|++.
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 5777888888888888888765
No 30
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.06 E-value=0.00025 Score=42.99 Aligned_cols=24 Identities=25% Similarity=0.661 Sum_probs=17.1
Q ss_pred ccccccccCCCChhhHHHHhhhhc
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQVH 59 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~hH 59 (405)
|+|.+|++.|.+...|.+|++++|
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 578888888888888888877665
No 31
>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=97.00 E-value=0.00089 Score=49.93 Aligned_cols=53 Identities=19% Similarity=0.327 Sum_probs=41.0
Q ss_pred cccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCCCChHHHHHHHhhhcC
Q 015552 35 HFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVLAAHYGEEEE 100 (405)
Q Consensus 35 PfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F~~~s~L~~H~r~h~~ 100 (405)
-|.|.+|++. .+...|..|....|... ++.+.|.+|...+. ++|.+|++.+++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~----------~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSE----------SKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCC----------CCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 4899999994 55678999988888654 22488999998654 489999987653
No 32
>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=96.71 E-value=0.00066 Score=43.09 Aligned_cols=25 Identities=24% Similarity=0.460 Sum_probs=19.7
Q ss_pred cccccccccCCCChhhHHHHhhhhc
Q 015552 35 HFKCHVCHKKLSTAGGMAIHVLQVH 59 (405)
Q Consensus 35 PfkC~~CgKsFs~~s~L~rH~r~hH 59 (405)
+|+|..|++.|.....|..|++.|+
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 4788888888888888888876665
No 33
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.68 E-value=0.00051 Score=68.24 Aligned_cols=47 Identities=26% Similarity=0.677 Sum_probs=42.6
Q ss_pred CCccc-ccc--cCcccCChhHHHHHhh-----------------------cCcccccccccCCCChhhHHHHh
Q 015552 9 SSKVW-CYY--CDREFDDEKILVQHQK-----------------------AKHFKCHVCHKKLSTAGGMAIHV 55 (405)
Q Consensus 9 geKp~-C~~--CgK~F~~ks~Lk~H~R-----------------------EKPfkC~~CgKsFs~~s~L~rH~ 55 (405)
++|+| |.+ |+|+++....|+-|+. .|||+|.+|+|++...-.|+-|.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 46888 987 9999999999999887 59999999999999999999884
No 34
>PHA00616 hypothetical protein
Probab=96.52 E-value=0.0012 Score=47.61 Aligned_cols=30 Identities=7% Similarity=-0.190 Sum_probs=27.4
Q ss_pred cccccCCCCCCChHHHHHHHhhhcCCCccc
Q 015552 76 TDIEIYGMQGIPPDVLAAHYGEEEEEVPSK 105 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H~r~h~~e~~~k 105 (405)
|+|..||+.|+...+|.+|++.|+++++..
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 889999999999999999999999986553
No 35
>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=96.28 E-value=0.0017 Score=39.59 Aligned_cols=23 Identities=17% Similarity=0.083 Sum_probs=21.2
Q ss_pred cccccCCCCCCChHHHHHHHhhh
Q 015552 76 TDIEIYGMQGIPPDVLAAHYGEE 98 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H~r~h 98 (405)
|.|.+|++.|.....|.+|++.|
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 57999999999999999999874
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.97 E-value=0.0049 Score=37.52 Aligned_cols=22 Identities=18% Similarity=0.563 Sum_probs=16.6
Q ss_pred ccccccccCCCChhhHHHHhhh
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQ 57 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~ 57 (405)
|+|..|++.|.....|.+|++.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH
Confidence 5677788888888888888753
No 37
>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=95.86 E-value=0.0034 Score=46.55 Aligned_cols=31 Identities=13% Similarity=0.288 Sum_probs=23.5
Q ss_pred cCcccccccccCCCChhhHHHHhhhhccccc
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENV 63 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp 63 (405)
++|..|.+|+..+.+..+|+||+..+|+.|+
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 8999999999999999999999999998774
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=95.59 E-value=0.0066 Score=36.56 Aligned_cols=24 Identities=17% Similarity=0.079 Sum_probs=20.0
Q ss_pred cccccCCCCCCChHHHHHHHhhhc
Q 015552 76 TDIEIYGMQGIPPDVLAAHYGEEE 99 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H~r~h~ 99 (405)
|.|.+|++.|.....|++|++.|+
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 579999999999999999998874
No 39
>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=95.46 E-value=0.0049 Score=39.36 Aligned_cols=21 Identities=43% Similarity=0.803 Sum_probs=11.5
Q ss_pred ccccccCcccCChhHHHHHhh
Q 015552 12 VWCYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~R 32 (405)
++|..|++.|.....|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 345555555555555555554
No 40
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=95.36 E-value=1.3 Score=47.00 Aligned_cols=18 Identities=22% Similarity=0.257 Sum_probs=13.8
Q ss_pred hHHHhhccCceeeecccc
Q 015552 331 MEERRMSSVKYQVHDETS 348 (405)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~ 348 (405)
|++|||+|=+..-.||-+
T Consensus 541 m~ara~a~~i~~tkd~de 558 (569)
T KOG3671|consen 541 MDARASALAIHSTKDEDE 558 (569)
T ss_pred HHHHHHhhcccccccccc
Confidence 899999999888544433
No 41
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=95.21 E-value=0.27 Score=54.45 Aligned_cols=12 Identities=17% Similarity=0.271 Sum_probs=6.5
Q ss_pred CCCCCCCCCCCC
Q 015552 240 APIPSTSIALSS 251 (405)
Q Consensus 240 ~~~~p~~~p~~~ 251 (405)
++..|=++..--
T Consensus 607 aPvlP~gLkpKK 618 (1102)
T KOG1924|consen 607 APVLPFGLKPKK 618 (1102)
T ss_pred cccCCCCCCccc
Confidence 355566665544
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.49 E-value=0.018 Score=35.50 Aligned_cols=24 Identities=25% Similarity=0.527 Sum_probs=17.6
Q ss_pred ccccccccCCCChhhHHHHhhhhcc
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQVHK 60 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~hH~ 60 (405)
|+|..|+.... +..|.+|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 67888887777 7888888887764
No 43
>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=94.46 E-value=0.016 Score=36.65 Aligned_cols=25 Identities=12% Similarity=0.001 Sum_probs=23.0
Q ss_pred cccccCCCCCCChHHHHHHHhhhcC
Q 015552 76 TDIEIYGMQGIPPDVLAAHYGEEEE 100 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H~r~h~~ 100 (405)
|+|.+|++.|.....|.+|++.|..
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhcC
Confidence 7899999999999999999988864
No 44
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.46 E-value=0.036 Score=60.61 Aligned_cols=22 Identities=23% Similarity=0.558 Sum_probs=11.6
Q ss_pred ccccccCCCChhhHHHHhhhhc
Q 015552 38 CHVCHKKLSTAGGMAIHVLQVH 59 (405)
Q Consensus 38 C~~CgKsFs~~s~L~rH~r~hH 59 (405)
|..|...|.....|.+|++.+|
T Consensus 185 C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred chhhhhhhccHHHHHHhhccce
Confidence 4555555555555555554444
No 45
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.45 E-value=0.037 Score=33.45 Aligned_cols=24 Identities=13% Similarity=-0.011 Sum_probs=21.6
Q ss_pred cccccCCCCCCChHHHHHHHhhhc
Q 015552 76 TDIEIYGMQGIPPDVLAAHYGEEE 99 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H~r~h~ 99 (405)
|+|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998764
No 46
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=94.40 E-value=0.36 Score=53.51 Aligned_cols=10 Identities=10% Similarity=0.218 Sum_probs=4.7
Q ss_pred CCCCCCCCCC
Q 015552 243 PSTSIALSSS 252 (405)
Q Consensus 243 ~p~~~p~~~p 252 (405)
|+++....+|
T Consensus 599 P~~gm~pmaP 608 (1102)
T KOG1924|consen 599 PPPGMFPMAP 608 (1102)
T ss_pred CCCCcccccc
Confidence 3444444554
No 47
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.36 E-value=0.019 Score=35.61 Aligned_cols=21 Identities=29% Similarity=0.767 Sum_probs=12.9
Q ss_pred ccccccccCCCChhhHHHHhh
Q 015552 36 FKCHVCHKKLSTAGGMAIHVL 56 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r 56 (405)
|.|.+|++.|.....|..|++
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 48
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.31 E-value=0.036 Score=60.58 Aligned_cols=69 Identities=20% Similarity=0.299 Sum_probs=53.2
Q ss_pred ccccccCcccCChhHHHHHhhcCcccccccc------cCCCChhhHHHHhhhhccccccccCCCCCCCCccccc--cC-C
Q 015552 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCH------KKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIE--IY-G 82 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~REKPfkC~~Cg------KsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~--iC-g 82 (405)
+.|.+|...|.....|.+|++...|.|..|. .-|..-+.|..|.|..| |.|+ .| .
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~H----------------flCE~~~C~~ 246 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----------------FLCEEEFCRT 246 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhcC----------------cccccccccc
Confidence 4599999999999999999998888999985 34677789999998887 5555 55 3
Q ss_pred CCCCChHHHHHHHh
Q 015552 83 MQGIPPDVLAAHYG 96 (405)
Q Consensus 83 k~F~~~s~L~~H~r 96 (405)
+.|.....++.|++
T Consensus 247 ~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 247 KKFYVAFELEIELK 260 (669)
T ss_pred ceeeehhHHHHHHH
Confidence 45655555555555
No 49
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=94.17 E-value=0.026 Score=56.85 Aligned_cols=89 Identities=19% Similarity=0.376 Sum_probs=59.7
Q ss_pred CcccccccCcccCChhHHHHHhh-cCc-----------------------------------------------------
Q 015552 10 SKVWCYYCDREFDDEKILVQHQK-AKH----------------------------------------------------- 35 (405)
Q Consensus 10 eKp~C~~CgK~F~~ks~Lk~H~R-EKP----------------------------------------------------- 35 (405)
++..|-+|.|.|..+..|+.||| .++
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed 273 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNED 273 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcC
Confidence 45569999999999999999999 000
Q ss_pred ------ccccccccCCCChhhHHHHhhhhccccccccCCC---------------CCCCCccccccCCCCCCChHHHHHH
Q 015552 36 ------FKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNA---------------KPGRESTDIEIYGMQGIPPDVLAAH 94 (405)
Q Consensus 36 ------fkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~---------------kpgRk~~~C~iCgk~F~~~s~L~~H 94 (405)
-+|..|.+..-....|..||+.+|.-.-.+.-.. ....+-..|-.|...|.....|..|
T Consensus 274 ~a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~h 353 (423)
T KOG2482|consen 274 DAEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIH 353 (423)
T ss_pred CCCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhh
Confidence 1688888777777888888887775321111000 0111225577788888888888888
Q ss_pred Hhhh
Q 015552 95 YGEE 98 (405)
Q Consensus 95 ~r~h 98 (405)
+..+
T Consensus 354 m~e~ 357 (423)
T KOG2482|consen 354 MVED 357 (423)
T ss_pred cccc
Confidence 7543
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=93.99 E-value=0.024 Score=65.47 Aligned_cols=84 Identities=14% Similarity=0.163 Sum_probs=63.8
Q ss_pred ccccCcccCChhHHHHHhh-----cCcccccccccCCCChhhHHHHhhhhccccc-cccC-------CC-----CCCCCc
Q 015552 14 CYYCDREFDDEKILVQHQK-----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENV-TKVP-------NA-----KPGRES 75 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R-----EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp-~~cp-------~~-----kpgRk~ 75 (405)
|..|+..|.++..+-.|+. .|-|+|.+|+-.|.....|..|+|..|-+-. .-|. .+ .-+++.
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p 518 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP 518 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc
Confidence 5567777777777777666 7899999999999999999999999765422 1111 10 113355
Q ss_pred cccccCCCCCCChHHHHHHHhh
Q 015552 76 TDIEIYGMQGIPPDVLAAHYGE 97 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H~r~ 97 (405)
|.|..|.-.+.....|.+|++.
T Consensus 519 ~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 519 YPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccceeeeeeeecchHHHHHHHH
Confidence 9999999999999999999875
No 51
>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=93.33 E-value=0.038 Score=35.16 Aligned_cols=22 Identities=27% Similarity=0.625 Sum_probs=18.2
Q ss_pred ccccccccCCCChhhHHHHhhh
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQ 57 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~ 57 (405)
|.|..|++.|.....|..|++.
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 6788888888888888888754
No 52
>PRK04860 hypothetical protein; Provisional
Probab=93.12 E-value=0.035 Score=50.76 Aligned_cols=40 Identities=18% Similarity=0.209 Sum_probs=32.0
Q ss_pred CcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCCCChH
Q 015552 34 KHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPD 89 (405)
Q Consensus 34 KPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F~~~s 89 (405)
-+|+|. |++ ....+.+|.++|.+++. |.|..|+..|...+
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~------------YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAV------------YRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCcc------------EECCCCCceeEEec
Confidence 469998 987 77788999988888775 88888988876543
No 53
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=92.93 E-value=0.062 Score=33.21 Aligned_cols=21 Identities=33% Similarity=0.812 Sum_probs=19.4
Q ss_pred ccccccCcccCChhHHHHHhh
Q 015552 12 VWCYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~R 32 (405)
++|..|++.|.....|+.|++
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 359999999999999999987
No 54
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.54 E-value=0.048 Score=54.18 Aligned_cols=55 Identities=24% Similarity=0.422 Sum_probs=47.7
Q ss_pred ccccccCcccCChhHHHHHhh------c--Cccccc--ccccCCCChhhHHHHhhhhcccccccc
Q 015552 12 VWCYYCDREFDDEKILVQHQK------A--KHFKCH--VCHKKLSTAGGMAIHVLQVHKENVTKV 66 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~R------E--KPfkC~--~CgKsFs~~s~L~rH~r~hH~ekp~~c 66 (405)
..|..|.+.|.+...|.+|.+ + ++|.|. .|++.|.+.+.+.+|.++|...+...|
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 339999999999999998887 6 999999 799999999999999988877665444
No 55
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.11 E-value=0.14 Score=51.76 Aligned_cols=72 Identities=21% Similarity=0.356 Sum_probs=52.5
Q ss_pred cccccCcccCChhHHHHHhhcCcccccccccC-------CCChhhHHHHhhhhccccccccCCCCCCCCccccc--cC--
Q 015552 13 WCYYCDREFDDEKILVQHQKAKHFKCHVCHKK-------LSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIE--IY-- 81 (405)
Q Consensus 13 ~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKs-------Fs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~--iC-- 81 (405)
.|.+|.+.|-+...|.+|+|+|+-+|.+|++. |..-..|.+|.+.-| |-|. .|
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----------------y~ct~qtc~~ 285 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNAH----------------YCCTFQTCRV 285 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcCc----------------eEEEEEEEec
Confidence 39999999999999999999777778888763 666677888864434 3332 12
Q ss_pred C--CCCCChHHHHHHHhhhcC
Q 015552 82 G--MQGIPPDVLAAHYGEEEE 100 (405)
Q Consensus 82 g--k~F~~~s~L~~H~r~h~~ 100 (405)
| ..|.....|..|+...++
T Consensus 286 ~k~~vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 286 GKCYVFPYHTELLEHLTRFHK 306 (493)
T ss_pred CcEEEeccHHHHHHHHHHHhh
Confidence 1 247788888899876654
No 56
>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=91.15 E-value=0.16 Score=33.72 Aligned_cols=21 Identities=33% Similarity=0.697 Sum_probs=11.5
Q ss_pred ccccccCcccCChhHHHHHhh
Q 015552 12 VWCYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~R 32 (405)
++|.+|++.|.....+..|++
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 345555555555555555554
No 57
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=89.35 E-value=0.22 Score=40.05 Aligned_cols=37 Identities=22% Similarity=0.503 Sum_probs=22.4
Q ss_pred ChhHHHHHhh---cCcccccccccCCCChhhHHHHhhhhc
Q 015552 23 DEKILVQHQK---AKHFKCHVCHKKLSTAGGMAIHVLQVH 59 (405)
Q Consensus 23 ~ks~Lk~H~R---EKPfkC~~CgKsFs~~s~L~rH~r~hH 59 (405)
....+..+.+ ...+.|.+|++.|.....|..|++.++
T Consensus 35 ~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 35 DPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp --------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred cccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 4444445555 457999999999999999999998653
No 58
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=88.94 E-value=0.25 Score=50.10 Aligned_cols=60 Identities=20% Similarity=0.280 Sum_probs=42.4
Q ss_pred ChhHHHHHhh----cCcc----cccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCC-------CCC
Q 015552 23 DEKILVQHQK----AKHF----KCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQ-------GIP 87 (405)
Q Consensus 23 ~ks~Lk~H~R----EKPf----kC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~-------F~~ 87 (405)
+++.|..|.. |.-| +|..|.+.|...+.|.+|+|..| -+|.||++. |..
T Consensus 200 ~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~H----------------E~ChICD~v~p~~~QYFK~ 263 (493)
T COG5236 200 RSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRH----------------EACHICDMVGPIRYQYFKS 263 (493)
T ss_pred ecccccccccCCccccCcCCCchhhhccceecChHHHHHHHHhhh----------------hhhhhhhccCccchhhhhC
Confidence 4566777766 3233 59999999999999999987766 346777664 456
Q ss_pred hHHHHHHHhhh
Q 015552 88 PDVLAAHYGEE 98 (405)
Q Consensus 88 ~s~L~~H~r~h 98 (405)
-++|.+|.+..
T Consensus 264 Y~~Le~HF~~~ 274 (493)
T COG5236 264 YEDLEAHFRNA 274 (493)
T ss_pred HHHHHHHhhcC
Confidence 67788887643
No 59
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=88.83 E-value=0.14 Score=50.86 Aligned_cols=59 Identities=17% Similarity=0.152 Sum_probs=49.9
Q ss_pred CcccccccccCCCChhhHHHHhh--hhccc--cccccCCCCCCCCccccc--cCCCCCCChHHHHHHHhhhcCCCcc
Q 015552 34 KHFKCHVCHKKLSTAGGMAIHVL--QVHKE--NVTKVPNAKPGRESTDIE--IYGMQGIPPDVLAAHYGEEEEEVPS 104 (405)
Q Consensus 34 KPfkC~~CgKsFs~~s~L~rH~r--~hH~e--kp~~cp~~kpgRk~~~C~--iCgk~F~~~s~L~~H~r~h~~e~~~ 104 (405)
..+.|..|.+.|.+...|.+|.+ .|..+ ++ +.|. .|++.|.+.+.+..|...|.+....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~------------~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP------------FSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCc------------eeeeccCCCccccccccccCCcccccCCCcc
Confidence 47999999999999999999998 57776 55 5555 7999999999999999998775543
No 60
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=88.02 E-value=0.18 Score=58.52 Aligned_cols=88 Identities=10% Similarity=0.070 Sum_probs=64.9
Q ss_pred ccccccCcccCChhHHHHHhh-cCcccccccccCCCChhhHHHHhhhhcc-cccccc----CCCCCCCCccccccCCCCC
Q 015552 12 VWCYYCDREFDDEKILVQHQK-AKHFKCHVCHKKLSTAGGMAIHVLQVHK-ENVTKV----PNAKPGRESTDIEIYGMQG 85 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~R-EKPfkC~~CgKsFs~~s~L~rH~r~hH~-ekp~~c----p~~kpgRk~~~C~iCgk~F 85 (405)
..|..|++.|.-...+. |.. +++|+|.+|...|.....|..|.+..-. .+...- +.-.+.++-| |.+|...|
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~ 1338 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLDVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLL 1338 (1406)
T ss_pred chhhhccccccCcccee-ecccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhc
Confidence 34999999999888877 777 9999999999999999999999732210 000000 0012334446 99999999
Q ss_pred CChHHHHHHHhhhcCC
Q 015552 86 IPPDVLAAHYGEEEEE 101 (405)
Q Consensus 86 ~~~s~L~~H~r~h~~e 101 (405)
.....|..|+++.+.+
T Consensus 1339 ~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1339 SGREALQIHMRSSAHR 1354 (1406)
T ss_pred chhHHHHHHHHHhhhc
Confidence 9999999999986543
No 61
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.20 E-value=0.27 Score=46.57 Aligned_cols=84 Identities=18% Similarity=0.216 Sum_probs=60.7
Q ss_pred cccccc--cCcccCChhHHHHHhh-cCcccccccccCCCChhhHHHHhhhhcccc-ccccCCCCCCCCcccc--ccCCCC
Q 015552 11 KVWCYY--CDREFDDEKILVQHQK-AKHFKCHVCHKKLSTAGGMAIHVLQVHKEN-VTKVPNAKPGRESTDI--EIYGMQ 84 (405)
Q Consensus 11 Kp~C~~--CgK~F~~ks~Lk~H~R-EKPfkC~~CgKsFs~~s~L~rH~r~hH~ek-p~~cp~~kpgRk~~~C--~iCgk~ 84 (405)
++.|++ |-+.|....++..|.. ..--.|.+|.+.|-+...|..|+.-.|..- ..++ ..|.+.|+| +.|+..
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~v---eRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALV---ERGQDMYQCLVEGCTEK 155 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHH---HcCccHHHHHHHhhhhh
Confidence 344887 8888888888777776 334579999999999999999986555321 0011 224566999 689999
Q ss_pred CCChHHHHHHHhh
Q 015552 85 GIPPDVLAAHYGE 97 (405)
Q Consensus 85 F~~~s~L~~H~r~ 97 (405)
|......+.|+-.
T Consensus 156 FkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 156 FKTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhhHHHH
Confidence 9888888888644
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=86.78 E-value=0.4 Score=41.12 Aligned_cols=37 Identities=19% Similarity=0.429 Sum_probs=29.5
Q ss_pred CCCcccccccCcccCChhHHHHHhhcCcccccccccCCCChhhH
Q 015552 8 VSSKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGM 51 (405)
Q Consensus 8 ~geKp~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s~L 51 (405)
.|.|..|..||++|-... ..|-.|.+||..|.-...+
T Consensus 6 lGtKR~Cp~CG~kFYDLn-------k~PivCP~CG~~~~~~~~~ 42 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYDLN-------KDPIVCPKCGTEFPPEPPL 42 (108)
T ss_pred cCCcccCCCCcchhccCC-------CCCccCCCCCCccCccccc
Confidence 466777999999997754 4688999999999887333
No 63
>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=86.43 E-value=0.48 Score=31.42 Aligned_cols=23 Identities=17% Similarity=0.485 Sum_probs=17.2
Q ss_pred cccccccccCCCChhhHHHHhhh
Q 015552 35 HFKCHVCHKKLSTAGGMAIHVLQ 57 (405)
Q Consensus 35 PfkC~~CgKsFs~~s~L~rH~r~ 57 (405)
.|.|.+|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46788888888888788777643
No 64
>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=85.70 E-value=0.75 Score=34.35 Aligned_cols=25 Identities=20% Similarity=0.329 Sum_probs=17.7
Q ss_pred CCCccc-ccccCcccCChhHHHHHhh
Q 015552 8 VSSKVW-CYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 8 ~geKp~-C~~CgK~F~~ks~Lk~H~R 32 (405)
..+.+- |.+|+..+.+..+|++|+.
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHH
T ss_pred ccCCCCCCCcchhhccchhhHHHHHH
Confidence 356666 9999999999999999987
No 65
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=85.19 E-value=0.54 Score=29.67 Aligned_cols=18 Identities=22% Similarity=0.659 Sum_probs=9.7
Q ss_pred cccccccCCCChhhHHHHh
Q 015552 37 KCHVCHKKLSTAGGMAIHV 55 (405)
Q Consensus 37 kC~~CgKsFs~~s~L~rH~ 55 (405)
.|..||++| ..+.|.+|+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 455566666 334555554
No 66
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=84.55 E-value=0.21 Score=42.17 Aligned_cols=17 Identities=24% Similarity=0.552 Sum_probs=10.3
Q ss_pred cCcccccccccCCCChh
Q 015552 33 AKHFKCHVCHKKLSTAG 49 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s 49 (405)
+|-|.|..|+..-....
T Consensus 20 ~k~FtCp~Cghe~vs~c 36 (104)
T COG4888 20 PKTFTCPRCGHEKVSSC 36 (104)
T ss_pred CceEecCccCCeeeeEE
Confidence 56677777765544433
No 67
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=84.32 E-value=0.58 Score=28.64 Aligned_cols=24 Identities=8% Similarity=-0.024 Sum_probs=18.4
Q ss_pred cccccCCCCCCChHHHHHHHhhhcC
Q 015552 76 TDIEIYGMQGIPPDVLAAHYGEEEE 100 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H~r~h~~ 100 (405)
|+|..|+.... ...|.+|++.+++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 57899998887 8899999998753
No 68
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=83.14 E-value=57 Score=33.18 Aligned_cols=25 Identities=12% Similarity=-0.116 Sum_probs=19.5
Q ss_pred ccc---ccCCCCCCChHHHHHHHhhhcC
Q 015552 76 TDI---EIYGMQGIPPDVLAAHYGEEEE 100 (405)
Q Consensus 76 ~~C---~iCgk~F~~~s~L~~H~r~h~~ 100 (405)
|.| ..|.+.|....+|++|+...++
T Consensus 145 FmC~~~~GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 145 FMCAAPHGCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred EEeecchhHHHHHhhHHHHHHHhhhhhc
Confidence 556 3588999999999999876554
No 69
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=82.45 E-value=0.93 Score=28.60 Aligned_cols=19 Identities=37% Similarity=0.728 Sum_probs=15.9
Q ss_pred cccccCcccCChhHHHHHhh
Q 015552 13 WCYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 13 ~C~~CgK~F~~ks~Lk~H~R 32 (405)
.|..||+.| ..+.|.+|++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 499999999 6677888975
No 70
>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=81.36 E-value=0.91 Score=39.96 Aligned_cols=38 Identities=11% Similarity=0.159 Sum_probs=30.0
Q ss_pred CCCcccccccCcccCChhHHHHHhhcCcccccccccCCCChhhHH
Q 015552 8 VSSKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMA 52 (405)
Q Consensus 8 ~geKp~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s~L~ 52 (405)
.|-|..|..||++|-... ..|-.|.+||..|.....++
T Consensus 6 lGtKr~Cp~cg~kFYDLn-------k~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 6 LGTKRICPNTGSKFYDLN-------RRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred hCccccCCCcCccccccC-------CCCccCCCcCCccCcchhhc
Confidence 466777999999997654 57899999999987775544
No 71
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=80.90 E-value=0.88 Score=44.43 Aligned_cols=42 Identities=19% Similarity=0.378 Sum_probs=27.0
Q ss_pred ccccCcccCChhHHHHHhh---cCcccccccccCCCChhhHHHHhhh
Q 015552 14 CYYCDREFDDEKILVQHQK---AKHFKCHVCHKKLSTAGGMAIHVLQ 57 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R---EKPfkC~~CgKsFs~~s~L~rH~r~ 57 (405)
|..||..... -.+-+|+. ..-|.|-.|++.|.+ ...+.|...
T Consensus 6 CnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 6 CNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred hhhhhhhccc-cchHHHHHhccCCeeEEeeccccccc-chhhhhhhh
Confidence 7777765443 34555665 556777778888777 556666533
No 72
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=80.38 E-value=1.4 Score=44.95 Aligned_cols=24 Identities=38% Similarity=0.753 Sum_probs=19.4
Q ss_pred CCcccccccCcccCChhHHHHHhh
Q 015552 9 SSKVWCYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 9 geKp~C~~CgK~F~~ks~Lk~H~R 32 (405)
.++.||..|+|.|.+.+-+..|..
T Consensus 236 ~~~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 236 FPKVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred ccceeeHhhhhHhhhhHHHHHHHh
Confidence 467889999999999877766655
No 73
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=77.87 E-value=1 Score=34.28 Aligned_cols=26 Identities=23% Similarity=0.433 Sum_probs=17.8
Q ss_pred CCCCccc-ccccCcccCChhHHHHHhh
Q 015552 7 RVSSKVW-CYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 7 r~geKp~-C~~CgK~F~~ks~Lk~H~R 32 (405)
|.||.+. |.-||+.|.+...+.+|..
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 4466666 7777777777777776665
No 74
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=77.27 E-value=1.9 Score=43.95 Aligned_cols=74 Identities=20% Similarity=0.215 Sum_probs=49.3
Q ss_pred hHHHHHhh---c--CcccccccccCC-CChhhHHHHhhhhccccccccCCC----------CCCCCccccccCCCCCCCh
Q 015552 25 KILVQHQK---A--KHFKCHVCHKKL-STAGGMAIHVLQVHKENVTKVPNA----------KPGRESTDIEIYGMQGIPP 88 (405)
Q Consensus 25 s~Lk~H~R---E--KPfkC~~CgKsF-s~~s~L~rH~r~hH~ekp~~cp~~----------kpgRk~~~C~iCgk~F~~~ 88 (405)
..|.+|++ + +.-.|..|+..+ ..++....|+-.+|+-....-.+- +..-.+++|-.|.|.|.++
T Consensus 129 eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdk 208 (423)
T KOG2482|consen 129 EALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDK 208 (423)
T ss_pred HHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCc
Confidence 45566666 2 345699998755 455777788877776442111110 1223458899999999999
Q ss_pred HHHHHHHhhh
Q 015552 89 DVLAAHYGEE 98 (405)
Q Consensus 89 s~L~~H~r~h 98 (405)
..|+.||+..
T Consensus 209 ntLkeHMrkK 218 (423)
T KOG2482|consen 209 NTLKEHMRKK 218 (423)
T ss_pred HHHHHHHHhc
Confidence 9999999863
No 75
>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=76.42 E-value=1.4 Score=31.04 Aligned_cols=26 Identities=23% Similarity=0.453 Sum_probs=13.8
Q ss_pred cCcccccccccCCCCh----hhHHHHhhhh
Q 015552 33 AKHFKCHVCHKKLSTA----GGMAIHVLQV 58 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~----s~L~rH~r~h 58 (405)
++-.+|.+|++.+... ++|.+|++..
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~ 43 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKK 43 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhh
Confidence 3445677777766653 6777777443
No 76
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=76.10 E-value=0.87 Score=50.30 Aligned_cols=53 Identities=19% Similarity=0.371 Sum_probs=27.9
Q ss_pred ccccCcccCChhHHHHHhh---cCccc-ccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCC
Q 015552 14 CYYCDREFDDEKILVQHQK---AKHFK-CHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQ 84 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R---EKPfk-C~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~ 84 (405)
|..||=+|+-...|--.+. -+.|. |..|.+.|..-.+ |+.|.+- ..|.+||-.
T Consensus 126 CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~n-----RRfHAQp-------------~aCp~CGP~ 182 (750)
T COG0068 126 CTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLN-----RRFHAQP-------------IACPKCGPH 182 (750)
T ss_pred cCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccc-----ccccccc-------------ccCcccCCC
Confidence 6666666665554432222 33343 6666665555443 4455543 567777753
No 77
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=73.10 E-value=2 Score=31.35 Aligned_cols=21 Identities=38% Similarity=0.722 Sum_probs=12.5
Q ss_pred cccccccCCCCh-----hhHHHHhhh
Q 015552 37 KCHVCHKKLSTA-----GGMAIHVLQ 57 (405)
Q Consensus 37 kC~~CgKsFs~~-----s~L~rH~r~ 57 (405)
.|.+|++.+... ++|.+|++.
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 466666655443 577777653
No 78
>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=73.10 E-value=2.4 Score=29.54 Aligned_cols=22 Identities=32% Similarity=0.824 Sum_probs=10.4
Q ss_pred cccccccCcccC-Ch-hHHHHHhh
Q 015552 11 KVWCYYCDREFD-DE-KILVQHQK 32 (405)
Q Consensus 11 Kp~C~~CgK~F~-~k-s~Lk~H~R 32 (405)
|+||++|++-|. +. ...+.|.+
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT-
T ss_pred CeecccccceecCCChHHHHHhhc
Confidence 577999999984 33 45577776
No 79
>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=72.06 E-value=7.4 Score=32.77 Aligned_cols=29 Identities=10% Similarity=0.095 Sum_probs=25.1
Q ss_pred CCCcccc----ccCCCCCCChHHHHHHHhhhcC
Q 015552 72 GRESTDI----EIYGMQGIPPDVLAAHYGEEEE 100 (405)
Q Consensus 72 gRk~~~C----~iCgk~F~~~s~L~~H~r~h~~ 100 (405)
.-+.|.| ..|+......+.+.+|.+.+++
T Consensus 77 ~~~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 77 VYDGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3366999 9999999999999999998875
No 80
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.91 E-value=1.3 Score=42.02 Aligned_cols=47 Identities=30% Similarity=0.719 Sum_probs=40.4
Q ss_pred ccccCcccCChhHHHHHhh-----------cC---cccccc--cccCCCChhhHHHHhhhhcc
Q 015552 14 CYYCDREFDDEKILVQHQK-----------AK---HFKCHV--CHKKLSTAGGMAIHVLQVHK 60 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R-----------EK---PfkC~~--CgKsFs~~s~L~rH~r~hH~ 60 (405)
|.+|.|.|.....|..|+- || =|.|.+ |+-+|.+...-++|+-..|.
T Consensus 109 Cs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 109 CSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred hHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 9999999999999999987 44 388987 99999999999999865553
No 81
>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=69.49 E-value=1.9 Score=38.28 Aligned_cols=28 Identities=25% Similarity=0.367 Sum_probs=17.7
Q ss_pred cCcccccccccCCCChhhHHHHhhhhccccc
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENV 63 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp 63 (405)
+.--.|..|||.|.. |++|++.||+-.+
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 444679999999976 4999999988764
No 82
>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=68.77 E-value=1.7 Score=41.64 Aligned_cols=30 Identities=20% Similarity=0.500 Sum_probs=23.6
Q ss_pred cCcccccccccCCCChhhHHHHhhhhcccc
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKEN 62 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH~r~hH~ek 62 (405)
+..|.|..|+|.|.-......|+...|.++
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 445899999999999999999999999887
No 83
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=68.57 E-value=2.4 Score=35.89 Aligned_cols=8 Identities=50% Similarity=0.866 Sum_probs=5.7
Q ss_pred CCCCCCCC
Q 015552 1 MGKKKKRV 8 (405)
Q Consensus 1 mgkKkrr~ 8 (405)
|||+|.+.
T Consensus 1 MgkRk~K~ 8 (109)
T KOG3214|consen 1 MGKRKSKR 8 (109)
T ss_pred CCcccccc
Confidence 78877764
No 84
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=66.69 E-value=2.1 Score=38.28 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=13.5
Q ss_pred CcccccccccCCCChhhH
Q 015552 34 KHFKCHVCHKKLSTAGGM 51 (405)
Q Consensus 34 KPfkC~~CgKsFs~~s~L 51 (405)
.-|.|..|+++|.....+
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~ 115 (147)
T smart00531 98 AYYKCPNCQSKYTFLEAN 115 (147)
T ss_pred cEEECcCCCCEeeHHHHH
Confidence 458899999888866544
No 85
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=65.96 E-value=7.5 Score=33.63 Aligned_cols=72 Identities=13% Similarity=0.057 Sum_probs=42.2
Q ss_pred ccccCcccCChhHHHHHhh----cCcc------------cccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccc
Q 015552 14 CYYCDREFDDEKILVQHQK----AKHF------------KCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTD 77 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R----EKPf------------kC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~ 77 (405)
|..||-..-..-+|.+... -++| .|.-|.+.|........ ++ .....+|+
T Consensus 18 CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~------~~--------~~~~~~y~ 83 (112)
T TIGR00622 18 CPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF------DE--------LKDSHRYV 83 (112)
T ss_pred CCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc------cc--------ccccccee
Confidence 7777777777777765443 2222 26666666655431110 00 00122488
Q ss_pred cccCCCCCCChHHHHHHHhhhc
Q 015552 78 IEIYGMQGIPPDVLAAHYGEEE 99 (405)
Q Consensus 78 C~iCgk~F~~~s~L~~H~r~h~ 99 (405)
|..|...|-..-+.-.|+..|.
T Consensus 84 C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 84 CAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred CCCCCCccccccchhhhhhccC
Confidence 9999999977777778877664
No 86
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=65.19 E-value=2.1 Score=40.75 Aligned_cols=54 Identities=19% Similarity=0.280 Sum_probs=29.4
Q ss_pred cCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCc-----cccccCCCCCCCh
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRES-----TDIEIYGMQGIPP 88 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~-----~~C~iCgk~F~~~ 88 (405)
+|...|.+|++.|.++.-+....|....+. .-|+.-. +-.+ .-|..||..|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~-D~~~~Y~-~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDS-DFCPRYK-GVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecC-CCccccC-CCCCeeeeEEECCCCCCccccc
Confidence 456778888888888766665554433222 1222100 0001 3488999877544
No 87
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=65.11 E-value=2.9 Score=36.56 Aligned_cols=23 Identities=22% Similarity=0.431 Sum_probs=17.9
Q ss_pred ccccccccCCCChhhHHHHhhhh
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQV 58 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~h 58 (405)
|-|-.|.+-|.....|+.|.++.
T Consensus 58 fyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred eehhhhhhhhcchHHHHHHHhcc
Confidence 77888888888888888886554
No 88
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=64.23 E-value=5.1 Score=43.52 Aligned_cols=19 Identities=32% Similarity=0.635 Sum_probs=13.8
Q ss_pred ccccCcccCChhHHHHHhh
Q 015552 14 CYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R 32 (405)
|..||++|.+.....+|+.
T Consensus 421 C~~CG~R~~~~ee~sk~md 439 (579)
T KOG2071|consen 421 CKSCGLRFDDSEERSKHMD 439 (579)
T ss_pred hcccccccccchhhhhHhh
Confidence 8888888887766666555
No 89
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.19 E-value=4.9 Score=34.65 Aligned_cols=38 Identities=11% Similarity=-0.026 Sum_probs=29.0
Q ss_pred CCCcccccccCcccCChhHHHHHhhcCcccccccccCCCChhhHHH
Q 015552 8 VSSKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMAI 53 (405)
Q Consensus 8 ~geKp~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s~L~r 53 (405)
.|-|-.|..|||.|-... .+|..|.+||++| -++.|..
T Consensus 6 LGtKridPetg~KFYDLN-------rdPiVsPytG~s~-P~s~fe~ 43 (129)
T COG4530 6 LGTKRIDPETGKKFYDLN-------RDPIVSPYTGKSY-PRSYFEE 43 (129)
T ss_pred ccccccCccccchhhccC-------CCccccCcccccc-hHHHHHh
Confidence 455666999999987643 6799999999999 4555543
No 90
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=62.86 E-value=1.9 Score=41.11 Aligned_cols=36 Identities=19% Similarity=0.441 Sum_probs=27.3
Q ss_pred cccccCcccCChhHHHHHhh--------------cCc-----ccccccccCCCCh
Q 015552 13 WCYYCDREFDDEKILVQHQK--------------AKH-----FKCHVCHKKLSTA 48 (405)
Q Consensus 13 ~C~~CgK~F~~ks~Lk~H~R--------------EKP-----fkC~~CgKsFs~~ 48 (405)
.|.+|++.|..+.-+....| .-| ..|..||.+|...
T Consensus 7 ~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 7 TCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred ECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 39999999998876666555 112 4699999988766
No 91
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=62.44 E-value=6.6 Score=40.56 Aligned_cols=45 Identities=20% Similarity=0.491 Sum_probs=36.8
Q ss_pred c-ccccCcccCChhHHHHHhh---------------------------cCcccccccc---cCCCChhhHHHHhhh
Q 015552 13 W-CYYCDREFDDEKILVQHQK---------------------------AKHFKCHVCH---KKLSTAGGMAIHVLQ 57 (405)
Q Consensus 13 ~-C~~CgK~F~~ks~Lk~H~R---------------------------EKPfkC~~Cg---KsFs~~s~L~rH~r~ 57 (405)
. |-+|++.|.....-..||. .+-|.|..|. +.|.+....+.||+.
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 5 9999999999988888987 3457888888 888888888888743
No 92
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=61.70 E-value=2 Score=39.04 Aligned_cols=39 Identities=15% Similarity=0.370 Sum_probs=23.9
Q ss_pred cccccCcccCC--hhHH-HH--HhhcCcccccccccCCCChhhHH
Q 015552 13 WCYYCDREFDD--EKIL-VQ--HQKAKHFKCHVCHKKLSTAGGMA 52 (405)
Q Consensus 13 ~C~~CgK~F~~--ks~L-k~--H~REKPfkC~~CgKsFs~~s~L~ 52 (405)
.|.+||..+.. .+.+ .. +. .|.++|..||++|.+-..+.
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~-~~~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAI-RRRRECLACGKRFTTFERVE 45 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCce-eeeeeccccCCcceEeEecc
Confidence 39999976621 1111 11 11 34489999999998775543
No 93
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=61.66 E-value=3.5 Score=34.84 Aligned_cols=7 Identities=43% Similarity=1.184 Sum_probs=5.4
Q ss_pred CCCCCCC
Q 015552 1 MGKKKKR 7 (405)
Q Consensus 1 mgkKkrr 7 (405)
|||+|++
T Consensus 1 MGkRk~~ 7 (99)
T PRK14892 1 MGRRRKK 7 (99)
T ss_pred CCCcccc
Confidence 8887766
No 94
>PRK04023 DNA polymerase II large subunit; Validated
Probab=59.55 E-value=8.9 Score=44.26 Aligned_cols=23 Identities=22% Similarity=0.255 Sum_probs=14.2
Q ss_pred ccccCCCCCCCCccccccCCCCC
Q 015552 63 VTKVPNAKPGRESTDIEIYGMQG 85 (405)
Q Consensus 63 p~~cp~~kpgRk~~~C~iCgk~F 85 (405)
.+.|+.|......+.|..||..-
T Consensus 651 i~fCP~CG~~~~~y~CPKCG~El 673 (1121)
T PRK04023 651 VYRCPRCGIEVEEDECEKCGREP 673 (1121)
T ss_pred ceeCccccCcCCCCcCCCCCCCC
Confidence 34666654444447788888654
No 95
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=58.80 E-value=5.3 Score=37.11 Aligned_cols=33 Identities=18% Similarity=0.231 Sum_probs=24.3
Q ss_pred CcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCCCC
Q 015552 34 KHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIP 87 (405)
Q Consensus 34 KPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F~~ 87 (405)
.-|.|..|+++|+....+.. . |.|..||.....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~--------~-------------F~Cp~Cg~~L~~ 148 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEY--------G-------------FRCPQCGEMLEE 148 (178)
T ss_pred CEEECCCCCcEEeHHHHhhc--------C-------------CcCCCCCCCCee
Confidence 45889999999988876531 1 888889876543
No 96
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=57.34 E-value=4.4 Score=36.13 Aligned_cols=25 Identities=16% Similarity=0.109 Sum_probs=20.9
Q ss_pred ccccccccCCCChhhHHHHhhhhccccc
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQVHKENV 63 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~hH~ekp 63 (405)
..|..|||+|. .|+||+++|++-.+
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 46999999996 58999999998765
No 97
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=54.65 E-value=14 Score=38.17 Aligned_cols=62 Identities=13% Similarity=0.072 Sum_probs=44.9
Q ss_pred ccccccccCCCChhhHHHHhhhhccccccccCC-----------CCCCCCccccccCC---CCCCChHHHHHHHhh
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPN-----------AKPGRESTDIEIYG---MQGIPPDVLAAHYGE 97 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~-----------~kpgRk~~~C~iCg---k~F~~~s~L~~H~r~ 97 (405)
=.|..|++.|.+-.....||..+|+-..-.-.. +..-...+-|-.|+ +.|..-...++||+.
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 359999999999999999998888753210000 01122347788888 899999999999875
No 98
>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=54.29 E-value=6.2 Score=35.87 Aligned_cols=33 Identities=15% Similarity=0.120 Sum_probs=24.2
Q ss_pred cCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCCC
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGI 86 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F~ 86 (405)
..-|.|..|+++|+....+.. . |.|..||....
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~--------~-------------F~Cp~Cg~~L~ 139 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMEL--------N-------------FTCPRCGAMLD 139 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHc--------C-------------CcCCCCCCEee
Confidence 355889999999888887741 1 88888887553
No 99
>PF10716 NdhL: NADH dehydrogenase transmembrane subunit; InterPro: IPR019654 NAD(P)H-quinone oxidoreductase subunit L (NdhL) is a component of the NDH-1L complex that is one of the proton-pumping NADH:ubiquinone oxidoreductases that catalyse the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. NDH-1L is essential for photoheterotrophic cell growth. NdhL appears to contain two transmembrane helices and it is necessary for the functioning of though not the correct assembly of the NDH-1 complex in Synechocystis 6803. The conservation between cyanobacteria and green plants suggests that chloroplast NDH-1 complexes contain related subunits []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=54.18 E-value=8.9 Score=31.19 Aligned_cols=19 Identities=37% Similarity=0.824 Sum_probs=17.1
Q ss_pred hhhHHHHHHHHHHHHhhhe
Q 015552 382 RFVTYLERYFLYEFQFFFF 400 (405)
Q Consensus 382 ~~~~~~~~~~~~~~~~~~~ 400 (405)
++.+-+|||+.|-+.||||
T Consensus 45 y~~~~~Er~~~y~lvF~FF 63 (81)
T PF10716_consen 45 YVMSSFERLFMYFLVFLFF 63 (81)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6778899999999999887
No 100
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=53.69 E-value=6 Score=27.11 Aligned_cols=31 Identities=16% Similarity=0.597 Sum_probs=15.4
Q ss_pred ccccCcccCChhHHHHHhhcCcccccccccCC
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKKL 45 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsF 45 (405)
|..|+..|.-...... .+.+-.+|..|+..|
T Consensus 5 Cp~C~~~y~i~d~~ip-~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 5 CPNCQAKYEIDDEKIP-PKGRKVRCSKCGHVF 35 (36)
T ss_pred CCCCCCEEeCCHHHCC-CCCcEEECCCCCCEe
Confidence 5666666655544321 113445566665554
No 101
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=53.49 E-value=8.4 Score=39.38 Aligned_cols=30 Identities=17% Similarity=0.231 Sum_probs=22.2
Q ss_pred CCCccccccCCCCCCChHHHHHHHhhhcCC
Q 015552 72 GRESTDIEIYGMQGIPPDVLAAHYGEEEEE 101 (405)
Q Consensus 72 gRk~~~C~iCgk~F~~~s~L~~H~r~h~~e 101 (405)
....|.|..|++.......|..|....|-+
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpd 105 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPE 105 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcc
Confidence 345688999998888888888887665433
No 102
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=52.64 E-value=5.5 Score=27.26 Aligned_cols=26 Identities=31% Similarity=0.620 Sum_probs=12.0
Q ss_pred ccccccCcccCChhHHHHHhhcCccccccccc
Q 015552 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHK 43 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgK 43 (405)
..|.+|++.|..+.- -+.|.+.+|++
T Consensus 4 ~~C~eC~~~f~dSyL------~~~F~~~VCD~ 29 (34)
T PF01286_consen 4 PKCDECGKPFMDSYL------LNNFDLPVCDK 29 (34)
T ss_dssp EE-TTT--EES-SSC------CCCTS-S--TT
T ss_pred chHhHhCCHHHHHHH------HHhCCcccccc
Confidence 348888888877654 33566666654
No 103
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=50.90 E-value=6.5 Score=32.70 Aligned_cols=12 Identities=25% Similarity=0.711 Sum_probs=8.8
Q ss_pred cCcccccccccC
Q 015552 33 AKHFKCHVCHKK 44 (405)
Q Consensus 33 EKPfkC~~CgKs 44 (405)
...|.|..|++.
T Consensus 34 ~a~y~CpfCgk~ 45 (90)
T PTZ00255 34 HAKYFCPFCGKH 45 (90)
T ss_pred hCCccCCCCCCC
Confidence 566889888753
No 104
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=50.51 E-value=8.3 Score=40.45 Aligned_cols=20 Identities=20% Similarity=0.552 Sum_probs=17.1
Q ss_pred cCcccccccccCCCChhhHH
Q 015552 33 AKHFKCHVCHKKLSTAGGMA 52 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~ 52 (405)
..-|+|..|.++|+....++
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred cccccCCccccchhhhHHHH
Confidence 46799999999999987765
No 105
>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=48.91 E-value=9.6 Score=36.55 Aligned_cols=24 Identities=21% Similarity=0.432 Sum_probs=18.6
Q ss_pred CCcccccccCcccCChhHHHHHhh
Q 015552 9 SSKVWCYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 9 geKp~C~~CgK~F~~ks~Lk~H~R 32 (405)
..|+.|..|+|.|.-.....+|+.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~ 98 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIF 98 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHh
Confidence 345559999999999999999997
No 106
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=48.68 E-value=7.5 Score=43.70 Aligned_cols=35 Identities=20% Similarity=0.350 Sum_probs=23.4
Q ss_pred cccccCcccCChhHHHHHhhcCcccccccccCCCChhh
Q 015552 13 WCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGG 50 (405)
Q Consensus 13 ~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s~ 50 (405)
.|..|++.|.....+. -.|.|.|..||+.|.....
T Consensus 462 tC~~C~kkFfSlsK~L---~~RKHHCRkCGrVFC~~CS 496 (1374)
T PTZ00303 462 SCPSCGRAFISLSRPL---GTRAHHCRSCGIRLCVFCI 496 (1374)
T ss_pred cccCcCCccccccccc---ccccccccCCccccCcccc
Confidence 3999999997542100 1356778888888877654
No 107
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=48.50 E-value=3.9 Score=41.80 Aligned_cols=65 Identities=23% Similarity=0.295 Sum_probs=44.0
Q ss_pred cCcccccc--cccCCCChhhHHHHhhhhcccc---ccccCCC----CCCCCccccccCCCCCCChHHHHHHHhh
Q 015552 33 AKHFKCHV--CHKKLSTAGGMAIHVLQVHKEN---VTKVPNA----KPGRESTDIEIYGMQGIPPDVLAAHYGE 97 (405)
Q Consensus 33 EKPfkC~~--CgKsFs~~s~L~rH~r~hH~ek---p~~cp~~----kpgRk~~~C~iCgk~F~~~s~L~~H~r~ 97 (405)
.|+|+|.+ |+|.+.....|+.|...-|... +.+++.. .-..|.|+|++|.++......|.-|+..
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~~ 420 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRTH 420 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceeeh
Confidence 89999998 9999999889998864444321 1222211 1134559999999998777767666443
No 108
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=48.23 E-value=4.9 Score=41.16 Aligned_cols=34 Identities=18% Similarity=0.405 Sum_probs=15.2
Q ss_pred ccccCcccCChhHHHHHhh---------cCcccccccccCCCC
Q 015552 14 CYYCDREFDDEKILVQHQK---------AKHFKCHVCHKKLST 47 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R---------EKPfkC~~CgKsFs~ 47 (405)
|..|+++......+.+-.+ .|=|+|..|+++...
T Consensus 255 C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 255 CKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTIS 297 (344)
T ss_dssp ETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEE
T ss_pred cCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeee
Confidence 7778777665555443222 455778888776443
No 109
>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=48.22 E-value=6.4 Score=26.75 Aligned_cols=32 Identities=16% Similarity=0.379 Sum_probs=16.7
Q ss_pred ccccCcccCChhHHHHHhhcCcccccccccCCC
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKKLS 46 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs 46 (405)
|..|+..|.-........ ....+|..|+..|.
T Consensus 5 CP~C~~~~~v~~~~~~~~-~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 5 CPNCKTSFRVVDSQLGAN-GGKVRCGKCGHVWY 36 (38)
T ss_pred CCCCCCEEEeCHHHcCCC-CCEEECCCCCCEEE
Confidence 666776666554432111 22356666666553
No 110
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=47.80 E-value=9.6 Score=40.03 Aligned_cols=33 Identities=15% Similarity=0.415 Sum_probs=22.7
Q ss_pred CcccccccCcccCChhHHHHHhhcCcccccccccCCCChh
Q 015552 10 SKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAG 49 (405)
Q Consensus 10 eKp~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s 49 (405)
+++.|..||++..++. .+-|+|..||.++....
T Consensus 349 ~~p~Cp~Cg~~m~S~G-------~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 349 VNPVCPRCGGRMKSAG-------RNGFRCKKCGTRARETL 381 (421)
T ss_pred cCCCCCccCCchhhcC-------CCCcccccccccCCccc
Confidence 4566888887655543 22788888888877654
No 111
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=47.73 E-value=5.5 Score=35.12 Aligned_cols=37 Identities=19% Similarity=0.422 Sum_probs=21.8
Q ss_pred cccccccCcccCChhHHHHHhh-cCcccccccccCCCChh
Q 015552 11 KVWCYYCDREFDDEKILVQHQK-AKHFKCHVCHKKLSTAG 49 (405)
Q Consensus 11 Kp~C~~CgK~F~~ks~Lk~H~R-EKPfkC~~CgKsFs~~s 49 (405)
+.+|..|+... ...+..+.+ ...|+|..|++.|....
T Consensus 30 ~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 30 KVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred cCcCCCCCccc--eeeECCccccccccccCCcCcceeeec
Confidence 45588887543 111111222 45589999999887663
No 112
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=47.61 E-value=6.9 Score=33.53 Aligned_cols=20 Identities=20% Similarity=0.373 Sum_probs=12.0
Q ss_pred ccccccccCCCChhhHHHHh
Q 015552 36 FKCHVCHKKLSTAGGMAIHV 55 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~ 55 (405)
|-|-.|.+-|.+...|..|.
T Consensus 56 hYCieCaryf~t~~aL~~Hk 75 (126)
T COG5112 56 HYCIECARYFITEKALMEHK 75 (126)
T ss_pred eeeehhHHHHHHHHHHHHHh
Confidence 44555666666666666664
No 113
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=47.27 E-value=11 Score=37.07 Aligned_cols=45 Identities=16% Similarity=0.199 Sum_probs=24.0
Q ss_pred ccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCCCCChHHHHHHH
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVLAAHY 95 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~F~~~s~L~~H~ 95 (405)
|.|.+||-...- -.|-+|+-+.++.. |.|-.|++.|.+ .....|.
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn~~-------------fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRNAY-------------FSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccCCe-------------eEEeeccccccc-chhhhhh
Confidence 556666655443 24455654444433 666666666666 4445553
No 114
>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=46.70 E-value=11 Score=31.71 Aligned_cols=25 Identities=20% Similarity=0.359 Sum_probs=23.1
Q ss_pred ccc----cccccCCCChhhHHHHhhhhcc
Q 015552 36 FKC----HVCHKKLSTAGGMAIHVLQVHK 60 (405)
Q Consensus 36 fkC----~~CgKsFs~~s~L~rH~r~hH~ 60 (405)
|.| ..|+..+.+...|.+|.+.+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 8999999999999999998885
No 115
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=46.66 E-value=11 Score=39.56 Aligned_cols=29 Identities=21% Similarity=0.627 Sum_probs=11.9
Q ss_pred ccccCcccCChhHHHHHhh-cCcccccccc
Q 015552 14 CYYCDREFDDEKILVQHQK-AKHFKCHVCH 42 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R-EKPfkC~~Cg 42 (405)
|..|+|.|+....++.-.. +--|.|..|+
T Consensus 131 Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 131 CPNCQKKYTSLEALQLLDNETGEFHCENCG 160 (436)
T ss_pred CCccccchhhhHHHHhhcccCceEEEecCC
Confidence 4444444444444332222 2334444444
No 116
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=46.31 E-value=3.6e+02 Score=28.05 Aligned_cols=13 Identities=31% Similarity=0.805 Sum_probs=6.9
Q ss_pred CCCCCcccCCCCC
Q 015552 300 IGPPPVIANKAPA 312 (405)
Q Consensus 300 ~~~~~~~~~~~p~ 312 (405)
.|++|..+.+.++
T Consensus 328 ~GppP~~~~~~~p 340 (498)
T KOG4849|consen 328 MGPPPQMNTAMRP 340 (498)
T ss_pred CCCCCCCccCCCC
Confidence 4555555555543
No 117
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=45.93 E-value=7.3 Score=29.69 Aligned_cols=29 Identities=17% Similarity=0.305 Sum_probs=23.7
Q ss_pred cCcccccccccCCCChhhHHHHhhhhccc
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKE 61 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH~r~hH~e 61 (405)
|--++|.-||+-|.......+|+...|+-
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 66688999999999999999998666654
No 118
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=45.83 E-value=9.7 Score=26.14 Aligned_cols=31 Identities=16% Similarity=0.475 Sum_probs=16.5
Q ss_pred ccccCcccCChhHHHHHhhcCcccccccccCC
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKKL 45 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsF 45 (405)
|..|+..|.-...... ...+..+|..|+..|
T Consensus 5 CP~C~~~f~v~~~~l~-~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 5 CPNCQTRFRVPDDKLP-AGGRKVRCPKCGHVF 35 (37)
T ss_pred CCCCCceEEcCHHHcc-cCCcEEECCCCCcEe
Confidence 6666666665544211 113456666666555
No 119
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=45.22 E-value=8.9 Score=31.99 Aligned_cols=15 Identities=13% Similarity=0.496 Sum_probs=12.8
Q ss_pred cCcccccccccCCCC
Q 015552 33 AKHFKCHVCHKKLST 47 (405)
Q Consensus 33 EKPfkC~~CgKsFs~ 47 (405)
.+|-+|..||..|..
T Consensus 56 v~Pa~CkkCGfef~~ 70 (97)
T COG3357 56 VRPARCKKCGFEFRD 70 (97)
T ss_pred ecChhhcccCccccc
Confidence 678899999988876
No 120
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=45.16 E-value=6.5 Score=27.07 Aligned_cols=32 Identities=22% Similarity=0.282 Sum_probs=19.9
Q ss_pred cccccCcccCChhHHHHHhhcCcccccccccCCCCh
Q 015552 13 WCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTA 48 (405)
Q Consensus 13 ~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~ 48 (405)
.|..||+.|.....-- ...-+|..||..+.++
T Consensus 3 ~C~~Cg~~Yh~~~~pP----~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPP----KVEGVCDNCGGELVQR 34 (36)
T ss_dssp EETTTTEEEETTTB------SSTTBCTTTTEBEBEE
T ss_pred CcCCCCCccccccCCC----CCCCccCCCCCeeEeC
Confidence 4788888776544311 4556788888766554
No 121
>PF14353 CpXC: CpXC protein
Probab=45.14 E-value=2.5 Score=36.58 Aligned_cols=45 Identities=22% Similarity=0.335 Sum_probs=30.5
Q ss_pred cccccCcccCChhHHHHHhh-------------cCcccccccccCCCChhhHHHHhhh
Q 015552 13 WCYYCDREFDDEKILVQHQK-------------AKHFKCHVCHKKLSTAGGMAIHVLQ 57 (405)
Q Consensus 13 ~C~~CgK~F~~ks~Lk~H~R-------------EKPfkC~~CgKsFs~~s~L~rH~r~ 57 (405)
.|..|++.|...-....... ---|.|..||+.|.-...+.-|...
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCC
Confidence 39999999875543322211 2358899999999888777766533
No 122
>PF04404 ERF: ERF superfamily; InterPro: IPR007499 The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to ERF [].
Probab=44.82 E-value=14 Score=33.07 Aligned_cols=67 Identities=21% Similarity=0.257 Sum_probs=34.0
Q ss_pred ceEEEEEcccccChHHHhhccCceeeecccccccchhhchhccccccccccccccccc-----cccceehhhHHHHHHHH
Q 015552 318 NEVYLVWEDEAMSMEERRMSSVKYQVHDETSQVSYNYLFKIWSWFVFSNQMDRPYVSC-----FQISCLRFVTYLERYFL 392 (405)
Q Consensus 318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~ 392 (405)
+.+.|+|+++...+|+.-.---++.+.++.-. ..|+.++...+.--... ...| -..||++||.|
T Consensus 45 ~gl~~~~~~~~~~~~~~~~~~v~~~l~~~~g~---------~e~~~~~~~~~~~~~k~~~~~~Q~~G--sa~TYArRY~l 113 (160)
T PF04404_consen 45 HGLSLTQEFEEIETEENGIVKVTTTLTHASGP---------SEWIEFPGPADENGSKNQMDDPQATG--SAITYARRYAL 113 (160)
T ss_pred cCCeEEEEeecceecccceEEEEEEEEECCCC---------cEEEEEEEEeecccccccCcHHHHHH--HHHHHHHHHHH
Confidence 56788898888776633322233333333221 12333333333211111 2222 46899999998
Q ss_pred HHH
Q 015552 393 YEF 395 (405)
Q Consensus 393 ~~~ 395 (405)
-..
T Consensus 114 ~~~ 116 (160)
T PF04404_consen 114 SAA 116 (160)
T ss_pred HHh
Confidence 654
No 123
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.41 E-value=9.1 Score=35.54 Aligned_cols=36 Identities=19% Similarity=0.501 Sum_probs=28.3
Q ss_pred Cccc-ccccCcccCChhHHHHHhhcCcccccccccCCCChhh
Q 015552 10 SKVW-CYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGG 50 (405)
Q Consensus 10 eKp~-C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s~ 50 (405)
..+| |..|++.|+....+. --|.|..||..+..-++
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~-----~~F~Cp~Cg~~L~~~dn 151 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME-----YGFRCPQCGEMLEEYDN 151 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh-----cCCcCCCCCCCCeeccc
Confidence 4567 999999999887753 47999999987765543
No 124
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]
Probab=42.91 E-value=20 Score=40.06 Aligned_cols=20 Identities=25% Similarity=0.607 Sum_probs=14.3
Q ss_pred ccccccccCCCC------hhhHHHHh
Q 015552 36 FKCHVCHKKLST------AGGMAIHV 55 (405)
Q Consensus 36 fkC~~CgKsFs~------~s~L~rH~ 55 (405)
-+|..|+|.|.. .+++..|+
T Consensus 75 ~kc~~c~Kwfcn~r~gtsgshIv~hl 100 (935)
T KOG1802|consen 75 IKCNTCGKWFCNSRGGTSGSHIVNHL 100 (935)
T ss_pred eeccccCceeecCCCCCchhHHHHHH
Confidence 468889888854 36677775
No 125
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=42.29 E-value=15 Score=32.56 Aligned_cols=15 Identities=13% Similarity=0.534 Sum_probs=9.1
Q ss_pred cccccccccCCCChh
Q 015552 35 HFKCHVCHKKLSTAG 49 (405)
Q Consensus 35 PfkC~~CgKsFs~~s 49 (405)
||+|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 456666666666543
No 126
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=42.07 E-value=7.2 Score=27.84 Aligned_cols=27 Identities=22% Similarity=0.643 Sum_probs=15.7
Q ss_pred ccccCcccCChhHHHHHhhcCcccccccccCCC
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKKLS 46 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs 46 (405)
|..||..|..... ...++|..||..+.
T Consensus 6 C~~CG~~~~~~~~------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 6 CARCGREVELDEY------GTGVRCPYCGYRIL 32 (46)
T ss_pred CCCCCCEEEECCC------CCceECCCCCCeEE
Confidence 7777776655432 11466777775543
No 127
>PF15269 zf-C2H2_7: Zinc-finger
Probab=41.99 E-value=15 Score=26.86 Aligned_cols=21 Identities=19% Similarity=0.422 Sum_probs=16.8
Q ss_pred ccccccccCCCChhhHHHHhh
Q 015552 36 FKCHVCHKKLSTAGGMAIHVL 56 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r 56 (405)
|+|-+|..+...+++|-.|++
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 568888888888888888874
No 128
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=41.86 E-value=5 Score=41.06 Aligned_cols=46 Identities=28% Similarity=0.712 Sum_probs=36.3
Q ss_pred Cccc-ccc--cCcccCChhHHHHHhh-----------------------cCcccccccccCCCChhhHHHHh
Q 015552 10 SKVW-CYY--CDREFDDEKILVQHQK-----------------------AKHFKCHVCHKKLSTAGGMAIHV 55 (405)
Q Consensus 10 eKp~-C~~--CgK~F~~ks~Lk~H~R-----------------------EKPfkC~~CgKsFs~~s~L~rH~ 55 (405)
.+.+ |.+ |+|.++....|+.|.. .|+|+|.+|.|++.-.-+|+-|.
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 4555 865 9999988877776644 58899999999998888887774
No 129
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=41.38 E-value=16 Score=36.53 Aligned_cols=42 Identities=29% Similarity=0.530 Sum_probs=29.2
Q ss_pred CcccccccCcccCChhHHHHHhh---cCcccccccc-----cCCCChhhH
Q 015552 10 SKVWCYYCDREFDDEKILVQHQK---AKHFKCHVCH-----KKLSTAGGM 51 (405)
Q Consensus 10 eKp~C~~CgK~F~~ks~Lk~H~R---EKPfkC~~Cg-----KsFs~~s~L 51 (405)
+.+.|.-|++...++..|+.-.| .+-.+|..|. +.|.+...+
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~ 81 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSREGSV 81 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhcCCce
Confidence 56679999998888888876666 5555666664 456666554
No 130
>PF14369 zf-RING_3: zinc-finger
Probab=41.30 E-value=12 Score=25.50 Aligned_cols=32 Identities=22% Similarity=0.578 Sum_probs=18.8
Q ss_pred cccccccCcccCChhHHHHHhhcCcccccccccCCCC
Q 015552 11 KVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLST 47 (405)
Q Consensus 11 Kp~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~ 47 (405)
++||..|++...-... ....-.|..|+..|..
T Consensus 2 ~ywCh~C~~~V~~~~~-----~~~~~~CP~C~~gFvE 33 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPS-----PDSDVACPRCHGGFVE 33 (35)
T ss_pred CEeCccCCCEeEeCcC-----CCCCcCCcCCCCcEeE
Confidence 4668888877654321 0111248888888764
No 131
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.26 E-value=8.4 Score=31.10 Aligned_cols=28 Identities=29% Similarity=0.669 Sum_probs=19.5
Q ss_pred ccccCcccCChhHHHHHhhcCcc-cccccccCC
Q 015552 14 CYYCDREFDDEKILVQHQKAKHF-KCHVCHKKL 45 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPf-kC~~CgKsF 45 (405)
|..|+..| .+.+|+++-|+ .|..|+..|
T Consensus 15 c~~cg~~~----dvvq~~~ddplt~ce~c~a~~ 43 (82)
T COG2331 15 CTECGNRF----DVVQAMTDDPLTTCEECGARL 43 (82)
T ss_pred ecccchHH----HHHHhcccCccccChhhChHH
Confidence 88888654 56777775554 488887644
No 132
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=41.17 E-value=12 Score=27.73 Aligned_cols=25 Identities=24% Similarity=0.740 Sum_probs=14.2
Q ss_pred ccccCcccCChhHHHHHhhcCcccccccccC
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKK 44 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKs 44 (405)
|..||+.|..... .....|.+||.+
T Consensus 9 C~~Cg~~~~~~~~------~~~irCp~Cg~r 33 (49)
T COG1996 9 CARCGREVELDQE------TRGIRCPYCGSR 33 (49)
T ss_pred hhhcCCeeehhhc------cCceeCCCCCcE
Confidence 7777777732221 445667777643
No 133
>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=39.75 E-value=17 Score=24.19 Aligned_cols=9 Identities=33% Similarity=0.899 Sum_probs=4.9
Q ss_pred Ccccccccc
Q 015552 34 KHFKCHVCH 42 (405)
Q Consensus 34 KPfkC~~Cg 42 (405)
.+++|.+||
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 355565554
No 134
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=39.37 E-value=14 Score=30.62 Aligned_cols=12 Identities=17% Similarity=0.589 Sum_probs=8.1
Q ss_pred cCcccccccccC
Q 015552 33 AKHFKCHVCHKK 44 (405)
Q Consensus 33 EKPfkC~~CgKs 44 (405)
...|.|..|++.
T Consensus 33 ~~~~~Cp~C~~~ 44 (89)
T COG1997 33 RAKHVCPFCGRT 44 (89)
T ss_pred hcCCcCCCCCCc
Confidence 456778888765
No 135
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=38.95 E-value=13 Score=38.05 Aligned_cols=60 Identities=23% Similarity=0.224 Sum_probs=38.0
Q ss_pred cCcccccccccCCCChhhHHHHhhhhcccccccc--CCCCCCCCccccccCCCCCCChHHHHHH
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKV--PNAKPGRESTDIEIYGMQGIPPDVLAAH 94 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~c--p~~kpgRk~~~C~iCgk~F~~~s~L~~H 94 (405)
++-|.|.+|++.=.+...|..|+...|.+..+.| +.+- ...+.|.+|.|.-........|
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~--~~~~~qp~~~~~~~~~~~~~~~ 138 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA--ANPEMQPIHSKETENLSVHWTE 138 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc--cCcccCchhhhhhhhhhhhhhh
Confidence 5679999999988888899999988887764322 3321 1125556666544433333333
No 136
>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=38.91 E-value=13 Score=33.79 Aligned_cols=36 Identities=17% Similarity=0.321 Sum_probs=28.0
Q ss_pred CCccc-ccccCcccCChhHHHHHhhcCcccccccccCCCChh
Q 015552 9 SSKVW-CYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAG 49 (405)
Q Consensus 9 geKp~-C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s 49 (405)
...+| |..|++.|+....+. --|.|..||..+..-+
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~-----~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME-----LNFTCPRCGAMLDYLD 142 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH-----cCCcCCCCCCEeeecc
Confidence 34567 999999999888775 3699999998755443
No 137
>PF04573 SPC22: Signal peptidase subunit; InterPro: IPR007653 Translocation of polypeptide chains across the endoplasmic reticulum membrane is triggered by signal sequences. During translocation of the nascent chain through the membrane, the signal sequence of most secretory and membrane proteins is cleaved off. Cleavage occurs by the signal peptidase complex (SPC), which consists of four subunits in yeast and five in mammals. This family is is described as similar to microsomal signal peptidase 23 kDa subunit. Found in eukaryotes [, ].; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0005787 signal peptidase complex, 0016021 integral to membrane
Probab=35.79 E-value=28 Score=32.37 Aligned_cols=36 Identities=25% Similarity=0.441 Sum_probs=30.6
Q ss_pred CCceEEEEEcccccChHHHhhccC----ceeeecccccccc
Q 015552 316 AVNEVYLVWEDEAMSMEERRMSSV----KYQVHDETSQVSY 352 (405)
Q Consensus 316 ~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~ 352 (405)
..||| .+||+=.-+.|+-++.|. ||.++|....+..
T Consensus 99 ~~Nev-viWD~Ii~~~~~a~~~~~~~~~KY~~~d~~~~l~~ 138 (175)
T PF04573_consen 99 PVNEV-VIWDKIIRRKEDAVLNLKNVKSKYPFWDDGNGLRG 138 (175)
T ss_pred CcceE-EEehHhhcccchhhhhhhccccceeeECCCCcccC
Confidence 37898 679999999999888877 9999999887766
No 138
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=35.61 E-value=8.8 Score=30.61 Aligned_cols=18 Identities=17% Similarity=0.436 Sum_probs=10.2
Q ss_pred cCccccc--ccccCCCChhh
Q 015552 33 AKHFKCH--VCHKKLSTAGG 50 (405)
Q Consensus 33 EKPfkC~--~CgKsFs~~s~ 50 (405)
|+-+.|. .||.+|.....
T Consensus 25 ~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 25 ERYHQCQNVNCSATFITYES 44 (72)
T ss_pred eeeeecCCCCCCCEEEEEEE
Confidence 5556666 56666655433
No 139
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=35.57 E-value=1.4e+02 Score=33.89 Aligned_cols=33 Identities=36% Similarity=0.391 Sum_probs=18.5
Q ss_pred eEEEEEcccc------cChHHHhhccCc--eeeeccccccc
Q 015552 319 EVYLVWEDEA------MSMEERRMSSVK--YQVHDETSQVS 351 (405)
Q Consensus 319 ~~~~~~~~~~------~~~~~~~~~~~~--~~~~~~~~~~~ 351 (405)
-||---|||- |+|-|-++-+.| -++-||.++.+
T Consensus 387 tvf~~~~De~Il~~lD~~~~ee~Fk~~~s~~~~~~e~~a~~ 427 (830)
T KOG1923|consen 387 TVFHELNDEKILEALDFSRFEEQFKILKSNGQILDESSAVS 427 (830)
T ss_pred chhhhhhHHHHHHhhhHHHHHHHHHhhhcccchhhhHHHHH
Confidence 4566667764 455555565543 34567766543
No 140
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=35.11 E-value=19 Score=25.91 Aligned_cols=24 Identities=25% Similarity=0.606 Sum_probs=13.3
Q ss_pred ccccCcccCChhHHHHHhhcCcccccccccC
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKK 44 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKs 44 (405)
|..||..|..+. .-..+|..||.+
T Consensus 5 C~~Cg~~~~~~~-------~~~irC~~CG~r 28 (44)
T smart00659 5 CGECGRENEIKS-------KDVVRCRECGYR 28 (44)
T ss_pred CCCCCCEeecCC-------CCceECCCCCce
Confidence 666666665441 234566666643
No 141
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=35.03 E-value=12 Score=38.63 Aligned_cols=17 Identities=24% Similarity=0.341 Sum_probs=7.9
Q ss_pred ccccccCCCChhhHHHHh
Q 015552 38 CHVCHKKLSTAGGMAIHV 55 (405)
Q Consensus 38 C~~CgKsFs~~s~L~rH~ 55 (405)
|+.| |.|.+++-.++|+
T Consensus 39 CdGC-KGFFRRSVrk~~~ 55 (432)
T KOG4215|consen 39 CDGC-KGFFRRSVRKNHQ 55 (432)
T ss_pred cCcc-hHHHHHHHHhcce
Confidence 4444 4444444444443
No 142
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=34.87 E-value=20 Score=38.09 Aligned_cols=29 Identities=31% Similarity=0.725 Sum_probs=23.3
Q ss_pred CCcccccccCcccCChhHHHHHhhcCccc
Q 015552 9 SSKVWCYYCDREFDDEKILVQHQKAKHFK 37 (405)
Q Consensus 9 geKp~C~~CgK~F~~ks~Lk~H~REKPfk 37 (405)
++-.||-.|+|.|.....|+.|..-|.|+
T Consensus 290 ge~lyC~vCnKsFKseKq~kNHEnSKKHk 318 (508)
T KOG0717|consen 290 GEVLYCVVCNKSFKSEKQLKNHENSKKHK 318 (508)
T ss_pred CCceEEeeccccccchHHHHhhHHHHHHH
Confidence 55578999999999999999998833333
No 143
>PHA00626 hypothetical protein
Probab=34.83 E-value=12 Score=28.47 Aligned_cols=15 Identities=20% Similarity=0.410 Sum_probs=9.2
Q ss_pred CcccccccccCCCCh
Q 015552 34 KHFKCHVCHKKLSTA 48 (405)
Q Consensus 34 KPfkC~~CgKsFs~~ 48 (405)
..|+|..||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 356677776666543
No 144
>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=33.90 E-value=24 Score=23.69 Aligned_cols=24 Identities=21% Similarity=0.616 Sum_probs=11.4
Q ss_pred ccccCcccCChhHHHHHhhcCcccccccccC
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKK 44 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKs 44 (405)
|..||..+..+. .-+-+|..||.+
T Consensus 3 C~~Cg~~~~~~~-------~~~irC~~CG~R 26 (32)
T PF03604_consen 3 CGECGAEVELKP-------GDPIRCPECGHR 26 (32)
T ss_dssp ESSSSSSE-BST-------SSTSSBSSSS-S
T ss_pred CCcCCCeeEcCC-------CCcEECCcCCCe
Confidence 666666655322 224456666543
No 145
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=33.81 E-value=44 Score=25.79 Aligned_cols=50 Identities=18% Similarity=0.286 Sum_probs=32.2
Q ss_pred ccccccCcccCChhHHHHHhhcCcccccccccCCCChhhHHHHhhhhccccccccCCCCCCCCccccccCCCC
Q 015552 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQ 84 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~kpgRk~~~C~iCgk~ 84 (405)
..|.-||+...-.+. .-.|.|..||+.-..+..-.|-+ +. .|.|..||..
T Consensus 10 ~~CtSCg~~i~p~e~------~v~F~CPnCGe~~I~Rc~~CRk~----g~-------------~Y~Cp~CGF~ 59 (61)
T COG2888 10 PVCTSCGREIAPGET------AVKFPCPNCGEVEIYRCAKCRKL----GN-------------PYRCPKCGFE 59 (61)
T ss_pred ceeccCCCEeccCCc------eeEeeCCCCCceeeehhhhHHHc----CC-------------ceECCCcCcc
Confidence 459999987633222 34589999998777766544332 21 1888888854
No 146
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=33.49 E-value=25 Score=25.63 Aligned_cols=27 Identities=19% Similarity=0.630 Sum_probs=19.4
Q ss_pred ccccCcccCChhHHHHHhhcCcccccccccCCCCh
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTA 48 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~ 48 (405)
|..|++.|... .+.+.|..||+.|-..
T Consensus 5 C~~C~~~F~~~--------~rk~~Cr~Cg~~~C~~ 31 (57)
T cd00065 5 CMGCGKPFTLT--------RRRHHCRNCGRIFCSK 31 (57)
T ss_pred CcccCccccCC--------ccccccCcCcCCcChH
Confidence 77888888762 3456788888887764
No 147
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.44 E-value=88 Score=31.69 Aligned_cols=6 Identities=33% Similarity=1.004 Sum_probs=3.3
Q ss_pred ccccCc
Q 015552 14 CYYCDR 19 (405)
Q Consensus 14 C~~CgK 19 (405)
|..|++
T Consensus 277 Cplc~~ 282 (427)
T COG5222 277 CPLCHC 282 (427)
T ss_pred Ccchhh
Confidence 666553
No 148
>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=33.00 E-value=13 Score=26.94 Aligned_cols=12 Identities=17% Similarity=0.963 Sum_probs=8.3
Q ss_pred ccccccccCCCC
Q 015552 36 FKCHVCHKKLST 47 (405)
Q Consensus 36 fkC~~CgKsFs~ 47 (405)
|+|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 677777776664
No 149
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=32.95 E-value=17 Score=31.16 Aligned_cols=26 Identities=27% Similarity=0.811 Sum_probs=14.4
Q ss_pred cccccccCcccCChhHHHHHhhcCcccccccccC
Q 015552 11 KVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKK 44 (405)
Q Consensus 11 Kp~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKs 44 (405)
+.+|..||+.|..... .+.|..||..
T Consensus 70 ~~~C~~Cg~~~~~~~~--------~~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEF--------DFSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECHHC--------CHH-SSSSSS
T ss_pred cEECCCCCCEEecCCC--------CCCCcCCcCC
Confidence 3457777777766543 2557777654
No 150
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=32.60 E-value=6e+02 Score=26.54 Aligned_cols=9 Identities=11% Similarity=0.039 Sum_probs=5.3
Q ss_pred ccCCCCCCC
Q 015552 79 EIYGMQGIP 87 (405)
Q Consensus 79 ~iCgk~F~~ 87 (405)
.-|+|.|..
T Consensus 157 ~~~NK~~~a 165 (498)
T KOG4849|consen 157 LSYNKTNQA 165 (498)
T ss_pred eccchhhHH
Confidence 357776643
No 151
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=31.76 E-value=9.9 Score=42.38 Aligned_cols=26 Identities=19% Similarity=0.392 Sum_probs=21.3
Q ss_pred ccccccccCCCChhhHHHHhhhhccc
Q 015552 36 FKCHVCHKKLSTAGGMAIHVLQVHKE 61 (405)
Q Consensus 36 fkC~~CgKsFs~~s~L~rH~r~hH~e 61 (405)
|.|..|+|.|.....+..||++|...
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 88999999998888888888777543
No 152
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=31.11 E-value=13 Score=41.73 Aligned_cols=35 Identities=20% Similarity=0.376 Sum_probs=19.9
Q ss_pred ccccCcccCChhHHHHHhhcCccc-ccccccCCCChhhH
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFK-CHVCHKKLSTAGGM 51 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfk-C~~CgKsFs~~s~L 51 (405)
|..|-+.+.+..+.+- .-||. |..||-+|+-...|
T Consensus 71 C~~Cl~E~~dp~~Rry---~YpF~nCt~CGPr~~i~~~l 106 (711)
T TIGR00143 71 CSDCLEEMLDKNDRRY---LYPFISCTHCGPRFTIIEAL 106 (711)
T ss_pred HHHHHHHhcCCCcccc---cCCcccccCCCCCeEEeecC
Confidence 7777766655544211 33554 77777776655544
No 153
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=30.91 E-value=25 Score=34.78 Aligned_cols=81 Identities=21% Similarity=0.377 Sum_probs=48.0
Q ss_pred CCCccc-ccccCcccCChhHHHHHhh------cCcccccccccCCCChhhHH-------HHhhhhccccccccCCCCCCC
Q 015552 8 VSSKVW-CYYCDREFDDEKILVQHQK------AKHFKCHVCHKKLSTAGGMA-------IHVLQVHKENVTKVPNAKPGR 73 (405)
Q Consensus 8 ~geKp~-C~~CgK~F~~ks~Lk~H~R------EKPfkC~~CgKsFs~~s~L~-------rH~r~hH~ekp~~cp~~kpgR 73 (405)
+|.|.+ |.+|+. |.-...--.|+. .--|||.-|++ +.+-+-|+ .|+|+.- ++-.. .
T Consensus 138 hGGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNr-lGq~sCLRCK~cfCddHvrrKg----~ky~k----~ 207 (314)
T PF06524_consen 138 HGGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNR-LGQYSCLRCKICFCDDHVRRKG----FKYEK----G 207 (314)
T ss_pred CCCeEEEeecCCC-eeeccchhhhhhhhhhhhccccccccccc-ccchhhhheeeeehhhhhhhcc----ccccc----C
Confidence 355666 999985 554555556776 45689988864 33333343 4543321 22222 2
Q ss_pred CccccccCCCCCCChHHHHHHHhhh
Q 015552 74 ESTDIEIYGMQGIPPDVLAAHYGEE 98 (405)
Q Consensus 74 k~~~C~iCgk~F~~~s~L~~H~r~h 98 (405)
+.+.|..||........|..-.|+|
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCcccccccceeeeecc
Confidence 3388999998777766676555554
No 154
>KOG3815 consensus Transcription factor Doublesex [Transcription]
Probab=30.28 E-value=22 Score=36.01 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=32.5
Q ss_pred CCcccccccCcccCChhHHHHHhh---cCcccccccccCCCChhhHH
Q 015552 9 SSKVWCYYCDREFDDEKILVQHQK---AKHFKCHVCHKKLSTAGGMA 52 (405)
Q Consensus 9 geKp~C~~CgK~F~~ks~Lk~H~R---EKPfkC~~CgKsFs~~s~L~ 52 (405)
..+++|..|. -+.....||.|.| -|.-.|.+|+....++..+.
T Consensus 34 ~r~p~CaRCr-nHG~~~~LKGHk~~C~~~~C~C~kC~li~eRqrvma 79 (322)
T KOG3815|consen 34 ARGPKCARCE-NHGVLSRLKGHKRSCPYRDCPCEKCGLVEERRRVMA 79 (322)
T ss_pred cccchhhhhh-ccCcceeccCCCCCCCCCCCCchHhcchHHHHHHHH
Confidence 4556799985 4566788999998 67777999998887775554
No 155
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the smart00531 TFIIE Transcription initiation factor IIE.
Probab=29.89 E-value=26 Score=31.25 Aligned_cols=37 Identities=16% Similarity=0.403 Sum_probs=24.8
Q ss_pred ccc-ccccCcccCChhHHHH-HhhcCcccccccccCCCCh
Q 015552 11 KVW-CYYCDREFDDEKILVQ-HQKAKHFKCHVCHKKLSTA 48 (405)
Q Consensus 11 Kp~-C~~CgK~F~~ks~Lk~-H~REKPfkC~~CgKsFs~~ 48 (405)
..| |..|++.|.....+.. +. +..|.|..||......
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d~-~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLDM-DGTFTCPRCGEELEED 136 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcCC-CCcEECCCCCCEEEEc
Confidence 455 8888888887665443 22 4448888888766443
No 157
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.68 E-value=30 Score=34.79 Aligned_cols=57 Identities=19% Similarity=0.141 Sum_probs=33.4
Q ss_pred cCcccccccccCCCChhhHHHHhhhhccccccccCCC--CCCCCccccccCCCC----CCChHHHHHHHhh
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNA--KPGRESTDIEIYGMQ----GIPPDVLAAHYGE 97 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH~r~hH~ekp~~cp~~--kpgRk~~~C~iCgk~----F~~~s~L~~H~r~ 97 (405)
.-||+|.+|++.|.+.- ++.-+.+=|..| ++.++.-.|-+|++. |.....|..-+..
T Consensus 239 ~~Pf~c~icr~~f~~pV--------vt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~~akeL~~~L~~ 301 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRPV--------VTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFNVAKELLVSLKL 301 (313)
T ss_pred cCCccccccccccccch--------hhcCCceeehhhhccccccCCcceecccccccccchHHHHHHHHHh
Confidence 45899999999987751 222222234332 455666778889874 3444445444433
No 158
>KOG4217 consensus Nuclear receptors of the nerve growth factor-induced protein B type [Transcription]
Probab=29.10 E-value=32 Score=36.80 Aligned_cols=23 Identities=26% Similarity=0.683 Sum_probs=14.6
Q ss_pred cccccCcccCChhHHHHHhhcCcccccccc
Q 015552 13 WCYYCDREFDDEKILVQHQKAKHFKCHVCH 42 (405)
Q Consensus 13 ~C~~CgK~F~~ks~Lk~H~REKPfkC~~Cg 42 (405)
.|-+||- ..-.+|...| .|+.|.
T Consensus 271 ~CAVCgD-----nAaCqHYGvR--TCEGCK 293 (605)
T KOG4217|consen 271 LCAVCGD-----NAACQHYGVR--TCEGCK 293 (605)
T ss_pred eeeecCC-----hHHhhhcCcc--ccccch
Confidence 4999983 3445666544 488883
No 159
>PRK14873 primosome assembly protein PriA; Provisional
Probab=28.93 E-value=40 Score=37.62 Aligned_cols=10 Identities=10% Similarity=-0.054 Sum_probs=7.1
Q ss_pred ccccccCCCC
Q 015552 75 STDIEIYGMQ 84 (405)
Q Consensus 75 ~~~C~iCgk~ 84 (405)
...|..||..
T Consensus 422 p~~Cp~Cgs~ 431 (665)
T PRK14873 422 DWRCPRCGSD 431 (665)
T ss_pred CccCCCCcCC
Confidence 4678888765
No 160
>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=28.83 E-value=31 Score=30.71 Aligned_cols=21 Identities=24% Similarity=0.564 Sum_probs=10.8
Q ss_pred Cccc-ccccCcccCCh-hHHHHH
Q 015552 10 SKVW-CYYCDREFDDE-KILVQH 30 (405)
Q Consensus 10 eKp~-C~~CgK~F~~k-s~Lk~H 30 (405)
+.+. |-+|||.|+.. .||..|
T Consensus 70 ~d~i~clecGk~~k~LkrHL~~~ 92 (132)
T PF05443_consen 70 PDYIICLECGKKFKTLKRHLRTH 92 (132)
T ss_dssp SS-EE-TBT--EESBHHHHHHHT
T ss_pred cCeeEEccCCcccchHHHHHHHc
Confidence 3444 99999999874 344444
No 161
>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=28.48 E-value=27 Score=23.56 Aligned_cols=22 Identities=27% Similarity=0.632 Sum_probs=11.4
Q ss_pred ccccCcccCChhHHHHHhhcCccccccccc
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHK 43 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgK 43 (405)
|..||..+... +.|.+|.+|+.
T Consensus 5 C~~CG~i~~g~--------~~p~~CP~Cg~ 26 (34)
T cd00729 5 CPVCGYIHEGE--------EAPEKCPICGA 26 (34)
T ss_pred CCCCCCEeECC--------cCCCcCcCCCC
Confidence 66666443321 23456666653
No 162
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.25 E-value=22 Score=40.12 Aligned_cols=8 Identities=25% Similarity=0.488 Sum_probs=5.9
Q ss_pred ccccCccc
Q 015552 14 CYYCDREF 21 (405)
Q Consensus 14 C~~CgK~F 21 (405)
|..||..|
T Consensus 438 C~~Cg~v~ 445 (730)
T COG1198 438 CRDCGYIA 445 (730)
T ss_pred cccCCCcc
Confidence 88888653
No 163
>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=27.76 E-value=16 Score=36.28 Aligned_cols=14 Identities=21% Similarity=0.487 Sum_probs=5.0
Q ss_pred cccccccccCCCCh
Q 015552 35 HFKCHVCHKKLSTA 48 (405)
Q Consensus 35 PfkC~~CgKsFs~~ 48 (405)
..+|..||..-..+
T Consensus 211 R~~Cp~Cg~~~~~~ 224 (290)
T PF04216_consen 211 RIKCPYCGNTDHEK 224 (290)
T ss_dssp TTS-TTT---SS-E
T ss_pred CCCCcCCCCCCCcc
Confidence 34677777654433
No 164
>KOG4672 consensus Uncharacterized conserved low complexity protein [Function unknown]
Probab=27.52 E-value=3.8e+02 Score=28.43 Aligned_cols=23 Identities=17% Similarity=-0.029 Sum_probs=12.4
Q ss_pred CCCccc-ccccCcccCChhHHHHH
Q 015552 8 VSSKVW-CYYCDREFDDEKILVQH 30 (405)
Q Consensus 8 ~geKp~-C~~CgK~F~~ks~Lk~H 30 (405)
.+.|+. |..-.|.-.++..|++.
T Consensus 9 k~gk~mnPTDqaRKe~RKkElKrN 32 (487)
T KOG4672|consen 9 KGGKYMNPTDQARKEARKKELKRN 32 (487)
T ss_pred cCCcccCccHHHHHHHHHHHhhhh
Confidence 356666 76555554555555443
No 165
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=27.48 E-value=34 Score=29.23 Aligned_cols=14 Identities=14% Similarity=0.527 Sum_probs=8.6
Q ss_pred cccccccccCCCCh
Q 015552 35 HFKCHVCHKKLSTA 48 (405)
Q Consensus 35 PfkC~~CgKsFs~~ 48 (405)
+|.|..||..|..-
T Consensus 2 pH~CtrCG~vf~~g 15 (112)
T COG3364 2 PHQCTRCGEVFDDG 15 (112)
T ss_pred Cceecccccccccc
Confidence 45666666666654
No 166
>PRK04860 hypothetical protein; Provisional
Probab=26.94 E-value=44 Score=30.59 Aligned_cols=32 Identities=6% Similarity=-0.070 Sum_probs=26.7
Q ss_pred cccccCCCCCCChHHHHHHHhhhcCCCcccccccCC
Q 015552 76 TDIEIYGMQGIPPDVLAAHYGEEEEEVPSKMAKVDT 111 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H~r~h~~e~~~k~ak~~~ 111 (405)
|.|. |++ ....+.+|.++|.+++.+++.++..
T Consensus 120 Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~ 151 (160)
T PRK04860 120 YRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGE 151 (160)
T ss_pred EEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCc
Confidence 8998 987 6777899999999998888776643
No 167
>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=26.94 E-value=20 Score=29.90 Aligned_cols=12 Identities=33% Similarity=0.838 Sum_probs=8.5
Q ss_pred cCcccccccccC
Q 015552 33 AKHFKCHVCHKK 44 (405)
Q Consensus 33 EKPfkC~~CgKs 44 (405)
...|.|..|++.
T Consensus 33 ~a~y~CpfCgk~ 44 (91)
T TIGR00280 33 KAKYVCPFCGKK 44 (91)
T ss_pred hcCccCCCCCCC
Confidence 456888888753
No 168
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=26.88 E-value=31 Score=32.10 Aligned_cols=21 Identities=24% Similarity=0.523 Sum_probs=19.3
Q ss_pred ccccccCcccCChhHHHHHhh
Q 015552 12 VWCYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~R 32 (405)
+||.+|+-.|.+.-++..|+.
T Consensus 76 yyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 76 YYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred eeeeecceeehhhHHHHHHhc
Confidence 669999999999999998888
No 169
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=26.75 E-value=51 Score=23.19 Aligned_cols=24 Identities=25% Similarity=0.239 Sum_probs=16.9
Q ss_pred cccccCCCCCCC--hHHHHHHHhhhc
Q 015552 76 TDIEIYGMQGIP--PDVLAAHYGEEE 99 (405)
Q Consensus 76 ~~C~iCgk~F~~--~s~L~~H~r~h~ 99 (405)
..|..||+.+.. .++.+.|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 578999998853 455667777664
No 170
>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=26.64 E-value=36 Score=21.77 Aligned_cols=10 Identities=20% Similarity=0.527 Sum_probs=5.7
Q ss_pred cccccccCCC
Q 015552 37 KCHVCHKKLS 46 (405)
Q Consensus 37 kC~~CgKsFs 46 (405)
.|..||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666666553
No 171
>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=26.08 E-value=16 Score=25.70 Aligned_cols=13 Identities=15% Similarity=0.787 Sum_probs=7.9
Q ss_pred ccccccccCCCCh
Q 015552 36 FKCHVCHKKLSTA 48 (405)
Q Consensus 36 fkC~~CgKsFs~~ 48 (405)
|+|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 6 YRCEECGHEFEVL 18 (42)
T ss_pred EEeCCCCCEEEEE
Confidence 5666666666544
No 172
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=25.80 E-value=21 Score=36.91 Aligned_cols=18 Identities=28% Similarity=0.506 Sum_probs=14.6
Q ss_pred ccccCcccCChhHHHHHhh
Q 015552 14 CYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R 32 (405)
|.-| |.|.+++.+++|+-
T Consensus 39 CdGC-KGFFRRSVrk~~~Y 56 (432)
T KOG4215|consen 39 CDGC-KGFFRRSVRKNHQY 56 (432)
T ss_pred cCcc-hHHHHHHHHhccee
Confidence 7778 57888888998876
No 173
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=25.66 E-value=37 Score=30.41 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=15.3
Q ss_pred CCccc-ccccCcccCChhHHHHHhh
Q 015552 9 SSKVW-CYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 9 geKp~-C~~CgK~F~~ks~Lk~H~R 32 (405)
..-+. |-+|||.|+. |++|.+
T Consensus 73 tpD~IicLEDGkkfKS---LKRHL~ 94 (148)
T COG4957 73 TPDYIICLEDGKKFKS---LKRHLT 94 (148)
T ss_pred CCCeEEEeccCcchHH---HHHHHh
Confidence 44455 9999999975 666655
No 174
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=25.55 E-value=13 Score=41.42 Aligned_cols=25 Identities=12% Similarity=-0.051 Sum_probs=22.6
Q ss_pred cccccCCCCCCChHHHHHHHhhhcC
Q 015552 76 TDIEIYGMQGIPPDVLAAHYGEEEE 100 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H~r~h~~ 100 (405)
|.|.+|+|.|..-..+.+||++|.-
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHHH
Confidence 8899999999999999999999853
No 175
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.37 E-value=36 Score=29.47 Aligned_cols=46 Identities=17% Similarity=0.458 Sum_probs=33.9
Q ss_pred cccccCcccCChhHHHHH-hh-cCcccccccccCCCChhhHHHHhhhh
Q 015552 13 WCYYCDREFDDEKILVQH-QK-AKHFKCHVCHKKLSTAGGMAIHVLQV 58 (405)
Q Consensus 13 ~C~~CgK~F~~ks~Lk~H-~R-EKPfkC~~CgKsFs~~s~L~rH~r~h 58 (405)
.|.-|++.|........- .. ...|+|..|.+.|--.-++-.|+..|
T Consensus 57 ~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhcc
Confidence 499999999865322111 11 45699999999999999999998544
No 176
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=25.12 E-value=32 Score=38.50 Aligned_cols=19 Identities=16% Similarity=-0.066 Sum_probs=11.0
Q ss_pred cccccCCCCCCChHHHHHH
Q 015552 76 TDIEIYGMQGIPPDVLAAH 94 (405)
Q Consensus 76 ~~C~iCgk~F~~~s~L~~H 94 (405)
-+|..|+..|...+.+..|
T Consensus 679 RKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 679 RKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred CCCCCCCCCCCcccccccC
Confidence 3466677777665554433
No 177
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.10 E-value=29 Score=29.74 Aligned_cols=12 Identities=25% Similarity=1.046 Sum_probs=6.0
Q ss_pred ccccccCcccCC
Q 015552 12 VWCYYCDREFDD 23 (405)
Q Consensus 12 p~C~~CgK~F~~ 23 (405)
.+|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PRK12380 71 AWCWDCSQVVEI 82 (113)
T ss_pred EEcccCCCEEec
Confidence 335555555444
No 178
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=25.04 E-value=37 Score=20.98 Aligned_cols=7 Identities=43% Similarity=1.027 Sum_probs=3.4
Q ss_pred ccccCcc
Q 015552 14 CYYCDRE 20 (405)
Q Consensus 14 C~~CgK~ 20 (405)
|..||+.
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 4455543
No 179
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.47 E-value=29 Score=30.67 Aligned_cols=10 Identities=30% Similarity=0.796 Sum_probs=5.4
Q ss_pred ccccCcccCC
Q 015552 14 CYYCDREFDD 23 (405)
Q Consensus 14 C~~CgK~F~~ 23 (405)
|..||..|..
T Consensus 73 C~~CG~~~~~ 82 (135)
T PRK03824 73 CRNCGNEWSL 82 (135)
T ss_pred CCCCCCEEec
Confidence 5555555544
No 180
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=24.46 E-value=39 Score=34.32 Aligned_cols=26 Identities=8% Similarity=-0.225 Sum_probs=20.8
Q ss_pred CccccccCCCCCCChHHHHHHHhhhc
Q 015552 74 ESTDIEIYGMQGIPPDVLAAHYGEEE 99 (405)
Q Consensus 74 k~~~C~iCgk~F~~~s~L~~H~r~h~ 99 (405)
.+|+|+.|...|-...+.-.|+..|.
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHhh
Confidence 44999999999987777778877764
No 181
>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=24.45 E-value=24 Score=26.88 Aligned_cols=30 Identities=17% Similarity=0.532 Sum_probs=14.4
Q ss_pred ccccccCcccCChhHHHHHhhcCcccccccccCCCChh
Q 015552 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAG 49 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s 49 (405)
..|..|++.|... .|.+.|..||+.|-..-
T Consensus 10 ~~C~~C~~~F~~~--------~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 10 SNCMICGKKFSLF--------RRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp SB-TTT--B-BSS--------S-EEE-TTT--EEECCC
T ss_pred CcCcCcCCcCCCc--------eeeEccCCCCCEECCch
Confidence 3488899998542 34577888888776553
No 182
>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=24.10 E-value=48 Score=30.23 Aligned_cols=48 Identities=23% Similarity=0.392 Sum_probs=17.5
Q ss_pred ccccccccCC------CChhhHHHHh-hhhccccccccCCCCCCCCccccccCCCC
Q 015552 36 FKCHVCHKKL------STAGGMAIHV-LQVHKENVTKVPNAKPGRESTDIEIYGMQ 84 (405)
Q Consensus 36 fkC~~CgKsF------s~~s~L~rH~-r~hH~ekp~~cp~~kpgRk~~~C~iCgk~ 84 (405)
.+|..|+|-| +..+++..|+ +.+|.+.- .-+...=+...++|-.||-+
T Consensus 15 v~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~-LH~~s~lgdt~leCy~Cg~~ 69 (152)
T PF09416_consen 15 VKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVS-LHPDSPLGDTVLECYNCGSR 69 (152)
T ss_dssp EEETTTTEEEES--TTSSS-HHHHHHHHHT---EE-E-TTSTT-S-B---TTT---
T ss_pred eEcCCCCcEeecCCCCCcccHHHHHHHHccCCcee-eCCCCCCCCcEEEEEecCCC
Confidence 4566666655 3567788885 33343311 00111113344777777654
No 183
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=23.60 E-value=35 Score=31.45 Aligned_cols=9 Identities=44% Similarity=1.412 Sum_probs=5.8
Q ss_pred cccccccCc
Q 015552 11 KVWCYYCDR 19 (405)
Q Consensus 11 Kp~C~~CgK 19 (405)
|+||++|+.
T Consensus 3 RYyCDYCdt 11 (165)
T KOG3454|consen 3 RYYCDYCDT 11 (165)
T ss_pred cchhhhhhh
Confidence 566777773
No 184
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=23.19 E-value=87 Score=32.07 Aligned_cols=65 Identities=12% Similarity=0.007 Sum_probs=43.6
Q ss_pred cCcccccccccCCCChhhHHHHhhhhcc-------cc----------ccccCCCCCCCCccccccCCCCCCChHHHHHHH
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHK-------EN----------VTKVPNAKPGRESTDIEIYGMQGIPPDVLAAHY 95 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH~r~hH~-------ek----------p~~cp~~kpgRk~~~C~iCgk~F~~~s~L~~H~ 95 (405)
+-|-.|..|+-.+...-+|.|-. ||- |. .|.|-........|.|+.|...|--.-+.-.|.
T Consensus 288 sLP~eCpiC~ltLVss~hLARSy--hhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 288 SLPIECPICSLTLVSSPHLARSY--HHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHE 365 (378)
T ss_pred cCCccCCccceeEecchHHHHHH--HhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHh
Confidence 56789999999999999998764 221 11 133322223344599999999997666666787
Q ss_pred hhhc
Q 015552 96 GEEE 99 (405)
Q Consensus 96 r~h~ 99 (405)
..|.
T Consensus 366 sLh~ 369 (378)
T KOG2807|consen 366 SLHN 369 (378)
T ss_pred hhhc
Confidence 7664
No 185
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=23.08 E-value=46 Score=29.30 Aligned_cols=30 Identities=17% Similarity=0.109 Sum_probs=25.9
Q ss_pred CCCCCCccccccCCCCCCChHHHHHHHhhh
Q 015552 69 AKPGRESTDIEIYGMQGIPPDVLAAHYGEE 98 (405)
Q Consensus 69 ~kpgRk~~~C~iCgk~F~~~s~L~~H~r~h 98 (405)
.+||.-.|-|-.|.+-|++...|..|.++.
T Consensus 51 dlPG~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 51 DLPGGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCCCCceeehhhhhhhhcchHHHHHHHhcc
Confidence 366777799999999999999999998764
No 186
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=22.82 E-value=26 Score=29.20 Aligned_cols=12 Identities=25% Similarity=0.661 Sum_probs=8.4
Q ss_pred cCcccccccccC
Q 015552 33 AKHFKCHVCHKK 44 (405)
Q Consensus 33 EKPfkC~~CgKs 44 (405)
...|.|..|++.
T Consensus 34 ~a~y~CpfCgk~ 45 (90)
T PRK03976 34 RAKHVCPVCGRP 45 (90)
T ss_pred hcCccCCCCCCC
Confidence 456888888654
No 187
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=22.65 E-value=67 Score=24.74 Aligned_cols=33 Identities=21% Similarity=0.351 Sum_probs=20.0
Q ss_pred cccccccCcccCChhHHHHHhhcCcccccccccCCCChh
Q 015552 11 KVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAG 49 (405)
Q Consensus 11 Kp~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s 49 (405)
+..|.-||+...-... .-.|.|..||+....+.
T Consensus 7 ~~~CtSCg~~i~~~~~------~~~F~CPnCG~~~I~RC 39 (59)
T PRK14890 7 PPKCTSCGIEIAPREK------AVKFLCPNCGEVIIYRC 39 (59)
T ss_pred CccccCCCCcccCCCc------cCEeeCCCCCCeeEeec
Confidence 3458888865443221 23588999987744443
No 188
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=22.59 E-value=22 Score=29.46 Aligned_cols=37 Identities=22% Similarity=0.282 Sum_probs=25.3
Q ss_pred Cceeeecccccccchhhchhccccccccccccccccccccc---eehhhHHHHH
Q 015552 339 VKYQVHDETSQVSYNYLFKIWSWFVFSNQMDRPYVSCFQIS---CLRFVTYLER 389 (405)
Q Consensus 339 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~ 389 (405)
-||.+|||-.+..-= |.. +|.|+|=.. .|.||..+++
T Consensus 45 kK~~aHde~~~~k~G-----------D~V---~I~EtRPLSKtK~~~vv~i~~~ 84 (87)
T COG0186 45 KKYHAHDECNEAKVG-----------DIV---RIAETRPLSKTKRFVVVEIVEK 84 (87)
T ss_pred eeeEeecccccCCCC-----------CEE---EEEEccccCCcceEEEEEEeee
Confidence 378999987765443 322 688888766 7887766654
No 189
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=22.54 E-value=3.7e+02 Score=30.73 Aligned_cols=8 Identities=25% Similarity=-0.002 Sum_probs=3.3
Q ss_pred Hhhhhccc
Q 015552 54 HVLQVHKE 61 (405)
Q Consensus 54 H~r~hH~e 61 (405)
|+|..+.+
T Consensus 177 her~~~v~ 184 (830)
T KOG1923|consen 177 HERLQAVE 184 (830)
T ss_pred HHHHHHHH
Confidence 34444433
No 190
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=22.46 E-value=8.6e+02 Score=28.02 Aligned_cols=10 Identities=40% Similarity=0.527 Sum_probs=4.6
Q ss_pred CCCCCChHHH
Q 015552 82 GMQGIPPDVL 91 (405)
Q Consensus 82 gk~F~~~s~L 91 (405)
|..+|.-+.|
T Consensus 510 GVt~IP~~kL 519 (894)
T KOG0132|consen 510 GVTYIPWEKL 519 (894)
T ss_pred CeeEeehHhc
Confidence 4445544444
No 191
>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=22.23 E-value=32 Score=22.33 Aligned_cols=10 Identities=10% Similarity=-0.150 Sum_probs=5.6
Q ss_pred cccccCCCCC
Q 015552 76 TDIEIYGMQG 85 (405)
Q Consensus 76 ~~C~iCgk~F 85 (405)
|.|..|++.+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 5566665544
No 192
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=22.07 E-value=77 Score=27.02 Aligned_cols=37 Identities=16% Similarity=0.275 Sum_probs=24.4
Q ss_pred Cceeeecccccccchhhchhccccccccccccccccccccc---eehhhHHHHH
Q 015552 339 VKYQVHDETSQVSYNYLFKIWSWFVFSNQMDRPYVSCFQIS---CLRFVTYLER 389 (405)
Q Consensus 339 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~ 389 (405)
-||+||||-.|-+-- |.. ||.-+|-.. .|-|..-|++
T Consensus 39 ~kymahD~~n~cnvG-----------D~V---rlepsRPlSk~K~f~i~eII~~ 78 (107)
T KOG1740|consen 39 SKYMAHDDKNQCNVG-----------DRV---RLEPSRPLSKTKHFIIAEIIKK 78 (107)
T ss_pred hheeecCcccccccc-----------ceE---EeccCCcccccceeehHHHHHH
Confidence 589999999887655 432 666677655 5555555543
No 193
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=21.96 E-value=30 Score=25.83 Aligned_cols=43 Identities=19% Similarity=0.498 Sum_probs=19.5
Q ss_pred ccccCcccCChhHHHHHhhcCcccccccccCCCChhhHHHHhhhh
Q 015552 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMAIHVLQV 58 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~REKPfkC~~CgKsFs~~s~L~rH~r~h 58 (405)
|.-|.+.|.....-..- ...|+|..|++.|--.-.+-.|+..|
T Consensus 2 CfgC~~~~~~~~~~~~~--~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKAD--SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp ETTTTEE-TTS---------EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CccCCCCCCCccccccc--CCeEECCCCCCccccCcChhhhcccc
Confidence 45566666654321100 24578888888888777777776443
No 194
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=21.92 E-value=45 Score=35.30 Aligned_cols=29 Identities=31% Similarity=0.407 Sum_probs=18.2
Q ss_pred CCCCCCCCCCcccccccCcccCChhHHHHHhhcCccccccccc
Q 015552 1 MGKKKKRVSSKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHK 43 (405)
Q Consensus 1 mgkKkrr~geKp~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgK 43 (405)
|.|+| + .|.|+.||..+.+= --+|..|+.
T Consensus 1 MaK~~-t---~f~C~~CG~~s~KW----------~GkCp~Cg~ 29 (456)
T COG1066 1 MAKKK-T---AFVCQECGYVSPKW----------LGKCPACGA 29 (456)
T ss_pred CCCcc-c---EEEcccCCCCCccc----------cccCCCCCC
Confidence 56666 2 24499999654332 237999984
No 195
>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=21.88 E-value=29 Score=31.47 Aligned_cols=22 Identities=18% Similarity=0.484 Sum_probs=15.4
Q ss_pred cCcccccccccCCCChhhHHHH
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIH 54 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH 54 (405)
.|-=.|..|+++|++-.-+..-
T Consensus 26 RRRReC~~C~~RFTTyErve~~ 47 (147)
T TIGR00244 26 RRRRECLECHERFTTFERAELL 47 (147)
T ss_pred eecccCCccCCccceeeecccc
Confidence 3445799999999887555433
No 196
>PRK11823 DNA repair protein RadA; Provisional
Probab=21.84 E-value=52 Score=34.76 Aligned_cols=22 Identities=23% Similarity=0.385 Sum_probs=15.1
Q ss_pred ccccccCcccCChhHHHHHhhcCccccccccc
Q 015552 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHK 43 (405)
Q Consensus 12 p~C~~CgK~F~~ks~Lk~H~REKPfkC~~CgK 43 (405)
|.|..||..+.+ .-.+|..|+.
T Consensus 8 y~C~~Cg~~~~~----------~~g~Cp~C~~ 29 (446)
T PRK11823 8 YVCQECGAESPK----------WLGRCPECGA 29 (446)
T ss_pred EECCcCCCCCcc----------cCeeCcCCCC
Confidence 449999965433 2367999975
No 197
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=21.74 E-value=31 Score=29.59 Aligned_cols=12 Identities=25% Similarity=0.789 Sum_probs=5.9
Q ss_pred ccccccCcccCC
Q 015552 12 VWCYYCDREFDD 23 (405)
Q Consensus 12 p~C~~CgK~F~~ 23 (405)
.+|..||+.|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (114)
T PRK03681 71 CWCETCQQYVTL 82 (114)
T ss_pred EEcccCCCeeec
Confidence 345555554443
No 198
>PF14051 Requiem_N: N-terminal domain of DPF2/REQ.
Probab=21.15 E-value=44 Score=26.84 Aligned_cols=22 Identities=18% Similarity=0.134 Sum_probs=20.4
Q ss_pred hHHHhhccCceeeecccccccc
Q 015552 331 MEERRMSSVKYQVHDETSQVSY 352 (405)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~ 352 (405)
|+|||+-||-+.-.-++.|-++
T Consensus 21 ~~ERr~R~PflD~QTgVAQ~~~ 42 (74)
T PF14051_consen 21 CAERRLRLPFLDSQTGVAQNHC 42 (74)
T ss_pred HHHHhhcccccccccchhhhHH
Confidence 7899999999999999999877
No 199
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=21.07 E-value=23 Score=29.06 Aligned_cols=55 Identities=16% Similarity=0.079 Sum_probs=32.8
Q ss_pred ceE-EEEEcccccChHHHhhccCceeeecccccccchhhchhccccccccccccccccccccc---eehhhHHHHH
Q 015552 318 NEV-YLVWEDEAMSMEERRMSSVKYQVHDETSQVSYNYLFKIWSWFVFSNQMDRPYVSCFQIS---CLRFVTYLER 389 (405)
Q Consensus 318 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~ 389 (405)
=|| |++|+ ...--.+||- -||.||||.....-= |- =+|.|+|=.+ .|.++.-|++
T Consensus 21 V~v~r~~~h-~kY~K~~~r~--kk~~aHDe~n~~~~G-----------D~---V~I~e~RPlSKtK~~~v~~i~~~ 79 (84)
T CHL00142 21 VAVENRYKH-PIYGKIITKT--KKYLVHDEENECNIG-----------DQ---VLIEETRPLSKTKRWILKEILSK 79 (84)
T ss_pred EEEEEEEEc-CcccEEEEee--EEEEEeCCCCCCCCC-----------CE---EEEEEcCCCCCcEEEEEEEEEEe
Confidence 344 77887 3444444443 389999998753322 22 1577888766 6766655543
No 200
>PF15168 TRIQK: Triple QxxK/R motif-containing protein family
Probab=20.95 E-value=44 Score=26.98 Aligned_cols=15 Identities=40% Similarity=0.799 Sum_probs=11.3
Q ss_pred HHHHHHhhheeeccC
Q 015552 391 FLYEFQFFFFLIFTK 405 (405)
Q Consensus 391 ~~~~~~~~~~~~~~~ 405 (405)
+|..|..||||+|++
T Consensus 61 lL~a~Ya~fyl~ls~ 75 (79)
T PF15168_consen 61 LLLAFYAFFYLNLSK 75 (79)
T ss_pred HHHHHHHHHHHhhcc
Confidence 566777788888875
No 201
>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=20.90 E-value=40 Score=28.94 Aligned_cols=11 Identities=27% Similarity=0.821 Sum_probs=4.9
Q ss_pred ccccccccCCC
Q 015552 36 FKCHVCHKKLS 46 (405)
Q Consensus 36 fkC~~CgKsFs 46 (405)
++|..|++.|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 34444444443
No 202
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=20.77 E-value=26 Score=30.15 Aligned_cols=67 Identities=21% Similarity=0.269 Sum_probs=37.3
Q ss_pred CCcccCCCCCCCCCCceE-EEEEcccccChHHHhhccCceeeeccc-ccccchhhchhccccccccccccccccccccc-
Q 015552 303 PPVIANKAPATQPAVNEV-YLVWEDEAMSMEERRMSSVKYQVHDET-SQVSYNYLFKIWSWFVFSNQMDRPYVSCFQIS- 379 (405)
Q Consensus 303 ~~~~~~~~p~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 379 (405)
+.|+++|.--+ .+=|| +++|+ ....-.+||- -||.||||. .+.+-= |- =+|.|+|=..
T Consensus 34 G~VvS~Km~KT--vvV~v~r~~~h-pkY~K~i~r~--kky~aHDe~cn~~kvG-----------D~---V~I~E~RPiSK 94 (108)
T PRK08572 34 GTVVSDKMHKT--VVVEREYLHYV-PKYERYEKRR--SRIHAHNPPCIDAKVG-----------DK---VKIAECRPLSK 94 (108)
T ss_pred EEEEecCCCce--EEEEEEEEEec-CCccEEEEEe--eeEEEECCCCCCCCCC-----------CE---EEEEEcCCCCC
Confidence 34566663322 33455 77776 4455555554 379999998 432221 11 1577777665
Q ss_pred --eehhhHHHH
Q 015552 380 --CLRFVTYLE 388 (405)
Q Consensus 380 --~~~~~~~~~ 388 (405)
.|.|+.-++
T Consensus 95 tK~w~v~~i~~ 105 (108)
T PRK08572 95 TKSFVVVEKKE 105 (108)
T ss_pred ceEEEEEEEEE
Confidence 666654443
No 203
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=20.70 E-value=45 Score=24.60 Aligned_cols=19 Identities=32% Similarity=0.735 Sum_probs=14.2
Q ss_pred cccccccCcccCChhHHHHHhh
Q 015552 11 KVWCYYCDREFDDEKILVQHQK 32 (405)
Q Consensus 11 Kp~C~~CgK~F~~ks~Lk~H~R 32 (405)
..||+.|...|.. |..|+.
T Consensus 5 ~GYCE~C~~ky~~---l~~Hi~ 23 (49)
T PF07535_consen 5 PGYCENCRVKYDD---LEEHIQ 23 (49)
T ss_pred CccCccccchhhh---HHHHhC
Confidence 3579999888764 777777
No 204
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=20.70 E-value=35 Score=25.10 Aligned_cols=33 Identities=21% Similarity=0.558 Sum_probs=15.0
Q ss_pred ccc--cCcccCChhHHHHHhh----cCcccccc----cccCCCC
Q 015552 14 CYY--CDREFDDEKILVQHQK----AKHFKCHV----CHKKLST 47 (405)
Q Consensus 14 C~~--CgK~F~~ks~Lk~H~R----EKPfkC~~----CgKsFs~ 47 (405)
|.. |.+.+.+ ..|..|.. .+...|.+ |+..+.+
T Consensus 12 C~~~cc~~~i~r-~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 12 CPNGCCNEMIPR-KELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp -TT--S-BEEEC-CCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred CCCCCcccceeH-HHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 655 4343443 34666666 45556666 6655544
No 205
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=20.65 E-value=30 Score=25.24 Aligned_cols=13 Identities=23% Similarity=0.700 Sum_probs=6.6
Q ss_pred ccccccccCCCCh
Q 015552 36 FKCHVCHKKLSTA 48 (405)
Q Consensus 36 fkC~~CgKsFs~~ 48 (405)
|+|.+|+..+...
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 4555555544444
No 206
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=20.62 E-value=20 Score=39.08 Aligned_cols=80 Identities=14% Similarity=0.210 Sum_probs=49.5
Q ss_pred CCCceE--EE----EEcccccCh------HHHhhccCceeeecccc----------cccc---hhhchhccccccccccc
Q 015552 315 PAVNEV--YL----VWEDEAMSM------EERRMSSVKYQVHDETS----------QVSY---NYLFKIWSWFVFSNQMD 369 (405)
Q Consensus 315 ~~~~~~--~~----~~~~~~~~~------~~~~~~~~~~~~~~~~~----------~~~~---~~~~~~~~~~~~~~~~~ 369 (405)
|++|.. .| ++.||-+|- ++--..|-++.+|-|-. -|-| +-+|.-+.=+-|||-+-
T Consensus 453 GTGNDLARtlnWGGgytDEPvSkil~~ve~gtvVqLDRW~lhvEpNp~~~pEe~ddG~~~~LPL~VfnNYFSlGfDAHVt 532 (1004)
T KOG0782|consen 453 GTGNDLARTLNWGGGYTDEPVSKILQAVEHGTVVQLDRWRLHVEPNPSCNPEEEDDGMQSALPLTVFNNYFSLGFDAHVT 532 (1004)
T ss_pred CCcchHHHhcccCCCcCcchHHHHHHHHhcCcEEeeeeeeecccCCCCCChhhhcccchhccchhHhhccccccccceEE
Confidence 667776 34 447888773 34445777888886643 2443 22344444557899888
Q ss_pred cccccccccceehhhHHHHHHHHHH
Q 015552 370 RPYVSCFQISCLRFVTYLERYFLYE 394 (405)
Q Consensus 370 ~~~~~~~~~~~~~~~~~~~~~~~~~ 394 (405)
-..-|+|-|--=.|-+-++.-+.|.
T Consensus 533 LeFHeSReANPekfNSRfrNkmfYa 557 (1004)
T KOG0782|consen 533 LEFHESREANPEKFNSRFRNKMFYA 557 (1004)
T ss_pred EEeccccccCHHHHHHHHhhhhhhc
Confidence 8888888887445555555544443
No 207
>PF12907 zf-met2: Zinc-binding
Probab=20.53 E-value=21 Score=25.27 Aligned_cols=27 Identities=19% Similarity=0.472 Sum_probs=17.4
Q ss_pred ccccccccCCCC---hhhHHHHhhhhcccc
Q 015552 36 FKCHVCHKKLST---AGGMAIHVLQVHKEN 62 (405)
Q Consensus 36 fkC~~CgKsFs~---~s~L~rH~r~hH~ek 62 (405)
++|.+|..+|.. ...|..|....|.+.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 578888865543 355888876566543
No 208
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=20.31 E-value=22 Score=25.77 Aligned_cols=36 Identities=25% Similarity=0.615 Sum_probs=20.4
Q ss_pred ccccCcccCChhHHHHHhh----cCcccccccccCCCChh
Q 015552 14 CYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAG 49 (405)
Q Consensus 14 C~~CgK~F~~ks~Lk~H~R----EKPfkC~~CgKsFs~~s 49 (405)
|..|++..........-.. +.-|+|..|++.+....
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSS
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCe
Confidence 5566666654333211111 56788888887776654
No 209
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=20.17 E-value=39 Score=24.99 Aligned_cols=13 Identities=23% Similarity=0.779 Sum_probs=7.1
Q ss_pred ccccccccCCCCh
Q 015552 36 FKCHVCHKKLSTA 48 (405)
Q Consensus 36 fkC~~CgKsFs~~ 48 (405)
|+|.+||..+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 4566666555543
No 210
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=20.05 E-value=55 Score=35.82 Aligned_cols=26 Identities=12% Similarity=0.231 Sum_probs=21.6
Q ss_pred cCcccccccccCCCChhhHHHHhhhh
Q 015552 33 AKHFKCHVCHKKLSTAGGMAIHVLQV 58 (405)
Q Consensus 33 EKPfkC~~CgKsFs~~s~L~rH~r~h 58 (405)
.++.+|..||.+|.......+|+..|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhh
Confidence 78899999999999987777776444
No 211
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=20.05 E-value=28 Score=28.48 Aligned_cols=51 Identities=22% Similarity=0.212 Sum_probs=30.8
Q ss_pred EEEEcccccChHHHhhccCceeeecccccccchhhchhccccccccccccccccccccc---eehhhHHHH
Q 015552 321 YLVWEDEAMSMEERRMSSVKYQVHDETSQVSYNYLFKIWSWFVFSNQMDRPYVSCFQIS---CLRFVTYLE 388 (405)
Q Consensus 321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ 388 (405)
+++| |......+||- -||.||||..+..-= |- =+|.|+|=.+ .|.|+.-|+
T Consensus 28 r~~~-h~kY~K~~~r~--kk~~aHD~~n~~k~G-----------D~---V~I~e~rPlSK~K~~~v~~i~~ 81 (84)
T PRK05610 28 RRVK-HPLYGKIVKRS--KKYHAHDENNEAKIG-----------DV---VRIMETRPLSKTKRWRLVEIVE 81 (84)
T ss_pred EEEE-eccccEEEEcc--eEEEEECCCCCCCCC-----------CE---EEEEEcccCCCCEEEEEEEEEe
Confidence 7788 45555555554 389999997532221 21 1577887766 666654443
Done!