Query 021090
Match_columns 317
No_of_seqs 151 out of 1227
Neff 9.7
Searched_HMMs 46136
Date Fri Mar 29 07:31:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021090.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021090hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 99.9 8.9E-26 1.9E-30 185.5 1.6 133 3-269 130-265 (279)
2 KOG1074 Transcriptional repres 99.9 1.1E-24 2.4E-29 201.5 4.9 253 3-279 605-939 (958)
3 KOG1074 Transcriptional repres 99.9 2.4E-22 5.2E-27 186.2 8.3 81 192-279 617-700 (958)
4 KOG2462 C2H2-type Zn-finger pr 99.8 7.9E-22 1.7E-26 162.4 2.4 130 63-287 126-255 (279)
5 KOG3623 Homeobox transcription 99.8 7.3E-21 1.6E-25 173.8 6.9 53 1-61 279-331 (1007)
6 KOG3608 Zn finger proteins [Ge 99.6 2.6E-17 5.7E-22 139.2 -5.9 192 4-273 178-378 (467)
7 KOG3623 Homeobox transcription 99.6 8.8E-17 1.9E-21 147.3 -3.4 54 205-269 278-331 (1007)
8 KOG3576 Ovo and related transc 99.5 1E-15 2.2E-20 120.2 -4.0 82 3-92 117-198 (267)
9 KOG3608 Zn finger proteins [Ge 99.3 3.1E-14 6.7E-19 120.8 -6.2 202 4-274 135-349 (467)
10 KOG3576 Ovo and related transc 99.3 6.6E-13 1.4E-17 104.5 0.1 83 180-273 117-200 (267)
11 PHA02768 hypothetical protein; 99.1 3.2E-11 7E-16 75.4 1.2 45 208-265 5-49 (55)
12 PHA02768 hypothetical protein; 99.1 3.7E-11 8.1E-16 75.1 0.6 43 3-55 5-47 (55)
13 PLN03086 PRLI-interacting fact 98.8 8.1E-10 1.8E-14 102.5 1.1 62 196-270 492-564 (567)
14 PF13465 zf-H2C2_2: Zinc-finge 98.8 1.5E-09 3.3E-14 58.1 0.7 26 223-259 1-26 (26)
15 PHA00733 hypothetical protein 98.7 4.7E-09 1E-13 79.7 1.5 61 197-271 63-123 (128)
16 PHA00616 hypothetical protein 98.7 2.2E-09 4.8E-14 63.9 -1.3 30 3-32 1-30 (44)
17 PHA00733 hypothetical protein 98.7 1.9E-09 4.2E-14 81.8 -1.9 82 2-93 39-125 (128)
18 KOG3993 Transcription factor ( 98.6 4.1E-09 8.9E-14 92.1 -1.3 54 41-94 269-322 (500)
19 PLN03086 PRLI-interacting fact 98.6 1.1E-08 2.4E-13 95.1 1.3 62 3-77 453-514 (567)
20 PHA00732 hypothetical protein 98.5 1.9E-08 4.1E-13 69.3 0.7 47 208-271 1-48 (79)
21 PHA00616 hypothetical protein 98.4 4.1E-08 8.8E-13 58.5 0.2 39 208-257 1-39 (44)
22 KOG3993 Transcription factor ( 98.4 3.2E-08 6.9E-13 86.7 -1.4 82 4-92 296-381 (500)
23 PF00096 zf-C2H2: Zinc finger, 98.3 2.9E-08 6.2E-13 51.7 -2.2 23 4-26 1-23 (23)
24 PF13465 zf-H2C2_2: Zinc-finge 98.3 5.9E-08 1.3E-12 51.9 -1.8 25 18-50 1-25 (26)
25 PHA00732 hypothetical protein 98.2 3.8E-07 8.3E-12 62.8 1.4 45 3-61 1-46 (79)
26 PF00096 zf-C2H2: Zinc finger, 98.1 4.1E-07 8.8E-12 47.2 -0.5 23 248-270 1-23 (23)
27 COG5189 SFP1 Putative transcri 98.0 3.4E-06 7.4E-11 71.5 2.3 64 205-268 346-419 (423)
28 PF13894 zf-C2H2_4: C2H2-type 97.9 7.8E-07 1.7E-11 46.6 -1.7 24 4-27 1-24 (24)
29 PF05605 zf-Di19: Drought indu 97.9 3.9E-06 8.4E-11 53.6 0.8 51 208-271 2-53 (54)
30 PF13912 zf-C2H2_6: C2H2-type 97.8 1.7E-06 3.8E-11 46.7 -1.5 26 3-28 1-26 (27)
31 PF13912 zf-C2H2_6: C2H2-type 97.7 5.9E-06 1.3E-10 44.6 -0.1 26 247-272 1-26 (27)
32 PF13894 zf-C2H2_4: C2H2-type 97.7 6.8E-06 1.5E-10 42.9 -0.1 23 248-270 1-23 (24)
33 smart00355 ZnF_C2H2 zinc finge 97.6 1.2E-05 2.7E-10 42.6 -0.4 24 4-27 1-24 (26)
34 PF12756 zf-C2H2_2: C2H2 type 97.5 2E-05 4.3E-10 57.3 0.2 61 210-271 1-74 (100)
35 PF05605 zf-Di19: Drought indu 97.5 2E-05 4.4E-10 50.3 -0.0 26 3-29 2-28 (54)
36 COG5189 SFP1 Putative transcri 97.5 9.3E-05 2E-09 63.0 3.4 70 2-89 348-420 (423)
37 PF09237 GAGA: GAGA factor; I 97.4 1.9E-05 4.2E-10 48.0 -1.4 30 2-31 23-52 (54)
38 smart00355 ZnF_C2H2 zinc finge 97.3 6.1E-05 1.3E-09 39.8 0.5 24 248-271 1-24 (26)
39 KOG2893 Zn finger protein [Gen 97.2 7E-05 1.5E-09 61.1 -0.1 51 209-274 11-62 (341)
40 PF12171 zf-C2H2_jaz: Zinc-fin 97.2 0.0001 2.2E-09 39.7 0.3 24 3-26 1-24 (27)
41 PRK04860 hypothetical protein; 97.0 0.00027 5.7E-09 55.8 1.1 41 207-262 118-158 (160)
42 PF09237 GAGA: GAGA factor; I 97.0 0.00023 5E-09 43.4 0.5 31 244-274 21-51 (54)
43 PF12874 zf-met: Zinc-finger o 97.0 5.8E-05 1.3E-09 39.8 -2.0 23 4-26 1-23 (25)
44 PF12756 zf-C2H2_2: C2H2 type 96.8 0.00012 2.5E-09 53.2 -2.0 72 5-90 1-73 (100)
45 PF12874 zf-met: Zinc-finger o 96.8 0.00024 5.3E-09 37.3 -0.5 23 248-270 1-23 (25)
46 COG5048 FOG: Zn-finger [Genera 96.5 0.014 3E-07 54.0 9.2 60 207-277 288-353 (467)
47 COG5048 FOG: Zn-finger [Genera 96.5 0.0089 1.9E-07 55.2 7.6 63 3-73 289-357 (467)
48 PF12171 zf-C2H2_jaz: Zinc-fin 96.4 0.00088 1.9E-08 35.9 0.3 22 248-269 2-23 (27)
49 PF13909 zf-H2C2_5: C2H2-type 96.4 0.00026 5.6E-09 36.9 -2.0 23 4-27 1-23 (24)
50 PF13909 zf-H2C2_5: C2H2-type 96.3 0.0008 1.7E-08 35.0 -0.4 23 248-271 1-23 (24)
51 PF13913 zf-C2HC_2: zinc-finge 96.0 0.0014 2.9E-08 34.4 -0.5 21 4-25 3-23 (25)
52 KOG1146 Homeobox protein [Gene 95.5 0.012 2.6E-07 59.7 3.4 76 18-93 414-491 (1406)
53 PF13913 zf-C2HC_2: zinc-finge 94.9 0.0083 1.8E-07 31.4 0.3 20 248-268 3-22 (25)
54 smart00451 ZnF_U1 U1-like zinc 94.7 0.0072 1.6E-07 34.5 -0.4 24 2-25 2-25 (35)
55 KOG2231 Predicted E3 ubiquitin 94.5 0.0029 6.3E-08 60.3 -3.5 26 3-28 99-140 (669)
56 KOG1146 Homeobox protein [Gene 94.0 0.016 3.6E-07 58.8 0.4 70 204-273 461-546 (1406)
57 smart00451 ZnF_U1 U1-like zinc 93.8 0.018 4E-07 32.7 0.1 22 247-268 3-24 (35)
58 KOG2785 C2H2-type Zn-finger pr 91.6 0.0052 1.1E-07 54.1 -6.1 64 205-268 163-241 (390)
59 PF09986 DUF2225: Uncharacteri 91.1 0.08 1.7E-06 44.2 0.6 52 206-260 3-61 (214)
60 KOG4167 Predicted DNA-binding 90.5 0.037 7.9E-07 52.8 -2.1 28 247-274 792-819 (907)
61 PF09986 DUF2225: Uncharacteri 90.0 0.23 5E-06 41.5 2.4 24 2-25 4-27 (214)
62 PF12013 DUF3505: Protein of u 89.4 0.18 3.8E-06 37.2 1.1 62 207-272 10-109 (109)
63 TIGR00622 ssl1 transcription f 87.0 1.7 3.6E-05 32.0 4.9 86 3-90 15-104 (112)
64 smart00614 ZnF_BED BED zinc fi 86.3 0.16 3.5E-06 31.6 -0.6 23 5-27 20-48 (50)
65 PRK00398 rpoP DNA-directed RNA 85.8 0.35 7.7E-06 29.4 0.8 31 208-259 3-33 (46)
66 cd00729 rubredoxin_SM Rubredox 85.7 0.43 9.4E-06 27.0 1.0 10 246-255 17-26 (34)
67 COG1996 RPC10 DNA-directed RNA 85.3 0.41 8.9E-06 29.4 0.9 30 206-256 4-33 (49)
68 KOG4124 Putative transcription 84.5 0.5 1.1E-05 41.4 1.4 64 205-268 346-419 (442)
69 KOG2071 mRNA cleavage and poly 83.2 0.67 1.5E-05 43.8 1.7 28 205-232 415-442 (579)
70 PF09538 FYDLN_acid: Protein o 82.9 0.67 1.4E-05 34.0 1.3 33 208-262 9-41 (108)
71 PRK04860 hypothetical protein; 82.3 0.21 4.5E-06 39.5 -1.7 10 41-50 145-154 (160)
72 TIGR02098 MJ0042_CXXC MJ0042 f 82.2 0.46 1E-05 27.5 0.2 34 209-258 3-36 (38)
73 KOG2186 Cell growth-regulating 82.0 0.76 1.7E-05 38.5 1.4 47 209-269 4-50 (276)
74 cd00350 rubredoxin_like Rubred 81.5 1.2 2.6E-05 24.9 1.7 13 3-15 1-13 (33)
75 PRK00464 nrdR transcriptional 81.0 0.46 9.9E-06 37.3 -0.2 20 246-265 27-46 (154)
76 smart00734 ZnF_Rad18 Rad18-lik 80.6 0.44 9.6E-06 25.1 -0.3 20 4-24 2-21 (26)
77 COG4049 Uncharacterized protei 80.2 0.46 1E-05 29.7 -0.3 27 242-268 12-38 (65)
78 PHA00626 hypothetical protein 80.1 0.66 1.4E-05 29.1 0.3 17 245-261 21-37 (59)
79 KOG2893 Zn finger protein [Gen 79.9 0.55 1.2E-05 38.9 -0.1 46 6-63 13-59 (341)
80 COG4957 Predicted transcriptio 79.4 0.47 1E-05 35.6 -0.5 24 5-31 78-101 (148)
81 COG4049 Uncharacterized protei 78.9 0.67 1.5E-05 29.0 0.1 27 205-231 14-40 (65)
82 KOG2231 Predicted E3 ubiquitin 78.3 0.61 1.3E-05 45.0 -0.3 49 208-271 206-263 (669)
83 PF05443 ROS_MUCR: ROS/MUCR tr 78.2 0.42 9.1E-06 36.4 -1.1 25 4-31 73-97 (132)
84 PF09723 Zn-ribbon_8: Zinc rib 78.2 0.84 1.8E-05 27.2 0.4 30 208-255 5-34 (42)
85 PF14353 CpXC: CpXC protein 78.0 0.67 1.4E-05 35.2 -0.1 58 209-269 2-60 (128)
86 TIGR02300 FYDLN_acid conserved 77.5 1.3 2.7E-05 33.2 1.2 35 208-264 9-43 (129)
87 COG1773 Rubredoxin [Energy pro 77.1 0.82 1.8E-05 28.8 0.1 14 1-14 1-14 (55)
88 KOG2785 C2H2-type Zn-finger pr 76.8 0.6 1.3E-05 41.6 -0.7 62 208-269 3-90 (390)
89 PF02892 zf-BED: BED zinc fing 76.6 0.8 1.7E-05 27.5 -0.0 15 206-220 14-28 (45)
90 COG1592 Rubrerythrin [Energy p 76.6 1.3 2.9E-05 35.1 1.2 24 208-255 134-157 (166)
91 smart00834 CxxC_CXXC_SSSS Puta 76.4 1 2.3E-05 26.3 0.5 31 208-256 5-35 (41)
92 COG2888 Predicted Zn-ribbon RN 75.6 1.3 2.8E-05 28.3 0.7 33 207-255 26-58 (61)
93 smart00531 TFIIE Transcription 75.6 1.6 3.5E-05 34.0 1.4 41 204-259 95-135 (147)
94 TIGR02605 CxxC_CxxC_SSSS putat 75.4 1.2 2.6E-05 27.8 0.5 30 208-255 5-34 (52)
95 smart00659 RPOLCX RNA polymera 74.7 1.6 3.4E-05 26.3 0.9 28 208-257 2-29 (44)
96 PF07754 DUF1610: Domain of un 73.3 1.4 3.1E-05 22.7 0.4 9 3-11 16-24 (24)
97 PRK00464 nrdR transcriptional 73.1 1.9 4.1E-05 33.9 1.3 12 41-52 30-41 (154)
98 KOG4167 Predicted DNA-binding 72.7 1.1 2.3E-05 43.4 -0.2 27 206-232 790-816 (907)
99 KOG2482 Predicted C2H2-type Zn 70.0 1.3 2.8E-05 38.9 -0.3 30 2-31 194-225 (423)
100 PF09538 FYDLN_acid: Protein o 69.4 6.3 0.00014 28.9 3.2 31 39-80 9-39 (108)
101 PF10571 UPF0547: Uncharacteri 68.9 2.7 5.9E-05 22.1 0.9 10 5-14 16-25 (26)
102 PF15269 zf-C2H2_7: Zinc-finge 68.6 1.2 2.5E-05 26.6 -0.6 23 3-25 20-42 (54)
103 PF03604 DNA_RNApol_7kD: DNA d 67.9 2.5 5.5E-05 23.5 0.7 27 209-257 1-27 (32)
104 KOG2482 Predicted C2H2-type Zn 67.3 1.7 3.7E-05 38.2 -0.1 67 207-273 194-306 (423)
105 PF13717 zinc_ribbon_4: zinc-r 65.7 2.8 6.2E-05 23.9 0.6 34 209-258 3-36 (36)
106 PF13719 zinc_ribbon_5: zinc-r 65.2 2.6 5.7E-05 24.2 0.4 34 209-258 3-36 (37)
107 COG1997 RPL43A Ribosomal prote 65.2 2.8 6.2E-05 29.0 0.7 36 207-263 34-69 (89)
108 COG4530 Uncharacterized protei 64.8 2.7 5.8E-05 30.4 0.5 34 209-265 10-43 (129)
109 PRK09678 DNA-binding transcrip 63.3 2.1 4.6E-05 28.8 -0.2 42 209-263 2-45 (72)
110 PF05443 ROS_MUCR: ROS/MUCR tr 62.1 2.8 6.1E-05 31.9 0.2 20 248-270 73-92 (132)
111 PRK14890 putative Zn-ribbon RN 60.7 3.9 8.5E-05 26.1 0.7 33 207-255 24-56 (59)
112 KOG4173 Alpha-SNAP protein [In 60.7 0.44 9.5E-06 38.6 -4.5 78 2-91 78-170 (253)
113 PRK06266 transcription initiat 59.9 4.6 0.0001 32.6 1.1 35 205-259 114-148 (178)
114 TIGR00280 L37a ribosomal prote 59.2 3.2 6.9E-05 29.2 0.1 37 206-263 33-69 (91)
115 TIGR00373 conserved hypothetic 59.2 5.2 0.00011 31.6 1.3 35 204-258 105-139 (158)
116 PTZ00255 60S ribosomal protein 59.0 3.6 7.9E-05 28.9 0.3 37 206-263 34-70 (90)
117 PF09845 DUF2072: Zn-ribbon co 58.1 5.6 0.00012 30.1 1.2 15 3-17 1-15 (131)
118 PRK03976 rpl37ae 50S ribosomal 57.4 3.1 6.8E-05 29.2 -0.2 36 207-263 35-70 (90)
119 COG5188 PRP9 Splicing factor 3 57.0 4.1 8.8E-05 36.0 0.3 52 241-292 368-422 (470)
120 KOG4173 Alpha-SNAP protein [In 56.3 2.9 6.3E-05 34.0 -0.6 63 209-273 107-173 (253)
121 TIGR02300 FYDLN_acid conserved 56.2 12 0.00026 28.1 2.6 34 39-83 9-42 (129)
122 PF01780 Ribosomal_L37ae: Ribo 56.0 2.4 5.1E-05 29.8 -1.0 36 207-263 34-69 (90)
123 PF01286 XPA_N: XPA protein N- 55.6 6.3 0.00014 22.2 0.9 16 209-224 4-19 (34)
124 KOG2593 Transcription initiati 54.8 6.7 0.00015 35.8 1.4 41 203-257 123-163 (436)
125 COG5236 Uncharacterized conser 53.8 2.1 4.5E-05 37.7 -1.9 81 3-93 151-246 (493)
126 TIGR01206 lysW lysine biosynth 52.9 5.3 0.00012 25.2 0.3 31 209-258 3-33 (54)
127 KOG2071 mRNA cleavage and poly 52.7 5.4 0.00012 38.0 0.4 28 2-29 417-444 (579)
128 PF06220 zf-U1: U1 zinc finger 52.2 3.6 7.8E-05 23.9 -0.5 24 1-24 1-26 (38)
129 PF05741 zf-nanos: Nanos RNA b 52.1 4.8 0.0001 25.5 0.0 12 1-12 31-42 (55)
130 smart00154 ZnF_AN1 AN1-like Zi 51.9 7.5 0.00016 22.7 0.8 16 3-18 12-27 (39)
131 COG4888 Uncharacterized Zn rib 50.5 5 0.00011 28.6 -0.1 40 205-259 19-58 (104)
132 KOG4124 Putative transcription 50.0 20 0.00043 31.8 3.4 75 2-94 348-425 (442)
133 PRK03824 hypA hydrogenase nick 49.4 7.7 0.00017 29.8 0.8 45 205-256 67-116 (135)
134 PF10013 DUF2256: Uncharacteri 49.2 6.8 0.00015 23.2 0.3 16 4-19 9-24 (42)
135 PF14446 Prok-RING_1: Prokaryo 49.1 12 0.00026 23.6 1.4 15 4-18 6-20 (54)
136 PRK06266 transcription initiat 48.8 6.2 0.00014 31.9 0.2 12 67-78 136-147 (178)
137 PF04959 ARS2: Arsenite-resist 48.7 1.4 3E-05 36.6 -3.6 26 3-28 77-102 (214)
138 COG3364 Zn-ribbon containing p 48.2 7.7 0.00017 27.7 0.5 16 3-18 2-17 (112)
139 COG5236 Uncharacterized conser 47.3 3.1 6.6E-05 36.7 -1.9 19 6-24 223-241 (493)
140 PF08790 zf-LYAR: LYAR-type C2 47.0 5.9 0.00013 21.2 -0.1 19 248-267 1-19 (28)
141 PF01428 zf-AN1: AN1-like Zinc 45.8 6.9 0.00015 23.3 0.0 17 246-262 12-28 (43)
142 PF12230 PRP21_like_P: Pre-mRN 45.7 6.9 0.00015 33.0 0.0 28 4-32 169-196 (229)
143 KOG2461 Transcription factor B 45.4 84 0.0018 29.0 6.9 62 200-272 323-384 (396)
144 PF14787 zf-CCHC_5: GAG-polypr 44.3 14 0.0003 21.0 1.1 16 4-19 3-18 (36)
145 PF13451 zf-trcl: Probable zin 44.2 8.3 0.00018 23.8 0.2 17 245-261 2-18 (49)
146 COG2331 Uncharacterized protei 43.5 6.8 0.00015 26.4 -0.3 33 208-258 12-44 (82)
147 COG1571 Predicted DNA-binding 42.3 12 0.00027 34.3 1.1 35 207-263 349-383 (421)
148 smart00661 RPOL9 RNA polymeras 42.0 14 0.0003 22.7 1.0 16 247-262 20-35 (52)
149 PF07975 C1_4: TFIIH C1-like d 40.6 8.1 0.00018 24.1 -0.2 24 247-270 21-44 (51)
150 COG3357 Predicted transcriptio 39.1 24 0.00052 24.7 1.8 25 41-75 60-84 (97)
151 COG3091 SprT Zn-dependent meta 38.9 12 0.00027 29.0 0.5 38 205-258 114-151 (156)
152 PRK12380 hydrogenase nickel in 38.9 16 0.00035 27.0 1.1 17 205-221 67-83 (113)
153 PF09963 DUF2197: Uncharacteri 38.6 12 0.00026 23.8 0.3 39 209-257 3-41 (56)
154 cd00924 Cyt_c_Oxidase_Vb Cytoc 38.5 14 0.00031 26.5 0.7 19 241-260 74-92 (97)
155 PF10276 zf-CHCC: Zinc-finger 38.2 12 0.00026 22.0 0.2 12 246-257 28-39 (40)
156 PRK03681 hypA hydrogenase nick 37.4 18 0.00038 26.9 1.1 16 205-220 67-82 (114)
157 PF01363 FYVE: FYVE zinc finge 37.0 15 0.00033 24.2 0.6 31 208-261 9-39 (69)
158 KOG2636 Splicing factor 3a, su 36.8 14 0.00031 33.9 0.6 52 242-293 396-450 (497)
159 PF04423 Rad50_zn_hook: Rad50 36.7 12 0.00027 23.4 0.1 12 249-260 22-33 (54)
160 PF04959 ARS2: Arsenite-resist 36.7 12 0.00026 31.2 0.1 28 205-232 74-101 (214)
161 KOG3408 U1-like Zn-finger-cont 36.5 15 0.00033 27.2 0.6 26 205-230 54-79 (129)
162 COG4306 Uncharacterized protei 36.5 20 0.00044 26.7 1.2 41 40-80 40-81 (160)
163 COG1198 PriA Primosomal protei 36.1 34 0.00074 34.1 3.1 45 5-76 437-484 (730)
164 PRK12496 hypothetical protein; 35.6 19 0.00041 28.6 1.1 13 208-220 127-139 (164)
165 PF01155 HypA: Hydrogenase exp 35.4 12 0.00026 27.7 -0.1 18 205-222 67-84 (113)
166 PRK14892 putative transcriptio 35.1 19 0.00042 25.9 0.9 12 69-80 44-55 (99)
167 COG3677 Transposase and inacti 34.7 19 0.00042 27.3 0.9 14 2-15 52-65 (129)
168 PF12013 DUF3505: Protein of u 34.6 14 0.00029 27.1 0.1 25 208-232 80-108 (109)
169 KOG3408 U1-like Zn-finger-cont 34.5 12 0.00027 27.7 -0.1 26 244-269 54-79 (129)
170 KOG0717 Molecular chaperone (D 34.5 11 0.00023 34.9 -0.6 22 4-25 293-314 (508)
171 PRK01343 zinc-binding protein; 34.2 28 0.00061 22.2 1.5 13 3-15 9-21 (57)
172 PF11494 Ta0938: Ta0938; Inte 33.8 21 0.00045 25.3 0.9 40 205-261 11-51 (105)
173 COG5151 SSL1 RNA polymerase II 33.8 18 0.0004 31.5 0.7 82 3-86 322-407 (421)
174 TIGR00100 hypA hydrogenase nic 32.6 22 0.00047 26.4 0.9 17 205-221 67-83 (115)
175 cd00730 rubredoxin Rubredoxin; 32.6 19 0.00042 22.3 0.5 12 3-14 1-12 (50)
176 PRK00564 hypA hydrogenase nick 32.3 27 0.00058 26.1 1.3 17 205-221 68-84 (117)
177 PRK04023 DNA polymerase II lar 32.2 41 0.00088 34.6 2.9 17 246-262 1036-1052(1121)
178 PF01844 HNH: HNH endonuclease 32.0 18 0.00039 21.5 0.4 17 6-22 1-17 (47)
179 COG4847 Uncharacterized protei 31.9 15 0.00032 25.9 -0.1 14 1-14 4-17 (103)
180 KOG0402 60S ribosomal protein 30.9 17 0.00038 24.9 0.1 36 207-263 35-70 (92)
181 PF09416 UPF1_Zn_bind: RNA hel 30.4 36 0.00079 26.6 1.8 52 205-256 11-69 (152)
182 KOG1280 Uncharacterized conser 30.2 37 0.00081 30.2 2.0 71 206-276 21-108 (381)
183 PLN02294 cytochrome c oxidase 30.2 19 0.00041 28.6 0.3 16 245-260 139-154 (174)
184 PF04618 HD-ZIP_N: HD-ZIP prot 30.1 25 0.00054 25.9 0.8 21 295-315 70-93 (111)
185 PF12760 Zn_Tnp_IS1595: Transp 30.0 21 0.00045 21.5 0.3 11 245-255 35-45 (46)
186 COG4338 Uncharacterized protei 29.7 12 0.00026 22.7 -0.7 13 5-17 14-26 (54)
187 PF00301 Rubredoxin: Rubredoxi 29.4 12 0.00027 22.8 -0.7 12 3-14 1-12 (47)
188 TIGR00595 priA primosomal prot 29.3 51 0.0011 31.5 3.0 45 5-76 215-262 (505)
189 PF09082 DUF1922: Domain of un 29.0 16 0.00034 24.2 -0.3 15 244-259 17-31 (68)
190 KOG0717 Molecular chaperone (D 29.0 20 0.00043 33.2 0.2 22 209-230 293-314 (508)
191 PF14255 Cys_rich_CPXG: Cystei 28.9 26 0.00057 21.9 0.7 10 5-14 2-11 (52)
192 PF07503 zf-HYPF: HypF finger; 28.9 35 0.00076 19.3 1.1 31 211-258 2-32 (35)
193 COG1779 C4-type Zn-finger prot 28.9 18 0.00039 29.5 -0.1 91 207-312 13-109 (201)
194 PRK00762 hypA hydrogenase nick 28.5 30 0.00065 26.1 1.1 17 205-222 67-83 (124)
195 PF15176 LRR19-TM: Leucine-ric 28.3 28 0.0006 25.0 0.8 53 248-316 38-90 (102)
196 PF06397 Desulfoferrod_N: Desu 28.3 21 0.00045 20.4 0.1 11 246-256 5-15 (36)
197 PF07282 OrfB_Zn_ribbon: Putat 27.2 31 0.00067 22.7 0.8 16 244-259 43-58 (69)
198 PF14447 Prok-RING_4: Prokaryo 27.2 35 0.00077 21.6 1.0 11 6-16 42-52 (55)
199 PRK00432 30S ribosomal protein 26.9 29 0.00062 21.5 0.6 12 246-257 36-47 (50)
200 PF02176 zf-TRAF: TRAF-type zi 26.4 44 0.00095 21.1 1.4 44 205-260 6-55 (60)
201 PF12907 zf-met2: Zinc-binding 26.0 30 0.00066 20.3 0.5 21 209-229 2-25 (40)
202 PRK14873 primosome assembly pr 25.6 52 0.0011 32.7 2.4 44 5-76 385-431 (665)
203 PRK04351 hypothetical protein; 25.2 28 0.00061 27.2 0.4 34 208-260 112-145 (149)
204 PF04780 DUF629: Protein of un 25.1 18 0.00038 33.9 -0.8 27 4-30 58-85 (466)
205 PF04810 zf-Sec23_Sec24: Sec23 25.0 25 0.00054 20.5 0.0 14 244-257 21-34 (40)
206 KOG0978 E3 ubiquitin ligase in 24.6 34 0.00073 33.8 0.9 56 207-267 642-698 (698)
207 PF08274 PhnA_Zn_Ribbon: PhnA 24.6 22 0.00047 19.4 -0.2 11 245-255 17-27 (30)
208 KOG1842 FYVE finger-containing 24.2 21 0.00045 32.9 -0.6 33 247-279 15-48 (505)
209 PF10263 SprT-like: SprT-like 24.2 26 0.00056 27.3 0.0 34 207-259 122-155 (157)
210 PF11931 DUF3449: Domain of un 24.1 26 0.00055 28.7 0.0 30 245-274 99-131 (196)
211 PF06524 NOA36: NOA36 protein; 23.6 33 0.00071 29.2 0.5 29 245-273 207-235 (314)
212 KOG2807 RNA polymerase II tran 22.8 45 0.00097 29.5 1.2 72 3-87 290-365 (378)
213 PF07295 DUF1451: Protein of u 22.8 45 0.00097 26.0 1.1 13 205-217 109-121 (146)
214 TIGR01384 TFS_arch transcripti 22.8 56 0.0012 23.5 1.6 13 4-16 17-29 (104)
215 PF04438 zf-HIT: HIT zinc fing 22.4 24 0.00052 19.2 -0.3 12 3-14 13-24 (30)
216 PTZ00448 hypothetical protein; 22.3 29 0.00063 31.2 -0.0 23 3-25 314-336 (373)
217 PF13878 zf-C2H2_3: zinc-finge 22.0 45 0.00098 19.6 0.8 25 247-271 13-39 (41)
218 PF14634 zf-RING_5: zinc-RING 21.5 31 0.00068 20.4 0.0 9 5-13 1-9 (44)
219 PHA02998 RNA polymerase subuni 21.3 33 0.00072 27.4 0.1 41 207-261 142-185 (195)
220 PF04606 Ogr_Delta: Ogr/Delta- 21.2 20 0.00044 21.7 -0.9 39 211-262 2-42 (47)
221 PLN02748 tRNA dimethylallyltra 20.8 37 0.0008 32.0 0.3 25 245-269 416-441 (468)
222 PF08271 TF_Zn_Ribbon: TFIIB z 20.2 48 0.001 19.5 0.6 8 4-11 1-8 (43)
223 PF13240 zinc_ribbon_2: zinc-r 20.1 39 0.00085 17.0 0.2 7 6-12 16-22 (23)
224 PF14369 zf-RING_3: zinc-finge 20.0 83 0.0018 17.8 1.5 10 69-78 23-32 (35)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.91 E-value=8.9e-26 Score=185.53 Aligned_cols=133 Identities=20% Similarity=0.261 Sum_probs=108.0
Q ss_pred CCCCCcccCcCCCccccccccccccC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCCC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLA---AHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYGL 79 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~---ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~~ 79 (317)
+|+|+.|||.+++.++|.+|..+|.. .+.+ +|..|++.+.+.+.|..|.++|. -+.+|.+|++.|..
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~--------~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSR 199 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAF--------SCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSR 199 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccc--------cCCCCCceeeehHHHhhHhhccC--CCcccccccccccc
Confidence 58999999999999999999999975 2334 67777777776666666666665 56666667666644
Q ss_pred CCCccccccccCCccccccCCCCeeecCCcccccccCCCcccccccccccchhhhhhhhhhhcCCCCCCCCCCCCCCCCC
Q 021090 80 RNNPKKSFRFADPEFSFAVDSGSVVVQDRESETESRNPTRRRSKRNRKLFTAHQDHHQKRMLKKPNFLESPAEPEPVSSV 159 (317)
Q Consensus 80 ~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (317)
.=.|
T Consensus 200 PWLL---------------------------------------------------------------------------- 203 (279)
T KOG2462|consen 200 PWLL---------------------------------------------------------------------------- 203 (279)
T ss_pred hHHh----------------------------------------------------------------------------
Confidence 3333
Q ss_pred CCCChhhHHHHHHhhhcccccccCCchhhhhHHHhhhhhhhhhhccCcceechhhhhhccCccchhhhhhhhhccccccc
Q 021090 160 SDTSPEEDVAMCLMMLSRDVWMRNNDEAQDHKIVEMVEESEEIKLTRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGT 239 (317)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~ 239 (317)
..|.++|+|++||.|..|+|.|..+++|..||++|.
T Consensus 204 -------------------------------------QGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS------- 239 (279)
T KOG2462|consen 204 -------------------------------------QGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHS------- 239 (279)
T ss_pred -------------------------------------hcccccccCCCCccCCcccchhcchHHHHHHHHhhc-------
Confidence 467777889999999999999999999999998776
Q ss_pred ccccCCccccCCccccccCCcccccchhhh
Q 021090 240 KVAADEKIFECPFCYKVFGSGQALGGHKRS 269 (317)
Q Consensus 240 ~~h~~ekpf~C~~C~k~F~~~~~L~~H~~~ 269 (317)
+.|+|+|..|+|+|.++++|.+|...
T Consensus 240 ----~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 240 ----DVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ----CCccccCcchhhHHHHHHHHHHhhhh
Confidence 89999999999999999999999764
No 2
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.90 E-value=1.1e-24 Score=201.50 Aligned_cols=253 Identities=17% Similarity=0.167 Sum_probs=154.1
Q ss_pred CCCCCcccCcCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCC----CCccC---cCCC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKS----PEVAE---EKSL 75 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~----~~~C~---~c~~ 75 (317)
|-.|-+|-|..+.++.|+.|.|+|+||||| +|.+|+..|.++++|+.||.+|.... .+.|+ +|.+
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPF--------kCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~ 676 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPF--------KCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQK 676 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCcc--------ccccccchhccccchhhcccccccCccccccccCCchhhhcc
Confidence 567999999999999999999999999999 99999999999999999999997664 47899 9999
Q ss_pred CCCCCCCccccccccCCccccccCCCCeeecCCcccccccCCCcccccccccccchhhhhhhhhhhcC----------CC
Q 021090 76 GYGLRNNPKKSFRFADPEFSFAVDSGSVVVQDRESETESRNPTRRRSKRNRKLFTAHQDHHQKRMLKK----------PN 145 (317)
Q Consensus 76 ~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~----------~~ 145 (317)
.|.....|..|+++|.+....+..... ......+.|..|.+.+.....+..+...+-...... .+
T Consensus 677 kftn~V~lpQhIriH~~~~~s~g~~a~-----e~~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s~~~~~~~~~t~t~~ 751 (958)
T KOG1074|consen 677 KFTNAVTLPQHIRIHLGGQISNGGTAA-----EGILAADQCSSCQKTFSDARSFSQQISEQPSPESEPDEQMDERTETEE 751 (958)
T ss_pred cccccccccceEEeecCCCCCCCcccc-----cccchhcccchhhhcccccccchhhhhccCCcccCCcccccccccccc
Confidence 999999999999998854433221111 112334455556555544444444433331111000 00
Q ss_pred CCCCC----------CCCCCCCCCCCCChhhH-----H------HHHH-hhhcccccc-------------cCCchhhhh
Q 021090 146 FLESP----------AEPEPVSSVSDTSPEED-----V------AMCL-MMLSRDVWM-------------RNNDEAQDH 190 (317)
Q Consensus 146 ~~~~~----------~~~~~~~~~~~~~~~~~-----~------~~~~-~~~~~~~~~-------------~~~~~~~~~ 190 (317)
....+ .+.+....+....++.. . .+.. ...+..... ...+.....
T Consensus 752 ~~~tp~~~e~~~~~~~~~e~~i~~~g~te~asa~~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~pvl~~ 831 (958)
T KOG1074|consen 752 LDVTPPPPENSCGRELEGEMAISVRGSTEEASANLDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDPVLWN 831 (958)
T ss_pred cccCCCccccccccccCcccccccccchhhhhcChhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCchhhc
Confidence 00000 00000000000000000 0 0000 000000000 000000000
Q ss_pred HHHhh--------------------hhhhhhhh----------ccCcceechhhhhhccCccchhhhhhhhhcccccccc
Q 021090 191 KIVEM--------------------VEESEEIK----------LTRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTK 240 (317)
Q Consensus 191 ~~~~~--------------------~~~~~~~~----------~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~ 240 (317)
....+ +......- .....+.|.+||+.|...+.|..|+++|+
T Consensus 832 ~~~~~l~eg~~t~~n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHt-------- 903 (958)
T KOG1074|consen 832 QETSMLNEGLATKTNEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHT-------- 903 (958)
T ss_pred ccccccccccccccccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCC--------
Confidence 00000 00000000 01234899999999999999999998876
Q ss_pred cccCCccccCCccccccCCcccccchhhhccCcccchhh
Q 021090 241 VAADEKIFECPFCYKVFGSGQALGGHKRSHLLANSSSTA 279 (317)
Q Consensus 241 ~h~~ekpf~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~a 279 (317)
|+|||.|.+|+++|..+.+|+.||.+|++....+-.
T Consensus 904 ---g~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 904 ---GPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred ---CCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 999999999999999999999999999998766543
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.87 E-value=2.4e-22 Score=186.19 Aligned_cols=81 Identities=23% Similarity=0.402 Sum_probs=64.4
Q ss_pred HHhhhhhhhhhhccCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCC---ccccccCCcccccchhh
Q 021090 192 IVEMVEESEEIKLTRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECP---FCYKVFGSGQALGGHKR 268 (317)
Q Consensus 192 ~~~~~~~~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~---~C~k~F~~~~~L~~H~~ 268 (317)
....+.-|.+.|+++|||+|.+||+.|+++.+|+.||-+|. ..+.-.-+|.|+ +|-+.|...-.|..|.+
T Consensus 617 C~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHk-------a~p~~R~q~ScP~~~ic~~kftn~V~lpQhIr 689 (958)
T KOG1074|consen 617 CPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHK-------AKPPARVQFSCPSTFICQKKFTNAVTLPQHIR 689 (958)
T ss_pred chhhhhhhhhcccCcCccccccccchhccccchhhcccccc-------cCccccccccCCchhhhcccccccccccceEE
Confidence 34456778888999999999999999999999999998875 334445578999 99999999999999999
Q ss_pred hccCcccchhh
Q 021090 269 SHLLANSSSTA 279 (317)
Q Consensus 269 ~H~~~~~~~~a 279 (317)
+|+++..+.+-
T Consensus 690 iH~~~~~s~g~ 700 (958)
T KOG1074|consen 690 IHLGGQISNGG 700 (958)
T ss_pred eecCCCCCCCc
Confidence 99977554443
No 4
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.83 E-value=7.9e-22 Score=162.36 Aligned_cols=130 Identities=18% Similarity=0.193 Sum_probs=103.5
Q ss_pred cCCCCCccCcCCCCCCCCCCccccccccCCccccccCCCCeeecCCcccccccCCCcccccccccccchhhhhhhhhhhc
Q 021090 63 KGKSPEVAEEKSLGYGLRNNPKKSFRFADPEFSFAVDSGSVVVQDRESETESRNPTRRRSKRNRKLFTAHQDHHQKRMLK 142 (317)
Q Consensus 63 ~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~ 142 (317)
.....|+|+.|++.|.+..+|-||.+.|-+.. +...+.|..|++.+.+...
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~---------------s~ka~~C~~C~K~YvSmpA-------------- 176 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLD---------------SKKAFSCKYCGKVYVSMPA-------------- 176 (279)
T ss_pred ccCCceeccccccccccccccchhhccccccc---------------ccccccCCCCCceeeehHH--------------
Confidence 34567899999999999999999988886521 1334566666665555422
Q ss_pred CCCCCCCCCCCCCCCCCCCCChhhHHHHHHhhhcccccccCCchhhhhHHHhhhhhhhhhhccCcceechhhhhhccCcc
Q 021090 143 KPNFLESPAEPEPVSSVSDTSPEEDVAMCLMMLSRDVWMRNNDEAQDHKIVEMVEESEEIKLTRGKYRCEKCKKAFRSYH 222 (317)
Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~f~~~~ 222 (317)
+.-|.++|+ -+++|.+|||.|.+..
T Consensus 177 -----------------------------------------------------LkMHirTH~--l~c~C~iCGKaFSRPW 201 (279)
T KOG2462|consen 177 -----------------------------------------------------LKMHIRTHT--LPCECGICGKAFSRPW 201 (279)
T ss_pred -----------------------------------------------------HhhHhhccC--CCcccccccccccchH
Confidence 234444443 6899999999999999
Q ss_pred chhhhhhhhhcccccccccccCCccccCCccccccCCcccccchhhhccCcccchhhhhhhcccC
Q 021090 223 ALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALGGHKRSHLLANSSSTAAAAAVVAT 287 (317)
Q Consensus 223 ~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~a~~~~~~~~ 287 (317)
.|+.|+|+|+ |||||.|+.|+|+|.-+++|..||++|.+.+--.+..++..+++
T Consensus 202 LLQGHiRTHT-----------GEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 202 LLQGHIRTHT-----------GEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred Hhhccccccc-----------CCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHH
Confidence 9999998877 99999999999999999999999999999998888888866654
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.83 E-value=7.3e-21 Score=173.75 Aligned_cols=53 Identities=25% Similarity=0.417 Sum_probs=50.2
Q ss_pred CCCCCCCcccCcCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 021090 1 MEKHKCKLCTRSFSNGRALGGHMKAHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVE 61 (317)
Q Consensus 1 ~k~~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 61 (317)
+|+|+|++|||.|..+..|+.|+|||.||||| .|+.|.+.|+.+++...||..
T Consensus 279 lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPf--------eCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 279 LRKFKCTECGKAFKFKHHLKEHLRIHSGEKPF--------ECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hccccccccchhhhhHHHHHhhheeecCCCCc--------CCcccccccccCCcccccccc
Confidence 58999999999999999999999999999999 999999999999998888776
No 6
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.57 E-value=2.6e-17 Score=139.24 Aligned_cols=192 Identities=16% Similarity=0.199 Sum_probs=135.4
Q ss_pred CCCC--cccCcCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccc--CCCCCccCcCCCCCCC
Q 021090 4 HKCK--LCTRSFSNGRALGGHMKAHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVK--GKSPEVAEEKSLGYGL 79 (317)
Q Consensus 4 ~~C~--~Cgk~F~~~~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~--~~~~~~C~~c~~~f~~ 79 (317)
+.|. .|-+.|.+++.|.+|+|+|++||.. .|+-|+..|+++..|-.|.+... ...+|.|..|.+.|.+
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvv--------ACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaT 249 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRTHSNEKVV--------ACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFAT 249 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHhcCCCeEE--------ecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhH
Confidence 4455 6999999999999999999999999 99999999999999988866544 4458999999999999
Q ss_pred CCCccccccccCCccccccCCCCeeecCCcccccccCCCcccccccccccchhhhh-hhhhhhcCCCCCCCCCCCCCCCC
Q 021090 80 RNNPKKSFRFADPEFSFAVDSGSVVVQDRESETESRNPTRRRSKRNRKLFTAHQDH-HQKRMLKKPNFLESPAEPEPVSS 158 (317)
Q Consensus 80 ~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 158 (317)
...|+-|+..|-. -+.||.|...-.....|..|.+. |......+
T Consensus 250 eklL~~Hv~rHvn--------------------~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfK--------------- 294 (467)
T KOG3608|consen 250 EKLLKSHVVRHVN--------------------CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFK--------------- 294 (467)
T ss_pred HHHHHHHHHHhhh--------------------cccccccccCCCChHHHHHHHHhhhccCCCcc---------------
Confidence 9999999887743 46777776666666666555555 32211111
Q ss_pred CCCCChhhHHHHHHhhhcccccccCCchhhhhHHHhhhhhhhhhhccCcceechh--hhhhccCccchhhhhhhhhcccc
Q 021090 159 VSDTSPEEDVAMCLMMLSRDVWMRNNDEAQDHKIVEMVEESEEIKLTRGKYRCEK--CKKAFRSYHALGGHKKVCETNIN 236 (317)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~--C~k~f~~~~~L~~H~~~H~~~~~ 236 (317)
+..++.......++..|...|+ +..|.|.. |...|++...|++|++.+
T Consensus 295 ------------------------Cd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~ev----- 344 (467)
T KOG3608|consen 295 ------------------------CDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEV----- 344 (467)
T ss_pred ------------------------ccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHh-----
Confidence 1222222233334445555553 55566655 666666666666665543
Q ss_pred cccccccC--CccccCCccccccCCcccccchhhhccCc
Q 021090 237 AGTKVAAD--EKIFECPFCYKVFGSGQALGGHKRSHLLA 273 (317)
Q Consensus 237 ~H~~~h~~--ekpf~C~~C~k~F~~~~~L~~H~~~H~~~ 273 (317)
|.| +-+|.|..|.+.|++..+|..|++.-++=
T Consensus 345 -----hEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f 378 (467)
T KOG3608|consen 345 -----HEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGF 378 (467)
T ss_pred -----ccCCCCCceeeecchhhhccchhHHHHHHHhhcc
Confidence 334 56799999999999999999996544333
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.57 E-value=8.8e-17 Score=147.35 Aligned_cols=54 Identities=37% Similarity=0.694 Sum_probs=49.4
Q ss_pred cCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccccchhhh
Q 021090 205 TRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALGGHKRS 269 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~~~ 269 (317)
..|.|+|..|||.|+.+..|+.|+|+|. |||||.|+-|+|+|.....+-.||..
T Consensus 278 ~lRKFKCtECgKAFKfKHHLKEHlRIHS-----------GEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 278 LLRKFKCTECGKAFKFKHHLKEHLRIHS-----------GEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhccccccccchhhhhHHHHHhhheeec-----------CCCCcCCcccccccccCCcccccccc
Confidence 5678999999999999999999997665 99999999999999999999999853
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.47 E-value=1e-15 Score=120.19 Aligned_cols=82 Identities=13% Similarity=0.181 Sum_probs=73.7
Q ss_pred CCCCCcccCcCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCCCCCC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYGLRNN 82 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~~~~~ 82 (317)
.|.|.+|||.|.....|++||+-|...+.| -|.-|++-|.....|.+|+++|.+.+||+|..|++.|..+-.
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~--------lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcs 188 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRH--------LCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCS 188 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHH--------HHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhcc
Confidence 588999999999999999999999999999 899999999988889999999998899999889888888888
Q ss_pred ccccccccCC
Q 021090 83 PKKSFRFADP 92 (317)
Q Consensus 83 l~~H~~~~~~ 92 (317)
|+-|++..|+
T Consensus 189 leshl~kvhg 198 (267)
T KOG3576|consen 189 LESHLKKVHG 198 (267)
T ss_pred HHHHHHHHcC
Confidence 8888776665
No 9
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.30 E-value=3.1e-14 Score=120.83 Aligned_cols=202 Identities=11% Similarity=0.095 Sum_probs=150.8
Q ss_pred CCCC--cccCcCCCccccccccccccCCCCCC--CCCC---CCCCCC--CCCCCCCCCCCCCCCCccccCCCCCccCcCC
Q 021090 4 HKCK--LCTRSFSNGRALGGHMKAHLAAHPLP--PKTN---QQQQPS--DSTESASTSSSSSGEGVEVKGKSPEVAEEKS 74 (317)
Q Consensus 4 ~~C~--~Cgk~F~~~~~L~~H~r~H~~ek~~~--~~~~---~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~ 74 (317)
|.|. .|+..|.+...|..|+-.|..---|. ..+. ....|. .|...+..+..|..|.+.|++++-..|+.|+
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg 214 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCG 214 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHH
Confidence 5565 69999999999999999887532332 1111 112343 5778888999999999999999999999999
Q ss_pred CCCCCCCCccccccccCCccccccCCCCeeecCCcccccccCCCcccccccccccchhhhhhhhhhhcCCCCCCCCCCCC
Q 021090 75 LGYGLRNNPKKSFRFADPEFSFAVDSGSVVVQDRESETESRNPTRRRSKRNRKLFTAHQDHHQKRMLKKPNFLESPAEPE 154 (317)
Q Consensus 75 ~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 154 (317)
..|+.+..|..|++.-..-. ...+.|..|.+.|...+.|..|.+.|..- .++..
T Consensus 215 ~~F~~~tkl~DH~rRqt~l~----------------~n~fqC~~C~KrFaTeklL~~Hv~rHvn~--ykCpl-------- 268 (467)
T KOG3608|consen 215 ELFRTKTKLFDHLRRQTELN----------------TNSFQCAQCFKRFATEKLLKSHVVRHVNC--YKCPL-------- 268 (467)
T ss_pred HHhccccHHHHHHHhhhhhc----------------CCchHHHHHHHHHhHHHHHHHHHHHhhhc--ccccc--------
Confidence 99999999999987654311 23578888888888888888887776321 11111
Q ss_pred CCCCCCCCChhhHHHHHHhhhcccccccCCchhhhhHHHhhhhhhhhh-hccCcceechhhhhhccCccchhhhhhhhhc
Q 021090 155 PVSSVSDTSPEEDVAMCLMMLSRDVWMRNNDEAQDHKIVEMVEESEEI-KLTRGKYRCEKCKKAFRSYHALGGHKKVCET 233 (317)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~ 233 (317)
++..-.....+..|.+. |+.++||+|+.|++.|.+.+.|.+|..+|.
T Consensus 269 -------------------------------Cdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS- 316 (467)
T KOG3608|consen 269 -------------------------------CDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS- 316 (467)
T ss_pred -------------------------------cccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-
Confidence 11111222334556655 678999999999999999999999998773
Q ss_pred ccccccccccCCccccCCc--cccccCCcccccchhhhcc-Ccc
Q 021090 234 NINAGTKVAADEKIFECPF--CYKVFGSGQALGGHKRSHL-LAN 274 (317)
Q Consensus 234 ~~~~H~~~h~~ekpf~C~~--C~k~F~~~~~L~~H~~~H~-~~~ 274 (317)
+-.|.|+. |..+|++...|++|++-|. |.+
T Consensus 317 -----------~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~n 349 (467)
T KOG3608|consen 317 -----------KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNN 349 (467)
T ss_pred -----------ccceecCCCCCcHHHHHHHHHHHHHHHhccCCC
Confidence 77899999 9999999999999987554 544
No 10
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.27 E-value=6.6e-13 Score=104.55 Aligned_cols=83 Identities=17% Similarity=0.306 Sum_probs=71.4
Q ss_pred cccCCchhhhhHHHhhhhhhhhhhccCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCC
Q 021090 180 WMRNNDEAQDHKIVEMVEESEEIKLTRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGS 259 (317)
Q Consensus 180 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~ 259 (317)
...+..+...+....++.+|..-|..-+.|-|..|||.|-....|++|+|+|+ |-|||+|..|+|+|++
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rtht-----------gvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHT-----------GVRPYKCSLCEKAFTQ 185 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhcccc-----------CccccchhhhhHHHHh
Confidence 34455677778888889999999998999999999999999999999997776 9999999999999999
Q ss_pred cccccchhh-hccCc
Q 021090 260 GQALGGHKR-SHLLA 273 (317)
Q Consensus 260 ~~~L~~H~~-~H~~~ 273 (317)
.-.|..|++ +|.-.
T Consensus 186 rcsleshl~kvhgv~ 200 (267)
T KOG3576|consen 186 RCSLESHLKKVHGVQ 200 (267)
T ss_pred hccHHHHHHHHcCch
Confidence 999999975 66543
No 11
>PHA02768 hypothetical protein; Provisional
Probab=99.08 E-value=3.2e-11 Score=75.43 Aligned_cols=45 Identities=11% Similarity=0.208 Sum_probs=40.6
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccccc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALGG 265 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~ 265 (317)
-|.|++||+.|...++|..|+++|+ +||+|..|++.|.+++.|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~-------------k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN-------------TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC-------------CcccCCcccceecccceeEE
Confidence 3899999999999999999998872 69999999999999988853
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.05 E-value=3.7e-11 Score=75.14 Aligned_cols=43 Identities=14% Similarity=0.335 Sum_probs=36.2
Q ss_pred CCCCCcccCcCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLAAHPLPPKTNQQQQPSDSTESASTSSSS 55 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l 55 (317)
-|.|++|||.|.+.+.|.+|||+|+ ++| .|..|+..|+..+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~--------kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNL--------KLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Ccc--------cCCcccceeccccee
Confidence 4899999999999999999999998 678 777777777655544
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.83 E-value=8.1e-10 Score=102.53 Aligned_cols=62 Identities=13% Similarity=0.338 Sum_probs=49.0
Q ss_pred hhhhhhhhccCcceechhhhhhccC----------ccchhhhhhhhhcccccccccccCCccccCCccccccCCcccccc
Q 021090 196 VEESEEIKLTRGKYRCEKCKKAFRS----------YHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALGG 265 (317)
Q Consensus 196 ~~~~~~~~~~~~~~~C~~C~k~f~~----------~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~ 265 (317)
+..|...|...+++.|.+|++.|.. .+.|..|+.++ |.+++.|..||+.|..+. |..
T Consensus 492 L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C------------G~rt~~C~~Cgk~Vrlrd-m~~ 558 (567)
T PLN03086 492 MVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC------------GSRTAPCDSCGRSVMLKE-MDI 558 (567)
T ss_pred HHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc------------CCcceEccccCCeeeehh-HHH
Confidence 4567777889999999999999963 34688888765 899999999999998765 446
Q ss_pred hh-hhc
Q 021090 266 HK-RSH 270 (317)
Q Consensus 266 H~-~~H 270 (317)
|+ .+|
T Consensus 559 H~~~~h 564 (567)
T PLN03086 559 HQIAVH 564 (567)
T ss_pred HHHHhh
Confidence 64 344
No 14
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.79 E-value=1.5e-09 Score=58.09 Aligned_cols=26 Identities=35% Similarity=0.774 Sum_probs=21.2
Q ss_pred chhhhhhhhhcccccccccccCCccccCCccccccCC
Q 021090 223 ALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGS 259 (317)
Q Consensus 223 ~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~ 259 (317)
+|.+|+++|+ |+|||+|++|+++|.+
T Consensus 1 ~l~~H~~~H~-----------~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHT-----------GEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHS-----------SSSSEEESSSSEEESS
T ss_pred CHHHHhhhcC-----------CCCCCCCCCCcCeeCc
Confidence 3667776655 9999999999999974
No 15
>PHA00733 hypothetical protein
Probab=98.71 E-value=4.7e-09 Score=79.75 Aligned_cols=61 Identities=25% Similarity=0.317 Sum_probs=50.9
Q ss_pred hhhhhhhccCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccccchhhhcc
Q 021090 197 EESEEIKLTRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALGGHKRSHL 271 (317)
Q Consensus 197 ~~~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~~~H~ 271 (317)
..+...+ +.++|.|..||+.|.+...|..|++.| +.+|.|++|++.|.+...|..|++..+
T Consensus 63 ~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h-------------~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 63 YKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT-------------EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred HhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcC-------------CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 3443333 588999999999999999999999764 347999999999999999999987544
No 16
>PHA00616 hypothetical protein
Probab=98.65 E-value=2.2e-09 Score=63.87 Aligned_cols=30 Identities=17% Similarity=0.294 Sum_probs=29.2
Q ss_pred CCCCCcccCcCCCccccccccccccCCCCC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLAAHPL 32 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~ 32 (317)
||+|+.||+.|..+++|.+|++.|++++++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~ 30 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKL 30 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcc
Confidence 799999999999999999999999999998
No 17
>PHA00733 hypothetical protein
Probab=98.65 E-value=1.9e-09 Score=81.83 Aligned_cols=82 Identities=10% Similarity=-0.060 Sum_probs=69.9
Q ss_pred CCCCCCcccCcCCCccccccc--cc---cccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCC
Q 021090 2 EKHKCKLCTRSFSNGRALGGH--MK---AHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLG 76 (317)
Q Consensus 2 k~~~C~~Cgk~F~~~~~L~~H--~r---~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~ 76 (317)
+++.|.+|.+.|..+..|..| ++ .+.+++|| .|..|+..|+....|..|+..+ ..+|.|+.|++.
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy--------~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~ 108 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPY--------VCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKE 108 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCc--------cCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCc
Confidence 568899999999998888877 22 33447899 9999999999999999998876 457999999999
Q ss_pred CCCCCCccccccccCCc
Q 021090 77 YGLRNNPKKSFRFADPE 93 (317)
Q Consensus 77 f~~~~~l~~H~~~~~~~ 93 (317)
|.....|.+|+...|..
T Consensus 109 F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 109 FRNTDSTLDHVCKKHNI 125 (128)
T ss_pred cCCHHHHHHHHHHhcCc
Confidence 99999999999877763
No 18
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.61 E-value=4.1e-09 Score=92.12 Aligned_cols=54 Identities=9% Similarity=-0.089 Sum_probs=46.5
Q ss_pred CCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCCCCCCccccccccCCcc
Q 021090 41 QPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYGLRNNPKKSFRFADPEF 94 (317)
Q Consensus 41 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~~ 94 (317)
.|+.|-..|-+...|.+|.=.-..-..|+|+.|++.|.-..||--|.|-|.+..
T Consensus 269 iCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~ 322 (500)
T KOG3993|consen 269 ICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRP 322 (500)
T ss_pred HHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCch
Confidence 788888888888888888666666678999999999999999999999887744
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.61 E-value=1.1e-08 Score=95.11 Aligned_cols=62 Identities=15% Similarity=0.101 Sum_probs=41.2
Q ss_pred CCCCCcccCcCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGY 77 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f 77 (317)
.+.|++||+.|. .+.|..|+++|+ +++ .|. |+..+ ....|..|+..+-..+++.|+.|+..|
T Consensus 453 H~~C~~Cgk~f~-~s~LekH~~~~H--kpv--------~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 453 HVHCEKCGQAFQ-QGEMEKHMKVFH--EPL--------QCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred CccCCCCCCccc-hHHHHHHHHhcC--CCc--------cCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 356777777774 566777777764 566 666 76533 446666777777777777777776666
No 20
>PHA00732 hypothetical protein
Probab=98.55 E-value=1.9e-08 Score=69.27 Aligned_cols=47 Identities=26% Similarity=0.525 Sum_probs=39.9
Q ss_pred ceechhhhhhccCccchhhhhhh-hhcccccccccccCCccccCCccccccCCcccccchhhhcc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKV-CETNINAGTKVAADEKIFECPFCYKVFGSGQALGGHKRSHL 271 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~-H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~~~H~ 271 (317)
||.|..||+.|.+...|..|++. |. ++.|+.||++|. .|..|++++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--------------~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--------------LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--------------CCccCCCCCEeC---ChhhhhcccC
Confidence 58999999999999999999974 42 468999999998 5888886654
No 21
>PHA00616 hypothetical protein
Probab=98.44 E-value=4.1e-08 Score=58.49 Aligned_cols=39 Identities=21% Similarity=0.450 Sum_probs=31.6
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCcccccc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVF 257 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F 257 (317)
||+|..||+.|..++.|..|++.|+ |++||.|+.---.|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~h-----------g~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVH-----------KQNKLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhc-----------CCCccceeEEEEEE
Confidence 5889999999999999999998876 88888887644333
No 22
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.40 E-value=3.2e-08 Score=86.66 Aligned_cols=82 Identities=12% Similarity=0.102 Sum_probs=52.7
Q ss_pred CCCCcccCcCCCccccccccccccCCCCCC--CCCCCCCC--CCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCCC
Q 021090 4 HKCKLCTRSFSNGRALGGHMKAHLAAHPLP--PKTNQQQQ--PSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYGL 79 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~~--~~~~~~~~--c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~~ 79 (317)
|+|++|+|.|+.+.+|-.|.|+|-....-. .....+.+ ...-.+.... .-....+..|.|..|++.|++
T Consensus 296 YrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r-------sg~dss~gi~~C~~C~KkFrR 368 (500)
T KOG3993|consen 296 YRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER-------SGDDSSSGIFSCHTCGKKFRR 368 (500)
T ss_pred ecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc-------cCCcccCceeecHHhhhhhHH
Confidence 899999999999999999999996432221 00110000 0000000000 011133458999999999999
Q ss_pred CCCccccccccCC
Q 021090 80 RNNPKKSFRFADP 92 (317)
Q Consensus 80 ~~~l~~H~~~~~~ 92 (317)
...|++|.-.|+.
T Consensus 369 qAYLrKHqlthq~ 381 (500)
T KOG3993|consen 369 QAYLRKHQLTHQR 381 (500)
T ss_pred HHHHHHhHHhhhc
Confidence 9999999877765
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.32 E-value=2.9e-08 Score=51.67 Aligned_cols=23 Identities=43% Similarity=0.852 Sum_probs=21.8
Q ss_pred CCCCcccCcCCCccccccccccc
Q 021090 4 HKCKLCTRSFSNGRALGGHMKAH 26 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r~H 26 (317)
|+|++|++.|.+++.|.+||++|
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 78999999999999999999976
No 24
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.26 E-value=5.9e-08 Score=51.90 Aligned_cols=25 Identities=28% Similarity=0.361 Sum_probs=21.4
Q ss_pred ccccccccccCCCCCCCCCCCCCCCCCCCCCCC
Q 021090 18 ALGGHMKAHLAAHPLPPKTNQQQQPSDSTESAS 50 (317)
Q Consensus 18 ~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~ 50 (317)
+|.+||++|++++|| .|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~--------~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPY--------KCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSE--------EESSSSEEES
T ss_pred CHHHHhhhcCCCCCC--------CCCCCcCeeC
Confidence 488999999999999 8888887765
No 25
>PHA00732 hypothetical protein
Probab=98.25 E-value=3.8e-07 Score=62.81 Aligned_cols=45 Identities=18% Similarity=0.121 Sum_probs=35.8
Q ss_pred CCCCCcccCcCCCcccccccccc-ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKA-HLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVE 61 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~-H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 61 (317)
||.|++||+.|.+.+.|+.|++. |. ++ .|+.|++.|. .+..|..+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~--------~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LT--------KCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CC--------ccCCCCCEeC---Chhhhhcc
Confidence 69999999999999999999994 65 34 6888888776 35566543
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.11 E-value=4.1e-07 Score=47.23 Aligned_cols=23 Identities=43% Similarity=0.891 Sum_probs=13.5
Q ss_pred ccCCccccccCCcccccchhhhc
Q 021090 248 FECPFCYKVFGSGQALGGHKRSH 270 (317)
Q Consensus 248 f~C~~C~k~F~~~~~L~~H~~~H 270 (317)
|+|++|++.|.++..|..|+++|
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 45666666666666666665543
No 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.98 E-value=3.4e-06 Score=71.48 Aligned_cols=64 Identities=22% Similarity=0.428 Sum_probs=48.4
Q ss_pred cCcceechh--hhhhccCccchhhhhhhhhccc--------ccccccccCCccccCCccccccCCcccccchhh
Q 021090 205 TRGKYRCEK--CKKAFRSYHALGGHKKVCETNI--------NAGTKVAADEKIFECPFCYKVFGSGQALGGHKR 268 (317)
Q Consensus 205 ~~~~~~C~~--C~k~f~~~~~L~~H~~~H~~~~--------~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~~ 268 (317)
+.+||+|.+ |.|.|+...-|+.|+.--+... ..+...-...|||+|++|+|.|....-|+-|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 359999988 9999999999999985311000 122222234599999999999999999999975
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.93 E-value=7.8e-07 Score=46.57 Aligned_cols=24 Identities=33% Similarity=0.784 Sum_probs=20.4
Q ss_pred CCCCcccCcCCCcccccccccccc
Q 021090 4 HKCKLCTRSFSNGRALGGHMKAHL 27 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r~H~ 27 (317)
|.|++|++.|.+...|..|+++|+
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 789999999999999999999874
No 29
>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=97.89 E-value=3.9e-06 Score=53.63 Aligned_cols=51 Identities=25% Similarity=0.309 Sum_probs=39.6
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccC-CccccCCccccccCCcccccchhhhcc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAAD-EKIFECPFCYKVFGSGQALGGHKRSHL 271 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~-ekpf~C~~C~k~F~~~~~L~~H~~~H~ 271 (317)
.|.|++|++ ......|..|.... |.. .+.+.|++|...+.. +|..|+..+.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~----------H~~~~~~v~CPiC~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDE----------HRSESKNVVCPICSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhH----------CcCCCCCccCCCchhhhhh--HHHHHHHHhc
Confidence 489999999 55567899997654 223 467999999997664 8889988764
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.82 E-value=1.7e-06 Score=46.73 Aligned_cols=26 Identities=31% Similarity=0.621 Sum_probs=24.2
Q ss_pred CCCCCcccCcCCCccccccccccccC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLA 28 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~ 28 (317)
+|.|..|++.|.+...|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 68999999999999999999998863
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.74 E-value=5.9e-06 Score=44.59 Aligned_cols=26 Identities=54% Similarity=0.694 Sum_probs=18.1
Q ss_pred cccCCccccccCCcccccchhhhccC
Q 021090 247 IFECPFCYKVFGSGQALGGHKRSHLL 272 (317)
Q Consensus 247 pf~C~~C~k~F~~~~~L~~H~~~H~~ 272 (317)
||+|.+|++.|.....|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 56777777777777777777776653
No 32
>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=97.72 E-value=6.8e-06 Score=42.85 Aligned_cols=23 Identities=48% Similarity=0.935 Sum_probs=13.9
Q ss_pred ccCCccccccCCcccccchhhhc
Q 021090 248 FECPFCYKVFGSGQALGGHKRSH 270 (317)
Q Consensus 248 f~C~~C~k~F~~~~~L~~H~~~H 270 (317)
|.|++|++.|.+...|+.|+++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 56666666666666666666654
No 33
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.58 E-value=1.2e-05 Score=42.65 Aligned_cols=24 Identities=33% Similarity=0.710 Sum_probs=22.6
Q ss_pred CCCCcccCcCCCcccccccccccc
Q 021090 4 HKCKLCTRSFSNGRALGGHMKAHL 27 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r~H~ 27 (317)
|.|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 789999999999999999999875
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.55 E-value=2e-05 Score=57.33 Aligned_cols=61 Identities=31% Similarity=0.448 Sum_probs=22.3
Q ss_pred echhhhhhccCccchhhhhhhhhccc-------------ccccccccCCccccCCccccccCCcccccchhhhcc
Q 021090 210 RCEKCKKAFRSYHALGGHKKVCETNI-------------NAGTKVAADEKIFECPFCYKVFGSGQALGGHKRSHL 271 (317)
Q Consensus 210 ~C~~C~k~f~~~~~L~~H~~~H~~~~-------------~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~~~H~ 271 (317)
.|.+|+..|.....|..|+...++-. ....+.. -...|.|.+|++.|.....|..||+.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp -------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Cccccccccccccccccccccccccccccccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 49999999999999999997644322 1111111 1226999999999999999999999653
No 35
>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=97.52 E-value=2e-05 Score=50.29 Aligned_cols=26 Identities=23% Similarity=0.560 Sum_probs=20.4
Q ss_pred CCCCCcccCcCCCccccccccc-cccCC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMK-AHLAA 29 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r-~H~~e 29 (317)
.|.||+||+.| +...|..|.. .|..+
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCEDEHRSE 28 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHhHCcCC
Confidence 59999999955 5688999988 46543
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.48 E-value=9.3e-05 Score=62.99 Aligned_cols=70 Identities=19% Similarity=0.217 Sum_probs=50.7
Q ss_pred CCCCCCc--ccCcCCCccccccccc-cccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCC
Q 021090 2 EKHKCKL--CTRSFSNGRALGGHMK-AHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYG 78 (317)
Q Consensus 2 k~~~C~~--Cgk~F~~~~~L~~H~r-~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~ 78 (317)
|||+|++ |.|.+.+..-|+-||. -|-..+..... .+.....| -..++||+|++|++.|.
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p------~p~~~~~F------------~~~~KPYrCevC~KRYK 409 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP------SPEKMNIF------------SAKDKPYRCEVCDKRYK 409 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCC------Cccccccc------------cccCCceeccccchhhc
Confidence 8999997 9999999999999998 45433333111 11111222 23478999999999999
Q ss_pred CCCCccccccc
Q 021090 79 LRNNPKKSFRF 89 (317)
Q Consensus 79 ~~~~l~~H~~~ 89 (317)
.-..|+-|.+-
T Consensus 410 NlNGLKYHr~H 420 (423)
T COG5189 410 NLNGLKYHRKH 420 (423)
T ss_pred cCccceecccc
Confidence 99999988653
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=97.37 E-value=1.9e-05 Score=48.03 Aligned_cols=30 Identities=20% Similarity=0.496 Sum_probs=22.4
Q ss_pred CCCCCCcccCcCCCccccccccccccCCCC
Q 021090 2 EKHKCKLCTRSFSNGRALGGHMKAHLAAHP 31 (317)
Q Consensus 2 k~~~C~~Cgk~F~~~~~L~~H~r~H~~ek~ 31 (317)
+|..|++|+..+.+..+|++|+.++++.||
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 577899999999999999999998888776
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.35 E-value=6.1e-05 Score=39.83 Aligned_cols=24 Identities=50% Similarity=0.873 Sum_probs=16.3
Q ss_pred ccCCccccccCCcccccchhhhcc
Q 021090 248 FECPFCYKVFGSGQALGGHKRSHL 271 (317)
Q Consensus 248 f~C~~C~k~F~~~~~L~~H~~~H~ 271 (317)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 567777777777777777766654
No 39
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=97.23 E-value=7e-05 Score=61.14 Aligned_cols=51 Identities=29% Similarity=0.442 Sum_probs=45.3
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccccch-hhhccCcc
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALGGH-KRSHLLAN 274 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H-~~~H~~~~ 274 (317)
-.|.+|++.|-....|..|+ ..|-|+|.+|.|..-+.--|.+| |++|...-
T Consensus 11 pwcwycnrefddekiliqhq---------------kakhfkchichkkl~sgpglsihcmqvhketi 62 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQ---------------KAKHFKCHICHKKLFSGPGLSIHCMQVHKETI 62 (341)
T ss_pred ceeeecccccchhhhhhhhh---------------hhccceeeeehhhhccCCCceeehhhhhhhhh
Confidence 36999999999999999998 46679999999999999999999 89997653
No 40
>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=97.18 E-value=0.0001 Score=39.66 Aligned_cols=24 Identities=33% Similarity=0.679 Sum_probs=21.6
Q ss_pred CCCCCcccCcCCCccccccccccc
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAH 26 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H 26 (317)
.|.|.+|++.|.+...|..|+++.
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCCcccCCCCcCCHHHHHHHHccC
Confidence 488999999999999999999964
No 41
>PRK04860 hypothetical protein; Provisional
Probab=97.00 E-value=0.00027 Score=55.78 Aligned_cols=41 Identities=22% Similarity=0.532 Sum_probs=34.4
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCccc
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQA 262 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~ 262 (317)
-+|.|. |++ ....+.+|.++|+ |+++|.|..|+..|.....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~-----------g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVR-----------GEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhc-----------CCccEECCCCCceeEEecc
Confidence 369998 998 7778888987776 9999999999999976543
No 42
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.99 E-value=0.00023 Score=43.42 Aligned_cols=31 Identities=23% Similarity=0.416 Sum_probs=22.0
Q ss_pred CCccccCCccccccCCcccccchhhhccCcc
Q 021090 244 DEKIFECPFCYKVFGSGQALGGHKRSHLLAN 274 (317)
Q Consensus 244 ~ekpf~C~~C~k~F~~~~~L~~H~~~H~~~~ 274 (317)
.+.|-.|++|+..+.+..+|.+|+.++++.+
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 5789999999999999999999997766554
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.97 E-value=5.8e-05 Score=39.79 Aligned_cols=23 Identities=30% Similarity=0.803 Sum_probs=21.5
Q ss_pred CCCCcccCcCCCccccccccccc
Q 021090 4 HKCKLCTRSFSNGRALGGHMKAH 26 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r~H 26 (317)
|.|.+|++.|.+...|+.|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 67999999999999999999975
No 44
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.84 E-value=0.00012 Score=53.24 Aligned_cols=72 Identities=18% Similarity=0.120 Sum_probs=21.6
Q ss_pred CCCcccCcCCCccccccccccccCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCCCCCCc
Q 021090 5 KCKLCTRSFSNGRALGGHMKAHLAA-HPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYGLRNNP 83 (317)
Q Consensus 5 ~C~~Cgk~F~~~~~L~~H~r~H~~e-k~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~~~~~l 83 (317)
.|.+|+..|.+...|..||+..++. .+- .........+..+.... ....+.|..|+..|.....|
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~-------------~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l 66 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPD-------------QKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREAL 66 (100)
T ss_dssp --------------------------------------------------------------SSEEBSSSS-EESSHHHH
T ss_pred Ccccccccccccccccccccccccccccc-------------ccccccccccccccccc-cCCCCCCCccCCCCcCHHHH
Confidence 5999999999999999999854432 221 00011111222222111 12268999999999999999
Q ss_pred ccccccc
Q 021090 84 KKSFRFA 90 (317)
Q Consensus 84 ~~H~~~~ 90 (317)
..||+.+
T Consensus 67 ~~Hm~~~ 73 (100)
T PF12756_consen 67 QEHMRSK 73 (100)
T ss_dssp HHHHHHT
T ss_pred HHHHcCc
Confidence 9999865
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.78 E-value=0.00024 Score=37.34 Aligned_cols=23 Identities=43% Similarity=0.759 Sum_probs=15.6
Q ss_pred ccCCccccccCCcccccchhhhc
Q 021090 248 FECPFCYKVFGSGQALGGHKRSH 270 (317)
Q Consensus 248 f~C~~C~k~F~~~~~L~~H~~~H 270 (317)
|.|.+|++.|.....|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 55777777777777777776654
No 46
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.55 E-value=0.014 Score=53.99 Aligned_cols=60 Identities=27% Similarity=0.461 Sum_probs=54.0
Q ss_pred cceechhhhhhccCccchhhhhh--hhhcccccccccccCC--ccccCC--ccccccCCcccccchhhhccCcccch
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKK--VCETNINAGTKVAADE--KIFECP--FCYKVFGSGQALGGHKRSHLLANSSS 277 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~--~H~~~~~~H~~~h~~e--kpf~C~--~C~k~F~~~~~L~~H~~~H~~~~~~~ 277 (317)
.++.|..|...|.....|.+|++ .|. ++ +||.|+ .|++.|.+...|..|..+|++.....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~-----------~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHS-----------GESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred cCCCCccccCCccccccccccccccccc-----------cccCCceeeeccCCCccccccccccCCcccccCCCccc
Confidence 47999999999999999999997 554 88 999999 89999999999999999999887433
No 47
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.50 E-value=0.0089 Score=55.25 Aligned_cols=63 Identities=21% Similarity=0.203 Sum_probs=57.0
Q ss_pred CCCCCcccCcCCCccccccccc--cccCC--CCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCccccCCCCCccCcC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMK--AHLAA--HPLPPKTNQQQQPS--DSTESASTSSSSSGEGVEVKGKSPEVAEEK 73 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r--~H~~e--k~~~~~~~~~~~c~--~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c 73 (317)
++.|..|...|.+...|.+|.+ .|+++ +|+ .|. .|+..|.....+.+|...+.....+.|...
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~--------~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 357 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPF--------SCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLL 357 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCce--------eeeccCCCccccccccccCCcccccCCCccccccc
Confidence 6899999999999999999999 89999 999 888 899999999999999999998888777543
No 48
>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=96.44 E-value=0.00088 Score=35.92 Aligned_cols=22 Identities=41% Similarity=0.671 Sum_probs=16.4
Q ss_pred ccCCccccccCCcccccchhhh
Q 021090 248 FECPFCYKVFGSGQALGGHKRS 269 (317)
Q Consensus 248 f~C~~C~k~F~~~~~L~~H~~~ 269 (317)
|.|.+|++.|.....|..|+++
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 6677777777777777777765
No 49
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.39 E-value=0.00026 Score=36.87 Aligned_cols=23 Identities=39% Similarity=0.569 Sum_probs=19.0
Q ss_pred CCCCcccCcCCCcccccccccccc
Q 021090 4 HKCKLCTRSFSNGRALGGHMKAHL 27 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r~H~ 27 (317)
|+|+.|+.... ++.|.+|++.|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999999998 999999999865
No 50
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.32 E-value=0.0008 Score=34.96 Aligned_cols=23 Identities=26% Similarity=0.598 Sum_probs=13.7
Q ss_pred ccCCccccccCCcccccchhhhcc
Q 021090 248 FECPFCYKVFGSGQALGGHKRSHL 271 (317)
Q Consensus 248 f~C~~C~k~F~~~~~L~~H~~~H~ 271 (317)
|+|+.|+.... ...|..|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 56777776666 666777766643
No 51
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.97 E-value=0.0014 Score=34.44 Aligned_cols=21 Identities=38% Similarity=0.684 Sum_probs=18.4
Q ss_pred CCCCcccCcCCCcccccccccc
Q 021090 4 HKCKLCTRSFSNGRALGGHMKA 25 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r~ 25 (317)
.+|+.||+.| ....|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 5799999999 78999999864
No 52
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=95.46 E-value=0.012 Score=59.74 Aligned_cols=76 Identities=13% Similarity=0.065 Sum_probs=51.0
Q ss_pred ccccccccccCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCcc-ccCCCCCccCcCCCCCCCCCCccccccccCCc
Q 021090 18 ALGGHMKAHLAAHPL-PPKTNQQQQPSDSTESASTSSSSSGEGVE-VKGKSPEVAEEKSLGYGLRNNPKKSFRFADPE 93 (317)
Q Consensus 18 ~L~~H~r~H~~ek~~-~~~~~~~~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~C~~c~~~f~~~~~l~~H~~~~~~~ 93 (317)
.+..|++.++..-.- ......-..|..|...+.....+.+++.. ++..+.|+|+.|...|.....|--|||..|+.
T Consensus 414 ~~~~~s~~~~~~~t~ee~~~~~l~e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~ 491 (1406)
T KOG1146|consen 414 ASDQHSNENTSSETKEEEDRGTLVELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPE 491 (1406)
T ss_pred cCcCCcccCCCccccccCCCCccccccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccc
Confidence 345666666543210 02222333455566666666677776544 56668999999999999999999999987773
No 53
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.93 E-value=0.0083 Score=31.43 Aligned_cols=20 Identities=30% Similarity=0.780 Sum_probs=12.7
Q ss_pred ccCCccccccCCcccccchhh
Q 021090 248 FECPFCYKVFGSGQALGGHKR 268 (317)
Q Consensus 248 f~C~~C~k~F~~~~~L~~H~~ 268 (317)
..|++||+.| ....|.+|++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4577777777 5556666654
No 54
>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=94.69 E-value=0.0072 Score=34.47 Aligned_cols=24 Identities=29% Similarity=0.677 Sum_probs=21.9
Q ss_pred CCCCCCcccCcCCCcccccccccc
Q 021090 2 EKHKCKLCTRSFSNGRALGGHMKA 25 (317)
Q Consensus 2 k~~~C~~Cgk~F~~~~~L~~H~r~ 25 (317)
-+|.|.+|++.|.+...|..|++.
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHCh
Confidence 478999999999999999999884
No 55
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.55 E-value=0.0029 Score=60.35 Aligned_cols=26 Identities=35% Similarity=0.781 Sum_probs=19.4
Q ss_pred CCCCCcccCcCC---------------Cccccccccc-cccC
Q 021090 3 KHKCKLCTRSFS---------------NGRALGGHMK-AHLA 28 (317)
Q Consensus 3 ~~~C~~Cgk~F~---------------~~~~L~~H~r-~H~~ 28 (317)
.+.|.+|++.|. +...|+.||+ .|..
T Consensus 99 ~~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~~ 140 (669)
T KOG2231|consen 99 HHSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHKL 140 (669)
T ss_pred hhhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhhh
Confidence 367888888874 7788999986 6754
No 56
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=94.05 E-value=0.016 Score=58.79 Aligned_cols=70 Identities=17% Similarity=0.254 Sum_probs=53.6
Q ss_pred ccCcceechhhhhhccCccchhhhhhhhhccc--------ccccc------cccCCccccCCccccccCCcccccchhh-
Q 021090 204 LTRGKYRCEKCKKAFRSYHALGGHKKVCETNI--------NAGTK------VAADEKIFECPFCYKVFGSGQALGGHKR- 268 (317)
Q Consensus 204 ~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~--------~~H~~------~h~~ekpf~C~~C~k~F~~~~~L~~H~~- 268 (317)
.-.+.|+|..|+-.|+....|..|||.-+-+- +.|.+ --.+.+||.|..|..+|..+.+|-+|++
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 34578999999999999999999999722111 22222 2234579999999999999999999987
Q ss_pred -hccCc
Q 021090 269 -SHLLA 273 (317)
Q Consensus 269 -~H~~~ 273 (317)
.|..+
T Consensus 541 ~~h~~~ 546 (1406)
T KOG1146|consen 541 DLHRNE 546 (1406)
T ss_pred HhhHHH
Confidence 46655
No 57
>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=93.81 E-value=0.018 Score=32.71 Aligned_cols=22 Identities=23% Similarity=0.516 Sum_probs=17.1
Q ss_pred cccCCccccccCCcccccchhh
Q 021090 247 IFECPFCYKVFGSGQALGGHKR 268 (317)
Q Consensus 247 pf~C~~C~k~F~~~~~L~~H~~ 268 (317)
+|.|++|++.|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4778888888887777777765
No 58
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=91.65 E-value=0.0052 Score=54.12 Aligned_cols=64 Identities=25% Similarity=0.239 Sum_probs=47.2
Q ss_pred cCcceechhhhhhccCccchhhhhhhhhccc---------ccccccccCC---ccccCCccc---cccCCcccccchhh
Q 021090 205 TRGKYRCEKCKKAFRSYHALGGHKKVCETNI---------NAGTKVAADE---KIFECPFCY---KVFGSGQALGGHKR 268 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~---------~~H~~~h~~e---kpf~C~~C~---k~F~~~~~L~~H~~ 268 (317)
..-|-.|-+|++.|..-..-..||..++|-. ..++..-.|+ +-|.|-+|+ +.|.+-...+.||+
T Consensus 163 e~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 163 ELIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred ccCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 3445779999999999999999999887544 1111111222 248999999 99999999999985
No 59
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=91.06 E-value=0.08 Score=44.19 Aligned_cols=52 Identities=19% Similarity=0.346 Sum_probs=34.5
Q ss_pred CcceechhhhhhccCccchhhhhhhhhcc--cccccccccCCcc-----ccCCccccccCCc
Q 021090 206 RGKYRCEKCKKAFRSYHALGGHKKVCETN--INAGTKVAADEKI-----FECPFCYKVFGSG 260 (317)
Q Consensus 206 ~~~~~C~~C~k~f~~~~~L~~H~~~H~~~--~~~H~~~h~~ekp-----f~C~~C~k~F~~~ 260 (317)
++.+.|++|++.|.++..+....+.-..+ ... .-.+.-| ..|+.||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~---~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCP---RYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCcc---ccCCCCCeeeeEEECCCCCCccccc
Confidence 46789999999999998888776542100 000 0112223 6899999999866
No 60
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=90.49 E-value=0.037 Score=52.85 Aligned_cols=28 Identities=32% Similarity=0.497 Sum_probs=25.9
Q ss_pred cccCCccccccCCcccccchhhhccCcc
Q 021090 247 IFECPFCYKVFGSGQALGGHKRSHLLAN 274 (317)
Q Consensus 247 pf~C~~C~k~F~~~~~L~~H~~~H~~~~ 274 (317)
-|.|..|+|.|-.-..+..||++|.-..
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~q~ 819 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQQE 819 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 4999999999999999999999998765
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.00 E-value=0.23 Score=41.48 Aligned_cols=24 Identities=21% Similarity=0.671 Sum_probs=21.4
Q ss_pred CCCCCCcccCcCCCcccccccccc
Q 021090 2 EKHKCKLCTRSFSNGRALGGHMKA 25 (317)
Q Consensus 2 k~~~C~~Cgk~F~~~~~L~~H~r~ 25 (317)
|.+.||+|++.|.++.-+....|+
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceE
Confidence 678999999999999998888874
No 62
>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=89.37 E-value=0.18 Score=37.23 Aligned_cols=62 Identities=19% Similarity=0.307 Sum_probs=43.6
Q ss_pred cceechhhhhhccCccchhhhhhh-hhccc---------------------------------ccccccccCCccccC--
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKV-CETNI---------------------------------NAGTKVAADEKIFEC-- 250 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~-H~~~~---------------------------------~~H~~~h~~ekpf~C-- 250 (317)
+-.-|..|+....- +.+..|++. |.... ..++.++. -|.|
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~---G~~C~~ 85 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYD---GYRCQC 85 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCC---Ceeeec
Confidence 45678888877666 778888884 32111 12222332 3999
Q ss_pred --CccccccCCcccccchhhhccC
Q 021090 251 --PFCYKVFGSGQALGGHKRSHLL 272 (317)
Q Consensus 251 --~~C~k~F~~~~~L~~H~~~H~~ 272 (317)
..|++.+.+...+.+|++.++|
T Consensus 86 ~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 86 DPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCCCcEeccHHHHHHHHHHhcC
Confidence 9999999999999999987654
No 63
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.00 E-value=1.7 Score=31.98 Aligned_cols=86 Identities=9% Similarity=0.025 Sum_probs=55.2
Q ss_pred CCCCCcccCcCCCccccccccccccCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLAAHPLPPK----TNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYG 78 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~~~~----~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~ 78 (317)
|-.|++||-.-.+...|.|--..=-..++|... ......|..|...|+........ .......|.|+.|...|-
T Consensus 15 P~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~--~~~~~~~y~C~~C~~~FC 92 (112)
T TIGR00622 15 PVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD--ELKDSHRYVCAVCKNVFC 92 (112)
T ss_pred CCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccccc--ccccccceeCCCCCCccc
Confidence 567999999988888887653221224445422 22234599999999865322211 123345899999999998
Q ss_pred CCCCcccccccc
Q 021090 79 LRNNPKKSFRFA 90 (317)
Q Consensus 79 ~~~~l~~H~~~~ 90 (317)
..-+.--|-.+|
T Consensus 93 ~dCD~fiHe~Lh 104 (112)
T TIGR00622 93 VDCDVFVHESLH 104 (112)
T ss_pred cccchhhhhhcc
Confidence 877777775444
No 64
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=86.31 E-value=0.16 Score=31.57 Aligned_cols=23 Identities=35% Similarity=0.758 Sum_probs=19.6
Q ss_pred CCCcccCcCCCc-----cccccccc-ccc
Q 021090 5 KCKLCTRSFSNG-----RALGGHMK-AHL 27 (317)
Q Consensus 5 ~C~~Cgk~F~~~-----~~L~~H~r-~H~ 27 (317)
.|.+|++.+... +.|.+|++ +|.
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 499999999887 59999998 675
No 65
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.84 E-value=0.35 Score=29.40 Aligned_cols=31 Identities=19% Similarity=0.526 Sum_probs=22.8
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCC
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGS 259 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~ 259 (317)
.|.|..||..|.... ....+.|+.||..+..
T Consensus 3 ~y~C~~CG~~~~~~~---------------------~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKCARCGREVELDE---------------------YGTGVRCPYCGYRILF 33 (46)
T ss_pred EEECCCCCCEEEECC---------------------CCCceECCCCCCeEEE
Confidence 589999998877654 1226899999976653
No 66
>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=85.70 E-value=0.43 Score=26.95 Aligned_cols=10 Identities=30% Similarity=0.717 Sum_probs=8.5
Q ss_pred ccccCCcccc
Q 021090 246 KIFECPFCYK 255 (317)
Q Consensus 246 kpf~C~~C~k 255 (317)
.|..|++||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 5789999986
No 67
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=85.28 E-value=0.41 Score=29.39 Aligned_cols=30 Identities=20% Similarity=0.696 Sum_probs=21.8
Q ss_pred CcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccc
Q 021090 206 RGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKV 256 (317)
Q Consensus 206 ~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~ 256 (317)
...|.|..||+.|.... ......|+.||..
T Consensus 4 ~~~Y~C~~Cg~~~~~~~---------------------~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQ---------------------ETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhh---------------------ccCceeCCCCCcE
Confidence 35699999999992111 4557899999864
No 68
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=84.48 E-value=0.5 Score=41.40 Aligned_cols=64 Identities=23% Similarity=0.441 Sum_probs=48.3
Q ss_pred cCcceechh--hhhhccCccchhhhhhh-hhccc-------ccccccccCCccccCCccccccCCcccccchhh
Q 021090 205 TRGKYRCEK--CKKAFRSYHALGGHKKV-CETNI-------NAGTKVAADEKIFECPFCYKVFGSGQALGGHKR 268 (317)
Q Consensus 205 ~~~~~~C~~--C~k~f~~~~~L~~H~~~-H~~~~-------~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~~ 268 (317)
..++|+|.+ |++.+....-|+.|... |.+.. ..|...-...|||+|++|.+++...-.|+-|+.
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceee
Confidence 568999976 99999999999888543 32222 455555566899999999999988777766654
No 69
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=83.16 E-value=0.67 Score=43.77 Aligned_cols=28 Identities=14% Similarity=0.389 Sum_probs=24.7
Q ss_pred cCcceechhhhhhccCccchhhhhhhhh
Q 021090 205 TRGKYRCEKCKKAFRSYHALGGHKKVCE 232 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~ 232 (317)
.+.+..|..||..|........||.+|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 5678999999999999999988888774
No 70
>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=82.94 E-value=0.67 Score=34.01 Aligned_cols=33 Identities=24% Similarity=0.552 Sum_probs=26.2
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCccc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQA 262 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~ 262 (317)
...|..||+.|--- +..|-.|+.||..|.....
T Consensus 9 KR~Cp~CG~kFYDL----------------------nk~PivCP~CG~~~~~~~~ 41 (108)
T PF09538_consen 9 KRTCPSCGAKFYDL----------------------NKDPIVCPKCGTEFPPEPP 41 (108)
T ss_pred cccCCCCcchhccC----------------------CCCCccCCCCCCccCcccc
Confidence 35799999998543 3569999999999998733
No 71
>PRK04860 hypothetical protein; Provisional
Probab=82.29 E-value=0.21 Score=39.55 Aligned_cols=10 Identities=10% Similarity=-0.004 Sum_probs=5.9
Q ss_pred CCCCCCCCCC
Q 021090 41 QPSDSTESAS 50 (317)
Q Consensus 41 ~c~~c~~~~~ 50 (317)
.|..|+..+.
T Consensus 145 rC~~C~~~l~ 154 (160)
T PRK04860 145 RCRRCGETLV 154 (160)
T ss_pred ECCCCCceeE
Confidence 6666665544
No 72
>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=82.17 E-value=0.46 Score=27.48 Aligned_cols=34 Identities=26% Similarity=0.548 Sum_probs=24.4
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccC
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFG 258 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~ 258 (317)
+.|..|+..|.-......- +...+.|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~----------------~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGA----------------NGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCC----------------CCCEEECCCCCCEEE
Confidence 6799999998877654321 223588999998874
No 73
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=82.00 E-value=0.76 Score=38.52 Aligned_cols=47 Identities=21% Similarity=0.575 Sum_probs=35.6
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccccchhhh
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALGGHKRS 269 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~~~ 269 (317)
|.|..||....... |.+|+-... + .-|.|-.||+.|.. -.+..|...
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCr-----------n-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCR-----------N-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhcc-----------C-CeeEEeeccccccc-chhhhhhhh
Confidence 78999998877654 666887664 4 57999999999988 555677653
No 74
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=81.47 E-value=1.2 Score=24.93 Aligned_cols=13 Identities=23% Similarity=0.636 Sum_probs=9.3
Q ss_pred CCCCCcccCcCCC
Q 021090 3 KHKCKLCTRSFSN 15 (317)
Q Consensus 3 ~~~C~~Cgk~F~~ 15 (317)
.|.|.+||..+.-
T Consensus 1 ~~~C~~CGy~y~~ 13 (33)
T cd00350 1 KYVCPVCGYIYDG 13 (33)
T ss_pred CEECCCCCCEECC
Confidence 3778888877654
No 75
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.00 E-value=0.46 Score=37.30 Aligned_cols=20 Identities=25% Similarity=0.271 Sum_probs=14.9
Q ss_pred ccccCCccccccCCcccccc
Q 021090 246 KIFECPFCYKVFGSGQALGG 265 (317)
Q Consensus 246 kpf~C~~C~k~F~~~~~L~~ 265 (317)
+.|+|+-||++|..--.+..
T Consensus 27 ~~~~c~~c~~~f~~~e~~~~ 46 (154)
T PRK00464 27 RRRECLACGKRFTTFERVEL 46 (154)
T ss_pred eeeeccccCCcceEeEeccC
Confidence 34999999999987655543
No 76
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=80.61 E-value=0.44 Score=25.09 Aligned_cols=20 Identities=20% Similarity=0.614 Sum_probs=16.4
Q ss_pred CCCCcccCcCCCccccccccc
Q 021090 4 HKCKLCTRSFSNGRALGGHMK 24 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r 24 (317)
..||+|++.+ ....++.|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 4699999999 5678888876
No 77
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=80.24 E-value=0.46 Score=29.68 Aligned_cols=27 Identities=26% Similarity=0.469 Sum_probs=20.7
Q ss_pred ccCCccccCCccccccCCcccccchhh
Q 021090 242 AADEKIFECPFCYKVFGSGQALGGHKR 268 (317)
Q Consensus 242 h~~ekpf~C~~C~k~F~~~~~L~~H~~ 268 (317)
..||--+.|+-||+-|.......+|..
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 347777888888888888877777764
No 78
>PHA00626 hypothetical protein
Probab=80.08 E-value=0.66 Score=29.10 Aligned_cols=17 Identities=12% Similarity=0.063 Sum_probs=13.3
Q ss_pred CccccCCccccccCCcc
Q 021090 245 EKIFECPFCYKVFGSGQ 261 (317)
Q Consensus 245 ekpf~C~~C~k~F~~~~ 261 (317)
...|+|+.||..|+...
T Consensus 21 snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CcceEcCCCCCeechhh
Confidence 34699999999997643
No 79
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=79.87 E-value=0.55 Score=38.91 Aligned_cols=46 Identities=22% Similarity=0.225 Sum_probs=37.4
Q ss_pred CCcccCcCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-Ccccc
Q 021090 6 CKLCTRSFSNGRALGGHMKAHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGE-GVEVK 63 (317)
Q Consensus 6 C~~Cgk~F~~~~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h-~~~~~ 63 (317)
|=+|++.|-...-|.+|++.- -| +|.+|.+...+...|.-| |.+|.
T Consensus 13 cwycnrefddekiliqhqkak----hf--------kchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAK----HF--------KCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeecccccchhhhhhhhhhhc----cc--------eeeeehhhhccCCCceeehhhhhh
Confidence 889999999999999999843 25 999999888877777655 66553
No 80
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=79.40 E-value=0.47 Score=35.61 Aligned_cols=24 Identities=25% Similarity=0.490 Sum_probs=21.1
Q ss_pred CCCcccCcCCCccccccccccccCCCC
Q 021090 5 KCKLCTRSFSNGRALGGHMKAHLAAHP 31 (317)
Q Consensus 5 ~C~~Cgk~F~~~~~L~~H~r~H~~ek~ 31 (317)
.|-+|||.|. +|++|+++|.+..|
T Consensus 78 icLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEeccCcchH---HHHHHHhcccCCCH
Confidence 5999999997 59999999998766
No 81
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=78.90 E-value=0.67 Score=28.98 Aligned_cols=27 Identities=22% Similarity=0.385 Sum_probs=24.0
Q ss_pred cCcceechhhhhhccCccchhhhhhhh
Q 021090 205 TRGKYRCEKCKKAFRSYHALGGHKKVC 231 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L~~H~~~H 231 (317)
++--+.|..||..|....+..+|...-
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 667799999999999999999998653
No 82
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.33 E-value=0.61 Score=45.03 Aligned_cols=49 Identities=27% Similarity=0.459 Sum_probs=31.0
Q ss_pred ceechhh------hhhccCccchhhhhhhhhcccccccccccCCccccCC--ccc-cccCCcccccchhhhcc
Q 021090 208 KYRCEKC------KKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECP--FCY-KVFGSGQALGGHKRSHL 271 (317)
Q Consensus 208 ~~~C~~C------~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~--~C~-k~F~~~~~L~~H~~~H~ 271 (317)
-|.|.+| +.-|.....|..|.+.+ -|.|+ .|. +.|.....+.+|++-|.
T Consensus 206 h~~chfC~~~~~~neyy~~~~dLe~HfR~~---------------HflCE~~~C~~~~f~~~~~~ei~lk~~~ 263 (669)
T KOG2231|consen 206 HEFCHFCDYKTGQNEYYNDYDDLEEHFRKG---------------HFLCEEEFCRTKKFYVAFELEIELKAHN 263 (669)
T ss_pred eeheeecCcccccchhcccchHHHHHhhhc---------------CccccccccccceeeehhHHHHHHHhhc
Confidence 3556665 34566666677777654 38999 773 56666666667776554
No 83
>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=78.24 E-value=0.42 Score=36.37 Aligned_cols=25 Identities=28% Similarity=0.638 Sum_probs=16.6
Q ss_pred CCCCcccCcCCCccccccccccccCCCC
Q 021090 4 HKCKLCTRSFSNGRALGGHMKAHLAAHP 31 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r~H~~ek~ 31 (317)
-.|-+|||.|.. |++|++.|+|..|
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eEEccCCcccch---HHHHHHHccCCCH
Confidence 359999999975 6999999988655
No 84
>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=78.20 E-value=0.84 Score=27.16 Aligned_cols=30 Identities=30% Similarity=0.873 Sum_probs=21.8
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCcccc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYK 255 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k 255 (317)
.|+|..||..|.....+. ...+-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~------------------~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSIS------------------EDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcC------------------CCCCCcCCCCCC
Confidence 389999998887655332 245688999987
No 85
>PF14353 CpXC: CpXC protein
Probab=78.00 E-value=0.67 Score=35.22 Aligned_cols=58 Identities=19% Similarity=0.223 Sum_probs=35.1
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCC-ccccCCccccccCCcccccchhhh
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADE-KIFECPFCYKVFGSGQALGGHKRS 269 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~e-kpf~C~~C~k~F~~~~~L~~H~~~ 269 (317)
..|..||..|...-.........-. .-.++-.|+ -.|.|+.||+.|.-...+.-|-..
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~---l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPE---LKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHH---HHHHHHcCCcCEEECCCCCCceecCCCEEEEcCC
Confidence 3699999988776654433211100 000112232 359999999999988888777543
No 86
>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=77.53 E-value=1.3 Score=33.21 Aligned_cols=35 Identities=20% Similarity=0.317 Sum_probs=27.5
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCccccc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALG 264 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~ 264 (317)
...|..||+.|--- +..|-.|+.||..|.....++
T Consensus 9 Kr~Cp~cg~kFYDL----------------------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 9 KRICPNTGSKFYDL----------------------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cccCCCcCcccccc----------------------CCCCccCCCcCCccCcchhhc
Confidence 45799999998542 357999999999998775554
No 87
>COG1773 Rubredoxin [Energy production and conversion]
Probab=77.15 E-value=0.82 Score=28.82 Aligned_cols=14 Identities=21% Similarity=0.873 Sum_probs=12.2
Q ss_pred CCCCCCCcccCcCC
Q 021090 1 MEKHKCKLCTRSFS 14 (317)
Q Consensus 1 ~k~~~C~~Cgk~F~ 14 (317)
|++|+|.+||..|.
T Consensus 1 m~~~~C~~CG~vYd 14 (55)
T COG1773 1 MKRWRCSVCGYVYD 14 (55)
T ss_pred CCceEecCCceEec
Confidence 67899999999886
No 88
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=76.83 E-value=0.6 Score=41.58 Aligned_cols=62 Identities=24% Similarity=0.442 Sum_probs=45.9
Q ss_pred ceechhhhhhccCccchhhhhhh--hhccc----------------cccc--------ccccCCccccCCccccccCCcc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKV--CETNI----------------NAGT--------KVAADEKIFECPFCYKVFGSGQ 261 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~--H~~~~----------------~~H~--------~~h~~ekpf~C~~C~k~F~~~~ 261 (317)
-|.|..|...|.....-+.|+++ |.=.+ .+++ ..-.++-+|.|.+|.|.|....
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~ 82 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPK 82 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChh
Confidence 38899999999999888889874 43221 1111 1234566899999999999999
Q ss_pred cccchhhh
Q 021090 262 ALGGHKRS 269 (317)
Q Consensus 262 ~L~~H~~~ 269 (317)
....|+..
T Consensus 83 a~~~hl~S 90 (390)
T KOG2785|consen 83 AHENHLKS 90 (390)
T ss_pred hHHHHHHH
Confidence 99888753
No 89
>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=76.58 E-value=0.8 Score=27.52 Aligned_cols=15 Identities=27% Similarity=0.698 Sum_probs=5.2
Q ss_pred CcceechhhhhhccC
Q 021090 206 RGKYRCEKCKKAFRS 220 (317)
Q Consensus 206 ~~~~~C~~C~k~f~~ 220 (317)
.....|..|++.+..
T Consensus 14 ~~~a~C~~C~~~~~~ 28 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKY 28 (45)
T ss_dssp SS-EEETTTTEE---
T ss_pred cCeEEeCCCCeEEee
Confidence 344444444444444
No 90
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=76.56 E-value=1.3 Score=35.08 Aligned_cols=24 Identities=25% Similarity=0.555 Sum_probs=19.8
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCcccc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYK 255 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k 255 (317)
-|.|.+||.. +.|+-|-+||+||.
T Consensus 134 ~~vC~vCGy~------------------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT------------------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc------------------------ccCCCCCcCCCCCC
Confidence 6999999854 33788999999983
No 91
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=76.43 E-value=1 Score=26.32 Aligned_cols=31 Identities=32% Similarity=0.830 Sum_probs=21.4
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKV 256 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~ 256 (317)
.|+|..||+.|....... ....-.|+.||..
T Consensus 5 ~y~C~~Cg~~fe~~~~~~------------------~~~~~~CP~Cg~~ 35 (41)
T smart00834 5 EYRCEDCGHTFEVLQKIS------------------DDPLATCPECGGD 35 (41)
T ss_pred EEEcCCCCCEEEEEEecC------------------CCCCCCCCCCCCc
Confidence 388999999887544331 1345779999873
No 92
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=75.64 E-value=1.3 Score=28.26 Aligned_cols=33 Identities=21% Similarity=0.336 Sum_probs=22.1
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCcccc
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYK 255 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k 255 (317)
-.|.|..||+.--.+-..-+- ...+|+|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~~CRk----------------~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKCRK----------------LGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhhhHHH----------------cCCceECCCcCc
Confidence 458899999765554433222 245899999984
No 93
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=75.55 E-value=1.6 Score=34.05 Aligned_cols=41 Identities=20% Similarity=0.458 Sum_probs=27.7
Q ss_pred ccCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCC
Q 021090 204 LTRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGS 259 (317)
Q Consensus 204 ~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~ 259 (317)
....-|.|+.|+..|.....+..- . ...-|.|+.||.....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~--------------d-~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLL--------------D-MDGTFTCPRCGEELEE 135 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhc--------------C-CCCcEECCCCCCEEEE
Confidence 355679999999999965443320 0 1233999999987643
No 94
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=75.40 E-value=1.2 Score=27.77 Aligned_cols=30 Identities=30% Similarity=0.825 Sum_probs=20.6
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCcccc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYK 255 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k 255 (317)
.|+|..||..|.....+. ...+-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~------------------~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMS------------------DDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecC------------------CCCCCCCCCCCC
Confidence 389999999887543221 234567999996
No 95
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=74.67 E-value=1.6 Score=26.33 Aligned_cols=28 Identities=18% Similarity=0.452 Sum_probs=20.7
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCcccccc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVF 257 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F 257 (317)
.|.|..||..|.... .-+.+|+.||..-
T Consensus 2 ~Y~C~~Cg~~~~~~~----------------------~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIKS----------------------KDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecCC----------------------CCceECCCCCceE
Confidence 489999999877541 2368899998653
No 96
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=73.27 E-value=1.4 Score=22.66 Aligned_cols=9 Identities=22% Similarity=0.512 Sum_probs=7.6
Q ss_pred CCCCCcccC
Q 021090 3 KHKCKLCTR 11 (317)
Q Consensus 3 ~~~C~~Cgk 11 (317)
+|.|+.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 589999985
No 97
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=73.12 E-value=1.9 Score=33.86 Aligned_cols=12 Identities=8% Similarity=-0.133 Sum_probs=8.6
Q ss_pred CCCCCCCCCCCC
Q 021090 41 QPSDSTESASTS 52 (317)
Q Consensus 41 ~c~~c~~~~~~~ 52 (317)
+|+.|+..|.+-
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 777777777654
No 98
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=72.75 E-value=1.1 Score=43.38 Aligned_cols=27 Identities=26% Similarity=0.566 Sum_probs=24.5
Q ss_pred CcceechhhhhhccCccchhhhhhhhh
Q 021090 206 RGKYRCEKCKKAFRSYHALGGHKKVCE 232 (317)
Q Consensus 206 ~~~~~C~~C~k~f~~~~~L~~H~~~H~ 232 (317)
.+-|.|.+|+|.|-.-.++..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 356999999999999999999999984
No 99
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=69.98 E-value=1.3 Score=38.89 Aligned_cols=30 Identities=30% Similarity=0.703 Sum_probs=25.0
Q ss_pred CCCCCCcccCcCCCccccccccc--cccCCCC
Q 021090 2 EKHKCKLCTRSFSNGRALGGHMK--AHLAAHP 31 (317)
Q Consensus 2 k~~~C~~Cgk~F~~~~~L~~H~r--~H~~ek~ 31 (317)
.++.|-+|.|.|+.+..|+.||| .|....|
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrkK~HrrinP 225 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRKKRHRRINP 225 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHhccCcccCC
Confidence 46889999999999999999999 4655444
No 100
>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=69.38 E-value=6.3 Score=28.93 Aligned_cols=31 Identities=10% Similarity=0.049 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCCCC
Q 021090 39 QQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYGLR 80 (317)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~~~ 80 (317)
+..|..||+.|..- +..|-.||.|+..|...
T Consensus 9 KR~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 44666676666542 23566788888888776
No 101
>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=68.93 E-value=2.7 Score=22.09 Aligned_cols=10 Identities=30% Similarity=0.733 Sum_probs=8.1
Q ss_pred CCCcccCcCC
Q 021090 5 KCKLCTRSFS 14 (317)
Q Consensus 5 ~C~~Cgk~F~ 14 (317)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5888998885
No 102
>PF15269 zf-C2H2_7: Zinc-finger
Probab=68.60 E-value=1.2 Score=26.56 Aligned_cols=23 Identities=35% Similarity=0.437 Sum_probs=20.2
Q ss_pred CCCCCcccCcCCCcccccccccc
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKA 25 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~ 25 (317)
+|+|-+|.-...-++.|-.||+-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 47899999999999999999984
No 103
>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=67.86 E-value=2.5 Score=23.47 Aligned_cols=27 Identities=22% Similarity=0.535 Sum_probs=16.9
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCcccccc
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVF 257 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F 257 (317)
|.|..||..+.... .-+.+|+.||..-
T Consensus 1 Y~C~~Cg~~~~~~~----------------------~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELKP----------------------GDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BST----------------------SSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEcCC----------------------CCcEECCcCCCeE
Confidence 67888888776221 2367899998653
No 104
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=67.25 E-value=1.7 Score=38.17 Aligned_cols=67 Identities=22% Similarity=0.413 Sum_probs=47.5
Q ss_pred cceechhhhhhccCccchhhhhhhhhccc--------------------------cccc--------cccc---------
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNI--------------------------NAGT--------KVAA--------- 243 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~--------------------------~~H~--------~~h~--------- 243 (317)
..+.|-.|.|.|+.+..|+.||+.-...+ ..+. ..+.
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 35899999999999999999998633222 0111 0010
Q ss_pred CCcc--ccCCccccccCCcccccchhh-hccCc
Q 021090 244 DEKI--FECPFCYKVFGSGQALGGHKR-SHLLA 273 (317)
Q Consensus 244 ~ekp--f~C~~C~k~F~~~~~L~~H~~-~H~~~ 273 (317)
+.-+ .+|-+|.....+...|..||. +|.-.
T Consensus 274 ~a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~D 306 (423)
T KOG2482|consen 274 DAEALSVVCLFCTNFYENPVFLFEHMKIVHEFD 306 (423)
T ss_pred CCCccceEEEeeccchhhHHHHHHHHHHHHHhh
Confidence 1122 699999999999999999998 56543
No 105
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=65.68 E-value=2.8 Score=23.93 Aligned_cols=34 Identities=18% Similarity=0.385 Sum_probs=23.5
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccC
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFG 258 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~ 258 (317)
..|..|+..|.-...... .+.+..+|+.|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~ip----------------~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP----------------PKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHHCC----------------CCCcEEECCCCCCEeC
Confidence 468888888877765422 1345688999988773
No 106
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=65.21 E-value=2.6 Score=24.23 Aligned_cols=34 Identities=29% Similarity=0.598 Sum_probs=23.7
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccC
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFG 258 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~ 258 (317)
..|..|+..|.-..... ..+.+..+|+.|+-.|.
T Consensus 3 i~CP~C~~~f~v~~~~l----------------~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKL----------------PAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHc----------------ccCCcEEECCCCCcEee
Confidence 46888888887776421 11456789999988774
No 107
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=65.17 E-value=2.8 Score=29.05 Aligned_cols=36 Identities=25% Similarity=0.534 Sum_probs=26.9
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccc
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQAL 263 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L 263 (317)
.+|.|..|++. .+.|+ +..-+.|..||..|.-..+.
T Consensus 34 ~~~~Cp~C~~~--------~VkR~-------------a~GIW~C~kCg~~fAGgay~ 69 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRI-------------ATGIWKCRKCGAKFAGGAYT 69 (89)
T ss_pred cCCcCCCCCCc--------ceeee-------------ccCeEEcCCCCCeecccccc
Confidence 57999999976 22322 45569999999999876664
No 108
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.83 E-value=2.7 Score=30.41 Aligned_cols=34 Identities=12% Similarity=0.131 Sum_probs=25.0
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccccc
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALGG 265 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~ 265 (317)
..|..||+.|--- ...|..|++||++| ..++|..
T Consensus 10 ridPetg~KFYDL----------------------NrdPiVsPytG~s~-P~s~fe~ 43 (129)
T COG4530 10 RIDPETGKKFYDL----------------------NRDPIVSPYTGKSY-PRSYFEE 43 (129)
T ss_pred ccCccccchhhcc----------------------CCCccccCcccccc-hHHHHHh
Confidence 3588888887432 47799999999999 4555543
No 109
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=63.33 E-value=2.1 Score=28.81 Aligned_cols=42 Identities=17% Similarity=0.389 Sum_probs=28.3
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCCccccCC--ccccccCCcccc
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECP--FCYKVFGSGQAL 263 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~--~C~k~F~~~~~L 263 (317)
+.|..||..-....+-..... +.++-|+|. .||.+|.....+
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~-------------~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT-------------TKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcChh-------------hheeeeecCCCCCCCEEEEEEEE
Confidence 468889876544443333321 257789999 999999986655
No 110
>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=62.11 E-value=2.8 Score=31.93 Aligned_cols=20 Identities=40% Similarity=0.634 Sum_probs=9.7
Q ss_pred ccCCccccccCCcccccchhhhc
Q 021090 248 FECPFCYKVFGSGQALGGHKRSH 270 (317)
Q Consensus 248 f~C~~C~k~F~~~~~L~~H~~~H 270 (317)
..|-+|||.|.. |++|++.|
T Consensus 73 i~clecGk~~k~---LkrHL~~~ 92 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTH 92 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHT
T ss_pred eEEccCCcccch---HHHHHHHc
Confidence 556666665554 35666666
No 111
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=60.74 E-value=3.9 Score=26.15 Aligned_cols=33 Identities=18% Similarity=0.402 Sum_probs=20.3
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCcccc
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYK 255 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k 255 (317)
-.|.|..||+.--.+-.--+- ...+|+|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~~CRk----------------~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEKCRK----------------QSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeechhHHh----------------cCCceECCCCCC
Confidence 458888888763333211111 245899999985
No 112
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.68 E-value=0.44 Score=38.57 Aligned_cols=78 Identities=14% Similarity=0.142 Sum_probs=55.0
Q ss_pred CCCCCCc--ccCcCCCcccccccccc-ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc----------ccCCCCC
Q 021090 2 EKHKCKL--CTRSFSNGRALGGHMKA-HLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVE----------VKGKSPE 68 (317)
Q Consensus 2 k~~~C~~--Cgk~F~~~~~L~~H~r~-H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~----------~~~~~~~ 68 (317)
+.|.|++ |...|........|-.+ |+. .|..|...|++..-|..|... ..+...|
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~------------sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy 145 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGN------------SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMY 145 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccc------------hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHH
Confidence 3466765 66777777766677653 432 788888888877777766544 2356789
Q ss_pred cc--CcCCCCCCCCCCccccccccC
Q 021090 69 VA--EEKSLGYGLRNNPKKSFRFAD 91 (317)
Q Consensus 69 ~C--~~c~~~f~~~~~l~~H~~~~~ 91 (317)
.| +.|...|.+...-++|+-..|
T Consensus 146 ~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 146 QCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred HHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 99 789999999888888865444
No 113
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.89 E-value=4.6 Score=32.60 Aligned_cols=35 Identities=23% Similarity=0.497 Sum_probs=27.3
Q ss_pred cCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCC
Q 021090 205 TRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGS 259 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~ 259 (317)
...-|.|..|+..|+.-..+. --|.|+.||-....
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~--------------------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME--------------------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh--------------------cCCcCCCCCCCCee
Confidence 445699999999998877652 24999999987654
No 114
>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=59.24 E-value=3.2 Score=29.23 Aligned_cols=37 Identities=27% Similarity=0.506 Sum_probs=26.7
Q ss_pred CcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccc
Q 021090 206 RGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQAL 263 (317)
Q Consensus 206 ~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L 263 (317)
...|.|++||+.-..+. +-..+.|..|++.|.-..+.
T Consensus 33 ~a~y~CpfCgk~~vkR~---------------------a~GIW~C~~C~~~~AGGAy~ 69 (91)
T TIGR00280 33 KAKYVCPFCGKKTVKRG---------------------STGIWTCRKCGAKFAGGAYT 69 (91)
T ss_pred hcCccCCCCCCCceEEE---------------------eeEEEEcCCCCCEEeCCccc
Confidence 35799999986521111 34569999999999987765
No 115
>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=59.15 E-value=5.2 Score=31.63 Aligned_cols=35 Identities=20% Similarity=0.356 Sum_probs=27.5
Q ss_pred ccCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccC
Q 021090 204 LTRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFG 258 (317)
Q Consensus 204 ~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~ 258 (317)
.+..-|.|..|+..|+.-.+|. --|.|+.||....
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~--------------------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME--------------------LNFTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH--------------------cCCcCCCCCCEee
Confidence 3556799999999998888774 1499999997654
No 116
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=58.99 E-value=3.6 Score=28.91 Aligned_cols=37 Identities=27% Similarity=0.452 Sum_probs=26.7
Q ss_pred CcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccc
Q 021090 206 RGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQAL 263 (317)
Q Consensus 206 ~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L 263 (317)
...|.|.+||+.-..+. +...+.|..|++.|.-..+.
T Consensus 34 ~a~y~CpfCgk~~vkR~---------------------a~GIW~C~~C~~~~AGGAy~ 70 (90)
T PTZ00255 34 HAKYFCPFCGKHAVKRQ---------------------AVGIWRCKGCKKTVAGGAWT 70 (90)
T ss_pred hCCccCCCCCCCceeee---------------------eeEEEEcCCCCCEEeCCccc
Confidence 35799999986421111 34579999999999977665
No 117
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=58.13 E-value=5.6 Score=30.06 Aligned_cols=15 Identities=40% Similarity=1.028 Sum_probs=11.3
Q ss_pred CCCCCcccCcCCCcc
Q 021090 3 KHKCKLCTRSFSNGR 17 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~ 17 (317)
||+|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678888888887644
No 118
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=57.35 E-value=3.1 Score=29.24 Aligned_cols=36 Identities=25% Similarity=0.434 Sum_probs=25.9
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccc
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQAL 263 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L 263 (317)
..|.|.+|++.-..+. +-..+.|..|++.|.-..+.
T Consensus 35 a~y~CpfCgk~~vkR~---------------------a~GIW~C~~C~~~~AGGAy~ 70 (90)
T PRK03976 35 AKHVCPVCGRPKVKRV---------------------GTGIWECRKCGAKFAGGAYT 70 (90)
T ss_pred cCccCCCCCCCceEEE---------------------EEEEEEcCCCCCEEeCCccc
Confidence 5799999986522111 34569999999999876665
No 119
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=56.97 E-value=4.1 Score=36.01 Aligned_cols=52 Identities=15% Similarity=0.222 Sum_probs=30.8
Q ss_pred cccCCccccCCccc-cccCCcccccchhh--hccCcccchhhhhhhcccCCccch
Q 021090 241 VAADEKIFECPFCY-KVFGSGQALGGHKR--SHLLANSSSTAAAAAVVATDPAVK 292 (317)
Q Consensus 241 ~h~~ekpf~C~~C~-k~F~~~~~L~~H~~--~H~~~~~~~~a~~~~~~~~~~~~~ 292 (317)
.|.-.+-|.|++|| +.+--...+.+|.. .|--.-.-.++.-..++...+...
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~E~rHiygl~clGi~ps~vfkgIT~I~ 422 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFEEDRHIYGLECLGIKPSRVFKGITRIG 422 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhhhhhhhhheeeccccchHHHhhhhhHH
Confidence 44445669999999 77777777777753 554444333333344444444433
No 120
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.30 E-value=2.9 Score=34.01 Aligned_cols=63 Identities=24% Similarity=0.479 Sum_probs=45.6
Q ss_pred eechhhhhhccCccchhhhhhh-hhcccccccccccCCccccCCc--cccccCCcccccchh-hhccCc
Q 021090 209 YRCEKCKKAFRSYHALGGHKKV-CETNINAGTKVAADEKIFECPF--CYKVFGSGQALGGHK-RSHLLA 273 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~-H~~~~~~H~~~h~~ekpf~C~~--C~k~F~~~~~L~~H~-~~H~~~ 273 (317)
..|.+|.+.|.+...|..|+.. |..-.+ ..+--|.-.|.|-+ |+-.|.+...-+.|+ +.|.-.
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fq--a~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk~P 173 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHILEWHDSLFQ--ALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHKYP 173 (253)
T ss_pred chhHHHHHhCCchhhhhHHHHHHHHHHHH--HHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhccCC
Confidence 4799999999999999999863 321000 01233556799975 999999999988996 577644
No 121
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=56.23 E-value=12 Score=28.13 Aligned_cols=34 Identities=6% Similarity=0.036 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCCCCCCc
Q 021090 39 QQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYGLRNNP 83 (317)
Q Consensus 39 ~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~~~~~l 83 (317)
+..|+.|++.|..- +..|-.|+.|+..|.....+
T Consensus 9 Kr~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 9 KRICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred cccCCCcCcccccc-----------CCCCccCCCcCCccCcchhh
Confidence 33566666666532 23566888888887666444
No 122
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=56.05 E-value=2.4 Score=29.83 Aligned_cols=36 Identities=31% Similarity=0.582 Sum_probs=23.7
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccc
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQAL 263 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L 263 (317)
..|.|++||+.- +.+. +.--+.|..|++.|.-..+.
T Consensus 34 ~ky~Cp~Cgk~~-----vkR~----------------a~GIW~C~~C~~~~AGGAy~ 69 (90)
T PF01780_consen 34 AKYTCPFCGKTS-----VKRV----------------ATGIWKCKKCGKKFAGGAYT 69 (90)
T ss_dssp S-BEESSSSSSE-----EEEE----------------ETTEEEETTTTEEEE-BSSS
T ss_pred CCCcCCCCCCce-----eEEe----------------eeEEeecCCCCCEEeCCCcc
Confidence 579999999762 2111 23349999999999865553
No 123
>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=55.64 E-value=6.3 Score=22.21 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=8.5
Q ss_pred eechhhhhhccCccch
Q 021090 209 YRCEKCKKAFRSYHAL 224 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L 224 (317)
-.|..|++.|.....+
T Consensus 4 ~~C~eC~~~f~dSyL~ 19 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLL 19 (34)
T ss_dssp EE-TTT--EES-SSCC
T ss_pred chHhHhCCHHHHHHHH
Confidence 4688888888877644
No 124
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=54.81 E-value=6.7 Score=35.82 Aligned_cols=41 Identities=24% Similarity=0.481 Sum_probs=29.4
Q ss_pred hccCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCcccccc
Q 021090 203 KLTRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVF 257 (317)
Q Consensus 203 ~~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F 257 (317)
.+...-|.|..|.+.|..-..|..--. ..-.|.|..|+--.
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L~~~--------------~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQLLDN--------------ETGEFHCENCGGEL 163 (436)
T ss_pred ccccccccCCccccchhhhHHHHhhcc--------------cCceEEEecCCCch
Confidence 345567999999999988777653321 34569999998533
No 125
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=53.84 E-value=2.1 Score=37.66 Aligned_cols=81 Identities=15% Similarity=0.095 Sum_probs=51.3
Q ss_pred CCCCCc--ccCcCCCccccccccccccCCCCCCCCCCCCCCCCCCCC---CC------CCCCCCCCCCccccCCCCC---
Q 021090 3 KHKCKL--CTRSFSNGRALGGHMKAHLAAHPLPPKTNQQQQPSDSTE---SA------STSSSSSGEGVEVKGKSPE--- 68 (317)
Q Consensus 3 ~~~C~~--Cgk~F~~~~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~---~~------~~~~~l~~h~~~~~~~~~~--- 68 (317)
.|.|+. |...-..+..|+.|.++-++- + -|..|.. .| .++..|..|......+..|
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~--~--------~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGH 220 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF--V--------LCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGH 220 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc--E--------EhHhhhcCcccCccceeeeecccccccccCCccccCcCCC
Confidence 467774 777777788899998853321 2 4444432 22 2455666665554444333
Q ss_pred -ccCcCCCCCCCCCCccccccccCCc
Q 021090 69 -VAEEKSLGYGLRNNPKKSFRFADPE 93 (317)
Q Consensus 69 -~C~~c~~~f~~~~~l~~H~~~~~~~ 93 (317)
.|..|..-|..-..|.+|+|..|..
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~HE~ 246 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRHEA 246 (493)
T ss_pred chhhhccceecChHHHHHHHHhhhhh
Confidence 5788888888888888888866643
No 126
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=52.89 E-value=5.3 Score=25.21 Aligned_cols=31 Identities=16% Similarity=0.379 Sum_probs=20.9
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccC
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFG 258 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~ 258 (317)
+.|..||..+.-..... |+ ...|+.||..|.
T Consensus 3 ~~CP~CG~~iev~~~~~------------------Ge-iV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPEL------------------GE-LVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCcc------------------CC-EEeCCCCCCEEE
Confidence 67899998775543221 34 468999987764
No 127
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=52.72 E-value=5.4 Score=37.96 Aligned_cols=28 Identities=25% Similarity=0.460 Sum_probs=24.8
Q ss_pred CCCCCCcccCcCCCccccccccccccCC
Q 021090 2 EKHKCKLCTRSFSNGRALGGHMKAHLAA 29 (317)
Q Consensus 2 k~~~C~~Cgk~F~~~~~L~~H~r~H~~e 29 (317)
++..|..||.+|........||-+|...
T Consensus 417 ~pnqC~~CG~R~~~~ee~sk~md~H~dw 444 (579)
T KOG2071|consen 417 SPNQCKSCGLRFDDSEERSKHMDIHDDW 444 (579)
T ss_pred CcchhcccccccccchhhhhHhhhhhhh
Confidence 4678999999999999999999999853
No 128
>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=52.21 E-value=3.6 Score=23.87 Aligned_cols=24 Identities=17% Similarity=0.456 Sum_probs=9.3
Q ss_pred CCCCCCCcccCcCCCcc--ccccccc
Q 021090 1 MEKHKCKLCTRSFSNGR--ALGGHMK 24 (317)
Q Consensus 1 ~k~~~C~~Cgk~F~~~~--~L~~H~r 24 (317)
|++|=|++|..-|..-+ .-+.|.+
T Consensus 1 m~ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp --S-B-TTT--B-S--SHHHHHHHT-
T ss_pred CcCeecccccceecCCChHHHHHhhc
Confidence 68899999999994433 2255554
No 129
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=52.10 E-value=4.8 Score=25.48 Aligned_cols=12 Identities=25% Similarity=0.764 Sum_probs=4.6
Q ss_pred CCCCCCCcccCc
Q 021090 1 MEKHKCKLCTRS 12 (317)
Q Consensus 1 ~k~~~C~~Cgk~ 12 (317)
||.|.|++||-.
T Consensus 31 Lr~y~Cp~CgAt 42 (55)
T PF05741_consen 31 LRKYVCPICGAT 42 (55)
T ss_dssp GGG---TTT---
T ss_pred HhcCcCCCCcCc
Confidence 577888888865
No 130
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=51.88 E-value=7.5 Score=22.65 Aligned_cols=16 Identities=25% Similarity=0.617 Sum_probs=13.2
Q ss_pred CCCCCcccCcCCCccc
Q 021090 3 KHKCKLCTRSFSNGRA 18 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~ 18 (317)
||+|..|++.|-....
T Consensus 12 ~f~C~~C~~~FC~~HR 27 (39)
T smart00154 12 GFKCRHCGNLFCGEHR 27 (39)
T ss_pred CeECCccCCccccccC
Confidence 7899999999987543
No 131
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=50.51 E-value=5 Score=28.62 Aligned_cols=40 Identities=15% Similarity=0.247 Sum_probs=27.4
Q ss_pred cCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCC
Q 021090 205 TRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGS 259 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~ 259 (317)
-++.|.|..||..-...-.++.-. +.-...|..||.+|.-
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~---------------~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTV---------------NIGTAVCGNCGLSFEC 58 (104)
T ss_pred CCceEecCccCCeeeeEEEEEecC---------------ceeEEEcccCcceEEE
Confidence 457799999998766655544332 3335789999988853
No 132
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=50.04 E-value=20 Score=31.83 Aligned_cols=75 Identities=20% Similarity=0.210 Sum_probs=49.7
Q ss_pred CCCCCCc--ccCcCCCcccccccccc-ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCC
Q 021090 2 EKHKCKL--CTRSFSNGRALGGHMKA-HLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYG 78 (317)
Q Consensus 2 k~~~C~~--Cgk~F~~~~~L~~H~r~-H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~ 78 (317)
++|+|++ |.|.+.....|+.|..+ |..- . ....+ .-.-|.......++|+|++|.+.+.
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~--i-------------~~~s~---~~~ph~~~~~~nk~~r~~i~~~~~k 409 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSP--I-------------TTPTP---APIPHQGFVVENKPYRCEVCSKRYK 409 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCC--C-------------CCCCC---CCCCcceeeeccCcccChhhhhhhc
Confidence 6788875 99999999999988773 4311 1 00000 1122333455678999999999999
Q ss_pred CCCCccccccccCCcc
Q 021090 79 LRNNPKKSFRFADPEF 94 (317)
Q Consensus 79 ~~~~l~~H~~~~~~~~ 94 (317)
.-..|+-|.-..+..+
T Consensus 410 ~~~~l~~~~~~~~~~~ 425 (442)
T KOG4124|consen 410 NLNGLKYHRTHSHLQV 425 (442)
T ss_pred cCCCCCceeehhhhhh
Confidence 8888888765555433
No 133
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=49.44 E-value=7.7 Score=29.78 Aligned_cols=45 Identities=13% Similarity=0.329 Sum_probs=25.7
Q ss_pred cCcceechhhhhhccCc---cchh--hhhhhhhcccccccccccCCccccCCccccc
Q 021090 205 TRGKYRCEKCKKAFRSY---HALG--GHKKVCETNINAGTKVAADEKIFECPFCYKV 256 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~---~~L~--~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~ 256 (317)
....+.|..||..|... ..|. .+.-+|- ---+...-+.|+.||..
T Consensus 67 ~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 67 EEAVLKCRNCGNEWSLKEVKESLDEEIREAIHF-------IPEVVHAFLKCPKCGSR 116 (135)
T ss_pred cceEEECCCCCCEEecccccccccccccccccc-------cccccccCcCCcCCCCC
Confidence 34679999999988775 2221 1111221 11112455889999954
No 134
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=49.15 E-value=6.8 Score=23.16 Aligned_cols=16 Identities=25% Similarity=0.671 Sum_probs=12.2
Q ss_pred CCCCcccCcCCCcccc
Q 021090 4 HKCKLCTRSFSNGRAL 19 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L 19 (317)
-.|.+||+-|.+....
T Consensus 9 K~C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKW 24 (42)
T ss_pred CcCcccCCcchHHHHH
Confidence 3599999999876543
No 135
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=49.11 E-value=12 Score=23.61 Aligned_cols=15 Identities=33% Similarity=0.957 Sum_probs=11.1
Q ss_pred CCCCcccCcCCCccc
Q 021090 4 HKCKLCTRSFSNGRA 18 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~ 18 (317)
-+|+.||+.|.....
T Consensus 6 ~~C~~Cg~~~~~~dD 20 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDD 20 (54)
T ss_pred ccChhhCCcccCCCC
Confidence 469999999975443
No 136
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=48.76 E-value=6.2 Score=31.87 Aligned_cols=12 Identities=0% Similarity=-0.421 Sum_probs=7.1
Q ss_pred CCccCcCCCCCC
Q 021090 67 PEVAEEKSLGYG 78 (317)
Q Consensus 67 ~~~C~~c~~~f~ 78 (317)
.|.|+.|+....
T Consensus 136 ~F~Cp~Cg~~L~ 147 (178)
T PRK06266 136 GFRCPQCGEMLE 147 (178)
T ss_pred CCcCCCCCCCCe
Confidence 456666665553
No 137
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=48.67 E-value=1.4 Score=36.60 Aligned_cols=26 Identities=23% Similarity=0.496 Sum_probs=20.6
Q ss_pred CCCCCcccCcCCCccccccccccccC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLA 28 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~ 28 (317)
+|.|+.|+|.|.-..-...|+..-+.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 68999999999999999999995443
No 138
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=48.16 E-value=7.7 Score=27.74 Aligned_cols=16 Identities=31% Similarity=0.879 Sum_probs=13.1
Q ss_pred CCCCCcccCcCCCccc
Q 021090 3 KHKCKLCTRSFSNGRA 18 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~ 18 (317)
||.|..||..|...+.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 7899999999987543
No 139
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=47.30 E-value=3.1 Score=36.66 Aligned_cols=19 Identities=26% Similarity=0.625 Sum_probs=13.5
Q ss_pred CCcccCcCCCccccccccc
Q 021090 6 CKLCTRSFSNGRALGGHMK 24 (317)
Q Consensus 6 C~~Cgk~F~~~~~L~~H~r 24 (317)
|..|.+.|-.-..|.+|+|
T Consensus 223 C~FC~~~FYdDDEL~~HcR 241 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCR 241 (493)
T ss_pred hhhccceecChHHHHHHHH
Confidence 6667777777777777777
No 140
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=47.03 E-value=5.9 Score=21.21 Aligned_cols=19 Identities=37% Similarity=0.754 Sum_probs=9.8
Q ss_pred ccCCccccccCCcccccchh
Q 021090 248 FECPFCYKVFGSGQALGGHK 267 (317)
Q Consensus 248 f~C~~C~k~F~~~~~L~~H~ 267 (317)
|.|-.|++.| .....+.|-
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 4566777777 334444443
No 141
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=45.84 E-value=6.9 Score=23.29 Aligned_cols=17 Identities=29% Similarity=0.518 Sum_probs=11.1
Q ss_pred ccccCCccccccCCccc
Q 021090 246 KIFECPFCYKVFGSGQA 262 (317)
Q Consensus 246 kpf~C~~C~k~F~~~~~ 262 (317)
-||.|+.|++.|=.+..
T Consensus 12 ~~~~C~~C~~~FC~~Hr 28 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHR 28 (43)
T ss_dssp SHEE-TTTS-EE-TTTH
T ss_pred CCeECCCCCcccCcccc
Confidence 58999999999977544
No 142
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=45.66 E-value=6.9 Score=33.01 Aligned_cols=28 Identities=14% Similarity=0.265 Sum_probs=0.0
Q ss_pred CCCCcccCcCCCccccccccccccCCCCC
Q 021090 4 HKCKLCTRSFSNGRALGGHMKAHLAAHPL 32 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~ 32 (317)
..|++||+..+- +.|..|||+.+....|
T Consensus 169 ~~cPitGe~IP~-~e~~eHmRi~LlDP~w 196 (229)
T PF12230_consen 169 IICPITGEMIPA-DEMDEHMRIELLDPRW 196 (229)
T ss_dssp -----------------------------
T ss_pred cccccccccccc-cccccccccccccccc
Confidence 579999999886 8999999999987777
No 143
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=45.39 E-value=84 Score=28.97 Aligned_cols=62 Identities=8% Similarity=-0.276 Sum_probs=30.3
Q ss_pred hhhhccCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccccchhhhccC
Q 021090 200 EEIKLTRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALGGHKRSHLL 272 (317)
Q Consensus 200 ~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~~~H~~ 272 (317)
...++....+.+.++.+.+.....+..|...+. ++.++.+..+...+.....+..+..+|..
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 384 (396)
T KOG2461|consen 323 EVPATVSVWTGETIPVRTPAGQLIYTQSHSMEV-----------AEPTDMAPNQIWKIYHTGVLGFLIITTDE 384 (396)
T ss_pred cccccccccCcCcccccccccccchhhhhhccc-----------CCCCcccccccccceeccccceeeeeccc
Confidence 333444455556666666666666666654443 44444444444444444444344444433
No 144
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=44.29 E-value=14 Score=21.03 Aligned_cols=16 Identities=19% Similarity=0.432 Sum_probs=10.0
Q ss_pred CCCCcccCcCCCcccc
Q 021090 4 HKCKLCTRSFSNGRAL 19 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L 19 (317)
=.|+.|+|.|-+.++-
T Consensus 3 ~~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 3 GLCPRCGKGFHWASEC 18 (36)
T ss_dssp -C-TTTSSSCS-TTT-
T ss_pred ccCcccCCCcchhhhh
Confidence 4699999999887653
No 145
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=44.19 E-value=8.3 Score=23.76 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=13.4
Q ss_pred CccccCCccccccCCcc
Q 021090 245 EKIFECPFCYKVFGSGQ 261 (317)
Q Consensus 245 ekpf~C~~C~k~F~~~~ 261 (317)
.+++.|..||..|....
T Consensus 2 Dk~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTA 18 (49)
T ss_pred CeeEEcccCCCeEEEeh
Confidence 56789999999887544
No 146
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.52 E-value=6.8 Score=26.36 Aligned_cols=33 Identities=21% Similarity=0.546 Sum_probs=22.2
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccC
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFG 258 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~ 258 (317)
.|.|..||..|. +..||. ..---.|+.|+..|.
T Consensus 12 ~Y~c~~cg~~~d----vvq~~~--------------ddplt~ce~c~a~~k 44 (82)
T COG2331 12 SYECTECGNRFD----VVQAMT--------------DDPLTTCEECGARLK 44 (82)
T ss_pred EEeecccchHHH----HHHhcc--------------cCccccChhhChHHH
Confidence 499999998763 455552 232357999987654
No 147
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=42.31 E-value=12 Score=34.29 Aligned_cols=35 Identities=17% Similarity=0.252 Sum_probs=26.5
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccc
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQAL 263 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L 263 (317)
..-.|..||.+..++. ..-|+|+.||+.+......
T Consensus 349 ~~p~Cp~Cg~~m~S~G----------------------~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 349 VNPVCPRCGGRMKSAG----------------------RNGFRCKKCGTRARETLIK 383 (421)
T ss_pred cCCCCCccCCchhhcC----------------------CCCcccccccccCCccccc
Confidence 3448999998755443 4489999999999887665
No 148
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=41.99 E-value=14 Score=22.71 Aligned_cols=16 Identities=25% Similarity=0.162 Sum_probs=12.6
Q ss_pred cccCCccccccCCccc
Q 021090 247 IFECPFCYKVFGSGQA 262 (317)
Q Consensus 247 pf~C~~C~k~F~~~~~ 262 (317)
.|.|+.||..+.-...
T Consensus 20 ~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 20 RFVCRKCGYEEPIEQK 35 (52)
T ss_pred EEECCcCCCeEECCCc
Confidence 6899999988776554
No 149
>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=40.57 E-value=8.1 Score=24.06 Aligned_cols=24 Identities=25% Similarity=0.427 Sum_probs=9.0
Q ss_pred cccCCccccccCCcccccchhhhc
Q 021090 247 IFECPFCYKVFGSGQALGGHKRSH 270 (317)
Q Consensus 247 pf~C~~C~k~F~~~~~L~~H~~~H 270 (317)
.|+|+.|+..|=..-.+-.|...|
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-
T ss_pred eEECCCCCCccccCcChhhhcccc
Confidence 455555555555444444444444
No 150
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=39.09 E-value=24 Score=24.74 Aligned_cols=25 Identities=8% Similarity=-0.049 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCC
Q 021090 41 QPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSL 75 (317)
Q Consensus 41 ~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~ 75 (317)
.|..||+.|..-.- ..|-+|+.|-.
T Consensus 60 ~CkkCGfef~~~~i----------k~pSRCP~CKS 84 (97)
T COG3357 60 RCKKCGFEFRDDKI----------KKPSRCPKCKS 84 (97)
T ss_pred hhcccCcccccccc----------CCcccCCcchh
Confidence 78888888875222 34668888854
No 151
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=38.91 E-value=12 Score=28.99 Aligned_cols=38 Identities=26% Similarity=0.615 Sum_probs=25.2
Q ss_pred cCcceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccC
Q 021090 205 TRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFG 258 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~ 258 (317)
..-+|.|. |+..|.+.- +|- .+-.|+ -|.|..|+-...
T Consensus 114 ~~~~Y~C~-C~q~~l~~R---Rhn-----------~~~~g~-~YrC~~C~gkL~ 151 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRIR---RHN-----------TVRRGE-VYRCGKCGGKLV 151 (156)
T ss_pred cceeEEee-cCCccchhh---hcc-----------cccccc-eEEeccCCceEE
Confidence 34579999 998865433 222 334477 899999986543
No 152
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=38.87 E-value=16 Score=27.01 Aligned_cols=17 Identities=12% Similarity=0.292 Sum_probs=12.6
Q ss_pred cCcceechhhhhhccCc
Q 021090 205 TRGKYRCEKCKKAFRSY 221 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~ 221 (317)
-.....|..||..|...
T Consensus 67 vp~~~~C~~Cg~~~~~~ 83 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIH 83 (113)
T ss_pred eCcEEEcccCCCEEecC
Confidence 45679999999776543
No 153
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=38.64 E-value=12 Score=23.76 Aligned_cols=39 Identities=15% Similarity=0.280 Sum_probs=23.1
Q ss_pred eechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCcccccc
Q 021090 209 YRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVF 257 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F 257 (317)
-+|.+|++.+.-......-.+.-. ---..|.|+.|.-.-
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrn----------rPi~tYmC~eC~~RI 41 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRN----------RPIHTYMCDECKERI 41 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhc----------CCCcceeChhHHHHH
Confidence 479999998876654433322110 012359999996543
No 154
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=38.50 E-value=14 Score=26.49 Aligned_cols=19 Identities=32% Similarity=0.464 Sum_probs=14.6
Q ss_pred cccCCccccCCccccccCCc
Q 021090 241 VAADEKIFECPFCYKVFGSG 260 (317)
Q Consensus 241 ~h~~ekpf~C~~C~k~F~~~ 260 (317)
++.| +|++|+.||.-|...
T Consensus 74 l~~g-~~~rC~eCG~~fkL~ 92 (97)
T cd00924 74 LEKG-KPKRCPECGHVFKLV 92 (97)
T ss_pred EeCC-CceeCCCCCcEEEEE
Confidence 3446 799999999988753
No 155
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=38.24 E-value=12 Score=22.00 Aligned_cols=12 Identities=25% Similarity=0.816 Sum_probs=9.1
Q ss_pred ccccCCcccccc
Q 021090 246 KIFECPFCYKVF 257 (317)
Q Consensus 246 kpf~C~~C~k~F 257 (317)
++-.|++||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 467888888776
No 156
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=37.39 E-value=18 Score=26.86 Aligned_cols=16 Identities=19% Similarity=0.528 Sum_probs=11.9
Q ss_pred cCcceechhhhhhccC
Q 021090 205 TRGKYRCEKCKKAFRS 220 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~ 220 (317)
......|..||..|..
T Consensus 67 ~p~~~~C~~Cg~~~~~ 82 (114)
T PRK03681 67 QEAECWCETCQQYVTL 82 (114)
T ss_pred eCcEEEcccCCCeeec
Confidence 4567999999976543
No 157
>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=36.96 E-value=15 Score=24.16 Aligned_cols=31 Identities=26% Similarity=0.423 Sum_probs=13.8
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQ 261 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~ 261 (317)
.-.|..|++.|.. -.+.+.|..||..|-..-
T Consensus 9 ~~~C~~C~~~F~~-----------------------~~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 9 ASNCMICGKKFSL-----------------------FRRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp -SB-TTT--B-BS-----------------------SS-EEE-TTT--EEECCC
T ss_pred CCcCcCcCCcCCC-----------------------ceeeEccCCCCCEECCch
Confidence 3469999999942 133466888888776443
No 158
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=36.80 E-value=14 Score=33.87 Aligned_cols=52 Identities=13% Similarity=0.186 Sum_probs=36.9
Q ss_pred ccCCccccCCccc-cccCCcccccchhh--hccCcccchhhhhhhcccCCccchh
Q 021090 242 AADEKIFECPFCY-KVFGSGQALGGHKR--SHLLANSSSTAAAAAVVATDPAVKF 293 (317)
Q Consensus 242 h~~ekpf~C~~C~-k~F~~~~~L~~H~~--~H~~~~~~~~a~~~~~~~~~~~~~~ 293 (317)
|--.+-|.|++|| +++.-...+.+|.. .|.-+-.=.++...+.++..+....
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrCLGIpnt~~F~~IT~I~e 450 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRCLGIPNTSVFKGITKIEE 450 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhHHHHHhhcceecCCCCcHHhcccccHHH
Confidence 3346779999999 88888888888863 6766665566666666666665543
No 159
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=36.75 E-value=12 Score=23.40 Aligned_cols=12 Identities=25% Similarity=0.778 Sum_probs=5.9
Q ss_pred cCCccccccCCc
Q 021090 249 ECPFCYKVFGSG 260 (317)
Q Consensus 249 ~C~~C~k~F~~~ 260 (317)
.||+|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 788888888753
No 160
>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=36.70 E-value=12 Score=31.18 Aligned_cols=28 Identities=25% Similarity=0.413 Sum_probs=21.7
Q ss_pred cCcceechhhhhhccCccchhhhhhhhh
Q 021090 205 TRGKYRCEKCKKAFRSYHALGGHKKVCE 232 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~ 232 (317)
.+..|.|..|+|.|+-..-...|+..-+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 5667999999999999999999988643
No 161
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=36.49 E-value=15 Score=27.23 Aligned_cols=26 Identities=31% Similarity=0.571 Sum_probs=23.8
Q ss_pred cCcceechhhhhhccCccchhhhhhh
Q 021090 205 TRGKYRCEKCKKAFRSYHALGGHKKV 230 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L~~H~~~ 230 (317)
|-+.|.|-.|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 67889999999999999999999874
No 162
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.47 E-value=20 Score=26.70 Aligned_cols=41 Identities=10% Similarity=-0.082 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCcc-ccCCCCCccCcCCCCCCCC
Q 021090 40 QQPSDSTESASTSSSSSGEGVE-VKGKSPEVAEEKSLGYGLR 80 (317)
Q Consensus 40 ~~c~~c~~~~~~~~~l~~h~~~-~~~~~~~~C~~c~~~f~~~ 80 (317)
.+|+.|+.+-+-..-..+-... +.=+.|--|.+|++.|.+-
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpwt 81 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWT 81 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcH
Confidence 3788887765543332222222 2223455699999999764
No 163
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=36.07 E-value=34 Score=34.15 Aligned_cols=45 Identities=16% Similarity=0.070 Sum_probs=30.4
Q ss_pred CCCcccCcCCCc---cccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCC
Q 021090 5 KCKLCTRSFSNG---RALGGHMKAHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLG 76 (317)
Q Consensus 5 ~C~~Cgk~F~~~---~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~ 76 (317)
.|..||..|..+ ..|.-|+..+. . .|..|+.. ...+..|+.|+..
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt~H~~~~~----L--------~CH~Cg~~---------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLTLHKATGQ----L--------RCHYCGYQ---------------EPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCCCcceEEecCCCe----e--------EeCCCCCC---------------CCCCCCCCCCCCC
Confidence 377777777554 45777776643 3 78888765 2457789999854
No 164
>PRK12496 hypothetical protein; Provisional
Probab=35.60 E-value=19 Score=28.63 Aligned_cols=13 Identities=31% Similarity=0.823 Sum_probs=10.5
Q ss_pred ceechhhhhhccC
Q 021090 208 KYRCEKCKKAFRS 220 (317)
Q Consensus 208 ~~~C~~C~k~f~~ 220 (317)
.|.|.-||+.|..
T Consensus 127 ~~~C~gC~~~~~~ 139 (164)
T PRK12496 127 RKVCKGCKKKYPE 139 (164)
T ss_pred eEECCCCCccccC
Confidence 3889999988854
No 165
>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=35.41 E-value=12 Score=27.66 Aligned_cols=18 Identities=22% Similarity=0.623 Sum_probs=11.5
Q ss_pred cCcceechhhhhhccCcc
Q 021090 205 TRGKYRCEKCKKAFRSYH 222 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~ 222 (317)
......|..||+.|....
T Consensus 67 ~p~~~~C~~Cg~~~~~~~ 84 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDE 84 (113)
T ss_dssp E--EEEETTTS-EEECHH
T ss_pred cCCcEECCCCCCEEecCC
Confidence 345699999999886543
No 166
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=35.06 E-value=19 Score=25.90 Aligned_cols=12 Identities=8% Similarity=-0.056 Sum_probs=6.3
Q ss_pred ccCcCCCCCCCC
Q 021090 69 VAEEKSLGYGLR 80 (317)
Q Consensus 69 ~C~~c~~~f~~~ 80 (317)
.|+.|+..|...
T Consensus 44 ~C~~CG~y~~~~ 55 (99)
T PRK14892 44 TCGNCGLYTEFE 55 (99)
T ss_pred ECCCCCCccCEE
Confidence 455565555443
No 167
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=34.74 E-value=19 Score=27.34 Aligned_cols=14 Identities=36% Similarity=0.857 Sum_probs=9.7
Q ss_pred CCCCCCcccCcCCC
Q 021090 2 EKHKCKLCTRSFSN 15 (317)
Q Consensus 2 k~~~C~~Cgk~F~~ 15 (317)
.+|+|+.|++.|..
T Consensus 52 qRyrC~~C~~tf~~ 65 (129)
T COG3677 52 QRYKCKSCGSTFTV 65 (129)
T ss_pred cccccCCcCcceee
Confidence 45777777777764
No 168
>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=34.64 E-value=14 Score=27.10 Aligned_cols=25 Identities=28% Similarity=0.480 Sum_probs=22.4
Q ss_pred ceec----hhhhhhccCccchhhhhhhhh
Q 021090 208 KYRC----EKCKKAFRSYHALGGHKKVCE 232 (317)
Q Consensus 208 ~~~C----~~C~k~f~~~~~L~~H~~~H~ 232 (317)
-|.| ..|+..+.+...|.+|.+.++
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 3899 999999999999999998764
No 169
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=34.54 E-value=12 Score=27.69 Aligned_cols=26 Identities=27% Similarity=0.419 Sum_probs=22.5
Q ss_pred CCccccCCccccccCCcccccchhhh
Q 021090 244 DEKIFECPFCYKVFGSGQALGGHKRS 269 (317)
Q Consensus 244 ~ekpf~C~~C~k~F~~~~~L~~H~~~ 269 (317)
|--.|-|-.|.+-|.....|+.|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 34459999999999999999999874
No 170
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=34.51 E-value=11 Score=34.91 Aligned_cols=22 Identities=27% Similarity=0.658 Sum_probs=20.1
Q ss_pred CCCCcccCcCCCcccccccccc
Q 021090 4 HKCKLCTRSFSNGRALGGHMKA 25 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r~ 25 (317)
+-|.+|.|.|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 5699999999999999999874
No 171
>PRK01343 zinc-binding protein; Provisional
Probab=34.17 E-value=28 Score=22.20 Aligned_cols=13 Identities=15% Similarity=0.531 Sum_probs=10.0
Q ss_pred CCCCCcccCcCCC
Q 021090 3 KHKCKLCTRSFSN 15 (317)
Q Consensus 3 ~~~C~~Cgk~F~~ 15 (317)
...|++|+|.|.+
T Consensus 9 ~~~CP~C~k~~~~ 21 (57)
T PRK01343 9 TRPCPECGKPSTR 21 (57)
T ss_pred CCcCCCCCCcCcC
Confidence 3579999998863
No 172
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=33.77 E-value=21 Score=25.30 Aligned_cols=40 Identities=25% Similarity=0.504 Sum_probs=16.8
Q ss_pred cCcceechhhhhhccCccchhhhhhhhhcccccccccccCCcc-ccCCccccccCCcc
Q 021090 205 TRGKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKI-FECPFCYKVFGSGQ 261 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekp-f~C~~C~k~F~~~~ 261 (317)
+.+.-.|.+||+++.-.. ..+- |+|. |-|.+|-+-|..--
T Consensus 11 g~ke~~CalCG~tWg~~y-----~Ev~------------G~rLfFCCd~ca~EF~nmi 51 (105)
T PF11494_consen 11 GTKEMGCALCGATWGDYY-----EEVD------------GERLFFCCDDCAKEFKNMI 51 (105)
T ss_dssp -SGGGS-SS---S---SS------B-T------------T--BSSS--SSSS-TTS-T
T ss_pred ccccccccccCCcHHHHH-----Hhhc------------CCEEEEEcHHHHHHHHHHH
Confidence 556678999999987433 2221 5664 78899999998743
No 173
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=33.76 E-value=18 Score=31.49 Aligned_cols=82 Identities=9% Similarity=0.026 Sum_probs=47.7
Q ss_pred CCCCCcccCcCCCccccccccccccCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLAAHPLPPKTN----QQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYG 78 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~~~~~~----~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~ 78 (317)
|..|+.|.-.......|.+-.+.=...|+|...+. ....|..|...|+......... -.....|.|+.|...|.
T Consensus 322 Pi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~~~~~--~~ss~rY~Ce~CK~~FC 399 (421)
T COG5151 322 PISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVSPFDE--STSSGRYQCELCKSTFC 399 (421)
T ss_pred CccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCCcccc--cccccceechhhhhhhh
Confidence 45577776666555555544333334556554333 2345888988887543322111 12245799999999987
Q ss_pred CCCCcccc
Q 021090 79 LRNNPKKS 86 (317)
Q Consensus 79 ~~~~l~~H 86 (317)
.--+.-.|
T Consensus 400 ~dCdvfiH 407 (421)
T COG5151 400 SDCDVFIH 407 (421)
T ss_pred hhhHHHHH
Confidence 66555445
No 174
>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=32.61 E-value=22 Score=26.43 Aligned_cols=17 Identities=18% Similarity=0.448 Sum_probs=12.8
Q ss_pred cCcceechhhhhhccCc
Q 021090 205 TRGKYRCEKCKKAFRSY 221 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~ 221 (317)
......|..||+.|...
T Consensus 67 ~p~~~~C~~Cg~~~~~~ 83 (115)
T TIGR00100 67 EPVECECEDCSEEVSPE 83 (115)
T ss_pred eCcEEEcccCCCEEecC
Confidence 45569999999777654
No 175
>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=32.57 E-value=19 Score=22.27 Aligned_cols=12 Identities=25% Similarity=0.877 Sum_probs=7.6
Q ss_pred CCCCCcccCcCC
Q 021090 3 KHKCKLCTRSFS 14 (317)
Q Consensus 3 ~~~C~~Cgk~F~ 14 (317)
.|.|.+||..+.
T Consensus 1 ~y~C~~CgyiYd 12 (50)
T cd00730 1 KYECRICGYIYD 12 (50)
T ss_pred CcCCCCCCeEEC
Confidence 366777776655
No 176
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.34 E-value=27 Score=26.05 Aligned_cols=17 Identities=18% Similarity=0.688 Sum_probs=12.9
Q ss_pred cCcceechhhhhhccCc
Q 021090 205 TRGKYRCEKCKKAFRSY 221 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~ 221 (317)
....+.|..||..|...
T Consensus 68 vp~~~~C~~Cg~~~~~~ 84 (117)
T PRK00564 68 EKVELECKDCSHVFKPN 84 (117)
T ss_pred cCCEEEhhhCCCccccC
Confidence 45679999999777554
No 177
>PRK04023 DNA polymerase II large subunit; Validated
Probab=32.16 E-value=41 Score=34.60 Aligned_cols=17 Identities=18% Similarity=0.409 Sum_probs=12.2
Q ss_pred ccccCCccccccCCccc
Q 021090 246 KIFECPFCYKVFGSGQA 262 (317)
Q Consensus 246 kpf~C~~C~k~F~~~~~ 262 (317)
.-|.|..||..|++.-.
T Consensus 1036 Q~fRC~kC~~kYRR~PL 1052 (1121)
T PRK04023 1036 QEFRCTKCGAKYRRPPL 1052 (1121)
T ss_pred cceeecccCcccccCCC
Confidence 35888888888876543
No 178
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=32.03 E-value=18 Score=21.45 Aligned_cols=17 Identities=29% Similarity=0.645 Sum_probs=7.2
Q ss_pred CCcccCcCCCccccccc
Q 021090 6 CKLCTRSFSNGRALGGH 22 (317)
Q Consensus 6 C~~Cgk~F~~~~~L~~H 22 (317)
|.+||+.|.....|..|
T Consensus 1 C~~C~~~~~~~~~~~v~ 17 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVH 17 (47)
T ss_dssp -TTT--B--GG-GEEEE
T ss_pred CCCCCCcCccCcceEeE
Confidence 78888888877444444
No 179
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.92 E-value=15 Score=25.93 Aligned_cols=14 Identities=21% Similarity=0.688 Sum_probs=9.7
Q ss_pred CCCCCCCcccCcCC
Q 021090 1 MEKHKCKLCTRSFS 14 (317)
Q Consensus 1 ~k~~~C~~Cgk~F~ 14 (317)
|+.|+|.+||..-.
T Consensus 4 lkewkC~VCg~~ii 17 (103)
T COG4847 4 LKEWKCYVCGGTII 17 (103)
T ss_pred cceeeEeeeCCEee
Confidence 56778888876544
No 180
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=30.92 E-value=17 Score=24.91 Aligned_cols=36 Identities=31% Similarity=0.557 Sum_probs=24.6
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCcccc
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQAL 263 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L 263 (317)
..|.|++|||.-..+. .---+.|.-|.+.|.-..++
T Consensus 35 aky~CsfCGK~~vKR~---------------------AvGiW~C~~C~kv~agga~~ 70 (92)
T KOG0402|consen 35 AKYTCSFCGKKTVKRK---------------------AVGIWKCGSCKKVVAGGAYT 70 (92)
T ss_pred hhhhhhhcchhhhhhh---------------------ceeEEecCCccceeccceEE
Confidence 4689999998632222 23358899999988765554
No 181
>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=30.38 E-value=36 Score=26.57 Aligned_cols=52 Identities=17% Similarity=0.312 Sum_probs=23.1
Q ss_pred cCcceechhhhhhccCccch--hhhhhhhh-----cccccccccccCCccccCCccccc
Q 021090 205 TRGKYRCEKCKKAFRSYHAL--GGHKKVCE-----TNINAGTKVAADEKIFECPFCYKV 256 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~~L--~~H~~~H~-----~~~~~H~~~h~~ekpf~C~~C~k~ 256 (317)
..--.+|..|+|-|-....- ..|+-.|. .+...|.....|+..++|-.||-+
T Consensus 11 p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~ 69 (152)
T PF09416_consen 11 PSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSR 69 (152)
T ss_dssp CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT---
T ss_pred cccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCC
Confidence 44567899999988654322 34544442 222334344456778999999864
No 182
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=30.24 E-value=37 Score=30.19 Aligned_cols=71 Identities=18% Similarity=0.272 Sum_probs=41.1
Q ss_pred Ccceech------hhhhhccCccchhhhhhhhhccc----------c-cccccccCCccccCCccccccCCcccccchhh
Q 021090 206 RGKYRCE------KCKKAFRSYHALGGHKKVCETNI----------N-AGTKVAADEKIFECPFCYKVFGSGQALGGHKR 268 (317)
Q Consensus 206 ~~~~~C~------~C~k~f~~~~~L~~H~~~H~~~~----------~-~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~~ 268 (317)
-+.|+|- +|-..|.+...-..|-.-|-... . .-.--|-...-|.|++|++.=-+...|..|..
T Consensus 21 ~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil~~~dfeL~f~Ge~i~~y~~qSftCPyC~~~Gfte~~f~~Hv~ 100 (381)
T KOG1280|consen 21 FRRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCILSRVDFELYFGGEPISHYDPQSFTCPYCGIMGFTERQFGTHVL 100 (381)
T ss_pred eeeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEeeccceeeEecCccccccccccccCCcccccccchhHHHHHhh
Confidence 3567773 35666666666666654442211 0 00012224557999999987777778888876
Q ss_pred hccCcccc
Q 021090 269 SHLLANSS 276 (317)
Q Consensus 269 ~H~~~~~~ 276 (317)
.-+.+...
T Consensus 101 s~Hpda~~ 108 (381)
T KOG1280|consen 101 SQHPEAST 108 (381)
T ss_pred hcCcccCc
Confidence 55555443
No 183
>PLN02294 cytochrome c oxidase subunit Vb
Probab=30.20 E-value=19 Score=28.56 Aligned_cols=16 Identities=44% Similarity=0.910 Sum_probs=13.2
Q ss_pred CccccCCccccccCCc
Q 021090 245 EKIFECPFCYKVFGSG 260 (317)
Q Consensus 245 ekpf~C~~C~k~F~~~ 260 (317)
.+|+.|+.||.-|..+
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 4699999999988754
No 184
>PF04618 HD-ZIP_N: HD-ZIP protein N terminus; InterPro: IPR006712 Homeodomain leucine zipper (HDZip) genes encode putative transcription factors that are unique to plants. This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events []. This domain is the N-terminal of plant homeobox-leucine zipper proteins. Its function is unknown.; GO: 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=30.09 E-value=25 Score=25.92 Aligned_cols=21 Identities=33% Similarity=0.420 Sum_probs=14.8
Q ss_pred cchhhcc-CCCCC--CCCCccccc
Q 021090 295 NNLIDLN-LPAPL--EEDDFSVVS 315 (317)
Q Consensus 295 ~~~~~~~-~~~~~--~~~~~~~~~ 315 (317)
-|-||+| +|+.. |.+|+..||
T Consensus 70 lRgiDVNr~p~~~~~d~eEe~gvS 93 (111)
T PF04618_consen 70 LRGIDVNRLPSTVEADCEEEAGVS 93 (111)
T ss_pred ccceeccCCCcccccccccccccc
Confidence 4778999 55555 677777775
No 185
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=30.01 E-value=21 Score=21.52 Aligned_cols=11 Identities=27% Similarity=0.724 Sum_probs=8.7
Q ss_pred CccccCCcccc
Q 021090 245 EKIFECPFCYK 255 (317)
Q Consensus 245 ekpf~C~~C~k 255 (317)
...|+|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 46799999876
No 186
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.66 E-value=12 Score=22.72 Aligned_cols=13 Identities=38% Similarity=0.884 Sum_probs=10.3
Q ss_pred CCCcccCcCCCcc
Q 021090 5 KCKLCTRSFSNGR 17 (317)
Q Consensus 5 ~C~~Cgk~F~~~~ 17 (317)
.|++|++-|.+..
T Consensus 14 ICpvCqRPFsWRk 26 (54)
T COG4338 14 ICPVCQRPFSWRK 26 (54)
T ss_pred hhhhhcCchHHHH
Confidence 4899999888754
No 187
>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=29.38 E-value=12 Score=22.80 Aligned_cols=12 Identities=25% Similarity=0.788 Sum_probs=6.8
Q ss_pred CCCCCcccCcCC
Q 021090 3 KHKCKLCTRSFS 14 (317)
Q Consensus 3 ~~~C~~Cgk~F~ 14 (317)
+|.|.+||..+.
T Consensus 1 ky~C~~CgyvYd 12 (47)
T PF00301_consen 1 KYQCPVCGYVYD 12 (47)
T ss_dssp EEEETTTSBEEE
T ss_pred CcCCCCCCEEEc
Confidence 356666665544
No 188
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.31 E-value=51 Score=31.50 Aligned_cols=45 Identities=13% Similarity=0.116 Sum_probs=26.0
Q ss_pred CCCcccCcCCCc---cccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCC
Q 021090 5 KCKLCTRSFSNG---RALGGHMKAHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLG 76 (317)
Q Consensus 5 ~C~~Cgk~F~~~---~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~ 76 (317)
.|..||.....+ ..|.-|. ..... .|..|+.... -+..|+.|+..
T Consensus 215 ~C~~Cg~~~~C~~C~~~l~~h~----~~~~l--------~Ch~Cg~~~~---------------~~~~Cp~C~s~ 262 (505)
T TIGR00595 215 LCRSCGYILCCPNCDVSLTYHK----KEGKL--------RCHYCGYQEP---------------IPKTCPQCGSE 262 (505)
T ss_pred EhhhCcCccCCCCCCCceEEec----CCCeE--------EcCCCcCcCC---------------CCCCCCCCCCC
Confidence 466666665543 3344443 33344 7888876543 34578888763
No 189
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=29.04 E-value=16 Score=24.22 Aligned_cols=15 Identities=27% Similarity=0.507 Sum_probs=9.8
Q ss_pred CCccccCCccccccCC
Q 021090 244 DEKIFECPFCYKVFGS 259 (317)
Q Consensus 244 ~ekpf~C~~C~k~F~~ 259 (317)
+.+.-+| +||+...-
T Consensus 17 ~~kTkkC-~CG~~l~v 31 (68)
T PF09082_consen 17 GAKTKKC-VCGKTLKV 31 (68)
T ss_dssp T-SEEEE-TTTEEEE-
T ss_pred CcceeEe-cCCCeeee
Confidence 6677788 88886543
No 190
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=28.96 E-value=20 Score=33.25 Aligned_cols=22 Identities=32% Similarity=0.646 Sum_probs=20.6
Q ss_pred eechhhhhhccCccchhhhhhh
Q 021090 209 YRCEKCKKAFRSYHALGGHKKV 230 (317)
Q Consensus 209 ~~C~~C~k~f~~~~~L~~H~~~ 230 (317)
+-|.+|+|+|++...|..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8999999999999999999875
No 191
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=28.93 E-value=26 Score=21.91 Aligned_cols=10 Identities=20% Similarity=0.826 Sum_probs=5.7
Q ss_pred CCCcccCcCC
Q 021090 5 KCKLCTRSFS 14 (317)
Q Consensus 5 ~C~~Cgk~F~ 14 (317)
.|++||..|.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 4666665553
No 192
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=28.91 E-value=35 Score=19.34 Aligned_cols=31 Identities=19% Similarity=0.470 Sum_probs=17.0
Q ss_pred chhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccC
Q 021090 211 CEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFG 258 (317)
Q Consensus 211 C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~ 258 (317)
|..|.+.+....+-.-| -.+..|..||-.|.
T Consensus 2 C~~C~~Ey~~p~~RR~~-----------------~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFH-----------------YQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCSTTSTTTT------------------TT--BTTCC-SCC
T ss_pred CHHHHHHHcCCCCCccc-----------------CcCccCCCCCCCEE
Confidence 67777777666653333 23577888887664
No 193
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=28.88 E-value=18 Score=29.47 Aligned_cols=91 Identities=19% Similarity=0.205 Sum_probs=49.2
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCC---ccccCCccccccCCcccccch--hhhccCcccchhhhh
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADE---KIFECPFCYKVFGSGQALGGH--KRSHLLANSSSTAAA 281 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~e---kpf~C~~C~k~F~~~~~L~~H--~~~H~~~~~~~~a~~ 281 (317)
..-.|..||.. |..|+.... --|-|+ ..+.|.-||+.+.--..|..- +++-..-.++. -.
T Consensus 13 ~~~~CPvCg~~------l~~~~~~~~-------IPyFG~V~i~t~~C~~CgYR~~DV~~~e~~eP~r~~lkve~~e--dL 77 (201)
T COG1779 13 TRIDCPVCGGT------LKAHMYLYD-------IPYFGEVLISTGVCERCGYRSTDVKTLEEREPRRYTLKVESEE--DL 77 (201)
T ss_pred eeecCCcccce------eeEEEeeec-------CCccceEEEEEEEccccCCcccceeecccCCCeEEEEEeCCHH--Hh
Confidence 34679999984 444443321 111232 358899999999876666433 22222222222 22
Q ss_pred hhcccCCccchhccchhhcc-CCCCCCCCCcc
Q 021090 282 AAVVATDPAVKFENNLIDLN-LPAPLEEDDFS 312 (317)
Q Consensus 282 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 312 (317)
-+...+..+..+-+-.+.+. .|+|..+-.+|
T Consensus 78 ~~~V~RS~s~~I~IPELg~~iePG~~s~G~IT 109 (201)
T COG1779 78 SARVVRSKSATIYIPELGLEIEPGPASEGFIT 109 (201)
T ss_pred hhheeecCCccEEcccCceEeccccccCceEe
Confidence 33455555666644444555 67777765554
No 194
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.54 E-value=30 Score=26.08 Aligned_cols=17 Identities=12% Similarity=0.130 Sum_probs=12.9
Q ss_pred cCcceechhhhhhccCcc
Q 021090 205 TRGKYRCEKCKKAFRSYH 222 (317)
Q Consensus 205 ~~~~~~C~~C~k~f~~~~ 222 (317)
......| .||..|....
T Consensus 67 vp~~~~C-~Cg~~~~~~~ 83 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDE 83 (124)
T ss_pred cCeeEEe-eCcCcccccc
Confidence 4567999 9998877653
No 195
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=28.30 E-value=28 Score=25.00 Aligned_cols=53 Identities=25% Similarity=0.259 Sum_probs=27.5
Q ss_pred ccCCccccccCCcccccchhhhccCcccchhhhhhhcccCCccchhccchhhccCCCCCCCCCcccccC
Q 021090 248 FECPFCYKVFGSGQALGGHKRSHLLANSSSTAAAAAVVATDPAVKFENNLIDLNLPAPLEEDDFSVVSD 316 (317)
Q Consensus 248 f~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 316 (317)
-+|++|-+-|.+ -+|.+.+..+...... -...++..+.+.+..++|||-++=|
T Consensus 38 aKC~~~~k~~~S----Y~H~rL~e~e~~~~~~------------g~~~~p~~~~~~~~~~eDDDGFIED 90 (102)
T PF15176_consen 38 AKCPVWYKYLAS----YRHHRLPETEAETYED------------GFTENPEVGSQIPDTNEDDDGFIED 90 (102)
T ss_pred HHhHHHHHHHhc----cccccCCccccccccc------------ccCCCCCccccCCCCCCCCCccccc
Confidence 568888776654 2466655444322211 1122333444555667777766544
No 196
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=28.28 E-value=21 Score=20.43 Aligned_cols=11 Identities=18% Similarity=0.932 Sum_probs=5.6
Q ss_pred ccccCCccccc
Q 021090 246 KIFECPFCYKV 256 (317)
Q Consensus 246 kpf~C~~C~k~ 256 (317)
+-|+|.+||.-
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 35888888754
No 197
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=27.19 E-value=31 Score=22.67 Aligned_cols=16 Identities=25% Similarity=0.671 Sum_probs=12.3
Q ss_pred CCccccCCccccccCC
Q 021090 244 DEKIFECPFCYKVFGS 259 (317)
Q Consensus 244 ~ekpf~C~~C~k~F~~ 259 (317)
..+-|.|+.||..+..
T Consensus 43 ~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 43 SGRVFTCPNCGFEMDR 58 (69)
T ss_pred ccceEEcCCCCCEECc
Confidence 4667999999987654
No 198
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=27.16 E-value=35 Score=21.55 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=9.3
Q ss_pred CCcccCcCCCc
Q 021090 6 CKLCTRSFSNG 16 (317)
Q Consensus 6 C~~Cgk~F~~~ 16 (317)
|+.||+.|...
T Consensus 42 CPfC~~~~~~~ 52 (55)
T PF14447_consen 42 CPFCGTPFEFD 52 (55)
T ss_pred CCCCCCcccCC
Confidence 99999998754
No 199
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=26.87 E-value=29 Score=21.48 Aligned_cols=12 Identities=17% Similarity=0.285 Sum_probs=9.4
Q ss_pred ccccCCcccccc
Q 021090 246 KIFECPFCYKVF 257 (317)
Q Consensus 246 kpf~C~~C~k~F 257 (317)
..|.|..||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 468899998765
No 200
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=26.38 E-value=44 Score=21.07 Aligned_cols=44 Identities=16% Similarity=0.368 Sum_probs=26.4
Q ss_pred cCcceechh--hhhhccCccchhhhhhhhhcccccccccccCCccccCCc----cccccCCc
Q 021090 205 TRGKYRCEK--CKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPF----CYKVFGSG 260 (317)
Q Consensus 205 ~~~~~~C~~--C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~----C~k~F~~~ 260 (317)
...+..|.. |...+. +..|..|+..-= ..++..|++ |+..+...
T Consensus 6 ~~~~v~C~~~cc~~~i~-r~~l~~H~~~~C-----------~~~~v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 6 PFRPVPCPNGCCNEMIP-RKELDDHLENEC-----------PKRPVPCPYSPYGCKERVPRE 55 (60)
T ss_dssp TTSEEE-TT--S-BEEE-CCCHHHHHHTTS-----------TTSEEE-SS----S--EEEHH
T ss_pred CCCEeeCCCCCccccee-HHHHHHHHHccC-----------CCCcEECCCCCCCCCCccchh
Confidence 345678887 545455 667899987322 567899999 98877653
No 201
>PF12907 zf-met2: Zinc-binding
Probab=25.96 E-value=30 Score=20.30 Aligned_cols=21 Identities=24% Similarity=0.569 Sum_probs=11.9
Q ss_pred eechhhhhhccCcc---chhhhhh
Q 021090 209 YRCEKCKKAFRSYH---ALGGHKK 229 (317)
Q Consensus 209 ~~C~~C~k~f~~~~---~L~~H~~ 229 (317)
+.|.+|..+|.... .|..|..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~e 25 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAE 25 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHH
Confidence 45777775554443 3666654
No 202
>PRK14873 primosome assembly protein PriA; Provisional
Probab=25.63 E-value=52 Score=32.67 Aligned_cols=44 Identities=11% Similarity=-0.001 Sum_probs=26.9
Q ss_pred CCCcccCcCCCc---cccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCC
Q 021090 5 KCKLCTRSFSNG---RALGGHMKAHLAAHPLPPKTNQQQQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLG 76 (317)
Q Consensus 5 ~C~~Cgk~F~~~---~~L~~H~r~H~~ek~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~ 76 (317)
.|..||..+..+ ..|..|.. .... .|.-|+... .+..|+.|+..
T Consensus 385 ~C~~Cg~~~~C~~C~~~L~~h~~----~~~l--------~Ch~CG~~~----------------~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRHCTGPLGLPSA----GGTP--------RCRWCGRAA----------------PDWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCCCCCceeEecC----CCee--------ECCCCcCCC----------------cCccCCCCcCC
Confidence 477777766543 35555543 2334 788887642 25589999864
No 203
>PRK04351 hypothetical protein; Provisional
Probab=25.19 E-value=28 Score=27.18 Aligned_cols=34 Identities=18% Similarity=0.493 Sum_probs=23.7
Q ss_pred ceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCCc
Q 021090 208 KYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGSG 260 (317)
Q Consensus 208 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~ 260 (317)
.|.|..||..+.+ + +.| +...|.|..|+-.+...
T Consensus 112 ~Y~C~~Cg~~~~r------~-Rr~------------n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 112 LYECQSCGQQYLR------K-RRI------------NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEECCCCCCEeee------e-eec------------CCCcEEeCCCCcEeeec
Confidence 4999999976543 2 223 35679999999777654
No 204
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=25.11 E-value=18 Score=33.88 Aligned_cols=27 Identities=30% Similarity=0.565 Sum_probs=23.5
Q ss_pred CCCCcccCcCCCccccccccc-cccCCC
Q 021090 4 HKCKLCTRSFSNGRALGGHMK-AHLAAH 30 (317)
Q Consensus 4 ~~C~~Cgk~F~~~~~L~~H~r-~H~~ek 30 (317)
+.|++|.+.|.....+..||. -|.+..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 469999999999999999999 677643
No 205
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=24.98 E-value=25 Score=20.51 Aligned_cols=14 Identities=29% Similarity=0.553 Sum_probs=8.7
Q ss_pred CCccccCCcccccc
Q 021090 244 DEKIFECPFCYKVF 257 (317)
Q Consensus 244 ~ekpf~C~~C~k~F 257 (317)
+.+.+.|.+|+...
T Consensus 21 ~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 21 GGKTWICNFCGTKN 34 (40)
T ss_dssp TTTEEEETTT--EE
T ss_pred CCCEEECcCCCCcC
Confidence 56678888887643
No 206
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=24.65 E-value=34 Score=33.77 Aligned_cols=56 Identities=20% Similarity=0.391 Sum_probs=32.6
Q ss_pred cceechhhhhhccCccchh-hhhhhhhcccccccccccCCccccCCccccccCCcccccchh
Q 021090 207 GKYRCEKCKKAFRSYHALG-GHKKVCETNINAGTKVAADEKIFECPFCYKVFGSGQALGGHK 267 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~-~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~~~~L~~H~ 267 (317)
...+|+.|...|+..-..+ .|..--. =++.-.+-|.-+||.|+.+|.....+..|+
T Consensus 642 ~~LkCs~Cn~R~Kd~vI~kC~H~FC~~-----Cvq~r~etRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKDAVITKCGHVFCEE-----CVQTRYETRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred hceeCCCccCchhhHHHHhcchHHHHH-----HHHHHHHHhcCCCCCCCCCCCcccccccCC
Confidence 3577888875554433222 2322100 001111446678999999999999887774
No 207
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=24.57 E-value=22 Score=19.42 Aligned_cols=11 Identities=27% Similarity=0.806 Sum_probs=7.3
Q ss_pred CccccCCcccc
Q 021090 245 EKIFECPFCYK 255 (317)
Q Consensus 245 ekpf~C~~C~k 255 (317)
.--|.|+.|+.
T Consensus 17 ~~~~vCp~C~~ 27 (30)
T PF08274_consen 17 GELLVCPECGH 27 (30)
T ss_dssp SSSEEETTTTE
T ss_pred CCEEeCCcccc
Confidence 34577887764
No 208
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=24.18 E-value=21 Score=32.88 Aligned_cols=33 Identities=24% Similarity=0.431 Sum_probs=22.2
Q ss_pred cccCCccccccCCcccccchhh-hccCcccchhh
Q 021090 247 IFECPFCYKVFGSGQALGGHKR-SHLLANSSSTA 279 (317)
Q Consensus 247 pf~C~~C~k~F~~~~~L~~H~~-~H~~~~~~~~a 279 (317)
-|.|++|.+-|..-..|.-|.- .|.++.....+
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ed~~D~l 48 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEEDEKDSL 48 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccccchhhHh
Confidence 5778888888888888888864 45555543333
No 209
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=24.16 E-value=26 Score=27.34 Aligned_cols=34 Identities=21% Similarity=0.551 Sum_probs=22.8
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCCccccCCccccccCC
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPFCYKVFGS 259 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~C~k~F~~ 259 (317)
-.|.|..|+..+.... +. ....|.|..|+-.|..
T Consensus 122 ~~~~C~~C~~~~~r~~------~~-------------~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHR------RS-------------KRKRYRCGRCGGPLVQ 155 (157)
T ss_pred eEEEcCCCCCEeeeec------cc-------------chhhEECCCCCCEEEE
Confidence 3589999998763333 21 2334999999977653
No 210
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=24.12 E-value=26 Score=28.73 Aligned_cols=30 Identities=17% Similarity=0.388 Sum_probs=0.0
Q ss_pred CccccCCccc-cccCCcccccchhh--hccCcc
Q 021090 245 EKIFECPFCY-KVFGSGQALGGHKR--SHLLAN 274 (317)
Q Consensus 245 ekpf~C~~C~-k~F~~~~~L~~H~~--~H~~~~ 274 (317)
.+-|.|++|| ..|.-...+.+|.. .|.-+-
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~E~rH~~Gl 131 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQEWRHAYGL 131 (196)
T ss_dssp ---------------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcChhHHHccC
Confidence 4568888886 45556666666743 555443
No 211
>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=23.56 E-value=33 Score=29.22 Aligned_cols=29 Identities=28% Similarity=0.332 Sum_probs=23.9
Q ss_pred CccccCCccccccCCcccccchhhhccCc
Q 021090 245 EKIFECPFCYKVFGSGQALGGHKRSHLLA 273 (317)
Q Consensus 245 ekpf~C~~C~k~F~~~~~L~~H~~~H~~~ 273 (317)
.+++.|+.||.-......|-+-.|+|.=+
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~hkyG 235 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSHKYG 235 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecchhc
Confidence 47999999999998888887777777544
No 212
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=22.81 E-value=45 Score=29.46 Aligned_cols=72 Identities=8% Similarity=0.053 Sum_probs=45.9
Q ss_pred CCCCCcccCcCCCccccccccccccCCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCccccCCCCCccCcCCCCCC
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKAHLAAHPLPPKTNQQ----QQPSDSTESASTSSSSSGEGVEVKGKSPEVAEEKSLGYG 78 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~H~~ek~~~~~~~~~----~~c~~c~~~~~~~~~l~~h~~~~~~~~~~~C~~c~~~f~ 78 (317)
|-.|++|+-.....-+|.+=.+.=-.-+||...+... ..|..|...- .+...|.|+.|...|-
T Consensus 290 P~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~-------------~~~~~y~C~~Ck~~FC 356 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGEL-------------LSSGRYRCESCKNVFC 356 (378)
T ss_pred CccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeecccc-------------CCCCcEEchhccceee
Confidence 5578899888888888876555444456665443332 3366772211 1245799999999997
Q ss_pred CCCCccccc
Q 021090 79 LRNNPKKSF 87 (317)
Q Consensus 79 ~~~~l~~H~ 87 (317)
.--+---|-
T Consensus 357 ldCDv~iHe 365 (378)
T KOG2807|consen 357 LDCDVFIHE 365 (378)
T ss_pred ccchHHHHh
Confidence 766665553
No 213
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=22.81 E-value=45 Score=25.97 Aligned_cols=13 Identities=31% Similarity=0.759 Sum_probs=10.8
Q ss_pred cCcceechhhhhh
Q 021090 205 TRGKYRCEKCKKA 217 (317)
Q Consensus 205 ~~~~~~C~~C~k~ 217 (317)
+.+.|.|..||..
T Consensus 109 g~G~l~C~~Cg~~ 121 (146)
T PF07295_consen 109 GPGTLVCENCGHE 121 (146)
T ss_pred cCceEecccCCCE
Confidence 5678999999975
No 214
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=22.78 E-value=56 Score=23.50 Aligned_cols=13 Identities=15% Similarity=0.266 Sum_probs=10.2
Q ss_pred CCCCcccCcCCCc
Q 021090 4 HKCKLCTRSFSNG 16 (317)
Q Consensus 4 ~~C~~Cgk~F~~~ 16 (317)
+.|+.||..+...
T Consensus 17 ~~C~~C~~~~~~~ 29 (104)
T TIGR01384 17 YVCPSCGYEKEKK 29 (104)
T ss_pred EECcCCCCccccc
Confidence 6799999887754
No 215
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=22.41 E-value=24 Score=19.19 Aligned_cols=12 Identities=25% Similarity=0.755 Sum_probs=6.0
Q ss_pred CCCCCcccCcCC
Q 021090 3 KHKCKLCTRSFS 14 (317)
Q Consensus 3 ~~~C~~Cgk~F~ 14 (317)
+|+|+.|+..+=
T Consensus 13 kY~Cp~C~~~~C 24 (30)
T PF04438_consen 13 KYRCPRCGARYC 24 (30)
T ss_dssp SEE-TTT--EES
T ss_pred EEECCCcCCcee
Confidence 577887776653
No 216
>PTZ00448 hypothetical protein; Provisional
Probab=22.30 E-value=29 Score=31.25 Aligned_cols=23 Identities=17% Similarity=0.437 Sum_probs=20.8
Q ss_pred CCCCCcccCcCCCcccccccccc
Q 021090 3 KHKCKLCTRSFSNGRALGGHMKA 25 (317)
Q Consensus 3 ~~~C~~Cgk~F~~~~~L~~H~r~ 25 (317)
.|.|..|+-.|.+....+.|+|+
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 48899999999999999999994
No 217
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=22.03 E-value=45 Score=19.56 Aligned_cols=25 Identities=28% Similarity=0.513 Sum_probs=16.4
Q ss_pred cccCCccccccCCccc--ccchhhhcc
Q 021090 247 IFECPFCYKVFGSGQA--LGGHKRSHL 271 (317)
Q Consensus 247 pf~C~~C~k~F~~~~~--L~~H~~~H~ 271 (317)
.-.|+.||..|..... -..|.+.|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 3689999988876543 334555553
No 218
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=21.48 E-value=31 Score=20.36 Aligned_cols=9 Identities=22% Similarity=1.132 Sum_probs=5.9
Q ss_pred CCCcccCcC
Q 021090 5 KCKLCTRSF 13 (317)
Q Consensus 5 ~C~~Cgk~F 13 (317)
.|++|.+.|
T Consensus 1 ~C~~C~~~~ 9 (44)
T PF14634_consen 1 HCNICFEKY 9 (44)
T ss_pred CCcCcCccc
Confidence 366776666
No 219
>PHA02998 RNA polymerase subunit; Provisional
Probab=21.30 E-value=33 Score=27.42 Aligned_cols=41 Identities=22% Similarity=0.340 Sum_probs=24.7
Q ss_pred cceechhhhhhccCccchhhhhhhhhcccccccccccCC---ccccCCccccccCCcc
Q 021090 207 GKYRCEKCKKAFRSYHALGGHKKVCETNINAGTKVAADE---KIFECPFCYKVFGSGQ 261 (317)
Q Consensus 207 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~e---kpf~C~~C~k~F~~~~ 261 (317)
..-+|..|+..= ...+...+|.- +| .-|.|..||+.|....
T Consensus 142 t~v~CPkCg~~~--A~f~qlQTRSA------------DEPmT~FYkC~~CG~~wkppk 185 (195)
T PHA02998 142 YNTPCPNCKSKN--TTPMMIQTRAA------------DEPPLVRHACRDCKKHFKPPK 185 (195)
T ss_pred cCCCCCCCCCCc--eEEEEEeeccC------------CCCceEEEEcCCCCCccCCcc
Confidence 456799998543 23233333321 22 3499999999987653
No 220
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=21.22 E-value=20 Score=21.72 Aligned_cols=39 Identities=18% Similarity=0.284 Sum_probs=23.4
Q ss_pred chhhhhhccCccchhhhhhhhhcccccccccccCCccccCCc--cccccCCccc
Q 021090 211 CEKCKKAFRSYHALGGHKKVCETNINAGTKVAADEKIFECPF--CYKVFGSGQA 262 (317)
Q Consensus 211 C~~C~k~f~~~~~L~~H~~~H~~~~~~H~~~h~~ekpf~C~~--C~k~F~~~~~ 262 (317)
|..||..-..+.+...+.. ..+.-|+|.- ||.+|.....
T Consensus 2 CP~Cg~~a~ir~S~~~s~~-------------~~~~Y~qC~N~~Cg~tfv~~~~ 42 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSPL-------------TRELYCQCTNPECGHTFVANLE 42 (47)
T ss_pred cCCCCCeeEEEEchhhCcc-------------eEEEEEEECCCcCCCEEEEEEE
Confidence 6777766555544433321 1355688886 8888876544
No 221
>PLN02748 tRNA dimethylallyltransferase
Probab=20.77 E-value=37 Score=32.03 Aligned_cols=25 Identities=20% Similarity=0.391 Sum_probs=21.5
Q ss_pred CccccCCcccc-ccCCcccccchhhh
Q 021090 245 EKIFECPFCYK-VFGSGQALGGHKRS 269 (317)
Q Consensus 245 ekpf~C~~C~k-~F~~~~~L~~H~~~ 269 (317)
-+.|.|++|++ .+.....+..|++.
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcc
Confidence 36799999997 89999999999864
No 222
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=20.21 E-value=48 Score=19.53 Aligned_cols=8 Identities=38% Similarity=0.833 Sum_probs=4.0
Q ss_pred CCCCcccC
Q 021090 4 HKCKLCTR 11 (317)
Q Consensus 4 ~~C~~Cgk 11 (317)
|+|+.||.
T Consensus 1 m~Cp~Cg~ 8 (43)
T PF08271_consen 1 MKCPNCGS 8 (43)
T ss_dssp ESBTTTSS
T ss_pred CCCcCCcC
Confidence 34555554
No 223
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.14 E-value=39 Score=17.03 Aligned_cols=7 Identities=29% Similarity=0.880 Sum_probs=3.9
Q ss_pred CCcccCc
Q 021090 6 CKLCTRS 12 (317)
Q Consensus 6 C~~Cgk~ 12 (317)
|+.||..
T Consensus 16 C~~CG~~ 22 (23)
T PF13240_consen 16 CPNCGTP 22 (23)
T ss_pred hhhhCCc
Confidence 5666653
No 224
>PF14369 zf-RING_3: zinc-finger
Probab=20.03 E-value=83 Score=17.76 Aligned_cols=10 Identities=10% Similarity=0.052 Sum_probs=8.0
Q ss_pred ccCcCCCCCC
Q 021090 69 VAEEKSLGYG 78 (317)
Q Consensus 69 ~C~~c~~~f~ 78 (317)
.|+.|+.+|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4899988884
Done!