Query 028830
Match_columns 203
No_of_seqs 230 out of 2709
Neff 10.1
Searched_HMMs 46136
Date Fri Mar 29 03:13:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028830.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028830hhsearch_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 100.0 3.9E-30 8.5E-35 190.1 8.2 129 7-135 128-266 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.8 7.8E-22 1.7E-26 146.2 4.0 100 7-108 159-265 (279)
3 KOG1074 Transcriptional repres 99.7 2.1E-19 4.5E-24 150.0 0.1 77 62-138 607-694 (958)
4 KOG1074 Transcriptional repres 99.7 1.9E-18 4.2E-23 144.3 4.5 54 87-140 879-935 (958)
5 KOG3608 Zn finger proteins [Ge 99.7 3.7E-18 8E-23 130.4 4.2 115 2-116 200-322 (467)
6 KOG3576 Ovo and related transc 99.7 2.6E-18 5.6E-23 122.0 2.1 107 33-139 115-239 (267)
7 KOG3608 Zn finger proteins [Ge 99.7 3.2E-17 7E-22 125.3 5.1 125 10-136 178-316 (467)
8 PLN03086 PRLI-interacting fact 99.7 1.9E-16 4.1E-21 130.6 9.1 128 10-138 408-566 (567)
9 KOG3623 Homeobox transcription 99.6 5.9E-16 1.3E-20 127.9 1.7 99 10-108 211-331 (1007)
10 KOG3576 Ovo and related transc 99.5 2.1E-15 4.6E-20 107.3 2.6 108 6-113 114-240 (267)
11 KOG3623 Homeobox transcription 99.5 2.9E-15 6.4E-20 123.9 2.4 73 60-132 894-970 (1007)
12 PLN03086 PRLI-interacting fact 99.2 1.6E-11 3.4E-16 101.8 6.7 100 6-110 450-565 (567)
13 PHA00733 hypothetical protein 99.2 1.4E-11 3E-16 84.2 3.6 62 75-138 62-125 (128)
14 KOG3993 Transcription factor ( 98.9 1.9E-10 4E-15 90.5 0.3 131 9-139 267-485 (500)
15 PHA00733 hypothetical protein 98.8 2.3E-09 4.9E-14 73.3 3.4 105 4-110 6-124 (128)
16 PHA02768 hypothetical protein; 98.8 1.2E-09 2.5E-14 62.2 1.4 38 87-125 5-43 (55)
17 PHA02768 hypothetical protein; 98.7 5.4E-09 1.2E-13 59.5 1.4 41 9-51 5-47 (55)
18 PF13465 zf-H2C2_2: Zinc-finge 98.5 2E-08 4.4E-13 48.8 0.4 23 75-97 2-24 (26)
19 PF05605 zf-Di19: Drought indu 98.5 3.6E-07 7.8E-12 52.8 4.7 50 87-137 2-54 (54)
20 PF13465 zf-H2C2_2: Zinc-finge 98.5 6.4E-08 1.4E-12 47.0 1.3 25 23-47 1-26 (26)
21 KOG3993 Transcription factor ( 98.4 1.5E-07 3.2E-12 74.5 2.0 104 36-139 268-383 (500)
22 PHA00616 hypothetical protein 98.3 3E-07 6.5E-12 49.8 1.2 31 87-117 1-33 (44)
23 PHA00616 hypothetical protein 98.3 5.6E-07 1.2E-11 48.8 1.9 33 60-92 1-34 (44)
24 PHA00732 hypothetical protein 98.2 5.6E-07 1.2E-11 56.0 1.8 35 61-98 2-38 (79)
25 PHA00732 hypothetical protein 98.1 1.9E-06 4.2E-11 53.6 1.8 35 9-46 1-38 (79)
26 PF05605 zf-Di19: Drought indu 97.8 1.7E-05 3.6E-10 45.8 2.9 8 88-95 32-39 (54)
27 PF00096 zf-C2H2: Zinc finger, 97.6 2.3E-05 5.1E-10 36.7 0.9 21 114-134 1-22 (23)
28 PF00096 zf-C2H2: Zinc finger, 97.5 7E-05 1.5E-09 35.0 1.6 21 88-108 1-22 (23)
29 COG5189 SFP1 Putative transcri 97.4 3.7E-05 8E-10 59.1 0.4 49 85-133 347-419 (423)
30 PF13912 zf-C2H2_6: C2H2-type 97.2 0.00017 3.7E-09 35.1 1.3 24 113-136 1-25 (27)
31 PF13894 zf-C2H2_4: C2H2-type 97.2 0.00026 5.7E-09 33.1 1.8 22 114-135 1-23 (24)
32 PF13894 zf-C2H2_4: C2H2-type 97.2 0.00022 4.7E-09 33.4 1.4 21 88-108 1-22 (24)
33 PF12756 zf-C2H2_2: C2H2 type 97.1 0.00043 9.3E-09 45.0 2.5 70 62-135 1-73 (100)
34 COG5189 SFP1 Putative transcri 97.1 0.00022 4.9E-09 55.0 1.2 65 6-79 346-418 (423)
35 PF13912 zf-C2H2_6: C2H2-type 96.9 0.00022 4.8E-09 34.7 -0.1 19 9-27 1-20 (27)
36 PF09237 GAGA: GAGA factor; I 96.9 0.00072 1.6E-08 37.6 1.8 29 85-113 22-52 (54)
37 smart00355 ZnF_C2H2 zinc finge 96.5 0.0025 5.4E-08 30.1 2.1 19 89-107 2-21 (26)
38 PF12756 zf-C2H2_2: C2H2 type 96.5 0.0016 3.4E-08 42.3 1.7 22 87-108 50-72 (100)
39 PF02176 zf-TRAF: TRAF-type zi 96.3 0.002 4.3E-08 37.8 1.1 49 83-131 5-60 (60)
40 KOG2231 Predicted E3 ubiquitin 96.2 0.0087 1.9E-07 51.4 5.2 84 21-109 127-236 (669)
41 PRK04860 hypothetical protein; 96.1 0.0042 9.1E-08 44.1 2.2 36 86-124 118-154 (160)
42 PRK04860 hypothetical protein; 96.0 0.0029 6.3E-08 44.9 1.0 36 60-98 119-154 (160)
43 smart00355 ZnF_C2H2 zinc finge 96.0 0.004 8.6E-08 29.3 1.2 21 10-30 1-23 (26)
44 PF13909 zf-H2C2_5: C2H2-type 95.8 0.0069 1.5E-07 28.4 1.7 23 114-136 1-23 (24)
45 PF13913 zf-C2HC_2: zinc-finge 95.8 0.0062 1.3E-07 29.0 1.4 19 115-133 4-22 (25)
46 PF13913 zf-C2HC_2: zinc-finge 95.7 0.0093 2E-07 28.3 1.8 21 88-108 3-23 (25)
47 PF09237 GAGA: GAGA factor; I 95.5 0.014 3.1E-07 32.5 2.3 29 110-138 21-50 (54)
48 PF12874 zf-met: Zinc-finger o 95.1 0.0071 1.5E-07 28.6 0.3 19 115-133 2-21 (25)
49 KOG2231 Predicted E3 ubiquitin 95.0 0.047 1E-06 47.1 5.1 71 37-108 117-204 (669)
50 PF13909 zf-H2C2_5: C2H2-type 95.0 0.018 4E-07 26.8 1.6 21 88-108 1-21 (24)
51 PF12874 zf-met: Zinc-finger o 94.7 0.019 4.2E-07 27.0 1.2 21 88-108 1-22 (25)
52 PF12171 zf-C2H2_jaz: Zinc-fin 94.3 0.0084 1.8E-07 29.0 -0.6 20 88-107 2-22 (27)
53 KOG2186 Cell growth-regulating 94.1 0.031 6.8E-07 42.0 1.9 49 9-57 3-51 (276)
54 KOG2186 Cell growth-regulating 93.7 0.037 8.1E-07 41.6 1.5 46 61-107 4-49 (276)
55 PF02176 zf-TRAF: TRAF-type zi 93.6 0.0094 2E-07 34.9 -1.4 46 60-105 9-60 (60)
56 COG4049 Uncharacterized protei 93.1 0.074 1.6E-06 30.2 1.8 28 110-137 14-42 (65)
57 smart00451 ZnF_U1 U1-like zinc 92.7 0.087 1.9E-06 26.9 1.7 22 87-108 3-25 (35)
58 KOG1146 Homeobox protein [Gene 92.4 0.064 1.4E-06 49.3 1.4 26 111-136 516-542 (1406)
59 KOG4173 Alpha-SNAP protein [In 92.1 0.17 3.7E-06 37.0 3.0 75 61-138 80-172 (253)
60 COG5236 Uncharacterized conser 91.7 0.12 2.6E-06 40.8 2.0 70 61-138 221-307 (493)
61 COG4049 Uncharacterized protei 90.9 0.083 1.8E-06 30.0 0.4 24 4-27 12-36 (65)
62 KOG2893 Zn finger protein [Gen 90.0 0.09 1.9E-06 39.4 -0.0 30 63-96 13-43 (341)
63 cd00350 rubredoxin_like Rubred 89.5 0.22 4.8E-06 25.3 1.2 10 10-19 2-11 (33)
64 TIGR00622 ssl1 transcription f 89.4 0.49 1.1E-05 31.4 3.0 27 10-48 2-28 (112)
65 PF09538 FYDLN_acid: Protein o 89.3 0.39 8.5E-06 31.8 2.5 15 34-48 25-39 (108)
66 KOG1146 Homeobox protein [Gene 89.1 0.14 3E-06 47.3 0.4 94 36-141 1261-1357(1406)
67 KOG2482 Predicted C2H2-type Zn 88.4 0.57 1.2E-05 37.1 3.3 127 9-135 144-357 (423)
68 KOG2893 Zn finger protein [Gen 88.1 0.11 2.5E-06 38.8 -0.6 34 38-72 13-46 (341)
69 COG2888 Predicted Zn-ribbon RN 88.1 0.32 7E-06 28.1 1.3 10 86-95 49-58 (61)
70 PF10571 UPF0547: Uncharacteri 87.6 0.3 6.5E-06 23.4 0.9 9 115-123 16-24 (26)
71 TIGR02098 MJ0042_CXXC MJ0042 f 87.6 0.24 5.1E-06 25.9 0.6 33 10-46 3-36 (38)
72 COG5048 FOG: Zn-finger [Genera 87.3 0.19 4E-06 41.2 0.1 51 8-58 288-346 (467)
73 PRK00398 rpoP DNA-directed RNA 87.0 0.24 5.2E-06 27.2 0.4 30 9-47 3-33 (46)
74 PHA00626 hypothetical protein 86.8 0.24 5.2E-06 28.2 0.3 16 112-127 22-37 (59)
75 PF13719 zinc_ribbon_5: zinc-r 86.8 0.28 6.1E-06 25.6 0.6 31 88-123 3-35 (37)
76 TIGR00622 ssl1 transcription f 86.7 0.99 2.1E-05 30.0 3.2 22 6-27 12-34 (112)
77 PF09986 DUF2225: Uncharacteri 85.1 0.29 6.4E-06 36.6 0.2 14 7-20 3-16 (214)
78 KOG4173 Alpha-SNAP protein [In 85.1 0.32 6.9E-06 35.6 0.4 76 34-109 78-170 (253)
79 cd00729 rubredoxin_SM Rubredox 84.6 0.72 1.6E-05 23.6 1.5 10 9-18 2-11 (34)
80 PRK00464 nrdR transcriptional 84.5 0.37 8.1E-06 34.0 0.5 13 36-48 29-41 (154)
81 PF13717 zinc_ribbon_4: zinc-r 84.4 0.5 1.1E-05 24.5 0.8 32 88-123 3-35 (36)
82 PF12013 DUF3505: Protein of u 83.8 2.2 4.8E-05 28.1 4.0 24 114-137 81-109 (109)
83 PF08209 Sgf11: Sgf11 (transcr 83.7 0.88 1.9E-05 23.1 1.5 25 113-137 4-28 (33)
84 COG5236 Uncharacterized conser 83.6 4 8.7E-05 32.6 5.8 70 37-110 222-306 (493)
85 TIGR02605 CxxC_CxxC_SSSS putat 83.6 0.45 9.7E-06 26.8 0.5 11 10-20 6-16 (52)
86 TIGR02300 FYDLN_acid conserved 83.4 1.2 2.5E-05 30.2 2.4 29 36-72 10-38 (129)
87 smart00734 ZnF_Rad18 Rad18-lik 83.4 1 2.2E-05 21.5 1.6 20 115-134 3-22 (26)
88 PF03145 Sina: Seven in absent 82.6 0.93 2E-05 33.4 2.0 53 87-139 14-74 (198)
89 smart00834 CxxC_CXXC_SSSS Puta 82.1 0.57 1.2E-05 24.8 0.5 11 10-20 6-16 (41)
90 TIGR00373 conserved hypothetic 81.6 1.4 3.1E-05 31.3 2.5 41 75-123 97-138 (158)
91 PF05290 Baculo_IE-1: Baculovi 81.5 1.9 4E-05 29.5 2.9 52 33-98 78-132 (140)
92 smart00659 RPOLCX RNA polymera 81.4 0.95 2E-05 24.7 1.2 26 10-45 3-29 (44)
93 smart00531 TFIIE Transcription 81.3 1.8 4E-05 30.3 3.0 45 76-123 88-133 (147)
94 COG5048 FOG: Zn-finger [Genera 80.9 0.34 7.4E-06 39.6 -1.0 57 60-116 289-354 (467)
95 PF09986 DUF2225: Uncharacteri 80.9 0.24 5.3E-06 37.1 -1.7 39 86-124 4-59 (214)
96 PRK14890 putative Zn-ribbon RN 80.3 1.2 2.6E-05 25.8 1.5 10 86-95 47-56 (59)
97 smart00531 TFIIE Transcription 80.3 0.84 1.8E-05 32.0 1.0 36 34-70 98-133 (147)
98 PF12013 DUF3505: Protein of u 79.1 2.4 5.2E-05 27.9 2.9 77 34-110 10-109 (109)
99 PRK06266 transcription initiat 78.6 1.7 3.7E-05 31.6 2.1 41 75-123 105-146 (178)
100 COG0068 HypF Hydrogenase matur 78.4 0.5 1.1E-05 41.2 -0.7 54 12-68 126-181 (750)
101 PF09723 Zn-ribbon_8: Zinc rib 77.4 0.62 1.3E-05 25.1 -0.3 11 10-20 6-16 (42)
102 TIGR00373 conserved hypothetic 75.7 1.3 2.8E-05 31.5 0.9 32 33-70 107-138 (158)
103 PF03604 DNA_RNApol_7kD: DNA d 75.7 2.1 4.5E-05 21.6 1.4 11 10-20 1-11 (32)
104 PRK09678 DNA-binding transcrip 75.3 1.3 2.7E-05 27.0 0.6 38 10-48 2-42 (72)
105 PF02892 zf-BED: BED zinc fing 73.9 2.3 5E-05 22.9 1.4 6 127-132 35-40 (45)
106 PRK06266 transcription initiat 73.5 1.8 4E-05 31.4 1.2 31 34-70 116-146 (178)
107 PF06524 NOA36: NOA36 protein; 72.0 2.6 5.6E-05 32.2 1.7 10 112-121 208-217 (314)
108 COG1592 Rubrerythrin [Energy p 71.8 2.3 5E-05 30.4 1.3 23 87-120 134-156 (166)
109 smart00614 ZnF_BED BED zinc fi 70.0 3.4 7.5E-05 23.0 1.6 22 87-108 18-45 (50)
110 COG1996 RPC10 DNA-directed RNA 69.9 1.6 3.4E-05 24.4 0.1 11 9-19 6-16 (49)
111 PRK04023 DNA polymerase II lar 69.2 4.3 9.3E-05 37.2 2.7 9 113-121 663-671 (1121)
112 PF04959 ARS2: Arsenite-resist 69.0 1.5 3.2E-05 32.9 -0.2 30 83-112 73-104 (214)
113 PF14353 CpXC: CpXC protein 68.5 3.9 8.5E-05 27.8 1.9 12 113-124 38-49 (128)
114 COG1198 PriA Primosomal protei 67.0 2.5 5.5E-05 37.6 0.9 11 86-96 474-484 (730)
115 PF09845 DUF2072: Zn-ribbon co 66.6 3.3 7.3E-05 28.2 1.2 28 87-124 1-31 (131)
116 KOG2785 C2H2-type Zn-finger pr 64.9 7.7 0.00017 31.5 3.1 49 60-108 166-242 (390)
117 KOG2593 Transcription initiati 63.4 9.1 0.0002 31.6 3.3 37 81-120 122-160 (436)
118 KOG3002 Zn finger protein [Gen 63.1 5.4 0.00012 31.5 1.9 98 10-108 49-161 (299)
119 COG3364 Zn-ribbon containing p 61.5 5.1 0.00011 26.0 1.3 30 86-124 1-32 (112)
120 KOG0297 TNF receptor-associate 61.2 11 0.00023 31.1 3.4 66 64-132 94-161 (391)
121 PF13878 zf-C2H2_3: zinc-finge 61.0 8.2 0.00018 20.6 1.8 22 88-109 14-38 (41)
122 PF07754 DUF1610: Domain of un 60.9 4.2 9E-05 19.0 0.6 10 8-17 15-24 (24)
123 PRK03824 hypA hydrogenase nick 60.5 3.7 8E-05 28.4 0.6 13 8-20 69-81 (135)
124 COG4530 Uncharacterized protei 60.3 6.1 0.00013 26.0 1.5 18 86-103 25-42 (129)
125 KOG4167 Predicted DNA-binding 60.3 4 8.6E-05 35.9 0.8 27 112-138 791-818 (907)
126 KOG2482 Predicted C2H2-type Zn 59.8 8.3 0.00018 30.9 2.4 61 75-135 131-218 (423)
127 PF04216 FdhE: Protein involve 58.3 0.59 1.3E-05 36.7 -4.2 73 36-123 173-248 (290)
128 KOG2593 Transcription initiati 58.0 6.2 0.00013 32.6 1.5 13 60-72 128-140 (436)
129 KOG0320 Predicted E3 ubiquitin 58.0 6.8 0.00015 28.3 1.5 50 33-98 129-178 (187)
130 PF03145 Sina: Seven in absent 58.0 7 0.00015 28.8 1.7 46 14-59 23-72 (198)
131 PF13240 zinc_ribbon_2: zinc-r 57.1 6.8 0.00015 18.0 1.0 7 12-18 2-8 (23)
132 COG2331 Uncharacterized protei 56.8 7.2 0.00016 23.8 1.3 9 61-69 13-21 (82)
133 COG3357 Predicted transcriptio 56.0 7.8 0.00017 24.6 1.4 13 35-47 58-70 (97)
134 PF09963 DUF2197: Uncharacteri 55.5 6.4 0.00014 22.6 0.9 36 88-123 3-41 (56)
135 TIGR01206 lysW lysine biosynth 55.2 5.7 0.00012 22.7 0.6 11 10-20 3-13 (54)
136 COG1655 Uncharacterized protei 55.2 3.1 6.6E-05 31.3 -0.6 39 86-124 18-74 (267)
137 KOG4167 Predicted DNA-binding 52.3 5.4 0.00012 35.1 0.4 24 60-83 792-816 (907)
138 COG3091 SprT Zn-dependent meta 51.7 7.2 0.00016 27.4 0.8 32 86-121 116-148 (156)
139 PF13451 zf-trcl: Probable zin 50.6 9 0.0002 21.4 1.0 13 8-20 3-15 (49)
140 PF15269 zf-C2H2_7: Zinc-finge 50.3 14 0.0003 20.1 1.6 21 88-108 21-42 (54)
141 TIGR00595 priA primosomal prot 50.2 4.1 8.9E-05 34.8 -0.7 23 86-121 239-261 (505)
142 PF05495 zf-CHY: CHY zinc fing 50.0 1.9 4.2E-05 26.1 -2.0 42 74-122 28-70 (71)
143 COG1997 RPL43A Ribosomal prote 49.8 7 0.00015 24.6 0.5 12 87-98 53-64 (89)
144 COG5151 SSL1 RNA polymerase II 49.7 12 0.00025 29.6 1.8 20 86-105 387-407 (421)
145 PF00301 Rubredoxin: Rubredoxi 49.6 4.7 0.0001 22.3 -0.3 11 10-20 2-12 (47)
146 PF03811 Zn_Tnp_IS1: InsA N-te 49.4 5 0.00011 20.8 -0.2 29 10-41 6-35 (36)
147 PF11789 zf-Nse: Zinc-finger o 49.1 14 0.00031 21.2 1.7 30 60-92 24-53 (57)
148 TIGR00595 priA primosomal prot 48.1 15 0.00033 31.4 2.4 10 9-18 222-231 (505)
149 PRK14873 primosome assembly pr 47.4 14 0.0003 32.9 2.1 13 7-19 390-402 (665)
150 KOG2807 RNA polymerase II tran 47.1 25 0.00054 28.1 3.2 13 35-47 290-302 (378)
151 KOG3002 Zn finger protein [Gen 46.9 6.4 0.00014 31.1 0.0 101 35-138 48-165 (299)
152 PRK14873 primosome assembly pr 46.7 4.6 9.9E-05 35.7 -0.9 9 113-121 422-430 (665)
153 KOG0782 Predicted diacylglycer 46.3 5.2 0.00011 34.3 -0.6 50 21-72 238-288 (1004)
154 COG1198 PriA Primosomal protei 45.5 9.9 0.00021 34.0 0.9 39 6-44 441-484 (730)
155 PF12907 zf-met2: Zinc-binding 44.7 22 0.00047 18.9 1.8 20 61-80 2-25 (40)
156 PF01286 XPA_N: XPA protein N- 44.1 7.8 0.00017 19.8 0.1 11 38-48 6-16 (34)
157 smart00504 Ubox Modified RING 44.0 30 0.00066 19.7 2.7 28 66-98 19-46 (63)
158 KOG0297 TNF receptor-associate 43.6 27 0.00059 28.8 3.1 62 59-121 113-176 (391)
159 KOG4124 Putative transcription 42.2 9.1 0.0002 30.7 0.2 25 7-31 347-376 (442)
160 COG5216 Uncharacterized conser 41.4 15 0.00032 21.3 0.9 28 88-121 23-52 (67)
161 KOG2636 Splicing factor 3a, su 41.3 15 0.00032 30.6 1.3 25 3-27 395-421 (497)
162 COG4896 Uncharacterized protei 41.2 9.6 0.00021 22.2 0.1 12 110-121 28-39 (68)
163 PF13248 zf-ribbon_3: zinc-rib 41.2 20 0.00043 16.8 1.2 7 11-17 4-10 (26)
164 PF07295 DUF1451: Protein of u 40.7 7.8 0.00017 27.2 -0.4 32 86-126 111-144 (146)
165 smart00154 ZnF_AN1 AN1-like Zi 40.6 14 0.00031 19.4 0.8 12 9-20 12-23 (39)
166 COG1675 TFA1 Transcription ini 40.4 47 0.001 24.1 3.6 41 74-122 100-141 (176)
167 PF12230 PRP21_like_P: Pre-mRN 38.9 10 0.00022 28.7 0.0 23 86-108 167-189 (229)
168 PTZ00255 60S ribosomal protein 38.3 11 0.00024 24.0 0.1 35 31-72 32-66 (90)
169 PF04959 ARS2: Arsenite-resist 38.0 23 0.0005 26.6 1.8 29 110-138 74-103 (214)
170 smart00440 ZnF_C2C2 C2C2 Zinc 38.0 8.3 0.00018 20.4 -0.4 10 36-45 29-38 (40)
171 PF01363 FYVE: FYVE zinc finge 38.0 12 0.00027 22.1 0.3 9 37-45 11-19 (69)
172 PF08790 zf-LYAR: LYAR-type C2 37.1 6.8 0.00015 19.0 -0.8 19 114-132 1-19 (28)
173 PF15135 UPF0515: Uncharacteri 37.1 23 0.0005 27.1 1.6 13 86-98 154-166 (278)
174 PRK14714 DNA polymerase II lar 37.0 30 0.00065 32.9 2.6 9 36-44 668-676 (1337)
175 COG1571 Predicted DNA-binding 36.5 27 0.00058 29.0 2.0 13 60-72 367-379 (421)
176 PF05443 ROS_MUCR: ROS/MUCR tr 36.4 23 0.0005 24.4 1.4 26 112-139 71-96 (132)
177 PF07800 DUF1644: Protein of u 35.7 24 0.00052 25.0 1.4 56 86-142 79-138 (162)
178 PF05191 ADK_lid: Adenylate ki 35.6 9.9 0.00022 19.6 -0.4 11 35-45 21-31 (36)
179 KOG2785 C2H2-type Zn-finger pr 35.4 47 0.001 27.1 3.2 49 86-134 165-242 (390)
180 TIGR00280 L37a ribosomal prote 35.1 12 0.00026 23.9 -0.1 34 32-72 32-65 (91)
181 PRK14559 putative protein seri 34.7 44 0.00094 29.7 3.1 8 11-18 3-10 (645)
182 TIGR01562 FdhE formate dehydro 34.6 10 0.00022 30.2 -0.6 12 112-123 251-262 (305)
183 KOG2923 Uncharacterized conser 34.4 26 0.00057 20.6 1.2 29 88-122 23-53 (67)
184 COG1327 Predicted transcriptio 34.2 17 0.00037 25.5 0.5 12 37-48 30-41 (156)
185 PF04780 DUF629: Protein of un 34.2 29 0.00063 29.3 1.9 24 86-109 56-81 (466)
186 PRK03564 formate dehydrogenase 33.6 15 0.00033 29.2 0.2 13 111-123 250-262 (309)
187 KOG0978 E3 ubiquitin ligase in 33.6 23 0.00049 31.5 1.2 12 87-98 678-689 (698)
188 PF12760 Zn_Tnp_IS1595: Transp 33.2 13 0.00028 20.2 -0.2 10 111-120 35-44 (46)
189 PF14445 Prok-RING_2: Prokaryo 33.1 21 0.00046 19.9 0.7 18 87-104 7-24 (57)
190 PF11672 DUF3268: Protein of u 33.1 25 0.00055 23.0 1.1 10 9-18 2-11 (102)
191 CHL00174 accD acetyl-CoA carbo 33.0 39 0.00084 26.8 2.4 30 36-71 39-68 (296)
192 TIGR00244 transcriptional regu 32.9 19 0.00042 25.2 0.6 12 37-48 30-41 (147)
193 COG1656 Uncharacterized conser 32.4 28 0.00061 24.9 1.4 11 37-47 99-109 (165)
194 PF13453 zf-TFIIB: Transcripti 32.4 22 0.00047 18.7 0.6 13 36-48 20-32 (41)
195 TIGR00515 accD acetyl-CoA carb 32.2 39 0.00084 26.6 2.2 30 36-71 27-56 (285)
196 TIGR00100 hypA hydrogenase nic 32.0 21 0.00046 23.8 0.7 9 37-45 72-80 (115)
197 PRK05978 hypothetical protein; 32.0 20 0.00043 25.2 0.6 11 61-71 53-63 (148)
198 PF12230 PRP21_like_P: Pre-mRN 31.8 15 0.00034 27.7 0.0 30 110-139 165-194 (229)
199 COG5188 PRP9 Splicing factor 3 31.7 22 0.00049 28.6 0.9 25 3-27 368-394 (470)
200 TIGR00143 hypF [NiFe] hydrogen 31.5 9.1 0.0002 34.2 -1.4 11 38-48 121-131 (711)
201 PF01155 HypA: Hydrogenase exp 31.0 10 0.00023 25.2 -0.9 12 87-98 70-81 (113)
202 TIGR00686 phnA alkylphosphonat 30.9 32 0.00068 22.7 1.3 14 35-48 19-32 (109)
203 PRK10220 hypothetical protein; 30.7 34 0.00074 22.6 1.4 14 35-48 20-33 (111)
204 PF04423 Rad50_zn_hook: Rad50 30.6 39 0.00085 18.9 1.6 18 115-132 22-42 (54)
205 COG5152 Uncharacterized conser 30.4 63 0.0014 23.9 2.9 13 35-47 196-208 (259)
206 PF11931 DUF3449: Domain of un 30.4 17 0.00037 26.9 0.0 25 3-27 95-121 (196)
207 PF07975 C1_4: TFIIH C1-like d 30.4 27 0.00058 19.7 0.8 24 59-82 20-44 (51)
208 PRK12380 hydrogenase nickel in 30.1 27 0.00058 23.3 0.9 8 37-44 72-79 (113)
209 PRK03681 hypA hydrogenase nick 29.8 30 0.00065 23.1 1.1 11 36-46 71-81 (114)
210 PF01428 zf-AN1: AN1-like Zinc 29.6 16 0.00034 19.6 -0.2 12 8-19 12-23 (43)
211 cd00065 FYVE FYVE domain; Zinc 29.6 32 0.00069 19.3 1.1 13 60-72 18-30 (57)
212 COG4957 Predicted transcriptio 29.6 35 0.00077 23.5 1.4 24 114-139 77-100 (148)
213 PRK00564 hypA hydrogenase nick 29.5 30 0.00065 23.2 1.1 12 36-47 72-83 (117)
214 KOG1280 Uncharacterized conser 29.3 59 0.0013 26.3 2.8 35 86-120 78-116 (381)
215 KOG3507 DNA-directed RNA polym 29.0 27 0.00059 20.2 0.7 11 60-70 37-47 (62)
216 KOG1280 Uncharacterized conser 28.9 36 0.00078 27.4 1.5 29 112-140 78-107 (381)
217 PF04806 EspF: EspF protein re 28.6 33 0.00072 18.4 0.9 22 153-174 9-30 (47)
218 smart00064 FYVE Protein presen 28.5 32 0.0007 20.2 1.0 10 37-46 12-21 (68)
219 PRK00432 30S ribosomal protein 28.4 30 0.00064 19.3 0.8 9 113-121 37-45 (50)
220 COG4888 Uncharacterized Zn rib 28.2 15 0.00032 23.9 -0.5 10 35-44 22-31 (104)
221 PF06397 Desulfoferrod_N: Desu 28.1 18 0.00039 18.7 -0.1 13 8-20 5-17 (36)
222 PRK05654 acetyl-CoA carboxylas 27.8 48 0.001 26.2 2.1 32 35-72 27-58 (292)
223 PF14446 Prok-RING_1: Prokaryo 27.8 31 0.00067 19.7 0.8 10 89-98 7-16 (54)
224 PF14369 zf-RING_3: zinc-finge 27.7 29 0.00063 17.7 0.6 30 9-46 2-32 (35)
225 PF13824 zf-Mss51: Zinc-finger 27.6 54 0.0012 18.8 1.7 9 35-43 14-22 (55)
226 PF10013 DUF2256: Uncharacteri 27.4 50 0.0011 17.7 1.5 15 89-103 10-25 (42)
227 PF14311 DUF4379: Domain of un 27.0 33 0.00073 19.3 0.9 11 88-98 29-39 (55)
228 PLN02294 cytochrome c oxidase 26.8 27 0.0006 25.1 0.6 16 109-124 137-152 (174)
229 PF15227 zf-C3HC4_4: zinc fing 26.5 55 0.0012 17.3 1.6 6 88-93 37-42 (42)
230 KOG0717 Molecular chaperone (D 25.8 41 0.00088 28.3 1.4 21 88-108 293-314 (508)
231 PRK04351 hypothetical protein; 25.8 24 0.00051 24.9 0.1 31 87-123 112-142 (149)
232 PF07282 OrfB_Zn_ribbon: Putat 25.8 28 0.0006 20.6 0.4 11 86-96 45-55 (69)
233 PF04810 zf-Sec23_Sec24: Sec23 24.9 17 0.00036 19.2 -0.6 9 86-94 23-31 (40)
234 cd00924 Cyt_c_Oxidase_Vb Cytoc 24.7 32 0.0007 22.3 0.5 14 111-124 77-90 (97)
235 PF09416 UPF1_Zn_bind: RNA hel 24.7 50 0.0011 23.3 1.5 10 112-121 59-68 (152)
236 COG1773 Rubredoxin [Energy pro 24.1 28 0.00061 19.9 0.2 12 9-20 3-14 (55)
237 KOG1729 FYVE finger containing 24.1 35 0.00076 26.9 0.7 7 37-43 170-176 (288)
238 KOG1701 Focal adhesion adaptor 23.9 1.7 3.8E-05 35.5 -6.5 10 11-20 276-285 (468)
239 PF08882 Acetone_carb_G: Aceto 23.7 24 0.00052 23.4 -0.2 18 14-31 28-48 (112)
240 KOG2272 Focal adhesion protein 23.5 36 0.00077 26.2 0.7 14 85-98 219-232 (332)
241 KOG2907 RNA polymerase I trans 23.4 40 0.00086 22.4 0.8 36 87-124 74-113 (116)
242 KOG1842 FYVE finger-containing 22.8 60 0.0013 27.2 1.8 28 86-113 14-43 (505)
243 PF10263 SprT-like: SprT-like 22.4 21 0.00045 25.0 -0.7 32 86-123 122-153 (157)
244 PF05129 Elf1: Transcription e 22.0 11 0.00025 23.4 -1.9 13 36-48 47-59 (81)
245 KOG1842 FYVE finger-containing 22.0 47 0.001 27.8 1.1 24 59-82 14-38 (505)
246 PRK12496 hypothetical protein; 21.9 43 0.00093 24.0 0.8 26 86-122 126-152 (164)
247 PF04606 Ogr_Delta: Ogr/Delta- 21.0 29 0.00063 19.0 -0.2 37 11-48 1-40 (47)
248 KOG4118 Uncharacterized conser 20.9 46 0.001 19.7 0.6 21 88-108 39-60 (74)
249 PF10276 zf-CHCC: Zinc-finger 20.3 31 0.00068 18.3 -0.1 12 34-45 28-39 (40)
250 KOG3183 Predicted Zn-finger pr 20.2 58 0.0013 24.8 1.2 11 9-19 23-33 (250)
251 PRK12722 transcriptional activ 20.2 68 0.0015 23.6 1.5 30 59-95 133-162 (187)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.96 E-value=3.9e-30 Score=190.07 Aligned_cols=129 Identities=22% Similarity=0.439 Sum_probs=120.0
Q ss_pred CCcccCccCCCcCc-cccHHHH-HhhcC---CCcccccccccccccccHHHHHHcCCC-CccCccChhhhhH-HHHHhhH
Q 028830 7 ETTKICSHCDRAIP-SSNIDLH-FAHCS---RNLERCKVCGDMVPRKYAEEHFLNTHA-PVACSQCSETMER-EILAIHK 79 (203)
Q Consensus 7 ~k~y~C~~C~~~f~-~~~l~~H-~~h~~---~~~~~C~~C~~~f~~~~~~~~~~~~h~-~~~C~~C~~~f~~-~~l~~H~ 79 (203)
...|+|+.|++.+. .++|.+| +.|+. .+.+.|++|++.|..-..|..|.++|+ +++|.+|||.|.+ +-|+.|+
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhccc
Confidence 44699999999998 9999999 89975 577999999999999988999999997 9999999999999 8999999
Q ss_pred hccCCCCcccCccCCCCCC-hhhHHHHHHHh-CCcceecccchhhcc-hhHHHHHHHhh
Q 028830 80 GENCPQRIVTCDFCEFPLP-AVDLAEHQEVC-GNRTELCHLCNRYIR-LRERYNHESRC 135 (203)
Q Consensus 80 ~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~-~~~~~~C~~C~~~f~-~~~l~~H~~~~ 135 (203)
++|+|||||.|+.|++.|. .++|+.|+++| +.++|+|+.|+|+|. .+-|.+|....
T Consensus 208 RTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 208 RTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred ccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 9999999999999999999 99999999995 889999999999999 57899998654
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.84 E-value=7.8e-22 Score=146.23 Aligned_cols=100 Identities=20% Similarity=0.457 Sum_probs=95.6
Q ss_pred CCcccCccCCCcCc-cccHHHH-HhhcCCCcccccccccccccccHHHHHHcCC---CCccCccChhhhhH-HHHHhhHh
Q 028830 7 ETTKICSHCDRAIP-SSNIDLH-FAHCSRNLERCKVCGDMVPRKYAEEHFLNTH---APVACSQCSETMER-EILAIHKG 80 (203)
Q Consensus 7 ~k~y~C~~C~~~f~-~~~l~~H-~~h~~~~~~~C~~C~~~f~~~~~~~~~~~~h---~~~~C~~C~~~f~~-~~l~~H~~ 80 (203)
.+.+.|+.|++.|. -..|+.| ++|+ -+++|.+||+.|.+.++|.-|.++| |||.|..|++.|.. ++|+.|+.
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQ 236 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQ 236 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHH
Confidence 67899999999998 9999999 9997 6899999999999999999999999 69999999999988 89999999
Q ss_pred ccCCCCcccCccCCCCCC-hhhHHHHHHH
Q 028830 81 ENCPQRIVTCDFCEFPLP-AVDLAEHQEV 108 (203)
Q Consensus 81 ~h~~~~~~~C~~C~~~f~-~~~l~~H~~~ 108 (203)
+|.+.|.|.|+.|+|.|. .+.|.+|...
T Consensus 237 THS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 237 THSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred hhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 999999999999999999 9999999887
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.74 E-value=2.1e-19 Score=149.96 Aligned_cols=77 Identities=18% Similarity=0.330 Sum_probs=65.0
Q ss_pred cCccChhhhhH-HHHHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHHhCCc-----ceecc---cchhhcch-hHHHH
Q 028830 62 ACSQCSETMER-EILAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEVCGNR-----TELCH---LCNRYIRL-RERYN 130 (203)
Q Consensus 62 ~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~-----~~~C~---~C~~~f~~-~~l~~ 130 (203)
+|-+|-++..= +.|+.|+++|+||+||+|.+||+.|. +.+|+.|+-+|..+ ++.|+ +|-+-|.. -.|-.
T Consensus 607 qCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQ 686 (958)
T KOG1074|consen 607 QCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQ 686 (958)
T ss_pred ceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccccc
Confidence 79999888766 78999999999999999999999999 99999999887543 48899 99988885 58888
Q ss_pred HHHhhcCC
Q 028830 131 HESRCTGV 138 (203)
Q Consensus 131 H~~~~~~~ 138 (203)
|++.|...
T Consensus 687 hIriH~~~ 694 (958)
T KOG1074|consen 687 HIRIHLGG 694 (958)
T ss_pred eEEeecCC
Confidence 88877643
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.73 E-value=1.9e-18 Score=144.30 Aligned_cols=54 Identities=19% Similarity=0.356 Sum_probs=48.3
Q ss_pred cccCccCCCCCC-hhhHHHHHHH-hCCcceecccchhhcc-hhHHHHHHHhhcCCCC
Q 028830 87 IVTCDFCEFPLP-AVDLAEHQEV-CGNRTELCHLCNRYIR-LRERYNHESRCTGVPE 140 (203)
Q Consensus 87 ~~~C~~C~~~f~-~~~l~~H~~~-~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~ 140 (203)
...|..|++.|. .+.|..|+++ .++|||.|..|++.|. +.+|+.||.+|+..+.
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCC
Confidence 368999999999 9999999999 5999999999999998 6799999987766543
No 5
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.72 E-value=3.7e-18 Score=130.39 Aligned_cols=115 Identities=21% Similarity=0.341 Sum_probs=61.2
Q ss_pred cccCCCCcccCccCCCcCc-cccHHHH-Hhh--cCCCcccccccccccccccHHHHHHcCC-CCccCccChhhhhH-HHH
Q 028830 2 AMTSDETTKICSHCDRAIP-SSNIDLH-FAH--CSRNLERCKVCGDMVPRKYAEEHFLNTH-APVACSQCSETMER-EIL 75 (203)
Q Consensus 2 ~~h~~~k~y~C~~C~~~f~-~~~l~~H-~~h--~~~~~~~C~~C~~~f~~~~~~~~~~~~h-~~~~C~~C~~~f~~-~~l 75 (203)
|.|++||.-.|+.|+..|. +..|-.| +.. ....+|.|..|.+.|.+..+|..|+..| ..|+|+.|..+... ++|
T Consensus 200 r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL 279 (467)
T KOG3608|consen 200 RTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSL 279 (467)
T ss_pred HhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHH
Confidence 4566666666666666666 6666666 322 2334566666666666555555555544 24444444444443 444
Q ss_pred HhhHhc-cCCCCcccCccCCCCCC-hhhHHHHHHHhCCcceec
Q 028830 76 AIHKGE-NCPQRIVTCDFCEFPLP-AVDLAEHQEVCGNRTELC 116 (203)
Q Consensus 76 ~~H~~~-h~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C 116 (203)
..|++. |...+||+|+.|++.|. .+.|.+|..+|.+-.|.|
T Consensus 280 ~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C 322 (467)
T KOG3608|consen 280 TTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQC 322 (467)
T ss_pred HHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceec
Confidence 444432 33445555555555554 555555555444433444
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.71 E-value=2.6e-18 Score=122.00 Aligned_cols=107 Identities=20% Similarity=0.331 Sum_probs=93.5
Q ss_pred CCcccccccccccccccHHHHHHcCC---CCccCccChhhhhH-HHHHhhHhccCCCCcccCccCCCCCC-hhhHHHHHH
Q 028830 33 RNLERCKVCGDMVPRKYAEEHFLNTH---APVACSQCSETMER-EILAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQE 107 (203)
Q Consensus 33 ~~~~~C~~C~~~f~~~~~~~~~~~~h---~~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~ 107 (203)
...|.|.+|++.|....++..|++.| +.|.|..||+.|.. -+|++|.++|+|.+||+|..|++.|. .-+|..|.+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 45689999999999999999999999 58999999999988 58999999999999999999999999 999999998
Q ss_pred H-hCC-----------cceecccchhhcc-hhHHHHHHHhhcCCC
Q 028830 108 V-CGN-----------RTELCHLCNRYIR-LRERYNHESRCTGVP 139 (203)
Q Consensus 108 ~-~~~-----------~~~~C~~C~~~f~-~~~l~~H~~~~~~~~ 139 (203)
. ||. +.|.|..||.+-. ...+..|++.+|...
T Consensus 195 kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 195 KVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred HHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 7 763 6799999998554 468888998877654
No 7
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.68 E-value=3.2e-17 Score=125.28 Aligned_cols=125 Identities=18% Similarity=0.419 Sum_probs=107.8
Q ss_pred ccC--ccCCCcCc-cccHHHH-HhhcCCCccccccccccccccc-HHHHHHcCC----CCccCccChhhhhH-HHHHhhH
Q 028830 10 KIC--SHCDRAIP-SSNIDLH-FAHCSRNLERCKVCGDMVPRKY-AEEHFLNTH----APVACSQCSETMER-EILAIHK 79 (203)
Q Consensus 10 y~C--~~C~~~f~-~~~l~~H-~~h~~~~~~~C~~C~~~f~~~~-~~~~~~~~h----~~~~C~~C~~~f~~-~~l~~H~ 79 (203)
+.| ..|-+.|. +.+|++| +.|++++...|+.||..|.++. +++|.++.- .+|.|..|.|.|.. ..|..|+
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv 257 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHV 257 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHH
Confidence 455 67889998 9999999 9999999999999999999995 445544422 49999999999988 7899999
Q ss_pred hccCCCCcccCccCCCCCC-hhhHHHHHHH-h-CCcceecccchhhcc-hhHHHHHHHhhc
Q 028830 80 GENCPQRIVTCDFCEFPLP-AVDLAEHQEV-C-GNRTELCHLCNRYIR-LRERYNHESRCT 136 (203)
Q Consensus 80 ~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~-~-~~~~~~C~~C~~~f~-~~~l~~H~~~~~ 136 (203)
..|. .-|+|+.|+.... .++|.+|++. | ..+||+|+.|++.|. .+.|.+|...|.
T Consensus 258 ~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 258 VRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 8875 6799999999999 9999999999 7 789999999999665 689999997654
No 8
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.67 E-value=1.9e-16 Score=130.60 Aligned_cols=128 Identities=34% Similarity=0.715 Sum_probs=106.8
Q ss_pred ccCccCCCcCccccHHHHHhhcC--------------------CCcccccccccccccccHHHHHHcCCCCccCccChhh
Q 028830 10 KICSHCDRAIPSSNIDLHFAHCS--------------------RNLERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSET 69 (203)
Q Consensus 10 y~C~~C~~~f~~~~l~~H~~h~~--------------------~~~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~ 69 (203)
-.|+.|.+.....+|..|..++. ++.+.|+.|++.|....+..|....|+++.|+ |++.
T Consensus 408 V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~ 486 (567)
T PLN03086 408 VECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVV 486 (567)
T ss_pred EECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccchHHHHHHHHhcCCCccCC-CCCC
Confidence 46999999988888888844442 24568899999997545544444447899999 9987
Q ss_pred hhHHHHHhhHhccCCCCcccCccCCCCCC-----------hhhHHHHHHHhCCcceecccchhhcchhHHHHHHHhhcCC
Q 028830 70 MEREILAIHKGENCPQRIVTCDFCEFPLP-----------AVDLAEHQEVCGNRTELCHLCNRYIRLRERYNHESRCTGV 138 (203)
Q Consensus 70 f~~~~l~~H~~~h~~~~~~~C~~C~~~f~-----------~~~l~~H~~~~~~~~~~C~~C~~~f~~~~l~~H~~~~~~~ 138 (203)
+....|..|+.+|++++++.|++|++.|. .+.|..|...+|.+++.|..||+.|....+..|+..+|..
T Consensus 487 ~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlrdm~~H~~~~h~~ 566 (567)
T PLN03086 487 LEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVMLKEMDIHQIAVHQK 566 (567)
T ss_pred cchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeeehhHHHHHHHhhcC
Confidence 76689999999999999999999999985 2479999999999999999999999999999999888764
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.57 E-value=5.9e-16 Score=127.95 Aligned_cols=99 Identities=17% Similarity=0.356 Sum_probs=79.1
Q ss_pred ccCccCCCcCc-cccHHHH-H-hh-cCCCcccccccccccccccHHHHHHcCCC----------------CccCccChhh
Q 028830 10 KICSHCDRAIP-SSNIDLH-F-AH-CSRNLERCKVCGDMVPRKYAEEHFLNTHA----------------PVACSQCSET 69 (203)
Q Consensus 10 y~C~~C~~~f~-~~~l~~H-~-~h-~~~~~~~C~~C~~~f~~~~~~~~~~~~h~----------------~~~C~~C~~~ 69 (203)
..|+.|++.+. ...|+.| + .| ..+..|.|..|..+|..+..|..|+.+|+ .|+|.+|+|.
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 57999999998 8899999 5 33 34567899999999999988888888883 5778888888
Q ss_pred hhH-HHHHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHH
Q 028830 70 MER-EILAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEV 108 (203)
Q Consensus 70 f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~ 108 (203)
|.. -+|+.|+++|.|||||.|+.|+|+|+ ..++..|+..
T Consensus 291 FKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 877 47888888888888888888888887 7777777654
No 10
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.55 E-value=2.1e-15 Score=107.29 Aligned_cols=108 Identities=18% Similarity=0.368 Sum_probs=94.6
Q ss_pred CCCcccCccCCCcCc-cccHHHH-HhhcCCCcccccccccccccccHHHHHHcCC---CCccCccChhhhhH-HHHHhhH
Q 028830 6 DETTKICSHCDRAIP-SSNIDLH-FAHCSRNLERCKVCGDMVPRKYAEEHFLNTH---APVACSQCSETMER-EILAIHK 79 (203)
Q Consensus 6 ~~k~y~C~~C~~~f~-~~~l~~H-~~h~~~~~~~C~~C~~~f~~~~~~~~~~~~h---~~~~C~~C~~~f~~-~~l~~H~ 79 (203)
+...|.|..|++.|. ..-|.+| .-|..-+.|.|..||+.|.....+..|.++| +||+|..|++.|++ -.|..|.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 456799999999999 9999999 8999999999999999999998888999999 69999999999998 4788887
Q ss_pred hccC-----------CCCcccCccCCCCCC-hhhHHHHHHH-hCCcc
Q 028830 80 GENC-----------PQRIVTCDFCEFPLP-AVDLAEHQEV-CGNRT 113 (203)
Q Consensus 80 ~~h~-----------~~~~~~C~~C~~~f~-~~~l~~H~~~-~~~~~ 113 (203)
..-+ .++.|.|..||..-. ...+..|.+. |...+
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 6533 458899999999988 8889999998 54433
No 11
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.53 E-value=2.9e-15 Score=123.91 Aligned_cols=73 Identities=27% Similarity=0.482 Sum_probs=69.6
Q ss_pred CccCccChhhhhH-HHHHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHHh-CCcceecccchhhcc-hhHHHHHH
Q 028830 60 PVACSQCSETMER-EILAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEVC-GNRTELCHLCNRYIR-LRERYNHE 132 (203)
Q Consensus 60 ~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~-~~~~~~C~~C~~~f~-~~~l~~H~ 132 (203)
.|.|+.|+|.|.. +.|.+|.-.|+|++||+|.+|.|.|. +..|..|+|.| |||||.|+.|+|.|+ +.++..||
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 8999999999977 89999999999999999999999999 99999999995 999999999999999 56999998
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.24 E-value=1.6e-11 Score=101.81 Aligned_cols=100 Identities=18% Similarity=0.404 Sum_probs=83.6
Q ss_pred CCCcccCccCCCcCccccHHHH-HhhcCCCcccccccccccccccHHHHHHcCC---CCccCccChhhhh----------
Q 028830 6 DETTKICSHCDRAIPSSNIDLH-FAHCSRNLERCKVCGDMVPRKYAEEHFLNTH---APVACSQCSETME---------- 71 (203)
Q Consensus 6 ~~k~y~C~~C~~~f~~~~l~~H-~~h~~~~~~~C~~C~~~f~~~~~~~~~~~~h---~~~~C~~C~~~f~---------- 71 (203)
.++.+.|+.|++.|....|..| +.+. .++.|+ ||..+ .+..+..|+..| +++.|.+|++.|.
T Consensus 450 l~~H~~C~~Cgk~f~~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d 525 (567)
T PLN03086 450 AKNHVHCEKCGQAFQQGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRD 525 (567)
T ss_pred cccCccCCCCCCccchHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhh
Confidence 4677899999999987789999 6653 799999 99766 456777777777 6999999999884
Q ss_pred -HHHHHhhHhccCCCCcccCccCCCCCChhhHHHHHHH-hC
Q 028830 72 -REILAIHKGENCPQRIVTCDFCEFPLPAVDLAEHQEV-CG 110 (203)
Q Consensus 72 -~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~l~~H~~~-~~ 110 (203)
.+.|..|+.. +|.+++.|..||+.|....+..|+.. |.
T Consensus 526 ~~s~Lt~HE~~-CG~rt~~C~~Cgk~Vrlrdm~~H~~~~h~ 565 (567)
T PLN03086 526 RLRGMSEHESI-CGSRTAPCDSCGRSVMLKEMDIHQIAVHQ 565 (567)
T ss_pred hhhhHHHHHHh-cCCcceEccccCCeeeehhHHHHHHHhhc
Confidence 1479999987 69999999999999997789999887 53
No 13
>PHA00733 hypothetical protein
Probab=99.20 E-value=1.4e-11 Score=84.17 Aligned_cols=62 Identities=18% Similarity=0.415 Sum_probs=47.5
Q ss_pred HHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHHhCCcceecccchhhcc-hhHHHHHHHhhcCC
Q 028830 75 LAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNRYIR-LRERYNHESRCTGV 138 (203)
Q Consensus 75 l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~ 138 (203)
|..|+.. .+.++|.|+.|++.|. ...|..|++.+ +.+|.|+.|++.|. ...|..|+...|..
T Consensus 62 l~~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~~CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 62 LYKLLTS-KAVSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCPVCGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred HHhhccc-CCCCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCCCCCCccCCHHHHHHHHHHhcCc
Confidence 4555443 3478899999999998 88888888865 45789999999888 46888898776653
No 14
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.93 E-value=1.9e-10 Score=90.51 Aligned_cols=131 Identities=15% Similarity=0.248 Sum_probs=87.3
Q ss_pred cccCccCCCcCc-cccHHHH-HhhcCCCcccccccccccccccHHHHHHcCCCC--------------------------
Q 028830 9 TKICSHCDRAIP-SSNIDLH-FAHCSRNLERCKVCGDMVPRKYAEEHFLNTHAP-------------------------- 60 (203)
Q Consensus 9 ~y~C~~C~~~f~-~~~l~~H-~~h~~~~~~~C~~C~~~f~~~~~~~~~~~~h~~-------------------------- 60 (203)
-|.|..|...|. ...|.+| -...-.-.|+|+.|++.|.-..+|..|++.|||
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 377888888887 7778887 333444468888888888888888888887731
Q ss_pred ----------ccCccChhhhhH-HHHHhhHhccCCC--------------------------------------------
Q 028830 61 ----------VACSQCSETMER-EILAIHKGENCPQ-------------------------------------------- 85 (203)
Q Consensus 61 ----------~~C~~C~~~f~~-~~l~~H~~~h~~~-------------------------------------------- 85 (203)
|.|.+|++.|.+ ..|+.|+.+|...
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~ 426 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAG 426 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeec
Confidence 678888888877 6777776654210
Q ss_pred --CcccCccCCCCCC-hhhHHHHHHH-hCCcceecccchhhcc-hhHHHHHHHhhcCCC
Q 028830 86 --RIVTCDFCEFPLP-AVDLAEHQEV-CGNRTELCHLCNRYIR-LRERYNHESRCTGVP 139 (203)
Q Consensus 86 --~~~~C~~C~~~f~-~~~l~~H~~~-~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~ 139 (203)
....|++|+..+. +..--.+.+. +.+.-|.|.+|--.|. +..|.+|+.++|..+
T Consensus 427 sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hpse 485 (500)
T KOG3993|consen 427 SAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPSE 485 (500)
T ss_pred cccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChHH
Confidence 1123455554444 3222233333 3445688999998776 579999998887644
No 15
>PHA00733 hypothetical protein
Probab=98.85 E-value=2.3e-09 Score=73.28 Aligned_cols=105 Identities=12% Similarity=0.115 Sum_probs=77.8
Q ss_pred cCCCCcccCccCCCcCc--cccHHHH-HhhcCCCcccccccccccccccHHHHH------HcCC--CCccCccChhhhhH
Q 028830 4 TSDETTKICSHCDRAIP--SSNIDLH-FAHCSRNLERCKVCGDMVPRKYAEEHF------LNTH--APVACSQCSETMER 72 (203)
Q Consensus 4 h~~~k~y~C~~C~~~f~--~~~l~~H-~~h~~~~~~~C~~C~~~f~~~~~~~~~------~~~h--~~~~C~~C~~~f~~ 72 (203)
..|.+.|.-+.=|-.|- ...|..+ ..-...+++.|.+|+..|....++.++ ...+ ++|.|..|++.|..
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss 85 (128)
T PHA00733 6 ESGSKKYLSNHKGIFIHVTLEELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSS 85 (128)
T ss_pred ccchHhhcccCCCeEEecCHHHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCC
Confidence 34566676444444443 4445554 333345789999999999988666554 1222 49999999999988
Q ss_pred -HHHHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHH-hC
Q 028830 73 -EILAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEV-CG 110 (203)
Q Consensus 73 -~~l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~-~~ 110 (203)
..|..|+..+ +.+|.|+.|++.|. ...|..|+.. |+
T Consensus 86 ~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 86 SVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 7899999876 46799999999999 9999999988 75
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.84 E-value=1.2e-09 Score=62.18 Aligned_cols=38 Identities=13% Similarity=0.097 Sum_probs=28.6
Q ss_pred cccCccCCCCCC-hhhHHHHHHHhCCcceecccchhhcch
Q 028830 87 IVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNRYIRL 125 (203)
Q Consensus 87 ~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~~f~~ 125 (203)
.|+|+.||+.|+ .++|..|+++|. ++|+|..|++.|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~ 43 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLR 43 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceecc
Confidence 467888888887 777888888755 57788888877763
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.71 E-value=5.4e-09 Score=59.49 Aligned_cols=41 Identities=15% Similarity=0.146 Sum_probs=32.0
Q ss_pred cccCccCCCcCc-cccHHHH-HhhcCCCcccccccccccccccHH
Q 028830 9 TKICSHCDRAIP-SSNIDLH-FAHCSRNLERCKVCGDMVPRKYAE 51 (203)
Q Consensus 9 ~y~C~~C~~~f~-~~~l~~H-~~h~~~~~~~C~~C~~~f~~~~~~ 51 (203)
-|.|+.||+.|. .++|..| +.|+ ++|+|..|++.|.+.+.+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 378888888888 8888888 7777 578888888888766443
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.53 E-value=2e-08 Score=48.83 Aligned_cols=23 Identities=17% Similarity=0.437 Sum_probs=10.8
Q ss_pred HHhhHhccCCCCcccCccCCCCC
Q 028830 75 LAIHKGENCPQRIVTCDFCEFPL 97 (203)
Q Consensus 75 l~~H~~~h~~~~~~~C~~C~~~f 97 (203)
|..|+++|++++||.|+.|++.|
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEE
T ss_pred HHHHhhhcCCCCCCCCCCCcCee
Confidence 34444444444444444444443
No 19
>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=98.47 E-value=3.6e-07 Score=52.82 Aligned_cols=50 Identities=20% Similarity=0.421 Sum_probs=38.8
Q ss_pred cccCccCCCCCChhhHHHHHHH-h--CCcceecccchhhcchhHHHHHHHhhcC
Q 028830 87 IVTCDFCEFPLPAVDLAEHQEV-C--GNRTELCHLCNRYIRLRERYNHESRCTG 137 (203)
Q Consensus 87 ~~~C~~C~~~f~~~~l~~H~~~-~--~~~~~~C~~C~~~f~~~~l~~H~~~~~~ 137 (203)
.|.|++|++.|....|..|... | ..+.+.|++|...++ .+|..|+...|+
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~-~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVT-DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhh-hHHHHHHHHhcC
Confidence 5789999997667789999888 7 345789999987544 488899877663
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.47 E-value=6.4e-08 Score=47.04 Aligned_cols=25 Identities=24% Similarity=0.535 Sum_probs=21.7
Q ss_pred cHHHH-HhhcCCCccccccccccccc
Q 028830 23 NIDLH-FAHCSRNLERCKVCGDMVPR 47 (203)
Q Consensus 23 ~l~~H-~~h~~~~~~~C~~C~~~f~~ 47 (203)
+|.+| +.|++++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47889 89999999999999998863
No 21
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.38 E-value=1.5e-07 Score=74.55 Aligned_cols=104 Identities=16% Similarity=0.275 Sum_probs=51.0
Q ss_pred ccccccccccccccHHHHHHc---CCCCccCccChhhhhH-HHHHhhHhccCCCCccc-Ccc-C-CCCCChhhH-HHHHH
Q 028830 36 ERCKVCGDMVPRKYAEEHFLN---THAPVACSQCSETMER-EILAIHKGENCPQRIVT-CDF-C-EFPLPAVDL-AEHQE 107 (203)
Q Consensus 36 ~~C~~C~~~f~~~~~~~~~~~---~h~~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~-C~~-C-~~~f~~~~l-~~H~~ 107 (203)
|.|..|...|.+...|..|+. +|--|+|++|+|.|.= .+|..|.++|.....-- -.. = .+......+ +.=.+
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 566666666666655555532 1235666666666655 56666666553211000 000 0 000000000 00000
Q ss_pred H---hCCcceecccchhhcch-hHHHHHHHhhcCCC
Q 028830 108 V---CGNRTELCHLCNRYIRL-RERYNHESRCTGVP 139 (203)
Q Consensus 108 ~---~~~~~~~C~~C~~~f~~-~~l~~H~~~~~~~~ 139 (203)
. ..+.-|.|..|++.|++ ..|..|+..|+...
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 0 01235899999999985 68888977776543
No 22
>PHA00616 hypothetical protein
Probab=98.28 E-value=3e-07 Score=49.83 Aligned_cols=31 Identities=13% Similarity=0.099 Sum_probs=16.8
Q ss_pred cccCccCCCCCC-hhhHHHHHHH-hCCcceecc
Q 028830 87 IVTCDFCEFPLP-AVDLAEHQEV-CGNRTELCH 117 (203)
Q Consensus 87 ~~~C~~C~~~f~-~~~l~~H~~~-~~~~~~~C~ 117 (203)
||+|+.||+.|. .+.|..|++. ||++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 355555555555 5555555555 455555554
No 23
>PHA00616 hypothetical protein
Probab=98.26 E-value=5.6e-07 Score=48.77 Aligned_cols=33 Identities=15% Similarity=0.267 Sum_probs=30.7
Q ss_pred CccCccChhhhhH-HHHHhhHhccCCCCcccCcc
Q 028830 60 PVACSQCSETMER-EILAIHKGENCPQRIVTCDF 92 (203)
Q Consensus 60 ~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~ 92 (203)
+|+|..||+.|.. ++|..|++.|+|++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999998 89999999999999999875
No 24
>PHA00732 hypothetical protein
Probab=98.24 E-value=5.6e-07 Score=56.01 Aligned_cols=35 Identities=20% Similarity=0.407 Sum_probs=16.1
Q ss_pred ccCccChhhhhH-HHHHhhHhc-cCCCCcccCccCCCCCC
Q 028830 61 VACSQCSETMER-EILAIHKGE-NCPQRIVTCDFCEFPLP 98 (203)
Q Consensus 61 ~~C~~C~~~f~~-~~l~~H~~~-h~~~~~~~C~~C~~~f~ 98 (203)
|.|..|++.|.. +.|..|++. |. ++.|+.|++.|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC
Confidence 445555555544 445555442 32 234555555543
No 25
>PHA00732 hypothetical protein
Probab=98.07 E-value=1.9e-06 Score=53.60 Aligned_cols=35 Identities=23% Similarity=0.427 Sum_probs=21.7
Q ss_pred cccCccCCCcCc-cccHHHH-H-hhcCCCcccccccccccc
Q 028830 9 TKICSHCDRAIP-SSNIDLH-F-AHCSRNLERCKVCGDMVP 46 (203)
Q Consensus 9 ~y~C~~C~~~f~-~~~l~~H-~-~h~~~~~~~C~~C~~~f~ 46 (203)
||.|+.|++.|. ..+|+.| + .|. ++.|+.|++.|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~ 38 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR 38 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC
Confidence 466777777776 6667766 4 243 245666666665
No 26
>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=97.85 E-value=1.7e-05 Score=45.81 Aligned_cols=8 Identities=38% Similarity=1.003 Sum_probs=3.5
Q ss_pred ccCccCCC
Q 028830 88 VTCDFCEF 95 (203)
Q Consensus 88 ~~C~~C~~ 95 (203)
+.|++|..
T Consensus 32 v~CPiC~~ 39 (54)
T PF05605_consen 32 VVCPICSS 39 (54)
T ss_pred ccCCCchh
Confidence 44444443
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.61 E-value=2.3e-05 Score=36.66 Aligned_cols=21 Identities=19% Similarity=0.398 Sum_probs=10.4
Q ss_pred eecccchhhcc-hhHHHHHHHh
Q 028830 114 ELCHLCNRYIR-LRERYNHESR 134 (203)
Q Consensus 114 ~~C~~C~~~f~-~~~l~~H~~~ 134 (203)
|.|+.|++.|. ...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 34555555554 2455555543
No 28
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.48 E-value=7e-05 Score=34.98 Aligned_cols=21 Identities=19% Similarity=0.464 Sum_probs=19.6
Q ss_pred ccCccCCCCCC-hhhHHHHHHH
Q 028830 88 VTCDFCEFPLP-AVDLAEHQEV 108 (203)
Q Consensus 88 ~~C~~C~~~f~-~~~l~~H~~~ 108 (203)
|.|+.|++.|. ...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 68999999999 9999999986
No 29
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.44 E-value=3.7e-05 Score=59.14 Aligned_cols=49 Identities=16% Similarity=0.329 Sum_probs=41.1
Q ss_pred CCcccCcc--CCCCCC-hhhHHHHHHH-hC-------------------Ccceecccchhhcc-hhHHHHHHH
Q 028830 85 QRIVTCDF--CEFPLP-AVDLAEHQEV-CG-------------------NRTELCHLCNRYIR-LRERYNHES 133 (203)
Q Consensus 85 ~~~~~C~~--C~~~f~-~~~l~~H~~~-~~-------------------~~~~~C~~C~~~f~-~~~l~~H~~ 133 (203)
+|||+|++ |+|.+. ...|+-|+.. |. .|||+|+.|+|.+. ...|+.|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 48999998 999998 9999999876 51 28999999999998 468888864
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=97.21 E-value=0.00017 Score=35.07 Aligned_cols=24 Identities=17% Similarity=0.303 Sum_probs=14.8
Q ss_pred ceecccchhhcc-hhHHHHHHHhhc
Q 028830 113 TELCHLCNRYIR-LRERYNHESRCT 136 (203)
Q Consensus 113 ~~~C~~C~~~f~-~~~l~~H~~~~~ 136 (203)
+|.|..|++.|. ...|..|++.++
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 466666766666 356666665543
No 31
>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=97.20 E-value=0.00026 Score=33.10 Aligned_cols=22 Identities=23% Similarity=0.401 Sum_probs=9.8
Q ss_pred eecccchhhcc-hhHHHHHHHhh
Q 028830 114 ELCHLCNRYIR-LRERYNHESRC 135 (203)
Q Consensus 114 ~~C~~C~~~f~-~~~l~~H~~~~ 135 (203)
|.|+.|++.|. ...|..|+..+
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 34555555554 24555555443
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=97.17 E-value=0.00022 Score=33.38 Aligned_cols=21 Identities=19% Similarity=0.518 Sum_probs=15.0
Q ss_pred ccCccCCCCCC-hhhHHHHHHH
Q 028830 88 VTCDFCEFPLP-AVDLAEHQEV 108 (203)
Q Consensus 88 ~~C~~C~~~f~-~~~l~~H~~~ 108 (203)
|.|+.|++.|. ...|..|++.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 56888888887 8888888776
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.08 E-value=0.00043 Score=44.96 Aligned_cols=70 Identities=19% Similarity=0.175 Sum_probs=16.0
Q ss_pred cCccChhhhhH-HHHHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHHhCCcceecccchhhcc-hhHHHHHHHhh
Q 028830 62 ACSQCSETMER-EILAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNRYIR-LRERYNHESRC 135 (203)
Q Consensus 62 ~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~~f~-~~~l~~H~~~~ 135 (203)
+|..|+..|.. ..|..|+...++...- ....+. ...+..+.+..-...+.|..|++.|. ...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc----cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 35666666655 5566666443332111 111111 23333333332222577777877776 46777777654
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.07 E-value=0.00022 Score=54.97 Aligned_cols=65 Identities=17% Similarity=0.410 Sum_probs=39.9
Q ss_pred CCCcccC--ccCCCcCc-cccHHHHH--hhcCCCccccc--ccccccccccHHHHHHcCCCCccCccChhhhhH-HHHHh
Q 028830 6 DETTKIC--SHCDRAIP-SSNIDLHF--AHCSRNLERCK--VCGDMVPRKYAEEHFLNTHAPVACSQCSETMER-EILAI 77 (203)
Q Consensus 6 ~~k~y~C--~~C~~~f~-~~~l~~H~--~h~~~~~~~C~--~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~-~~l~~ 77 (203)
++|||+| ..|++.|. ...|+.|+ .|...+...-+ +--..| ...-+||.|+.|+|.|.. ..|+-
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F---------~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIF---------SAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccc---------cccCCceeccccchhhccCcccee
Confidence 4699999 57999998 88999994 44433222111 111112 011168888888888877 56666
Q ss_pred hH
Q 028830 78 HK 79 (203)
Q Consensus 78 H~ 79 (203)
|.
T Consensus 417 Hr 418 (423)
T COG5189 417 HR 418 (423)
T ss_pred cc
Confidence 64
No 35
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.89 E-value=0.00022 Score=34.65 Aligned_cols=19 Identities=21% Similarity=0.497 Sum_probs=11.1
Q ss_pred cccCccCCCcCc-cccHHHH
Q 028830 9 TKICSHCDRAIP-SSNIDLH 27 (203)
Q Consensus 9 ~y~C~~C~~~f~-~~~l~~H 27 (203)
||.|..|++.|. ...|..|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H 20 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREH 20 (27)
T ss_dssp SEEETTTTEEESSHHHHHHH
T ss_pred CCCCCccCCccCChhHHHHH
Confidence 455666666665 5555555
No 36
>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=96.88 E-value=0.00072 Score=37.60 Aligned_cols=29 Identities=21% Similarity=0.424 Sum_probs=14.0
Q ss_pred CCcccCccCCCCCC-hhhHHHHHHH-hCCcc
Q 028830 85 QRIVTCDFCEFPLP-AVDLAEHQEV-CGNRT 113 (203)
Q Consensus 85 ~~~~~C~~C~~~f~-~~~l~~H~~~-~~~~~ 113 (203)
+.|-.|++|+..+. ..+|++|+.+ |+.+|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45566666666666 6666666665 55544
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.51 E-value=0.0025 Score=30.08 Aligned_cols=19 Identities=26% Similarity=0.433 Sum_probs=9.2
Q ss_pred cCccCCCCCC-hhhHHHHHH
Q 028830 89 TCDFCEFPLP-AVDLAEHQE 107 (203)
Q Consensus 89 ~C~~C~~~f~-~~~l~~H~~ 107 (203)
.|..|++.|. ...|..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 4444555554 444444444
No 38
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.47 E-value=0.0016 Score=42.26 Aligned_cols=22 Identities=23% Similarity=0.505 Sum_probs=18.4
Q ss_pred cccCccCCCCCC-hhhHHHHHHH
Q 028830 87 IVTCDFCEFPLP-AVDLAEHQEV 108 (203)
Q Consensus 87 ~~~C~~C~~~f~-~~~l~~H~~~ 108 (203)
.+.|..|++.|. ...|..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 688999999998 8889999887
No 39
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=96.26 E-value=0.002 Score=37.80 Aligned_cols=49 Identities=31% Similarity=0.657 Sum_probs=33.8
Q ss_pred CCCCcccCcc--CCCCCChhhHHHHHHH-hCCcceeccc----chhhcchhHHHHH
Q 028830 83 CPQRIVTCDF--CEFPLPAVDLAEHQEV-CGNRTELCHL----CNRYIRLRERYNH 131 (203)
Q Consensus 83 ~~~~~~~C~~--C~~~f~~~~l~~H~~~-~~~~~~~C~~----C~~~f~~~~l~~H 131 (203)
+...+..|+. |...+....|..|... +..++..|+. |+..+....|..|
T Consensus 5 C~~~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 5 CPFRPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp STTSEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CCCCEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 5667788887 5455667788899886 7888888888 8888877777665
No 40
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.24 E-value=0.0087 Score=51.41 Aligned_cols=84 Identities=21% Similarity=0.290 Sum_probs=52.7
Q ss_pred cccHHHHHhhcCCCcccccc----------cccccccccHHHHHHcCC------C-CccCccChhhhhH-HHHHhhHhcc
Q 028830 21 SSNIDLHFAHCSRNLERCKV----------CGDMVPRKYAEEHFLNTH------A-PVACSQCSETMER-EILAIHKGEN 82 (203)
Q Consensus 21 ~~~l~~H~~h~~~~~~~C~~----------C~~~f~~~~~~~~~~~~h------~-~~~C~~C~~~f~~-~~l~~H~~~h 82 (203)
...|+.|+.+..+ .+.|.. +.+.+....++.|++..- + --.|..|...|.. ..|..|++.
T Consensus 127 ~~~Lk~H~~~~H~-~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~- 204 (669)
T KOG2231|consen 127 VENLKNHMRDQHK-LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRF- 204 (669)
T ss_pred HHHHHHHHHHhhh-hhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhcc-
Confidence 5678888322221 233333 445555556666665421 2 3578889888876 678888876
Q ss_pred CCCCcccCccCC------CCCC-hhhHHHHHHH-h
Q 028830 83 CPQRIVTCDFCE------FPLP-AVDLAEHQEV-C 109 (203)
Q Consensus 83 ~~~~~~~C~~C~------~~f~-~~~l~~H~~~-~ 109 (203)
..|.|.+|. .-|. ...|..|.+. |
T Consensus 205 ---~h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 205 ---DHEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ---ceeheeecCcccccchhcccchHHHHHhhhcC
Confidence 467777773 3356 7889999887 6
No 41
>PRK04860 hypothetical protein; Provisional
Probab=96.08 E-value=0.0042 Score=44.13 Aligned_cols=36 Identities=19% Similarity=0.443 Sum_probs=28.8
Q ss_pred CcccCccCCCCCChhhHHHHHHH-hCCcceecccchhhcc
Q 028830 86 RIVTCDFCEFPLPAVDLAEHQEV-CGNRTELCHLCNRYIR 124 (203)
Q Consensus 86 ~~~~C~~C~~~f~~~~l~~H~~~-~~~~~~~C~~C~~~f~ 124 (203)
-+|.|. |+. ....+.+|.++ .++++|.|..|+..|.
T Consensus 118 ~~Y~C~-C~~--~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 118 FPYRCK-CQE--HQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEEcC-CCC--eeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 368897 886 45667899999 5888999999988775
No 42
>PRK04860 hypothetical protein; Provisional
Probab=95.98 E-value=0.0029 Score=44.93 Aligned_cols=36 Identities=22% Similarity=0.445 Sum_probs=31.6
Q ss_pred CccCccChhhhhHHHHHhhHhccCCCCcccCccCCCCCC
Q 028830 60 PVACSQCSETMEREILAIHKGENCPQRIVTCDFCEFPLP 98 (203)
Q Consensus 60 ~~~C~~C~~~f~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 98 (203)
+|.|. |+. ....+..|.+++.++++|.|..|+..|.
T Consensus 119 ~Y~C~-C~~--~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 119 PYRCK-CQE--HQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEcC-CCC--eeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 69998 987 3367889999999999999999999886
No 43
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.96 E-value=0.004 Score=29.33 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=13.8
Q ss_pred ccCccCCCcCc-cccHHHH-Hhh
Q 028830 10 KICSHCDRAIP-SSNIDLH-FAH 30 (203)
Q Consensus 10 y~C~~C~~~f~-~~~l~~H-~~h 30 (203)
|.|+.|++.|. ...|..| +.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 46777777776 6677777 444
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.83 E-value=0.0069 Score=28.35 Aligned_cols=23 Identities=17% Similarity=0.184 Sum_probs=12.5
Q ss_pred eecccchhhcchhHHHHHHHhhc
Q 028830 114 ELCHLCNRYIRLRERYNHESRCT 136 (203)
Q Consensus 114 ~~C~~C~~~f~~~~l~~H~~~~~ 136 (203)
|+|+.|+.......|..|++.+|
T Consensus 1 y~C~~C~y~t~~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTSKSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EESHHHHHHHHHHHH
T ss_pred CCCCCCCCcCCHHHHHHHHHhhC
Confidence 56667765334446777766654
No 45
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.79 E-value=0.0062 Score=28.97 Aligned_cols=19 Identities=26% Similarity=0.529 Sum_probs=9.7
Q ss_pred ecccchhhcchhHHHHHHH
Q 028830 115 LCHLCNRYIRLRERYNHES 133 (203)
Q Consensus 115 ~C~~C~~~f~~~~l~~H~~ 133 (203)
.|+.||+.|....|..|+.
T Consensus 4 ~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEECHHHHHHHHH
Confidence 4555555555455555543
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.71 E-value=0.0093 Score=28.35 Aligned_cols=21 Identities=24% Similarity=0.597 Sum_probs=15.2
Q ss_pred ccCccCCCCCChhhHHHHHHH
Q 028830 88 VTCDFCEFPLPAVDLAEHQEV 108 (203)
Q Consensus 88 ~~C~~C~~~f~~~~l~~H~~~ 108 (203)
..|+.||+.|..+.|..|+.+
T Consensus 3 ~~C~~CgR~F~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKFNPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEECHHHHHHHHHh
Confidence 467778877777777777654
No 47
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.51 E-value=0.014 Score=32.54 Aligned_cols=29 Identities=21% Similarity=0.296 Sum_probs=20.3
Q ss_pred CCcceecccchhhcch-hHHHHHHHhhcCC
Q 028830 110 GNRTELCHLCNRYIRL-RERYNHESRCTGV 138 (203)
Q Consensus 110 ~~~~~~C~~C~~~f~~-~~l~~H~~~~~~~ 138 (203)
.+.|..|++|+..+++ .+|.+|+...|..
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 5779999999999984 6999999887764
No 48
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.12 E-value=0.0071 Score=28.55 Aligned_cols=19 Identities=21% Similarity=0.509 Sum_probs=9.1
Q ss_pred ecccchhhcc-hhHHHHHHH
Q 028830 115 LCHLCNRYIR-LRERYNHES 133 (203)
Q Consensus 115 ~C~~C~~~f~-~~~l~~H~~ 133 (203)
.|..|++.|. ...|..|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 4555555554 235555543
No 49
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.00 E-value=0.047 Score=47.11 Aligned_cols=71 Identities=21% Similarity=0.366 Sum_probs=40.3
Q ss_pred cccccccccccccHHHHHH-cCCCCccCccC----------hhhhhHHHHHhhHhccCC-CC----cccCccCCCCCC-h
Q 028830 37 RCKVCGDMVPRKYAEEHFL-NTHAPVACSQC----------SETMEREILAIHKGENCP-QR----IVTCDFCEFPLP-A 99 (203)
Q Consensus 37 ~C~~C~~~f~~~~~~~~~~-~~h~~~~C~~C----------~~~f~~~~l~~H~~~h~~-~~----~~~C~~C~~~f~-~ 99 (203)
.|..| ..|.....|..|+ ..|+.+.|..| .+.|....|..|+..... ++ .-.|..|...|. .
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~ 195 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDD 195 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccH
Confidence 46667 5565554443333 56655554443 334445567777665432 11 235777777777 7
Q ss_pred hhHHHHHHH
Q 028830 100 VDLAEHQEV 108 (203)
Q Consensus 100 ~~l~~H~~~ 108 (203)
..|.+|++.
T Consensus 196 ~el~rH~~~ 204 (669)
T KOG2231|consen 196 DELYRHLRF 204 (669)
T ss_pred HHHHHhhcc
Confidence 777777775
No 50
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.99 E-value=0.018 Score=26.84 Aligned_cols=21 Identities=19% Similarity=0.547 Sum_probs=13.6
Q ss_pred ccCccCCCCCChhhHHHHHHH
Q 028830 88 VTCDFCEFPLPAVDLAEHQEV 108 (203)
Q Consensus 88 ~~C~~C~~~f~~~~l~~H~~~ 108 (203)
|+|+.|+.......|.+|++.
T Consensus 1 y~C~~C~y~t~~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTSKSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EESHHHHHHHHHH
T ss_pred CCCCCCCCcCCHHHHHHHHHh
Confidence 578888765555678888776
No 51
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.65 E-value=0.019 Score=26.99 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=18.7
Q ss_pred ccCccCCCCCC-hhhHHHHHHH
Q 028830 88 VTCDFCEFPLP-AVDLAEHQEV 108 (203)
Q Consensus 88 ~~C~~C~~~f~-~~~l~~H~~~ 108 (203)
|.|..|++.|. ...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 67999999999 9999999863
No 52
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.31 E-value=0.0084 Score=29.00 Aligned_cols=20 Identities=25% Similarity=0.542 Sum_probs=11.0
Q ss_pred ccCccCCCCCC-hhhHHHHHH
Q 028830 88 VTCDFCEFPLP-AVDLAEHQE 107 (203)
Q Consensus 88 ~~C~~C~~~f~-~~~l~~H~~ 107 (203)
|.|..|++.|. ...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 44555555555 555555543
No 53
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=94.14 E-value=0.031 Score=42.04 Aligned_cols=49 Identities=18% Similarity=0.448 Sum_probs=41.0
Q ss_pred cccCccCCCcCccccHHHHHhhcCCCcccccccccccccccHHHHHHcC
Q 028830 9 TKICSHCDRAIPSSNIDLHFAHCSRNLERCKVCGDMVPRKYAEEHFLNT 57 (203)
Q Consensus 9 ~y~C~~C~~~f~~~~l~~H~~h~~~~~~~C~~C~~~f~~~~~~~~~~~~ 57 (203)
.|.|+.||....+..+.+|+..+...-|.|-.|+..|..-....|...+
T Consensus 3 ~FtCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k~F~~~sYknH~kCI 51 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGKTFERVSYKNHTKCI 51 (276)
T ss_pred EEehhhhhhhccccchHHHHHhccCCeeEEeecccccccchhhhhhhhc
Confidence 4889999999988889999777777889999999999987666665443
No 54
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=93.67 E-value=0.037 Score=41.64 Aligned_cols=46 Identities=17% Similarity=0.403 Sum_probs=24.5
Q ss_pred ccCccChhhhhHHHHHhhHhccCCCCcccCccCCCCCChhhHHHHHH
Q 028830 61 VACSQCSETMEREILAIHKGENCPQRIVTCDFCEFPLPAVDLAEHQE 107 (203)
Q Consensus 61 ~~C~~C~~~f~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~l~~H~~ 107 (203)
|.|..||.......+..|+....+ .-|.|-.|++.|-..++..|..
T Consensus 4 FtCnvCgEsvKKp~vekH~srCrn-~~fSCIDC~k~F~~~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHMSRCRN-AYFSCIDCGKTFERVSYKNHTK 49 (276)
T ss_pred EehhhhhhhccccchHHHHHhccC-CeeEEeecccccccchhhhhhh
Confidence 455566655555455555554333 4555666666655444555544
No 55
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=93.57 E-value=0.0094 Score=34.87 Aligned_cols=46 Identities=41% Similarity=0.902 Sum_probs=24.0
Q ss_pred CccCcc--ChhhhhHHHHHhhHhccCCCCcccCcc----CCCCCChhhHHHH
Q 028830 60 PVACSQ--CSETMEREILAIHKGENCPQRIVTCDF----CEFPLPAVDLAEH 105 (203)
Q Consensus 60 ~~~C~~--C~~~f~~~~l~~H~~~h~~~~~~~C~~----C~~~f~~~~l~~H 105 (203)
+..|+. |...+.+..|..|....+..++..|++ |+..+....|.+|
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 445555 444455556666666666666777777 6666655555444
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.11 E-value=0.074 Score=30.18 Aligned_cols=28 Identities=21% Similarity=0.468 Sum_probs=17.8
Q ss_pred CCcceecccchhhcc-hhHHHHHHHhhcC
Q 028830 110 GNRTELCHLCNRYIR-LRERYNHESRCTG 137 (203)
Q Consensus 110 ~~~~~~C~~C~~~f~-~~~l~~H~~~~~~ 137 (203)
||--+.|+.||..|. +.++.+|.-..|+
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 555667777777776 4567777655444
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=92.73 E-value=0.087 Score=26.90 Aligned_cols=22 Identities=14% Similarity=0.457 Sum_probs=15.7
Q ss_pred cccCccCCCCCC-hhhHHHHHHH
Q 028830 87 IVTCDFCEFPLP-AVDLAEHQEV 108 (203)
Q Consensus 87 ~~~C~~C~~~f~-~~~l~~H~~~ 108 (203)
+|.|+.|++.|. ...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 466777777777 7777777654
No 58
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=92.40 E-value=0.064 Score=49.35 Aligned_cols=26 Identities=15% Similarity=0.112 Sum_probs=21.5
Q ss_pred Ccceecccchhhcc-hhHHHHHHHhhc
Q 028830 111 NRTELCHLCNRYIR-LRERYNHESRCT 136 (203)
Q Consensus 111 ~~~~~C~~C~~~f~-~~~l~~H~~~~~ 136 (203)
.++|.|..|...++ ..+|..|++..-
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS~~ 542 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQSDL 542 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHHHh
Confidence 47899999999888 579999997653
No 59
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.05 E-value=0.17 Score=37.03 Aligned_cols=75 Identities=23% Similarity=0.419 Sum_probs=39.5
Q ss_pred ccCcc--ChhhhhH-HHHHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHH-h----------CCcceec--ccchhhc
Q 028830 61 VACSQ--CSETMER-EILAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEV-C----------GNRTELC--HLCNRYI 123 (203)
Q Consensus 61 ~~C~~--C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~-~----------~~~~~~C--~~C~~~f 123 (203)
+.|.. |...|.. .+...|..+-++ -.|.+|.+.|. ..-|..|+.. | |.-+|.| ..|+..|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 44543 4444444 445555544222 25666666666 5555556543 3 3345666 4666666
Q ss_pred c-hhHHHHHHHhhcCC
Q 028830 124 R-LRERYNHESRCTGV 138 (203)
Q Consensus 124 ~-~~~l~~H~~~~~~~ 138 (203)
. ...-..|+...|.-
T Consensus 157 kT~r~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMHKY 172 (253)
T ss_pred hhhhhhhhHHHHhccC
Confidence 5 35666666555443
No 60
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.67 E-value=0.12 Score=40.82 Aligned_cols=70 Identities=23% Similarity=0.366 Sum_probs=40.3
Q ss_pred ccCccChhhhhH-HHHHhhHhccCCCCcccCccCCCC-------CC-hhhHHHHHHH-hCCcceecc--cc--hh--hcc
Q 028830 61 VACSQCSETMER-EILAIHKGENCPQRIVTCDFCEFP-------LP-AVDLAEHQEV-CGNRTELCH--LC--NR--YIR 124 (203)
Q Consensus 61 ~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~-------f~-~~~l~~H~~~-~~~~~~~C~--~C--~~--~f~ 124 (203)
-.|..|...|-. ..|..|.+. +.-.|-+|++. |. ..+|..|.+. | |.|. .| |+ .|.
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~----~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~k~~vf~ 292 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRL----RHEACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVGKCYVFP 292 (493)
T ss_pred chhhhccceecChHHHHHHHHh----hhhhhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecCcEEEec
Confidence 357777777766 567777664 44455555433 44 5666666665 4 4442 22 22 455
Q ss_pred h-hHHHHHHHhhcCC
Q 028830 125 L-RERYNHESRCTGV 138 (203)
Q Consensus 125 ~-~~l~~H~~~~~~~ 138 (203)
. ..|..|+..-|+.
T Consensus 293 ~~~el~~h~~~~h~~ 307 (493)
T COG5236 293 YHTELLEHLTRFHKV 307 (493)
T ss_pred cHHHHHHHHHHHhhc
Confidence 3 5888887665554
No 61
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.95 E-value=0.083 Score=29.99 Aligned_cols=24 Identities=17% Similarity=0.296 Sum_probs=18.9
Q ss_pred cCCCCcccCccCCCcCc-cccHHHH
Q 028830 4 TSDETTKICSHCDRAIP-SSNIDLH 27 (203)
Q Consensus 4 h~~~k~y~C~~C~~~f~-~~~l~~H 27 (203)
-.||..+.|+.|+..|. ..++.+|
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RH 36 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRH 36 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHH
Confidence 34677788888888887 7788888
No 62
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=90.01 E-value=0.09 Score=39.35 Aligned_cols=30 Identities=23% Similarity=0.641 Sum_probs=15.0
Q ss_pred CccChhhhhH-HHHHhhHhccCCCCcccCccCCCC
Q 028830 63 CSQCSETMER-EILAIHKGENCPQRIVTCDFCEFP 96 (203)
Q Consensus 63 C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~ 96 (203)
|-+|++.|.. +.|.+|++. +.|+|.+|-+.
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkk 43 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKK 43 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhh
Confidence 4455555544 445555543 45555555443
No 63
>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=89.52 E-value=0.22 Score=25.28 Aligned_cols=10 Identities=20% Similarity=0.640 Sum_probs=5.6
Q ss_pred ccCccCCCcC
Q 028830 10 KICSHCDRAI 19 (203)
Q Consensus 10 y~C~~C~~~f 19 (203)
|.|..||..+
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 4566666553
No 64
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.37 E-value=0.49 Score=31.39 Aligned_cols=27 Identities=19% Similarity=0.499 Sum_probs=17.0
Q ss_pred ccCccCCCcCccccHHHHHhhcCCCcccccccccccccc
Q 028830 10 KICSHCDRAIPSSNIDLHFAHCSRNLERCKVCGDMVPRK 48 (203)
Q Consensus 10 y~C~~C~~~f~~~~l~~H~~h~~~~~~~C~~C~~~f~~~ 48 (203)
|.|+.|+-..- +-|..|+.||......
T Consensus 2 Y~CPrC~skvC------------~LP~~CpiCgLtLVss 28 (112)
T TIGR00622 2 YFCPQCRAKVC------------ELPVECPICGLTLILS 28 (112)
T ss_pred ccCCCCCCCcc------------CCCCcCCcCCCEEecc
Confidence 66777765421 2366777787776666
No 65
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=89.25 E-value=0.39 Score=31.77 Aligned_cols=15 Identities=27% Similarity=0.634 Sum_probs=7.6
Q ss_pred Ccccccccccccccc
Q 028830 34 NLERCKVCGDMVPRK 48 (203)
Q Consensus 34 ~~~~C~~C~~~f~~~ 48 (203)
.|..|+.||..|...
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 345555555555443
No 66
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=89.07 E-value=0.14 Score=47.34 Aligned_cols=94 Identities=13% Similarity=0.176 Sum_probs=50.2
Q ss_pred ccccccccccccccHHHHHHcCCCCccCccChhhhhH-HHHHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHHhCCcc
Q 028830 36 ERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETMER-EILAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEVCGNRT 113 (203)
Q Consensus 36 ~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~ 113 (203)
+.|..|++.|.....+. +...-..|.|..|...|.. ..|..|.+ .|.+.+. .....-|...+....
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~l~~~~~-----------k~~~~~~~~~~~~~~~l~~~d~~ 1328 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLDVTHRYLCRQCKMAFDGEAPLTAHQR-----------KFCFAGRGSGGSMPPPLRVPDCT 1328 (1406)
T ss_pred chhhhccccccCcccee-ecccchhHHHHHHHhhhcchhHHHHHHH-----------HHHhccCccccCCCCcccCcccc
Confidence 45666665555553332 2222235556666655555 45555542 1222333 333333333332233
Q ss_pred eecccchhhcc-hhHHHHHHHhhcCCCCC
Q 028830 114 ELCHLCNRYIR-LRERYNHESRCTGVPEN 141 (203)
Q Consensus 114 ~~C~~C~~~f~-~~~l~~H~~~~~~~~~~ 141 (203)
|.|..|...|+ +..|..||+..+.....
T Consensus 1329 ~~c~~c~~~~~~~~alqihm~~~~~~~kt 1357 (1406)
T KOG1146|consen 1329 YHCLACEVLLSGREALQIHMRSSAHRRKT 1357 (1406)
T ss_pred ccchHHHhhcchhHHHHHHHHHhhhcccC
Confidence 44999999998 57999999877665543
No 67
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=88.44 E-value=0.57 Score=37.13 Aligned_cols=127 Identities=18% Similarity=0.216 Sum_probs=77.6
Q ss_pred cccCccCCCcCc--cccHHHH--Hhhc---C------------------CCcccccccccccccccHHHHHHcC--CC--
Q 028830 9 TKICSHCDRAIP--SSNIDLH--FAHC---S------------------RNLERCKVCGDMVPRKYAEEHFLNT--HA-- 59 (203)
Q Consensus 9 ~y~C~~C~~~f~--~~~l~~H--~~h~---~------------------~~~~~C~~C~~~f~~~~~~~~~~~~--h~-- 59 (203)
.-.|-.|...+. ++..-.| +.|- | -..+.|-.|.+.|..+..+..||+. |+
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrri 223 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRI 223 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCccc
Confidence 356888888885 7777777 4442 1 1236899999999999888888764 32
Q ss_pred -C--------ccC--ccChhhhhH--HHHH-----hhHhcc--------CCCCc--ccCccCCCCCC-hhhHHHHHHH-h
Q 028830 60 -P--------VAC--SQCSETMER--EILA-----IHKGEN--------CPQRI--VTCDFCEFPLP-AVDLAEHQEV-C 109 (203)
Q Consensus 60 -~--------~~C--~~C~~~f~~--~~l~-----~H~~~h--------~~~~~--~~C~~C~~~f~-~~~l~~H~~~-~ 109 (203)
| |.= ..-|++..- +.+. .+.... .+..+ .+|-.|....- ...|..||++ |
T Consensus 224 nPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 224 NPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred CCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHHHH
Confidence 1 110 112222211 1110 111100 12223 58999999887 8999999998 7
Q ss_pred CC---------------------------cceecccchhhcch-hHHHHHHHhh
Q 028830 110 GN---------------------------RTELCHLCNRYIRL-RERYNHESRC 135 (203)
Q Consensus 110 ~~---------------------------~~~~C~~C~~~f~~-~~l~~H~~~~ 135 (203)
.- +.-.|-.|...|-. ..|..||...
T Consensus 304 e~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 304 EFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred HhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 31 22457788888874 6899998543
No 68
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=88.10 E-value=0.11 Score=38.83 Aligned_cols=34 Identities=12% Similarity=0.278 Sum_probs=20.1
Q ss_pred ccccccccccccHHHHHHcCCCCccCccChhhhhH
Q 028830 38 CKVCGDMVPRKYAEEHFLNTHAPVACSQCSETMER 72 (203)
Q Consensus 38 C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~ 72 (203)
|=+|.+.|.....|..|++. +-|+|.+|-+..-+
T Consensus 13 cwycnrefddekiliqhqka-khfkchichkkl~s 46 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA-KHFKCHICHKKLFS 46 (341)
T ss_pred eeecccccchhhhhhhhhhh-ccceeeeehhhhcc
Confidence 66677777766555554432 45677777665433
No 69
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.10 E-value=0.32 Score=28.08 Aligned_cols=10 Identities=30% Similarity=0.720 Sum_probs=6.1
Q ss_pred CcccCccCCC
Q 028830 86 RIVTCDFCEF 95 (203)
Q Consensus 86 ~~~~C~~C~~ 95 (203)
.+|.|+.||.
T Consensus 49 ~~Y~Cp~CGF 58 (61)
T COG2888 49 NPYRCPKCGF 58 (61)
T ss_pred CceECCCcCc
Confidence 4666666664
No 70
>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=87.59 E-value=0.3 Score=23.36 Aligned_cols=9 Identities=22% Similarity=0.696 Sum_probs=4.2
Q ss_pred ecccchhhc
Q 028830 115 LCHLCNRYI 123 (203)
Q Consensus 115 ~C~~C~~~f 123 (203)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 345554444
No 71
>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=87.55 E-value=0.24 Score=25.94 Aligned_cols=33 Identities=18% Similarity=0.403 Sum_probs=17.9
Q ss_pred ccCccCCCcCc-cccHHHHHhhcCCCcccccccccccc
Q 028830 10 KICSHCDRAIP-SSNIDLHFAHCSRNLERCKVCGDMVP 46 (203)
Q Consensus 10 y~C~~C~~~f~-~~~l~~H~~h~~~~~~~C~~C~~~f~ 46 (203)
+.|+.|+..|. ..... ........|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~----~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL----GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc----CCCCCEEECCCCCCEEE
Confidence 56777777765 32211 11122466777776663
No 72
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=87.34 E-value=0.19 Score=41.16 Aligned_cols=51 Identities=22% Similarity=0.398 Sum_probs=44.2
Q ss_pred CcccCccCCCcCc-cccHHHH-H--hhcCC--Cccccc--ccccccccccHHHHHHcCC
Q 028830 8 TTKICSHCDRAIP-SSNIDLH-F--AHCSR--NLERCK--VCGDMVPRKYAEEHFLNTH 58 (203)
Q Consensus 8 k~y~C~~C~~~f~-~~~l~~H-~--~h~~~--~~~~C~--~C~~~f~~~~~~~~~~~~h 58 (203)
.++.|..|...|. ...|..| . .|.++ +++.|+ .|++.|.....+..|...|
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 346 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH 346 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccc
Confidence 5789999999998 9999999 7 79999 999999 7999999997776666666
No 73
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.03 E-value=0.24 Score=27.24 Aligned_cols=30 Identities=23% Similarity=0.473 Sum_probs=17.9
Q ss_pred cccCccCCCcCc-cccHHHHHhhcCCCccccccccccccc
Q 028830 9 TKICSHCDRAIP-SSNIDLHFAHCSRNLERCKVCGDMVPR 47 (203)
Q Consensus 9 ~y~C~~C~~~f~-~~~l~~H~~h~~~~~~~C~~C~~~f~~ 47 (203)
.|.|+.|+..|. .... ....|+.||..+..
T Consensus 3 ~y~C~~CG~~~~~~~~~---------~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKCARCGREVELDEYG---------TGVRCPYCGYRILF 33 (46)
T ss_pred EEECCCCCCEEEECCCC---------CceECCCCCCeEEE
Confidence 577778877764 2211 14667777765543
No 74
>PHA00626 hypothetical protein
Probab=86.85 E-value=0.24 Score=28.20 Aligned_cols=16 Identities=13% Similarity=0.154 Sum_probs=9.8
Q ss_pred cceecccchhhcchhH
Q 028830 112 RTELCHLCNRYIRLRE 127 (203)
Q Consensus 112 ~~~~C~~C~~~f~~~~ 127 (203)
..|.|+.||..|+...
T Consensus 22 nrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 22 DDYVCCDCGYNDSKDA 37 (59)
T ss_pred cceEcCCCCCeechhh
Confidence 3577777776666543
No 75
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.79 E-value=0.28 Score=25.62 Aligned_cols=31 Identities=29% Similarity=0.643 Sum_probs=16.9
Q ss_pred ccCccCCCCCC-hhh-HHHHHHHhCCcceecccchhhc
Q 028830 88 VTCDFCEFPLP-AVD-LAEHQEVCGNRTELCHLCNRYI 123 (203)
Q Consensus 88 ~~C~~C~~~f~-~~~-l~~H~~~~~~~~~~C~~C~~~f 123 (203)
..|+.|+..|. ..+ |. -+.+..+|+.|+..|
T Consensus 3 i~CP~C~~~f~v~~~~l~-----~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLP-----AGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcc-----cCCcEEECCCCCcEe
Confidence 35677776665 332 21 234456677776655
No 76
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.67 E-value=0.99 Score=29.97 Aligned_cols=22 Identities=18% Similarity=0.300 Sum_probs=16.5
Q ss_pred CCCcccCccCCCcCc-cccHHHH
Q 028830 6 DETTKICSHCDRAIP-SSNIDLH 27 (203)
Q Consensus 6 ~~k~y~C~~C~~~f~-~~~l~~H 27 (203)
.+-|-.|+.|+...- ...|.+.
T Consensus 12 C~LP~~CpiCgLtLVss~HLARS 34 (112)
T TIGR00622 12 CELPVECPICGLTLILSTHLARS 34 (112)
T ss_pred cCCCCcCCcCCCEEeccchHHHh
Confidence 356889999998875 6666654
No 77
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.10 E-value=0.29 Score=36.63 Aligned_cols=14 Identities=14% Similarity=0.591 Sum_probs=11.3
Q ss_pred CCcccCccCCCcCc
Q 028830 7 ETTKICSHCDRAIP 20 (203)
Q Consensus 7 ~k~y~C~~C~~~f~ 20 (203)
+|.+.||.|+..|.
T Consensus 3 ~k~~~CPvC~~~F~ 16 (214)
T PF09986_consen 3 DKKITCPVCGKEFK 16 (214)
T ss_pred CCceECCCCCCeee
Confidence 46788888888886
No 78
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.05 E-value=0.32 Score=35.65 Aligned_cols=76 Identities=22% Similarity=0.321 Sum_probs=52.1
Q ss_pred Ccccccc--cccccccccHHHHHHcCCCCccCccChhhhhHH-HHHhhHhc----------cCCCCcccCcc--CCCCCC
Q 028830 34 NLERCKV--CGDMVPRKYAEEHFLNTHAPVACSQCSETMERE-ILAIHKGE----------NCPQRIVTCDF--CEFPLP 98 (203)
Q Consensus 34 ~~~~C~~--C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~~-~l~~H~~~----------h~~~~~~~C~~--C~~~f~ 98 (203)
+.+.|++ |...|.......+|...--.-.|..|.+.|..+ -|..|+.. ..|.-.|.|-+ |+..|.
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFk 157 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFK 157 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhh
Confidence 3467876 666676654444443322245788999999773 55666543 34678899976 999998
Q ss_pred -hhhHHHHHHH-h
Q 028830 99 -AVDLAEHQEV-C 109 (203)
Q Consensus 99 -~~~l~~H~~~-~ 109 (203)
...-+.|+-. |
T Consensus 158 T~r~RkdH~I~~H 170 (253)
T KOG4173|consen 158 TSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhHHHHhc
Confidence 8888999877 5
No 79
>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=84.63 E-value=0.72 Score=23.58 Aligned_cols=10 Identities=20% Similarity=0.617 Sum_probs=5.9
Q ss_pred cccCccCCCc
Q 028830 9 TKICSHCDRA 18 (203)
Q Consensus 9 ~y~C~~C~~~ 18 (203)
.|+|..||..
T Consensus 2 ~~~C~~CG~i 11 (34)
T cd00729 2 VWVCPVCGYI 11 (34)
T ss_pred eEECCCCCCE
Confidence 3566666654
No 80
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=84.50 E-value=0.37 Score=34.03 Aligned_cols=13 Identities=23% Similarity=0.613 Sum_probs=6.6
Q ss_pred ccccccccccccc
Q 028830 36 ERCKVCGDMVPRK 48 (203)
Q Consensus 36 ~~C~~C~~~f~~~ 48 (203)
+.|+.||..|.+.
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 4555555555444
No 81
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=84.40 E-value=0.5 Score=24.50 Aligned_cols=32 Identities=19% Similarity=0.394 Sum_probs=15.9
Q ss_pred ccCccCCCCCC-hhhHHHHHHHhCCcceecccchhhc
Q 028830 88 VTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNRYI 123 (203)
Q Consensus 88 ~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~~f 123 (203)
..|+.|+..|. ...... -..+..+|+.|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~ip----~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP----PKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCC----CCCcEEECCCCCCEe
Confidence 35666666665 332110 223356666666554
No 82
>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=83.80 E-value=2.2 Score=28.12 Aligned_cols=24 Identities=21% Similarity=0.313 Sum_probs=19.4
Q ss_pred eec----ccchhhcc-hhHHHHHHHhhcC
Q 028830 114 ELC----HLCNRYIR-LRERYNHESRCTG 137 (203)
Q Consensus 114 ~~C----~~C~~~f~-~~~l~~H~~~~~~ 137 (203)
|.| ..|+.... ...+.+|.+..|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 99988666 5799999987764
No 83
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=83.68 E-value=0.88 Score=23.10 Aligned_cols=25 Identities=24% Similarity=0.442 Sum_probs=17.8
Q ss_pred ceecccchhhcchhHHHHHHHhhcC
Q 028830 113 TELCHLCNRYIRLRERYNHESRCTG 137 (203)
Q Consensus 113 ~~~C~~C~~~f~~~~l~~H~~~~~~ 137 (203)
.+.|+.|++.+...-+..|+..+.+
T Consensus 4 ~~~C~nC~R~v~a~RfA~HLekCmg 28 (33)
T PF08209_consen 4 YVECPNCGRPVAASRFAPHLEKCMG 28 (33)
T ss_dssp EEE-TTTSSEEEGGGHHHHHHHHTC
T ss_pred eEECCCCcCCcchhhhHHHHHHHHc
Confidence 4678888887777778888877654
No 84
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=83.65 E-value=4 Score=32.60 Aligned_cols=70 Identities=21% Similarity=0.302 Sum_probs=37.3
Q ss_pred cccccccccccccHHHHHHc-CC-CCccCccChh----hhhH-HHHHhhHhccCCCCcccCcc--CC--C--CCC-hhhH
Q 028830 37 RCKVCGDMVPRKYAEEHFLN-TH-APVACSQCSE----TMER-EILAIHKGENCPQRIVTCDF--CE--F--PLP-AVDL 102 (203)
Q Consensus 37 ~C~~C~~~f~~~~~~~~~~~-~h-~~~~C~~C~~----~f~~-~~l~~H~~~h~~~~~~~C~~--C~--~--~f~-~~~l 102 (203)
.|..|...|-....|..|.+ .| +-|.|+.-+. -|.. .+|..|.+. -.|.|.+ |- + .|. .-.|
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~----~hy~ct~qtc~~~k~~vf~~~~el 297 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRN----AHYCCTFQTCRVGKCYVFPYHTEL 297 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhc----CceEEEEEEEecCcEEEeccHHHH
Confidence 47777777766644444433 33 3444443332 2333 467777664 4566654 32 2 255 6667
Q ss_pred HHHHHH-hC
Q 028830 103 AEHQEV-CG 110 (203)
Q Consensus 103 ~~H~~~-~~ 110 (203)
..|+.. |+
T Consensus 298 ~~h~~~~h~ 306 (493)
T COG5236 298 LEHLTRFHK 306 (493)
T ss_pred HHHHHHHhh
Confidence 777766 63
No 85
>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=83.55 E-value=0.45 Score=26.79 Aligned_cols=11 Identities=18% Similarity=0.600 Sum_probs=7.1
Q ss_pred ccCccCCCcCc
Q 028830 10 KICSHCDRAIP 20 (203)
Q Consensus 10 y~C~~C~~~f~ 20 (203)
|+|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 66666666665
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=83.40 E-value=1.2 Score=30.20 Aligned_cols=29 Identities=14% Similarity=0.175 Sum_probs=15.3
Q ss_pred ccccccccccccccHHHHHHcCCCCccCccChhhhhH
Q 028830 36 ERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETMER 72 (203)
Q Consensus 36 ~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~ 72 (203)
..|+.||..|-..+ + .|..|++||..|.-
T Consensus 10 r~Cp~cg~kFYDLn------k--~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 10 RICPNTGSKFYDLN------R--RPAVSPYTGEQFPP 38 (129)
T ss_pred ccCCCcCccccccC------C--CCccCCCcCCccCc
Confidence 34666666664321 1 36666666665543
No 87
>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=83.36 E-value=1 Score=21.46 Aligned_cols=20 Identities=20% Similarity=0.310 Sum_probs=11.8
Q ss_pred ecccchhhcchhHHHHHHHh
Q 028830 115 LCHLCNRYIRLRERYNHESR 134 (203)
Q Consensus 115 ~C~~C~~~f~~~~l~~H~~~ 134 (203)
.||.|++.+....+..|+..
T Consensus 3 ~CPiC~~~v~~~~in~HLD~ 22 (26)
T smart00734 3 QCPVCFREVPENLINSHLDS 22 (26)
T ss_pred cCCCCcCcccHHHHHHHHHH
Confidence 46666666555566666543
No 88
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=82.57 E-value=0.93 Score=33.43 Aligned_cols=53 Identities=23% Similarity=0.387 Sum_probs=30.3
Q ss_pred cccCcc----CCCCCChhhHHHHHHHhCCcceeccc----chhhcchhHHHHHHHhhcCCC
Q 028830 87 IVTCDF----CEFPLPAVDLAEHQEVCGNRTELCHL----CNRYIRLRERYNHESRCTGVP 139 (203)
Q Consensus 87 ~~~C~~----C~~~f~~~~l~~H~~~~~~~~~~C~~----C~~~f~~~~l~~H~~~~~~~~ 139 (203)
.+.|.. |...+.......|.+.+.-+|+.|+. |+..=....|..|....|...
T Consensus 14 ~~pC~~~~~GC~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~ 74 (198)
T PF03145_consen 14 KFPCKNAKYGCTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWN 74 (198)
T ss_dssp -EE-CCGGGT---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTS
T ss_pred eecCCCCCCCCcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCc
Confidence 455655 77777777778888888888888877 643223468888888777653
No 89
>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=82.11 E-value=0.57 Score=24.76 Aligned_cols=11 Identities=18% Similarity=0.634 Sum_probs=7.1
Q ss_pred ccCccCCCcCc
Q 028830 10 KICSHCDRAIP 20 (203)
Q Consensus 10 y~C~~C~~~f~ 20 (203)
|+|+.|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 56666666664
No 90
>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=81.63 E-value=1.4 Score=31.31 Aligned_cols=41 Identities=10% Similarity=0.117 Sum_probs=28.4
Q ss_pred HHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHHhCCcceecccchhhc
Q 028830 75 LAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNRYI 123 (203)
Q Consensus 75 l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~~f 123 (203)
|..-+.......-|.|+.|+..|+ ...+. .-|.|+.||...
T Consensus 97 lk~~l~~e~~~~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 97 LREKLEFETNNMFFICPNMCVRFTFNEAME--------LNFTCPRCGAML 138 (158)
T ss_pred HHHHHhhccCCCeEECCCCCcEeeHHHHHH--------cCCcCCCCCCEe
Confidence 333334445557789999999998 66664 258999999743
No 91
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=81.51 E-value=1.9 Score=29.49 Aligned_cols=52 Identities=17% Similarity=0.390 Sum_probs=29.7
Q ss_pred CCcccccccccccccccHHHHHHcCCCCccCccChhhhhH---HHHHhhHhccCCCCcccCccCCCCCC
Q 028830 33 RNLERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETMER---EILAIHKGENCPQRIVTCDFCEFPLP 98 (203)
Q Consensus 33 ~~~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~---~~l~~H~~~h~~~~~~~C~~C~~~f~ 98 (203)
.+.|+|++|..+......+ +|-+| ||...-. ..|+.|-..| -+|+.|.-+|.
T Consensus 78 ~~lYeCnIC~etS~ee~FL-------KPneC--CgY~iCn~Cya~LWK~~~~y-----pvCPvCkTSFK 132 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFL-------KPNEC--CGYSICNACYANLWKFCNLY-----PVCPVCKTSFK 132 (140)
T ss_pred CCceeccCcccccchhhcC-------Ccccc--cchHHHHHHHHHHHHHcccC-----CCCCccccccc
Confidence 4667888887776554322 45555 5544433 3555554432 26777777775
No 92
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=81.40 E-value=0.95 Score=24.67 Aligned_cols=26 Identities=35% Similarity=0.871 Sum_probs=15.7
Q ss_pred ccCccCCCcCc-cccHHHHHhhcCCCccccccccccc
Q 028830 10 KICSHCDRAIP-SSNIDLHFAHCSRNLERCKVCGDMV 45 (203)
Q Consensus 10 y~C~~C~~~f~-~~~l~~H~~h~~~~~~~C~~C~~~f 45 (203)
|.|..|+..|. . ...+..|+.||...
T Consensus 3 Y~C~~Cg~~~~~~----------~~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRENEIK----------SKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCEeecC----------CCCceECCCCCceE
Confidence 67777777665 2 12356677776554
No 93
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=81.31 E-value=1.8 Score=30.29 Aligned_cols=45 Identities=11% Similarity=0.102 Sum_probs=26.6
Q ss_pred HhhHhccCCCCcccCccCCCCCC-hhhHHHHHHHhCCcceecccchhhc
Q 028830 76 AIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNRYI 123 (203)
Q Consensus 76 ~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~~f 123 (203)
..-........-|.|+.|+..|. ...+.. . .....|.|+.||...
T Consensus 88 ~~~l~~e~~~~~Y~Cp~C~~~y~~~ea~~~-~--d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 88 EDKLEDETNNAYYKCPNCQSKYTFLEANQL-L--DMDGTFTCPRCGEEL 133 (147)
T ss_pred HHHHhcccCCcEEECcCCCCEeeHHHHHHh-c--CCCCcEECCCCCCEE
Confidence 33333344556788999998887 433221 0 123348999998744
No 94
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=80.91 E-value=0.34 Score=39.58 Aligned_cols=57 Identities=18% Similarity=0.314 Sum_probs=36.6
Q ss_pred CccCccChhhhhH-HHHHhhHh--ccCCC--CcccCc--cCCCCCC-hhhHHHHHHH-hCCcceec
Q 028830 60 PVACSQCSETMER-EILAIHKG--ENCPQ--RIVTCD--FCEFPLP-AVDLAEHQEV-CGNRTELC 116 (203)
Q Consensus 60 ~~~C~~C~~~f~~-~~l~~H~~--~h~~~--~~~~C~--~C~~~f~-~~~l~~H~~~-~~~~~~~C 116 (203)
++.|..|...|.. ..|..|.. .|.++ +++.|+ .|++.|. ...+..|... .+..++.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 4666667666666 56666666 56666 677777 5777776 6666666666 34444444
No 95
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=80.90 E-value=0.24 Score=37.08 Aligned_cols=39 Identities=18% Similarity=0.287 Sum_probs=21.6
Q ss_pred CcccCccCCCCCC-hhhHHHHHHH-h----------CCc-----ceecccchhhcc
Q 028830 86 RIVTCDFCEFPLP-AVDLAEHQEV-C----------GNR-----TELCHLCNRYIR 124 (203)
Q Consensus 86 ~~~~C~~C~~~f~-~~~l~~H~~~-~----------~~~-----~~~C~~C~~~f~ 124 (203)
+.+.|++|++.|. ..-.....+. . +.. ...||.||.++.
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~ 59 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAF 59 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccc
Confidence 4567777777775 4333333322 1 112 257999998664
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=80.30 E-value=1.2 Score=25.77 Aligned_cols=10 Identities=40% Similarity=0.810 Sum_probs=6.2
Q ss_pred CcccCccCCC
Q 028830 86 RIVTCDFCEF 95 (203)
Q Consensus 86 ~~~~C~~C~~ 95 (203)
.+|+|+.||.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 4666666664
No 97
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=80.29 E-value=0.84 Score=32.00 Aligned_cols=36 Identities=17% Similarity=0.455 Sum_probs=15.9
Q ss_pred CcccccccccccccccHHHHHHcCCCCccCccChhhh
Q 028830 34 NLERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETM 70 (203)
Q Consensus 34 ~~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f 70 (203)
.-|.|+.|+..|.....+... ..-..|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~-d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLL-DMDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhc-CCCCcEECCCCCCEE
Confidence 345666666655543211110 001236666666544
No 98
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=79.12 E-value=2.4 Score=27.95 Aligned_cols=77 Identities=16% Similarity=0.215 Sum_probs=43.3
Q ss_pred CcccccccccccccccHHHHHHcCCCCccCccC---hhhhhH-HHH-HhhHhcc------------CCCCcccC----cc
Q 028830 34 NLERCKVCGDMVPRKYAEEHFLNTHAPVACSQC---SETMER-EIL-AIHKGEN------------CPQRIVTC----DF 92 (203)
Q Consensus 34 ~~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C---~~~f~~-~~l-~~H~~~h------------~~~~~~~C----~~ 92 (203)
+-..|..|+..........|....|....-..- .+.+.. ..| ....... ....-|.| ..
T Consensus 10 ~vlIC~~C~~av~~~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~~~~~ 89 (109)
T PF12013_consen 10 RVLICRQCQYAVQPSEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQCDPPH 89 (109)
T ss_pred CEEEeCCCCcccCchHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeecCCCC
Confidence 345689999988887666666656543221110 111111 111 0000000 01145899 89
Q ss_pred CCCCCC-hhhHHHHHHH-hC
Q 028830 93 CEFPLP-AVDLAEHQEV-CG 110 (203)
Q Consensus 93 C~~~f~-~~~l~~H~~~-~~ 110 (203)
|+..+. ...+.+|++. ||
T Consensus 90 C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 90 CGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCcEeccHHHHHHHHHHhcC
Confidence 999988 9999999988 65
No 99
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.57 E-value=1.7 Score=31.58 Aligned_cols=41 Identities=15% Similarity=0.282 Sum_probs=27.0
Q ss_pred HHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHHhCCcceecccchhhc
Q 028830 75 LAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNRYI 123 (203)
Q Consensus 75 l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~~f 123 (203)
|..-+.......-|.|+.|+..|+ ...+. ..|.|+.||...
T Consensus 105 lk~~l~~e~~~~~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L 146 (178)
T PRK06266 105 LKEQLEEEENNMFFFCPNCHIRFTFDEAME--------YGFRCPQCGEML 146 (178)
T ss_pred HHHHhhhccCCCEEECCCCCcEEeHHHHhh--------cCCcCCCCCCCC
Confidence 333333334456788999999988 65543 258999998633
No 100
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=78.43 E-value=0.5 Score=41.19 Aligned_cols=54 Identities=17% Similarity=0.434 Sum_probs=22.5
Q ss_pred CccCCCcCc-cccHHHHHhhcCCCccc-ccccccccccccHHHHHHcCCCCccCccChh
Q 028830 12 CSHCDRAIP-SSNIDLHFAHCSRNLER-CKVCGDMVPRKYAEEHFLNTHAPVACSQCSE 68 (203)
Q Consensus 12 C~~C~~~f~-~~~l~~H~~h~~~~~~~-C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~ 68 (203)
|..||-.|+ ...|-.-+.++.-+.|. |+.|.+.+......+.|. .+..|+.||-
T Consensus 126 CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfHA---Qp~aCp~CGP 181 (750)
T COG0068 126 CTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFHA---QPIACPKCGP 181 (750)
T ss_pred cCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCcccccccc---ccccCcccCC
Confidence 455555554 44433223333333332 555555544443322221 2445555554
No 101
>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=77.42 E-value=0.62 Score=25.05 Aligned_cols=11 Identities=18% Similarity=0.616 Sum_probs=5.4
Q ss_pred ccCccCCCcCc
Q 028830 10 KICSHCDRAIP 20 (203)
Q Consensus 10 y~C~~C~~~f~ 20 (203)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 44555555443
No 102
>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=75.70 E-value=1.3 Score=31.49 Aligned_cols=32 Identities=16% Similarity=0.212 Sum_probs=18.4
Q ss_pred CCcccccccccccccccHHHHHHcCCCCccCccChhhh
Q 028830 33 RNLERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETM 70 (203)
Q Consensus 33 ~~~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f 70 (203)
..-|.|+.|+..|+....+. .-|.|+.||...
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME------LNFTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH------cCCcCCCCCCEe
Confidence 34466777776665553332 256777777654
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=75.66 E-value=2.1 Score=21.56 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=5.6
Q ss_pred ccCccCCCcCc
Q 028830 10 KICSHCDRAIP 20 (203)
Q Consensus 10 y~C~~C~~~f~ 20 (203)
|.|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 45556665543
No 104
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=75.30 E-value=1.3 Score=27.01 Aligned_cols=38 Identities=13% Similarity=0.289 Sum_probs=20.9
Q ss_pred ccCccCCCcCc-cccHHHHHhhcCCCccccc--ccccccccc
Q 028830 10 KICSHCDRAIP-SSNIDLHFAHCSRNLERCK--VCGDMVPRK 48 (203)
Q Consensus 10 y~C~~C~~~f~-~~~l~~H~~h~~~~~~~C~--~C~~~f~~~ 48 (203)
+.|+.|+..-. ..+-..... ..++-+.|. .||..|...
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~-~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT-TKERYHQCQNVNCSATFITY 42 (72)
T ss_pred ccCCCCCCccEEEEChhcChh-hheeeeecCCCCCCCEEEEE
Confidence 46777776654 333222211 344556676 677777665
No 105
>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=73.86 E-value=2.3 Score=22.92 Aligned_cols=6 Identities=17% Similarity=0.008 Sum_probs=2.9
Q ss_pred HHHHHH
Q 028830 127 ERYNHE 132 (203)
Q Consensus 127 ~l~~H~ 132 (203)
.|..|+
T Consensus 35 ~l~~HL 40 (45)
T PF02892_consen 35 NLKRHL 40 (45)
T ss_dssp HHHHHH
T ss_pred HHHHhh
Confidence 444444
No 106
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=73.51 E-value=1.8 Score=31.39 Aligned_cols=31 Identities=26% Similarity=0.354 Sum_probs=16.7
Q ss_pred CcccccccccccccccHHHHHHcCCCCccCccChhhh
Q 028830 34 NLERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETM 70 (203)
Q Consensus 34 ~~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f 70 (203)
.-|.|+.|+..|+....+. .-|.|+.||...
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~------~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME------YGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHHHhh------cCCcCCCCCCCC
Confidence 3456666666665543221 246666666654
No 107
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=71.96 E-value=2.6 Score=32.24 Aligned_cols=10 Identities=20% Similarity=0.541 Sum_probs=6.0
Q ss_pred cceecccchh
Q 028830 112 RTELCHLCNR 121 (203)
Q Consensus 112 ~~~~C~~C~~ 121 (203)
+++.||.||.
T Consensus 208 k~~PCPKCg~ 217 (314)
T PF06524_consen 208 KPIPCPKCGY 217 (314)
T ss_pred CCCCCCCCCC
Confidence 4566666664
No 108
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=71.78 E-value=2.3 Score=30.44 Aligned_cols=23 Identities=26% Similarity=0.904 Sum_probs=15.5
Q ss_pred cccCccCCCCCChhhHHHHHHHhCCcceecccch
Q 028830 87 IVTCDFCEFPLPAVDLAEHQEVCGNRTELCHLCN 120 (203)
Q Consensus 87 ~~~C~~C~~~f~~~~l~~H~~~~~~~~~~C~~C~ 120 (203)
.|.|++||..+. |+-|-.||.||
T Consensus 134 ~~vC~vCGy~~~-----------ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHE-----------GEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCccc-----------CCCCCcCCCCC
Confidence 677888876542 34567788887
No 109
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=70.00 E-value=3.4 Score=22.96 Aligned_cols=22 Identities=23% Similarity=0.531 Sum_probs=14.7
Q ss_pred cccCccCCCCCC-h-----hhHHHHHHH
Q 028830 87 IVTCDFCEFPLP-A-----VDLAEHQEV 108 (203)
Q Consensus 87 ~~~C~~C~~~f~-~-----~~l~~H~~~ 108 (203)
-..|..|++.+. . +.|.+|++.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 456888887764 3 567777763
No 110
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=69.90 E-value=1.6 Score=24.36 Aligned_cols=11 Identities=27% Similarity=0.857 Sum_probs=6.4
Q ss_pred cccCccCCCcC
Q 028830 9 TKICSHCDRAI 19 (203)
Q Consensus 9 ~y~C~~C~~~f 19 (203)
.|.|..|++.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 45666666655
No 111
>PRK04023 DNA polymerase II large subunit; Validated
Probab=69.25 E-value=4.3 Score=37.19 Aligned_cols=9 Identities=33% Similarity=0.970 Sum_probs=5.9
Q ss_pred ceecccchh
Q 028830 113 TELCHLCNR 121 (203)
Q Consensus 113 ~~~C~~C~~ 121 (203)
++.|+.||.
T Consensus 663 ~y~CPKCG~ 671 (1121)
T PRK04023 663 EDECEKCGR 671 (1121)
T ss_pred CCcCCCCCC
Confidence 356777774
No 112
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=68.97 E-value=1.5 Score=32.85 Aligned_cols=30 Identities=10% Similarity=0.081 Sum_probs=22.9
Q ss_pred CCCCcccCccCCCCCC-hhhHHHHHHH-hCCc
Q 028830 83 CPQRIVTCDFCEFPLP-AVDLAEHQEV-CGNR 112 (203)
Q Consensus 83 ~~~~~~~C~~C~~~f~-~~~l~~H~~~-~~~~ 112 (203)
..+..|.|+.|+|.|. ..-...|+.. |.++
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 3556899999999999 9999999999 8654
No 113
>PF14353 CpXC: CpXC protein
Probab=68.46 E-value=3.9 Score=27.77 Aligned_cols=12 Identities=25% Similarity=0.576 Sum_probs=7.0
Q ss_pred ceecccchhhcc
Q 028830 113 TELCHLCNRYIR 124 (203)
Q Consensus 113 ~~~C~~C~~~f~ 124 (203)
.|.|+.||..|.
T Consensus 38 ~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 38 SFTCPSCGHKFR 49 (128)
T ss_pred EEECCCCCCcee
Confidence 466666666554
No 114
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=67.02 E-value=2.5 Score=37.56 Aligned_cols=11 Identities=18% Similarity=0.283 Sum_probs=6.3
Q ss_pred CcccCccCCCC
Q 028830 86 RIVTCDFCEFP 96 (203)
Q Consensus 86 ~~~~C~~C~~~ 96 (203)
.|..|+.||..
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 45566666544
No 115
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=66.57 E-value=3.3 Score=28.24 Aligned_cols=28 Identities=14% Similarity=0.350 Sum_probs=19.4
Q ss_pred cccCccCCCCCC-hh-hHHHHHHHhCCcceecccchh-hcc
Q 028830 87 IVTCDFCEFPLP-AV-DLAEHQEVCGNRTELCHLCNR-YIR 124 (203)
Q Consensus 87 ~~~C~~C~~~f~-~~-~l~~H~~~~~~~~~~C~~C~~-~f~ 124 (203)
|++|..||+.|. .+ .+.. -|+.||- .|.
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~----------GCP~CGg~kF~ 31 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILS----------GCPECGGNKFQ 31 (131)
T ss_pred CcccCcCCCCcCCCcHHHHc----------cCcccCCcceE
Confidence 578999999997 32 3332 4889985 664
No 116
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=64.94 E-value=7.7 Score=31.46 Aligned_cols=49 Identities=20% Similarity=0.302 Sum_probs=32.9
Q ss_pred CccCccChhhhhH-HHHHhhHhccCCC-----------------------CcccCccCC---CCCC-hhhHHHHHHH
Q 028830 60 PVACSQCSETMER-EILAIHKGENCPQ-----------------------RIVTCDFCE---FPLP-AVDLAEHQEV 108 (203)
Q Consensus 60 ~~~C~~C~~~f~~-~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~f~-~~~l~~H~~~ 108 (203)
|-.|-.|++.+.. ..-..||..++|- .-+.|-.|+ +.|. ....+.||..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 5678888888877 5566777766543 345666666 6666 6666777765
No 117
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=63.37 E-value=9.1 Score=31.61 Aligned_cols=37 Identities=14% Similarity=0.219 Sum_probs=22.5
Q ss_pred ccCCCCcccCccCCCCCC-hhhHHHHHHH-hCCcceecccch
Q 028830 81 ENCPQRIVTCDFCEFPLP-AVDLAEHQEV-CGNRTELCHLCN 120 (203)
Q Consensus 81 ~h~~~~~~~C~~C~~~f~-~~~l~~H~~~-~~~~~~~C~~C~ 120 (203)
..+....|.|+.|++.|+ ...++ .. -....|.|..|+
T Consensus 122 d~t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 122 DDTNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCG 160 (436)
T ss_pred hccccccccCCccccchhhhHHHH---hhcccCceEEEecCC
Confidence 344556788888888876 44332 22 233457787776
No 118
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=63.11 E-value=5.4 Score=31.55 Aligned_cols=98 Identities=16% Similarity=0.317 Sum_probs=47.9
Q ss_pred ccCccCCCcCccccHHHHHhh------cCCCccccccccccccccc-HHHHHHcCCCCccCc----cChhhhhHHHHHhh
Q 028830 10 KICSHCDRAIPSSNIDLHFAH------CSRNLERCKVCGDMVPRKY-AEEHFLNTHAPVACS----QCSETMEREILAIH 78 (203)
Q Consensus 10 y~C~~C~~~f~~~~l~~H~~h------~~~~~~~C~~C~~~f~~~~-~~~~~~~~h~~~~C~----~C~~~f~~~~l~~H 78 (203)
..||+|........++....| ..+...+|+.|...+.... +..........+.|+ .|.+.|....-..|
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~~~~H 128 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPTCRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCTKSFPYGEKSKH 128 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhhcccCCccccccccHHHHHHHHHHHhceecccccccCCceeecccccccc
Confidence 557777766554444443222 1256677777777766431 111111111234443 36666655222455
Q ss_pred HhccCCCCcccCcc----CCCCCChhhHHHHHHH
Q 028830 79 KGENCPQRIVTCDF----CEFPLPAVDLAEHQEV 108 (203)
Q Consensus 79 ~~~h~~~~~~~C~~----C~~~f~~~~l~~H~~~ 108 (203)
++. +.-.+|.|+. |...-....|..|...
T Consensus 129 E~~-C~f~~~~CP~p~~~C~~~G~~~~l~~H~~~ 161 (299)
T KOG3002|consen 129 EKV-CEFRPCSCPVPGAECKYTGSYKDLYAHLND 161 (299)
T ss_pred ccc-cccCCcCCCCCcccCCccCcHHHHHHHHHh
Confidence 553 2235666654 3322225566666665
No 119
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=61.46 E-value=5.1 Score=25.98 Aligned_cols=30 Identities=13% Similarity=0.164 Sum_probs=19.6
Q ss_pred CcccCccCCCCCC-hhhHHHHHHHhCCcceecccchh-hcc
Q 028830 86 RIVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNR-YIR 124 (203)
Q Consensus 86 ~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~-~f~ 124 (203)
+|+.|..||..|. -+.... --|+.||- .|.
T Consensus 1 MpH~CtrCG~vf~~g~~~il---------~GCp~CG~nkF~ 32 (112)
T COG3364 1 MPHQCTRCGEVFDDGSEEIL---------SGCPKCGCNKFL 32 (112)
T ss_pred CCceecccccccccccHHHH---------ccCccccchheE
Confidence 3678999999997 332221 25888886 564
No 120
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=61.18 E-value=11 Score=31.13 Aligned_cols=66 Identities=30% Similarity=0.503 Sum_probs=44.2
Q ss_pred ccChhhhhHHHHHhhHhccCCCCcccCcc-CCCCCChhhHHHHHHH-hCCcceecccchhhcchhHHHHHH
Q 028830 64 SQCSETMEREILAIHKGENCPQRIVTCDF-CEFPLPAVDLAEHQEV-CGNRTELCHLCNRYIRLRERYNHE 132 (203)
Q Consensus 64 ~~C~~~f~~~~l~~H~~~h~~~~~~~C~~-C~~~f~~~~l~~H~~~-~~~~~~~C~~C~~~f~~~~l~~H~ 132 (203)
..|........+..|+..- .+.+|+. |+..+....+..|++. +..+.-.|..|+..+....+..|.
T Consensus 94 ~GC~~~~~l~~~~~Hl~~c---~~~~C~~~C~~~~~~~d~~~hl~~~C~~~~~~c~~~~~~~~~~~~~~h~ 161 (391)
T KOG0297|consen 94 RGCRADLELEALQGHLSTC---DPLKCPHRCGVQVPRDDLEDHLEAECPRRSLKCSLCQSDSILILLEAHE 161 (391)
T ss_pred CCccccccHHHHHhHhccC---CcccCccccccccchHHHHHHHhcccccccccchhhcCccchhhhhhcC
Confidence 3455555556777777653 6777877 8877777778888866 777777777776655544444444
No 121
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=60.95 E-value=8.2 Score=20.56 Aligned_cols=22 Identities=23% Similarity=0.379 Sum_probs=15.0
Q ss_pred ccCccCCCCCC---hhhHHHHHHHh
Q 028830 88 VTCDFCEFPLP---AVDLAEHQEVC 109 (203)
Q Consensus 88 ~~C~~C~~~f~---~~~l~~H~~~~ 109 (203)
..|+.||..|. ..+-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 57888888874 56666666554
No 122
>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=60.88 E-value=4.2 Score=19.00 Aligned_cols=10 Identities=20% Similarity=0.524 Sum_probs=7.9
Q ss_pred CcccCccCCC
Q 028830 8 TTKICSHCDR 17 (203)
Q Consensus 8 k~y~C~~C~~ 17 (203)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 5788998874
No 123
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.47 E-value=3.7 Score=28.36 Aligned_cols=13 Identities=15% Similarity=0.498 Sum_probs=7.8
Q ss_pred CcccCccCCCcCc
Q 028830 8 TTKICSHCDRAIP 20 (203)
Q Consensus 8 k~y~C~~C~~~f~ 20 (203)
..+.|..|+..|.
T Consensus 69 ~~~~C~~CG~~~~ 81 (135)
T PRK03824 69 AVLKCRNCGNEWS 81 (135)
T ss_pred eEEECCCCCCEEe
Confidence 3466666666654
No 124
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.34 E-value=6.1 Score=25.98 Aligned_cols=18 Identities=6% Similarity=0.108 Sum_probs=10.2
Q ss_pred CcccCccCCCCCChhhHH
Q 028830 86 RIVTCDFCEFPLPAVDLA 103 (203)
Q Consensus 86 ~~~~C~~C~~~f~~~~l~ 103 (203)
.|..|++||++|..+.|.
T Consensus 25 dPiVsPytG~s~P~s~fe 42 (129)
T COG4530 25 DPIVSPYTGKSYPRSYFE 42 (129)
T ss_pred CccccCcccccchHHHHH
Confidence 466666666666544443
No 125
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=60.28 E-value=4 Score=35.93 Aligned_cols=27 Identities=15% Similarity=0.206 Sum_probs=21.8
Q ss_pred cceecccchhhcch-hHHHHHHHhhcCC
Q 028830 112 RTELCHLCNRYIRL-RERYNHESRCTGV 138 (203)
Q Consensus 112 ~~~~C~~C~~~f~~-~~l~~H~~~~~~~ 138 (203)
.-|.|.+|++.|-+ .++..||+.|...
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 34899999998874 7999999887543
No 126
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=59.82 E-value=8.3 Score=30.85 Aligned_cols=61 Identities=20% Similarity=0.252 Sum_probs=43.0
Q ss_pred HHhhHhccCC-CCcccCccCCCCCC--hhhHHHHHHH-hCC----------------------cceecccchhhcc-hhH
Q 028830 75 LAIHKGENCP-QRIVTCDFCEFPLP--AVDLAEHQEV-CGN----------------------RTELCHLCNRYIR-LRE 127 (203)
Q Consensus 75 l~~H~~~h~~-~~~~~C~~C~~~f~--~~~l~~H~~~-~~~----------------------~~~~C~~C~~~f~-~~~ 127 (203)
|..+++.-.+ ...-.|-.|+..+. .+.+..|+-. |+- ..+.|-.|.+.|+ +..
T Consensus 131 LeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdknt 210 (423)
T KOG2482|consen 131 LEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNT 210 (423)
T ss_pred HHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHH
Confidence 4455443221 23457999998875 7888888876 632 2478999999999 679
Q ss_pred HHHHHHhh
Q 028830 128 RYNHESRC 135 (203)
Q Consensus 128 l~~H~~~~ 135 (203)
|..||+..
T Consensus 211 LkeHMrkK 218 (423)
T KOG2482|consen 211 LKEHMRKK 218 (423)
T ss_pred HHHHHHhc
Confidence 99999754
No 127
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=58.31 E-value=0.59 Score=36.73 Aligned_cols=73 Identities=21% Similarity=0.372 Sum_probs=25.9
Q ss_pred ccccccccccccccHHHHHHcCCCCccCccChhhhhHHHHHhhHhccCCCCcccCccCCCCCC--hhhHHHHHHH-hCCc
Q 028830 36 ERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETMEREILAIHKGENCPQRIVTCDFCEFPLP--AVDLAEHQEV-CGNR 112 (203)
Q Consensus 36 ~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~~~l~~H~~~h~~~~~~~C~~C~~~f~--~~~l~~H~~~-~~~~ 112 (203)
-.|++||..-.-..+........+-..|..|+.... .....|+.||..-. ...+. ... -+.+
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~-------------~~R~~Cp~Cg~~~~~~l~~~~--~e~~~~~r 237 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWR-------------FVRIKCPYCGNTDHEKLEYFT--VEGEPAYR 237 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE---------------TTS-TTT---SS-EEE----------SEE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeee-------------ecCCCCcCCCCCCCcceeeEe--cCCCCcEE
Confidence 357777765433322211101224566777764211 13346777776543 12111 111 2456
Q ss_pred ceecccchhhc
Q 028830 113 TELCHLCNRYI 123 (203)
Q Consensus 113 ~~~C~~C~~~f 123 (203)
-+.|..|+..+
T Consensus 238 ve~C~~C~~Yl 248 (290)
T PF04216_consen 238 VEVCESCGSYL 248 (290)
T ss_dssp EEEETTTTEEE
T ss_pred EEECCcccchH
Confidence 67788887433
No 128
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=58.02 E-value=6.2 Score=32.56 Aligned_cols=13 Identities=15% Similarity=0.577 Sum_probs=6.2
Q ss_pred CccCccChhhhhH
Q 028830 60 PVACSQCSETMER 72 (203)
Q Consensus 60 ~~~C~~C~~~f~~ 72 (203)
-|.|+.|.+.|..
T Consensus 128 ~Y~Cp~C~kkyt~ 140 (436)
T KOG2593|consen 128 GYVCPNCQKKYTS 140 (436)
T ss_pred cccCCccccchhh
Confidence 3445555444444
No 129
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.01 E-value=6.8 Score=28.29 Aligned_cols=50 Identities=16% Similarity=0.379 Sum_probs=29.5
Q ss_pred CCcccccccccccccccHHHHHHcCCCCccCccChhhhhHHHHHhhHhccCCCCcccCccCCCCCC
Q 028830 33 RNLERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETMEREILAIHKGENCPQRIVTCDFCEFPLP 98 (203)
Q Consensus 33 ~~~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 98 (203)
+.-|.|++|-..+..+.. .-..||-.|-..-++.-++ ...+|+.|++...
T Consensus 129 ~~~~~CPiCl~~~sek~~-----------vsTkCGHvFC~~Cik~alk-----~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVP-----------VSTKCGHVFCSQCIKDALK-----NTNKCPTCRKKIT 178 (187)
T ss_pred ccccCCCceecchhhccc-----------cccccchhHHHHHHHHHHH-----hCCCCCCcccccc
Confidence 344788888777655421 2234777776654444333 3567888876554
No 130
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=57.95 E-value=7 Score=28.79 Aligned_cols=46 Identities=22% Similarity=0.348 Sum_probs=24.8
Q ss_pred cCCCcCccccHHHHHhhcCCCcccccc----cccccccccHHHHHHcCCC
Q 028830 14 HCDRAIPSSNIDLHFAHCSRNLERCKV----CGDMVPRKYAEEHFLNTHA 59 (203)
Q Consensus 14 ~C~~~f~~~~l~~H~~h~~~~~~~C~~----C~~~f~~~~~~~~~~~~h~ 59 (203)
.|...+.......|...+.-+|+.|+. |+..-....++.|....|.
T Consensus 23 GC~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~ 72 (198)
T PF03145_consen 23 GCTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDKHS 72 (198)
T ss_dssp T---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHHTT
T ss_pred CCcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHHCC
Confidence 477776666777776677777888876 6655555566666666663
No 131
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=57.12 E-value=6.8 Score=17.96 Aligned_cols=7 Identities=29% Similarity=1.146 Sum_probs=3.1
Q ss_pred CccCCCc
Q 028830 12 CSHCDRA 18 (203)
Q Consensus 12 C~~C~~~ 18 (203)
|+.|+..
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 4444443
No 132
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.77 E-value=7.2 Score=23.85 Aligned_cols=9 Identities=22% Similarity=0.970 Sum_probs=3.9
Q ss_pred ccCccChhh
Q 028830 61 VACSQCSET 69 (203)
Q Consensus 61 ~~C~~C~~~ 69 (203)
|.|..|+..
T Consensus 13 Y~c~~cg~~ 21 (82)
T COG2331 13 YECTECGNR 21 (82)
T ss_pred EeecccchH
Confidence 444444443
No 133
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=55.97 E-value=7.8 Score=24.59 Aligned_cols=13 Identities=38% Similarity=0.664 Sum_probs=7.1
Q ss_pred ccccccccccccc
Q 028830 35 LERCKVCGDMVPR 47 (203)
Q Consensus 35 ~~~C~~C~~~f~~ 47 (203)
|-.|..||..|..
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 4455566655544
No 134
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=55.54 E-value=6.4 Score=22.64 Aligned_cols=36 Identities=19% Similarity=0.306 Sum_probs=18.7
Q ss_pred ccCccCCCCCC--hhhHHHHHHH-hCCcceecccchhhc
Q 028830 88 VTCDFCEFPLP--AVDLAEHQEV-CGNRTELCHLCNRYI 123 (203)
Q Consensus 88 ~~C~~C~~~f~--~~~l~~H~~~-~~~~~~~C~~C~~~f 123 (203)
.+|-.|++.+. ...+..-... .....|.|+.|....
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI 41 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERI 41 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHH
Confidence 35667777664 2222222222 455567777776533
No 135
>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=55.17 E-value=5.7 Score=22.69 Aligned_cols=11 Identities=27% Similarity=0.631 Sum_probs=6.5
Q ss_pred ccCccCCCcCc
Q 028830 10 KICSHCDRAIP 20 (203)
Q Consensus 10 y~C~~C~~~f~ 20 (203)
++|+.|+..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 45666666554
No 136
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.15 E-value=3.1 Score=31.30 Aligned_cols=39 Identities=13% Similarity=0.456 Sum_probs=22.7
Q ss_pred CcccCccCCCCCC-hhhHHHHHHH-hCC---------------cceecccchh-hcc
Q 028830 86 RIVTCDFCEFPLP-AVDLAEHQEV-CGN---------------RTELCHLCNR-YIR 124 (203)
Q Consensus 86 ~~~~C~~C~~~f~-~~~l~~H~~~-~~~---------------~~~~C~~C~~-~f~ 124 (203)
+.+.|++|+..|. ...+..-.|+ .|+ ....||.|+. +|.
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yAaf~ 74 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYAAFK 74 (267)
T ss_pred ceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHHHhh
Confidence 5667777777776 4444433343 332 1256899987 554
No 137
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=52.35 E-value=5.4 Score=35.15 Aligned_cols=24 Identities=13% Similarity=0.318 Sum_probs=19.6
Q ss_pred CccCccChhhhhH-HHHHhhHhccC
Q 028830 60 PVACSQCSETMER-EILAIHKGENC 83 (203)
Q Consensus 60 ~~~C~~C~~~f~~-~~l~~H~~~h~ 83 (203)
.|.|..|++.|.. +++..|+++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 5889999999977 78888888763
No 138
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=51.68 E-value=7.2 Score=27.39 Aligned_cols=32 Identities=22% Similarity=0.475 Sum_probs=22.1
Q ss_pred CcccCccCCCCCChhhHHHHHHH-hCCcceecccchh
Q 028830 86 RIVTCDFCEFPLPAVDLAEHQEV-CGNRTELCHLCNR 121 (203)
Q Consensus 86 ~~~~C~~C~~~f~~~~l~~H~~~-~~~~~~~C~~C~~ 121 (203)
-+|.|. |+..|. ..++|-.+ -|+ .|.|..|+.
T Consensus 116 ~~Y~C~-C~q~~l--~~RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 116 YPYRCQ-CQQHYL--RIRRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred eeEEee-cCCccc--hhhhcccccccc-eEEeccCCc
Confidence 478898 988864 12355555 466 899999874
No 139
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=50.61 E-value=9 Score=21.37 Aligned_cols=13 Identities=23% Similarity=0.567 Sum_probs=7.2
Q ss_pred CcccCccCCCcCc
Q 028830 8 TTKICSHCDRAIP 20 (203)
Q Consensus 8 k~y~C~~C~~~f~ 20 (203)
+.+.|..||..|.
T Consensus 3 k~l~C~dCg~~Fv 15 (49)
T PF13451_consen 3 KTLTCKDCGAEFV 15 (49)
T ss_pred eeEEcccCCCeEE
Confidence 4455666665554
No 140
>PF15269 zf-C2H2_7: Zinc-finger
Probab=50.31 E-value=14 Score=20.10 Aligned_cols=21 Identities=24% Similarity=0.410 Sum_probs=15.4
Q ss_pred ccCccCCCCCC-hhhHHHHHHH
Q 028830 88 VTCDFCEFPLP-AVDLAEHQEV 108 (203)
Q Consensus 88 ~~C~~C~~~f~-~~~l~~H~~~ 108 (203)
|+|-+|..... .+.|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 56777777777 7778888764
No 141
>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=50.22 E-value=4.1 Score=34.77 Aligned_cols=23 Identities=17% Similarity=0.660 Sum_probs=13.2
Q ss_pred CcccCccCCCCCChhhHHHHHHHhCCcceecccchh
Q 028830 86 RIVTCDFCEFPLPAVDLAEHQEVCGNRTELCHLCNR 121 (203)
Q Consensus 86 ~~~~C~~C~~~f~~~~l~~H~~~~~~~~~~C~~C~~ 121 (203)
+...|.+||... ..|..|+.|+.
T Consensus 239 ~~l~Ch~Cg~~~-------------~~~~~Cp~C~s 261 (505)
T TIGR00595 239 GKLRCHYCGYQE-------------PIPKTCPQCGS 261 (505)
T ss_pred CeEEcCCCcCcC-------------CCCCCCCCCCC
Confidence 455666666543 22456777775
No 142
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=50.02 E-value=1.9 Score=26.11 Aligned_cols=42 Identities=29% Similarity=0.587 Sum_probs=18.6
Q ss_pred HHHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHHhCCcceecccchhh
Q 028830 74 ILAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNRY 122 (203)
Q Consensus 74 ~l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~~ 122 (203)
.+..|...........|..|+..++ ... ..+ ..|.|+.|+..
T Consensus 28 e~~~H~~~~~~~~~v~Cg~C~~~~~~~~~------~c~-~~~~C~~C~~~ 70 (71)
T PF05495_consen 28 ELEDHPFDRWPVKRVICGKCRTEQPIDEY------SCG-ADYFCPICGLY 70 (71)
T ss_dssp HCSSS---TTT--EEEETTT--EEES-SB------TT---SEEETTTTEE
T ss_pred HhccCccccccccCeECCCCCCccChhhh------hcC-CCccCcCcCCC
Confidence 3445544444445677888877765 322 112 45778877643
No 143
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=49.83 E-value=7 Score=24.62 Aligned_cols=12 Identities=25% Similarity=0.542 Sum_probs=7.1
Q ss_pred cccCccCCCCCC
Q 028830 87 IVTCDFCEFPLP 98 (203)
Q Consensus 87 ~~~C~~C~~~f~ 98 (203)
-+.|..|+..|.
T Consensus 53 IW~C~kCg~~fA 64 (89)
T COG1997 53 IWKCRKCGAKFA 64 (89)
T ss_pred eEEcCCCCCeec
Confidence 456666666654
No 144
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=49.74 E-value=12 Score=29.64 Aligned_cols=20 Identities=20% Similarity=0.464 Sum_probs=9.8
Q ss_pred CcccCccCCCCCC-hhhHHHH
Q 028830 86 RIVTCDFCEFPLP-AVDLAEH 105 (203)
Q Consensus 86 ~~~~C~~C~~~f~-~~~l~~H 105 (203)
..|.|+.|...|. .=+.-.|
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIH 407 (421)
T ss_pred cceechhhhhhhhhhhHHHHH
Confidence 3455555555554 4343444
No 145
>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=49.55 E-value=4.7 Score=22.29 Aligned_cols=11 Identities=18% Similarity=0.437 Sum_probs=7.1
Q ss_pred ccCccCCCcCc
Q 028830 10 KICSHCDRAIP 20 (203)
Q Consensus 10 y~C~~C~~~f~ 20 (203)
|.|..|+..+.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 66667776664
No 146
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=49.35 E-value=5 Score=20.78 Aligned_cols=29 Identities=21% Similarity=0.533 Sum_probs=15.6
Q ss_pred ccCccCCCcCccccHHHH-HhhcCCCccccccc
Q 028830 10 KICSHCDRAIPSSNIDLH-FAHCSRNLERCKVC 41 (203)
Q Consensus 10 y~C~~C~~~f~~~~l~~H-~~h~~~~~~~C~~C 41 (203)
-.|+.|+.. ..+.+| ....+...|.|..|
T Consensus 6 v~CP~C~s~---~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQST---EGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCC---CcceeCCCCCCCCEeEecCcC
Confidence 356666553 224455 55555556666665
No 147
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=49.08 E-value=14 Score=21.23 Aligned_cols=30 Identities=23% Similarity=0.426 Sum_probs=13.7
Q ss_pred CccCccChhhhhHHHHHhhHhccCCCCcccCcc
Q 028830 60 PVACSQCSETMEREILAIHKGENCPQRIVTCDF 92 (203)
Q Consensus 60 ~~~C~~C~~~f~~~~l~~H~~~h~~~~~~~C~~ 92 (203)
|+....|+..|..+.+...+. ..+...|++
T Consensus 24 PV~s~~C~H~fek~aI~~~i~---~~~~~~CPv 53 (57)
T PF11789_consen 24 PVKSKKCGHTFEKEAILQYIQ---RNGSKRCPV 53 (57)
T ss_dssp EEEESSS--EEEHHHHHHHCT---TTS-EE-SC
T ss_pred CcCcCCCCCeecHHHHHHHHH---hcCCCCCCC
Confidence 455555666666655544442 234556665
No 148
>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=48.10 E-value=15 Score=31.41 Aligned_cols=10 Identities=30% Similarity=0.820 Sum_probs=5.0
Q ss_pred cccCccCCCc
Q 028830 9 TKICSHCDRA 18 (203)
Q Consensus 9 ~y~C~~C~~~ 18 (203)
..+|+.|+..
T Consensus 222 ~~~C~~C~~~ 231 (505)
T TIGR00595 222 ILCCPNCDVS 231 (505)
T ss_pred ccCCCCCCCc
Confidence 3455555543
No 149
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.38 E-value=14 Score=32.86 Aligned_cols=13 Identities=31% Similarity=0.797 Sum_probs=7.0
Q ss_pred CCcccCccCCCcC
Q 028830 7 ETTKICSHCDRAI 19 (203)
Q Consensus 7 ~k~y~C~~C~~~f 19 (203)
....+|+.|+...
T Consensus 390 g~~~~C~~C~~~L 402 (665)
T PRK14873 390 RTPARCRHCTGPL 402 (665)
T ss_pred cCeeECCCCCCce
Confidence 3455566666543
No 150
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=47.11 E-value=25 Score=28.09 Aligned_cols=13 Identities=15% Similarity=0.424 Sum_probs=5.8
Q ss_pred ccccccccccccc
Q 028830 35 LERCKVCGDMVPR 47 (203)
Q Consensus 35 ~~~C~~C~~~f~~ 47 (203)
|-.|+.|+.....
T Consensus 290 P~eCpiC~ltLVs 302 (378)
T KOG2807|consen 290 PIECPICSLTLVS 302 (378)
T ss_pred CccCCccceeEec
Confidence 3444445444433
No 151
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=46.95 E-value=6.4 Score=31.13 Aligned_cols=101 Identities=18% Similarity=0.327 Sum_probs=61.4
Q ss_pred cccccccccccccccHHH--HHHcC-----CCCccCccChhhhhH-HHHHhhHhccCCCCcccCcc----CCCCCC-hhh
Q 028830 35 LERCKVCGDMVPRKYAEE--HFLNT-----HAPVACSQCSETMER-EILAIHKGENCPQRIVTCDF----CEFPLP-AVD 101 (203)
Q Consensus 35 ~~~C~~C~~~f~~~~~~~--~~~~~-----h~~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~----C~~~f~-~~~ 101 (203)
-..|++|........... -|... -....|+.|...+.. ..+ ++..-.....+.|+. |.+.|. ...
T Consensus 48 lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g~~R~~--amEkV~e~~~vpC~~~~~GC~~~~~Y~~~ 125 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPTCRLPIGNIRCR--AMEKVAEAVLVPCKNAKLGCTKSFPYGEK 125 (299)
T ss_pred hccCchhhccCcccceecCCCcEehhhhhhhhcccCCccccccccHHHH--HHHHHHHhceecccccccCCceeeccccc
Confidence 467999887766552111 11110 136789999887764 221 222122235677875 999998 444
Q ss_pred HHHHHHHhCCcceecccc----hhhcchhHHHHHHHhhcCC
Q 028830 102 LAEHQEVCGNRTELCHLC----NRYIRLRERYNHESRCTGV 138 (203)
Q Consensus 102 l~~H~~~~~~~~~~C~~C----~~~f~~~~l~~H~~~~~~~ 138 (203)
..|.+.+.-+||.|+.= ...=....|..|....|..
T Consensus 126 -~~HE~~C~f~~~~CP~p~~~C~~~G~~~~l~~H~~~~hk~ 165 (299)
T KOG3002|consen 126 -SKHEKVCEFRPCSCPVPGAECKYTGSYKDLYAHLNDTHKS 165 (299)
T ss_pred -cccccccccCCcCCCCCcccCCccCcHHHHHHHHHhhChh
Confidence 78888866688988744 3222347888998766554
No 152
>PRK14873 primosome assembly protein PriA; Provisional
Probab=46.69 E-value=4.6 Score=35.74 Aligned_cols=9 Identities=22% Similarity=0.497 Sum_probs=6.0
Q ss_pred ceecccchh
Q 028830 113 TELCHLCNR 121 (203)
Q Consensus 113 ~~~C~~C~~ 121 (203)
+..|+.||.
T Consensus 422 p~~Cp~Cgs 430 (665)
T PRK14873 422 DWRCPRCGS 430 (665)
T ss_pred CccCCCCcC
Confidence 456777775
No 153
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=46.27 E-value=5.2 Score=34.30 Aligned_cols=50 Identities=22% Similarity=0.446 Sum_probs=32.6
Q ss_pred cccHHHH-HhhcCCCcccccccccccccccHHHHHHcCCCCccCccChhhhhH
Q 028830 21 SSNIDLH-FAHCSRNLERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETMER 72 (203)
Q Consensus 21 ~~~l~~H-~~h~~~~~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~ 72 (203)
.+.|.+| -.|.....=+|..|++.|.++.....-. --...|.+|...|-.
T Consensus 238 E~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~FhsKE--ivAisCSWCKqayH~ 288 (1004)
T KOG0782|consen 238 ESGFVRHHWVHRRRQEGKCNTCGKGFQQKFFFHSKE--IVAISCSWCKQAYHL 288 (1004)
T ss_pred cccchHHhHhhHhhhccccchhhhhhhhheeecccc--EEEEEehHHHHHhhc
Confidence 3467777 7777666677999999887763221100 025678888888855
No 154
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=45.51 E-value=9.9 Score=34.00 Aligned_cols=39 Identities=18% Similarity=0.417 Sum_probs=19.9
Q ss_pred CCCcccCccCCCcCc----cccHHHH-HhhcCCCcccccccccc
Q 028830 6 DETTKICSHCDRAIP----SSNIDLH-FAHCSRNLERCKVCGDM 44 (203)
Q Consensus 6 ~~k~y~C~~C~~~f~----~~~l~~H-~~h~~~~~~~C~~C~~~ 44 (203)
+.-..+|+.|+..++ ...|.-| -.+....|..|+.||..
T Consensus 441 Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 441 CGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred CCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 344556677766543 2334444 33333455666666654
No 155
>PF12907 zf-met2: Zinc-binding
Probab=44.68 E-value=22 Score=18.92 Aligned_cols=20 Identities=25% Similarity=0.532 Sum_probs=10.3
Q ss_pred ccCccChhhhhH----HHHHhhHh
Q 028830 61 VACSQCSETMER----EILAIHKG 80 (203)
Q Consensus 61 ~~C~~C~~~f~~----~~l~~H~~ 80 (203)
+.|.+|...|.. ..|..|..
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 355566655533 24555554
No 156
>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=44.06 E-value=7.8 Score=19.80 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=2.9
Q ss_pred ccccccccccc
Q 028830 38 CKVCGDMVPRK 48 (203)
Q Consensus 38 C~~C~~~f~~~ 48 (203)
|..|++.|..+
T Consensus 6 C~eC~~~f~dS 16 (34)
T PF01286_consen 6 CDECGKPFMDS 16 (34)
T ss_dssp -TTT--EES-S
T ss_pred HhHhCCHHHHH
Confidence 44444444433
No 157
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=44.03 E-value=30 Score=19.71 Aligned_cols=28 Identities=21% Similarity=0.086 Sum_probs=12.9
Q ss_pred ChhhhhHHHHHhhHhccCCCCcccCccCCCCCC
Q 028830 66 CSETMEREILAIHKGENCPQRIVTCDFCEFPLP 98 (203)
Q Consensus 66 C~~~f~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 98 (203)
||..|....+..+... ...|+.|++.+.
T Consensus 19 ~G~v~~~~~i~~~~~~-----~~~cP~~~~~~~ 46 (63)
T smart00504 19 SGQTYERRAIEKWLLS-----HGTDPVTGQPLT 46 (63)
T ss_pred CCCEEeHHHHHHHHHH-----CCCCCCCcCCCC
Confidence 4455544444444332 124555655554
No 158
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=43.59 E-value=27 Score=28.84 Aligned_cols=62 Identities=27% Similarity=0.651 Sum_probs=45.9
Q ss_pred CCccCcc-ChhhhhHHHHHhhHhccCCCCcccCccCCCCCChhhHHHHHHHhCCcceeccc-chh
Q 028830 59 APVACSQ-CSETMEREILAIHKGENCPQRIVTCDFCEFPLPAVDLAEHQEVCGNRTELCHL-CNR 121 (203)
Q Consensus 59 ~~~~C~~-C~~~f~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~l~~H~~~~~~~~~~C~~-C~~ 121 (203)
.+.+|+. |+..+....+..|+...+..+.-.|..|+..+....+..|... ...+..|.. |+.
T Consensus 113 ~~~~C~~~C~~~~~~~d~~~hl~~~C~~~~~~c~~~~~~~~~~~~~~h~~~-~~~~~~c~~k~~~ 176 (391)
T KOG0297|consen 113 DPLKCPHRCGVQVPRDDLEDHLEAECPRRSLKCSLCQSDSILILLEAHEEN-PQAEVSCELKCGK 176 (391)
T ss_pred CcccCccccccccchHHHHHHHhcccccccccchhhcCccchhhhhhcCCC-CCccccccccchh
Confidence 4677766 8888888889999988888899999999988876666666554 344555643 544
No 159
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=42.19 E-value=9.1 Score=30.71 Aligned_cols=25 Identities=28% Similarity=0.834 Sum_probs=19.4
Q ss_pred CCcccC--ccCCCcCc-cccHHHH-H-hhc
Q 028830 7 ETTKIC--SHCDRAIP-SSNIDLH-F-AHC 31 (203)
Q Consensus 7 ~k~y~C--~~C~~~f~-~~~l~~H-~-~h~ 31 (203)
.++|+| +.|++.+. ...|+.| . .|+
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~ 376 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHC 376 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcC
Confidence 578999 78999988 7788888 3 454
No 160
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=41.44 E-value=15 Score=21.26 Aligned_cols=28 Identities=25% Similarity=0.528 Sum_probs=16.6
Q ss_pred ccCccCCCCCC--hhhHHHHHHHhCCcceecccchh
Q 028830 88 VTCDFCEFPLP--AVDLAEHQEVCGNRTELCHLCNR 121 (203)
Q Consensus 88 ~~C~~C~~~f~--~~~l~~H~~~~~~~~~~C~~C~~ 121 (203)
|.|+ ||-+|. ...|+. |+..-.|+.|..
T Consensus 23 yPCP-CGDRFeIsLeDl~~-----GE~VArCPSCSL 52 (67)
T COG5216 23 YPCP-CGDRFEISLEDLRN-----GEVVARCPSCSL 52 (67)
T ss_pred ecCC-CCCEeEEEHHHhhC-----CceEEEcCCceE
Confidence 4555 777774 333332 666777777764
No 161
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=41.33 E-value=15 Score=30.57 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=19.2
Q ss_pred ccCCCCcccCccCC-CcCc-cccHHHH
Q 028830 3 MTSDETTKICSHCD-RAIP-SSNIDLH 27 (203)
Q Consensus 3 ~h~~~k~y~C~~C~-~~f~-~~~l~~H 27 (203)
.|.-..-|.|.+|| +++. +..|++|
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHH
Confidence 46666778888888 6666 8888888
No 162
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.20 E-value=9.6 Score=22.21 Aligned_cols=12 Identities=33% Similarity=0.653 Sum_probs=6.1
Q ss_pred CCcceecccchh
Q 028830 110 GNRTELCHLCNR 121 (203)
Q Consensus 110 ~~~~~~C~~C~~ 121 (203)
..+.|.|++|..
T Consensus 28 PIrtymC~eC~~ 39 (68)
T COG4896 28 PIRTYMCPECEH 39 (68)
T ss_pred CceeEechhhHh
Confidence 344555555544
No 163
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=41.19 E-value=20 Score=16.83 Aligned_cols=7 Identities=29% Similarity=1.194 Sum_probs=3.7
Q ss_pred cCccCCC
Q 028830 11 ICSHCDR 17 (203)
Q Consensus 11 ~C~~C~~ 17 (203)
.|+.|+.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4555555
No 164
>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=40.68 E-value=7.8 Score=27.18 Aligned_cols=32 Identities=16% Similarity=0.419 Sum_probs=21.1
Q ss_pred CcccCccCCCCCC-hhhHHHHHHHhCCcceecccchh-hcchh
Q 028830 86 RIVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNR-YIRLR 126 (203)
Q Consensus 86 ~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~-~f~~~ 126 (203)
-.|.|..||.... . +...--.|+.||. .|.+.
T Consensus 111 G~l~C~~Cg~~~~~~---------~~~~l~~Cp~C~~~~F~R~ 144 (146)
T PF07295_consen 111 GTLVCENCGHEVELT---------HPERLPPCPKCGHTEFTRQ 144 (146)
T ss_pred ceEecccCCCEEEec---------CCCcCCCCCCCCCCeeeeC
Confidence 4689999997642 1 2233457999987 67643
No 165
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=40.61 E-value=14 Score=19.37 Aligned_cols=12 Identities=25% Similarity=0.539 Sum_probs=8.9
Q ss_pred cccCccCCCcCc
Q 028830 9 TKICSHCDRAIP 20 (203)
Q Consensus 9 ~y~C~~C~~~f~ 20 (203)
|+.|..|++.|=
T Consensus 12 ~f~C~~C~~~FC 23 (39)
T smart00154 12 GFKCRHCGNLFC 23 (39)
T ss_pred CeECCccCCccc
Confidence 677888887773
No 166
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=40.42 E-value=47 Score=24.12 Aligned_cols=41 Identities=12% Similarity=0.210 Sum_probs=26.9
Q ss_pred HHHhhHhccCCCCcccCccCCCCCC-hhhHHHHHHHhCCcceecccchhh
Q 028830 74 ILAIHKGENCPQRIVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNRY 122 (203)
Q Consensus 74 ~l~~H~~~h~~~~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~~ 122 (203)
.|..-.....+..-|.|+.|...|+ ..+... .|.|+.||..
T Consensus 100 ~Lk~~le~~~~~~~y~C~~~~~r~sfdeA~~~--------~F~Cp~Cg~~ 141 (176)
T COG1675 100 KLKRKLEKETENNYYVCPNCHVKYSFDEAMEL--------GFTCPKCGED 141 (176)
T ss_pred HHHHHHHhhccCCceeCCCCCCcccHHHHHHh--------CCCCCCCCch
Confidence 3444444455667899988888887 443222 3899999963
No 167
>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=38.90 E-value=10 Score=28.68 Aligned_cols=23 Identities=22% Similarity=0.567 Sum_probs=0.0
Q ss_pred CcccCccCCCCCChhhHHHHHHH
Q 028830 86 RIVTCDFCEFPLPAVDLAEHQEV 108 (203)
Q Consensus 86 ~~~~C~~C~~~f~~~~l~~H~~~ 108 (203)
....|+.||+....+.+..|+|+
T Consensus 167 ~~~~cPitGe~IP~~e~~eHmRi 189 (229)
T PF12230_consen 167 KMIICPITGEMIPADEMDEHMRI 189 (229)
T ss_dssp -----------------------
T ss_pred ccccccccccccccccccccccc
Confidence 34456666655555555556555
No 168
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=38.26 E-value=11 Score=23.97 Aligned_cols=35 Identities=20% Similarity=0.425 Sum_probs=22.0
Q ss_pred cCCCcccccccccccccccHHHHHHcCCCCccCccChhhhhH
Q 028830 31 CSRNLERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETMER 72 (203)
Q Consensus 31 ~~~~~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~ 72 (203)
.....|.|+.|++.-..... --.+.|..|++.|..
T Consensus 32 ~q~a~y~CpfCgk~~vkR~a-------~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 32 SQHAKYFCPFCGKHAVKRQA-------VGIWRCKGCKKTVAG 66 (90)
T ss_pred HHhCCccCCCCCCCceeeee-------eEEEEcCCCCCEEeC
Confidence 34567889999855322110 037888888888754
No 169
>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=38.01 E-value=23 Score=26.56 Aligned_cols=29 Identities=14% Similarity=0.121 Sum_probs=19.5
Q ss_pred CCcceecccchhhcch-hHHHHHHHhhcCC
Q 028830 110 GNRTELCHLCNRYIRL-RERYNHESRCTGV 138 (203)
Q Consensus 110 ~~~~~~C~~C~~~f~~-~~l~~H~~~~~~~ 138 (203)
.+..|.|+.|+|.|.- .-..+|+...|.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 4557999999999984 5667788766653
No 170
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=37.99 E-value=8.3 Score=20.40 Aligned_cols=10 Identities=30% Similarity=0.647 Sum_probs=5.5
Q ss_pred cccccccccc
Q 028830 36 ERCKVCGDMV 45 (203)
Q Consensus 36 ~~C~~C~~~f 45 (203)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5555555544
No 171
>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=37.99 E-value=12 Score=22.10 Aligned_cols=9 Identities=33% Similarity=1.139 Sum_probs=2.7
Q ss_pred ccccccccc
Q 028830 37 RCKVCGDMV 45 (203)
Q Consensus 37 ~C~~C~~~f 45 (203)
.|..|++.|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 455555555
No 172
>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=37.13 E-value=6.8 Score=19.04 Aligned_cols=19 Identities=16% Similarity=0.190 Sum_probs=12.7
Q ss_pred eecccchhhcchhHHHHHH
Q 028830 114 ELCHLCNRYIRLRERYNHE 132 (203)
Q Consensus 114 ~~C~~C~~~f~~~~l~~H~ 132 (203)
|.|-.|++.|...+...|.
T Consensus 1 ~sCiDC~~~F~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDFDGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEEEGGGTTT--
T ss_pred CeeecCCCCcCcCCcCCCC
Confidence 4677888888766777775
No 173
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=37.07 E-value=23 Score=27.10 Aligned_cols=13 Identities=15% Similarity=0.411 Sum_probs=7.8
Q ss_pred CcccCccCCCCCC
Q 028830 86 RIVTCDFCEFPLP 98 (203)
Q Consensus 86 ~~~~C~~C~~~f~ 98 (203)
--|.|+.|+..|.
T Consensus 154 aef~C~~C~h~F~ 166 (278)
T PF15135_consen 154 AEFHCPKCRHNFR 166 (278)
T ss_pred eeeecccccccch
Confidence 3466666666665
No 174
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=37.02 E-value=30 Score=32.92 Aligned_cols=9 Identities=44% Similarity=1.151 Sum_probs=5.1
Q ss_pred ccccccccc
Q 028830 36 ERCKVCGDM 44 (203)
Q Consensus 36 ~~C~~C~~~ 44 (203)
+.|+.||..
T Consensus 668 rkCPkCG~~ 676 (1337)
T PRK14714 668 RRCPSCGTE 676 (1337)
T ss_pred EECCCCCCc
Confidence 456666653
No 175
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=36.47 E-value=27 Score=29.03 Aligned_cols=13 Identities=15% Similarity=0.583 Sum_probs=6.6
Q ss_pred CccCccChhhhhH
Q 028830 60 PVACSQCSETMER 72 (203)
Q Consensus 60 ~~~C~~C~~~f~~ 72 (203)
-|.|+.||..+..
T Consensus 367 g~rC~kCg~~~~~ 379 (421)
T COG1571 367 GFRCKKCGTRARE 379 (421)
T ss_pred CcccccccccCCc
Confidence 3555555554443
No 176
>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=36.43 E-value=23 Score=24.39 Aligned_cols=26 Identities=15% Similarity=0.326 Sum_probs=14.6
Q ss_pred cceecccchhhcchhHHHHHHHhhcCCC
Q 028830 112 RTELCHLCNRYIRLRERYNHESRCTGVP 139 (203)
Q Consensus 112 ~~~~C~~C~~~f~~~~l~~H~~~~~~~~ 139 (203)
.-..|-+||+.|.. |.+|++.||+..
T Consensus 71 d~i~clecGk~~k~--LkrHL~~~~glt 96 (132)
T PF05443_consen 71 DYIICLECGKKFKT--LKRHLRTHHGLT 96 (132)
T ss_dssp S-EE-TBT--EESB--HHHHHHHTT-S-
T ss_pred CeeEEccCCcccch--HHHHHHHccCCC
Confidence 34678999998764 488888776644
No 177
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=35.69 E-value=24 Score=25.04 Aligned_cols=56 Identities=13% Similarity=0.167 Sum_probs=27.5
Q ss_pred CcccCccCCCCCC-hhhHHHHHHH-hCCcceecc--cchhhcchhHHHHHHHhhcCCCCCC
Q 028830 86 RIVTCDFCEFPLP-AVDLAEHQEV-CGNRTELCH--LCNRYIRLRERYNHESRCTGVPENT 142 (203)
Q Consensus 86 ~~~~C~~C~~~f~-~~~l~~H~~~-~~~~~~~C~--~C~~~f~~~~l~~H~~~~~~~~~~~ 142 (203)
....|+.|--... .... .--|. -..|+-.|. .|...=+...|.+|.+..|....+.
T Consensus 79 ~~L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~GtY~eLrKHar~~HP~~rP~ 138 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFSGTYSELRKHARSEHPSARPS 138 (162)
T ss_pred ccccCccccCceeceEEc-hHHHHHhccCCccCcccccccccCHHHHHHHHHhhCCCCCCc
Confidence 3456777754433 2111 11222 234444453 4433223578888887776655433
No 178
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=35.60 E-value=9.9 Score=19.63 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=5.6
Q ss_pred ccccccccccc
Q 028830 35 LERCKVCGDMV 45 (203)
Q Consensus 35 ~~~C~~C~~~f 45 (203)
.-.|+.||..+
T Consensus 21 ~~~Cd~cg~~L 31 (36)
T PF05191_consen 21 EGVCDNCGGEL 31 (36)
T ss_dssp TTBCTTTTEBE
T ss_pred CCccCCCCCee
Confidence 34566665543
No 179
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=35.37 E-value=47 Score=27.13 Aligned_cols=49 Identities=20% Similarity=0.258 Sum_probs=38.9
Q ss_pred CcccCccCCCCCC-hhhHHHHHHH-hCC-----------------------cceecccch---hhcch-hHHHHHHHh
Q 028830 86 RIVTCDFCEFPLP-AVDLAEHQEV-CGN-----------------------RTELCHLCN---RYIRL-RERYNHESR 134 (203)
Q Consensus 86 ~~~~C~~C~~~f~-~~~l~~H~~~-~~~-----------------------~~~~C~~C~---~~f~~-~~l~~H~~~ 134 (203)
-|-.|-.|++.+. ...-..||.. ||- .-+.|-.|+ +.|.+ .+...||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 4678999999998 8888899988 763 347788888 67764 689999963
No 180
>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=35.12 E-value=12 Score=23.86 Aligned_cols=34 Identities=15% Similarity=0.453 Sum_probs=20.9
Q ss_pred CCCcccccccccccccccHHHHHHcCCCCccCccChhhhhH
Q 028830 32 SRNLERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETMER 72 (203)
Q Consensus 32 ~~~~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~ 72 (203)
....|.|+.|++.-.... .--.+.|..|++.|..
T Consensus 32 q~a~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 32 QKAKYVCPFCGKKTVKRG-------STGIWTCRKCGAKFAG 65 (91)
T ss_pred HhcCccCCCCCCCceEEE-------eeEEEEcCCCCCEEeC
Confidence 345788888885532210 0036888888887754
No 181
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=34.67 E-value=44 Score=29.68 Aligned_cols=8 Identities=38% Similarity=1.095 Sum_probs=4.7
Q ss_pred cCccCCCc
Q 028830 11 ICSHCDRA 18 (203)
Q Consensus 11 ~C~~C~~~ 18 (203)
.|+.|+..
T Consensus 3 ~Cp~Cg~~ 10 (645)
T PRK14559 3 ICPQCQFE 10 (645)
T ss_pred cCCCCCCc
Confidence 46666654
No 182
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=34.60 E-value=10 Score=30.16 Aligned_cols=12 Identities=33% Similarity=1.032 Sum_probs=7.6
Q ss_pred cceecccchhhc
Q 028830 112 RTELCHLCNRYI 123 (203)
Q Consensus 112 ~~~~C~~C~~~f 123 (203)
+-..|..|+...
T Consensus 251 r~e~C~~C~~Yl 262 (305)
T TIGR01562 251 KAETCDSCQGYL 262 (305)
T ss_pred EEeeccccccch
Confidence 556788776433
No 183
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.38 E-value=26 Score=20.65 Aligned_cols=29 Identities=24% Similarity=0.532 Sum_probs=17.1
Q ss_pred ccCccCCCCCC--hhhHHHHHHHhCCcceecccchhh
Q 028830 88 VTCDFCEFPLP--AVDLAEHQEVCGNRTELCHLCNRY 122 (203)
Q Consensus 88 ~~C~~C~~~f~--~~~l~~H~~~~~~~~~~C~~C~~~ 122 (203)
|.|+ ||-.|. ...|.. |+..-.|+.|...
T Consensus 23 yPCp-CGDrf~It~edL~~-----ge~Va~CpsCSL~ 53 (67)
T KOG2923|consen 23 YPCP-CGDRFQITLEDLEN-----GEDVARCPSCSLI 53 (67)
T ss_pred cCCC-CCCeeeecHHHHhC-----CCeeecCCCceEE
Confidence 3444 777775 444433 6666777777643
No 184
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=34.23 E-value=17 Score=25.55 Aligned_cols=12 Identities=25% Similarity=0.659 Sum_probs=5.7
Q ss_pred cccccccccccc
Q 028830 37 RCKVCGDMVPRK 48 (203)
Q Consensus 37 ~C~~C~~~f~~~ 48 (203)
.|..|+..|++-
T Consensus 30 eC~~C~~RFTTf 41 (156)
T COG1327 30 ECLECGERFTTF 41 (156)
T ss_pred cccccccccchh
Confidence 355555554443
No 185
>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=34.22 E-value=29 Score=29.29 Aligned_cols=24 Identities=25% Similarity=0.343 Sum_probs=21.4
Q ss_pred CcccCccCCCCCC-hhhHHHHHHH-h
Q 028830 86 RIVTCDFCEFPLP-AVDLAEHQEV-C 109 (203)
Q Consensus 86 ~~~~C~~C~~~f~-~~~l~~H~~~-~ 109 (203)
+-+.|+.|++.|. ...+..|+.. |
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhh
Confidence 4578999999999 9999999998 7
No 186
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=33.59 E-value=15 Score=29.17 Aligned_cols=13 Identities=31% Similarity=0.795 Sum_probs=8.2
Q ss_pred Ccceecccchhhc
Q 028830 111 NRTELCHLCNRYI 123 (203)
Q Consensus 111 ~~~~~C~~C~~~f 123 (203)
.+-..|..|+..+
T Consensus 250 ~r~e~C~~C~~Yl 262 (309)
T PRK03564 250 VKAESCGDCGTYL 262 (309)
T ss_pred eEeeecccccccc
Confidence 3557788887543
No 187
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=33.58 E-value=23 Score=31.49 Aligned_cols=12 Identities=17% Similarity=0.404 Sum_probs=6.0
Q ss_pred cccCccCCCCCC
Q 028830 87 IVTCDFCEFPLP 98 (203)
Q Consensus 87 ~~~C~~C~~~f~ 98 (203)
.-+||.|+..|.
T Consensus 678 qRKCP~Cn~aFg 689 (698)
T KOG0978|consen 678 QRKCPKCNAAFG 689 (698)
T ss_pred cCCCCCCCCCCC
Confidence 335555555554
No 188
>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=33.19 E-value=13 Score=20.24 Aligned_cols=10 Identities=20% Similarity=0.564 Sum_probs=5.7
Q ss_pred Ccceecccch
Q 028830 111 NRTELCHLCN 120 (203)
Q Consensus 111 ~~~~~C~~C~ 120 (203)
...|+|..|+
T Consensus 35 ~~~~~C~~C~ 44 (46)
T PF12760_consen 35 RGRYRCKACR 44 (46)
T ss_pred CCeEECCCCC
Confidence 3456666664
No 189
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=33.15 E-value=21 Score=19.95 Aligned_cols=18 Identities=28% Similarity=0.702 Sum_probs=12.5
Q ss_pred cccCccCCCCCChhhHHH
Q 028830 87 IVTCDFCEFPLPAVDLAE 104 (203)
Q Consensus 87 ~~~C~~C~~~f~~~~l~~ 104 (203)
.|.|+.|+.+|+.+.|++
T Consensus 7 ry~CDLCn~~~p~~~LRQ 24 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQ 24 (57)
T ss_pred hHhHHhhcccCcHHHHHH
Confidence 477888888877555554
No 190
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=33.14 E-value=25 Score=22.99 Aligned_cols=10 Identities=30% Similarity=0.753 Sum_probs=5.3
Q ss_pred cccCccCCCc
Q 028830 9 TKICSHCDRA 18 (203)
Q Consensus 9 ~y~C~~C~~~ 18 (203)
|-.|+.|+..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 4455555554
No 191
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=33.00 E-value=39 Score=26.77 Aligned_cols=30 Identities=20% Similarity=0.533 Sum_probs=15.2
Q ss_pred ccccccccccccccHHHHHHcCCCCccCccChhhhh
Q 028830 36 ERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETME 71 (203)
Q Consensus 36 ~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~ 71 (203)
.+|+.|+.....+.+.. ..+.|+.|+..|.
T Consensus 39 ~kc~~C~~~~~~~~l~~------~~~vcp~c~~h~r 68 (296)
T CHL00174 39 VQCENCYGLNYKKFLKS------KMNICEQCGYHLK 68 (296)
T ss_pred eECCCccchhhHHHHHH------cCCCCCCCCCCcC
Confidence 45666665554433221 1356666666553
No 192
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=32.93 E-value=19 Score=25.19 Aligned_cols=12 Identities=17% Similarity=0.437 Sum_probs=6.3
Q ss_pred cccccccccccc
Q 028830 37 RCKVCGDMVPRK 48 (203)
Q Consensus 37 ~C~~C~~~f~~~ 48 (203)
.|..|++.|++.
T Consensus 30 eC~~C~~RFTTy 41 (147)
T TIGR00244 30 ECLECHERFTTF 41 (147)
T ss_pred cCCccCCcccee
Confidence 455555555544
No 193
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=32.44 E-value=28 Score=24.89 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=5.7
Q ss_pred ccccccccccc
Q 028830 37 RCKVCGDMVPR 47 (203)
Q Consensus 37 ~C~~C~~~f~~ 47 (203)
.|+.|+.....
T Consensus 99 RCp~CN~~L~~ 109 (165)
T COG1656 99 RCPECNGELEK 109 (165)
T ss_pred cCcccCCEecc
Confidence 46666555433
No 194
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=32.35 E-value=22 Score=18.74 Aligned_cols=13 Identities=23% Similarity=0.621 Sum_probs=6.9
Q ss_pred ccccccccccccc
Q 028830 36 ERCKVCGDMVPRK 48 (203)
Q Consensus 36 ~~C~~C~~~f~~~ 48 (203)
+.|+.|+-.|...
T Consensus 20 d~C~~C~G~W~d~ 32 (41)
T PF13453_consen 20 DVCPSCGGIWFDA 32 (41)
T ss_pred EECCCCCeEEccH
Confidence 3455555555544
No 195
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=32.18 E-value=39 Score=26.64 Aligned_cols=30 Identities=27% Similarity=0.683 Sum_probs=15.0
Q ss_pred ccccccccccccccHHHHHHcCCCCccCccChhhhh
Q 028830 36 ERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETME 71 (203)
Q Consensus 36 ~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~ 71 (203)
.+|+.|+.....+.+... .+.|+.|+..|.
T Consensus 27 ~~c~~c~~~~~~~~l~~~------~~vc~~c~~h~r 56 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERN------LEVCPKCDHHMR 56 (285)
T ss_pred eECCCCcchhhHHHHHhh------CCCCCCCCCcCc
Confidence 456666655544332211 355666666553
No 196
>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=32.01 E-value=21 Score=23.80 Aligned_cols=9 Identities=33% Similarity=0.970 Sum_probs=3.6
Q ss_pred ccccccccc
Q 028830 37 RCKVCGDMV 45 (203)
Q Consensus 37 ~C~~C~~~f 45 (203)
.|..|+..|
T Consensus 72 ~C~~Cg~~~ 80 (115)
T TIGR00100 72 ECEDCSEEV 80 (115)
T ss_pred EcccCCCEE
Confidence 344444333
No 197
>PRK05978 hypothetical protein; Provisional
Probab=31.96 E-value=20 Score=25.23 Aligned_cols=11 Identities=27% Similarity=0.779 Sum_probs=6.6
Q ss_pred ccCccChhhhh
Q 028830 61 VACSQCSETME 71 (203)
Q Consensus 61 ~~C~~C~~~f~ 71 (203)
-.|+.||..|.
T Consensus 53 ~~C~~CG~~~~ 63 (148)
T PRK05978 53 DHCAACGEDFT 63 (148)
T ss_pred CCccccCCccc
Confidence 45666766553
No 198
>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=31.77 E-value=15 Score=27.68 Aligned_cols=30 Identities=17% Similarity=0.161 Sum_probs=0.0
Q ss_pred CCcceecccchhhcchhHHHHHHHhhcCCC
Q 028830 110 GNRTELCHLCNRYIRLRERYNHESRCTGVP 139 (203)
Q Consensus 110 ~~~~~~C~~C~~~f~~~~l~~H~~~~~~~~ 139 (203)
+.....|+.||+.+..+.+..||+.....+
T Consensus 165 ~~~~~~cPitGe~IP~~e~~eHmRi~LlDP 194 (229)
T PF12230_consen 165 KEKMIICPITGEMIPADEMDEHMRIELLDP 194 (229)
T ss_dssp ------------------------------
T ss_pred cccccccccccccccccccccccccccccc
Confidence 445689999999999999999998765544
No 199
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=31.67 E-value=22 Score=28.63 Aligned_cols=25 Identities=16% Similarity=0.276 Sum_probs=14.7
Q ss_pred ccCCCCcccCccCC-CcCc-cccHHHH
Q 028830 3 MTSDETTKICSHCD-RAIP-SSNIDLH 27 (203)
Q Consensus 3 ~h~~~k~y~C~~C~-~~f~-~~~l~~H 27 (203)
.|.-++.|.|.+|+ +++. +..+.+|
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrH 394 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRH 394 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhh
Confidence 34445566666666 4444 6666666
No 200
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=31.54 E-value=9.1 Score=34.20 Aligned_cols=11 Identities=18% Similarity=0.483 Sum_probs=5.5
Q ss_pred ccccccccccc
Q 028830 38 CKVCGDMVPRK 48 (203)
Q Consensus 38 C~~C~~~f~~~ 48 (203)
|+.|.+.+...
T Consensus 121 C~~C~~ey~~p 131 (711)
T TIGR00143 121 CPDCAKEYKDP 131 (711)
T ss_pred CHHHHHHhcCC
Confidence 55555554443
No 201
>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=31.00 E-value=10 Score=25.19 Aligned_cols=12 Identities=17% Similarity=0.440 Sum_probs=7.4
Q ss_pred cccCccCCCCCC
Q 028830 87 IVTCDFCEFPLP 98 (203)
Q Consensus 87 ~~~C~~C~~~f~ 98 (203)
...|..||..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (113)
T PF01155_consen 70 RARCRDCGHEFE 81 (113)
T ss_dssp EEEETTTS-EEE
T ss_pred cEECCCCCCEEe
Confidence 456777777775
No 202
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=30.91 E-value=32 Score=22.72 Aligned_cols=14 Identities=14% Similarity=0.076 Sum_probs=7.5
Q ss_pred cccccccccccccc
Q 028830 35 LERCKVCGDMVPRK 48 (203)
Q Consensus 35 ~~~C~~C~~~f~~~ 48 (203)
.|.|+.|+..+...
T Consensus 19 ~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 19 QLICPSCLYEWNEN 32 (109)
T ss_pred eeECcccccccccc
Confidence 35566666555443
No 203
>PRK10220 hypothetical protein; Provisional
Probab=30.68 E-value=34 Score=22.59 Aligned_cols=14 Identities=14% Similarity=0.309 Sum_probs=7.8
Q ss_pred cccccccccccccc
Q 028830 35 LERCKVCGDMVPRK 48 (203)
Q Consensus 35 ~~~C~~C~~~f~~~ 48 (203)
.|.|+.|+..|...
T Consensus 20 ~~vCpeC~hEW~~~ 33 (111)
T PRK10220 20 MYICPECAHEWNDA 33 (111)
T ss_pred eEECCcccCcCCcc
Confidence 35566666655544
No 204
>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=30.59 E-value=39 Score=18.94 Aligned_cols=18 Identities=28% Similarity=0.501 Sum_probs=7.8
Q ss_pred ecccchhhcch---hHHHHHH
Q 028830 115 LCHLCNRYIRL---RERYNHE 132 (203)
Q Consensus 115 ~C~~C~~~f~~---~~l~~H~ 132 (203)
.||.|++.|.. ..|..+.
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~ 42 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKY 42 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHH
Confidence 67777776652 3444444
No 205
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=30.44 E-value=63 Score=23.89 Aligned_cols=13 Identities=15% Similarity=0.289 Sum_probs=6.3
Q ss_pred ccccccccccccc
Q 028830 35 LERCKVCGDMVPR 47 (203)
Q Consensus 35 ~~~C~~C~~~f~~ 47 (203)
||.|.+|.+.|..
T Consensus 196 PF~C~iCKkdy~s 208 (259)
T COG5152 196 PFLCGICKKDYES 208 (259)
T ss_pred ceeehhchhhccc
Confidence 4555555554433
No 206
>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=30.42 E-value=17 Score=26.86 Aligned_cols=25 Identities=12% Similarity=0.280 Sum_probs=0.0
Q ss_pred ccCCCCcccCccCCCc-Cc-cccHHHH
Q 028830 3 MTSDETTKICSHCDRA-IP-SSNIDLH 27 (203)
Q Consensus 3 ~h~~~k~y~C~~C~~~-f~-~~~l~~H 27 (203)
.|.-.+.|.|.+||.. |. +..|.+|
T Consensus 95 LhGL~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 95 LHGLGVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp ---------------------------
T ss_pred HhCCCCeeeeEeCCCcceecHHHHHHh
Confidence 4555677899999865 45 8888888
No 207
>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=30.39 E-value=27 Score=19.69 Aligned_cols=24 Identities=17% Similarity=0.379 Sum_probs=12.3
Q ss_pred CCccCccChhhhhHH-HHHhhHhcc
Q 028830 59 APVACSQCSETMERE-ILAIHKGEN 82 (203)
Q Consensus 59 ~~~~C~~C~~~f~~~-~l~~H~~~h 82 (203)
..|.|+.|...|-.. ++-.|...|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 368888888888663 666775543
No 208
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.06 E-value=27 Score=23.26 Aligned_cols=8 Identities=25% Similarity=0.746 Sum_probs=3.2
Q ss_pred cccccccc
Q 028830 37 RCKVCGDM 44 (203)
Q Consensus 37 ~C~~C~~~ 44 (203)
.|..||..
T Consensus 72 ~C~~Cg~~ 79 (113)
T PRK12380 72 WCWDCSQV 79 (113)
T ss_pred EcccCCCE
Confidence 34444433
No 209
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=29.77 E-value=30 Score=23.07 Aligned_cols=11 Identities=27% Similarity=0.691 Sum_probs=6.2
Q ss_pred ccccccccccc
Q 028830 36 ERCKVCGDMVP 46 (203)
Q Consensus 36 ~~C~~C~~~f~ 46 (203)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (114)
T PRK03681 71 CWCETCQQYVT 81 (114)
T ss_pred EEcccCCCeee
Confidence 45666665553
No 210
>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=29.65 E-value=16 Score=19.59 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=7.2
Q ss_pred CcccCccCCCcC
Q 028830 8 TTKICSHCDRAI 19 (203)
Q Consensus 8 k~y~C~~C~~~f 19 (203)
.|+.|+.|++.|
T Consensus 12 ~~~~C~~C~~~F 23 (43)
T PF01428_consen 12 LPFKCKHCGKSF 23 (43)
T ss_dssp SHEE-TTTS-EE
T ss_pred CCeECCCCCccc
Confidence 467777777776
No 211
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=29.65 E-value=32 Score=19.29 Aligned_cols=13 Identities=15% Similarity=0.473 Sum_probs=6.5
Q ss_pred CccCccChhhhhH
Q 028830 60 PVACSQCSETMER 72 (203)
Q Consensus 60 ~~~C~~C~~~f~~ 72 (203)
.+.|..||+.|-.
T Consensus 18 k~~Cr~Cg~~~C~ 30 (57)
T cd00065 18 RHHCRNCGRIFCS 30 (57)
T ss_pred ccccCcCcCCcCh
Confidence 3445555555533
No 212
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=29.58 E-value=35 Score=23.48 Aligned_cols=24 Identities=13% Similarity=0.202 Sum_probs=17.9
Q ss_pred eecccchhhcchhHHHHHHHhhcCCC
Q 028830 114 ELCHLCNRYIRLRERYNHESRCTGVP 139 (203)
Q Consensus 114 ~~C~~C~~~f~~~~l~~H~~~~~~~~ 139 (203)
..|-++|+.| .+|.+|+.+|++-.
T Consensus 77 IicLEDGkkf--KSLKRHL~t~~gmT 100 (148)
T COG4957 77 IICLEDGKKF--KSLKRHLTTHYGLT 100 (148)
T ss_pred EEEeccCcch--HHHHHHHhcccCCC
Confidence 5688899888 46888887776543
No 213
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.48 E-value=30 Score=23.20 Aligned_cols=12 Identities=25% Similarity=0.609 Sum_probs=6.3
Q ss_pred cccccccccccc
Q 028830 36 ERCKVCGDMVPR 47 (203)
Q Consensus 36 ~~C~~C~~~f~~ 47 (203)
+.|..||..|..
T Consensus 72 ~~C~~Cg~~~~~ 83 (117)
T PRK00564 72 LECKDCSHVFKP 83 (117)
T ss_pred EEhhhCCCcccc
Confidence 455555555543
No 214
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=29.30 E-value=59 Score=26.27 Aligned_cols=35 Identities=20% Similarity=0.543 Sum_probs=20.8
Q ss_pred CcccCccCCCC-CChhhHHHHHHH-hCCcc--eecccch
Q 028830 86 RIVTCDFCEFP-LPAVDLAEHQEV-CGNRT--ELCHLCN 120 (203)
Q Consensus 86 ~~~~C~~C~~~-f~~~~l~~H~~~-~~~~~--~~C~~C~ 120 (203)
..|.|++|+.. |+...|..|... |.+-. ..|+.|+
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 46777777766 447777777766 64322 2344444
No 215
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=29.03 E-value=27 Score=20.19 Aligned_cols=11 Identities=18% Similarity=0.764 Sum_probs=5.8
Q ss_pred CccCccChhhh
Q 028830 60 PVACSQCSETM 70 (203)
Q Consensus 60 ~~~C~~C~~~f 70 (203)
.+.|..||...
T Consensus 37 ~irCReCG~RI 47 (62)
T KOG3507|consen 37 VIRCRECGYRI 47 (62)
T ss_pred cEehhhcchHH
Confidence 45555555544
No 216
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=28.91 E-value=36 Score=27.44 Aligned_cols=29 Identities=14% Similarity=0.088 Sum_probs=24.1
Q ss_pred cceecccchh-hcchhHHHHHHHhhcCCCC
Q 028830 112 RTELCHLCNR-YIRLRERYNHESRCTGVPE 140 (203)
Q Consensus 112 ~~~~C~~C~~-~f~~~~l~~H~~~~~~~~~ 140 (203)
.-|.|++|+. .|+-..+..|+...|.+..
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~ 107 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEAS 107 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccC
Confidence 3599999998 8888999999987776543
No 217
>PF04806 EspF: EspF protein repeat; InterPro: IPR006891 Enteropathogenic Escherichia coli O127:H6 attaches to the intestinal muscosa through actin pedestals that are created after it has injected the Type III secretion protein EspF (E. coli secreted protein F-like protein from prophage U) into the cells. EspF recruits the actin machinery by activating the WASP (Wiscott-Aldrich syndrome protein) family of actin nucleating factors []. Subsequent cell-death (apoptosis) is caused by EspF being targeted to the mitochondria as a consequence of its mitochondrial targeting sequence. Import into mitochondria leads to a loss of membrane potential, leakage of cytochrome c and activation of the apoptotic caspase cascade. Mutation of leucine to glutamic at position 16 of EspF (L16E) resulted in the failure of EspF import into mitochondria; mitochondrial membrane potential was not affected and cell death abolished. This suggests that the targeting of EspF to mitochondria is essential for bacterial pathogenesis and apoptosis [, ].; PDB: 2KXC_B 2K42_B.
Probab=28.60 E-value=33 Score=18.39 Aligned_cols=22 Identities=41% Similarity=0.708 Sum_probs=2.1
Q ss_pred cccCCCCCCCCCCCCCcccccc
Q 028830 153 ESDQGAHRRPAPPPPNEFYRKR 174 (203)
Q Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~ 174 (203)
+-.++.|..|+|+|+......+
T Consensus 9 ehipp~P~rPAPpPPtQNnQs~ 30 (47)
T PF04806_consen 9 EHIPPTPNRPAPPPPTQNNQSR 30 (47)
T ss_dssp SS-----SS-------------
T ss_pred hcCCCCCCCCCCCCCCcccccC
Confidence 3345556666665544333333
No 218
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PRK00432 30S ribosomal protein S27ae; Validated
Probab=28.43 E-value=30 Score=19.34 Aligned_cols=9 Identities=22% Similarity=0.435 Sum_probs=5.1
Q ss_pred ceecccchh
Q 028830 113 TELCHLCNR 121 (203)
Q Consensus 113 ~~~C~~C~~ 121 (203)
.+.|..||.
T Consensus 37 r~~C~~Cgy 45 (50)
T PRK00432 37 RWHCGKCGY 45 (50)
T ss_pred cEECCCcCC
Confidence 355666654
No 220
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=28.21 E-value=15 Score=23.85 Aligned_cols=10 Identities=30% Similarity=0.667 Sum_probs=4.9
Q ss_pred cccccccccc
Q 028830 35 LERCKVCGDM 44 (203)
Q Consensus 35 ~~~C~~C~~~ 44 (203)
.|.|+.|+..
T Consensus 22 ~FtCp~Cghe 31 (104)
T COG4888 22 TFTCPRCGHE 31 (104)
T ss_pred eEecCccCCe
Confidence 3455555544
No 221
>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=28.11 E-value=18 Score=18.73 Aligned_cols=13 Identities=23% Similarity=0.639 Sum_probs=7.0
Q ss_pred CcccCccCCCcCc
Q 028830 8 TTKICSHCDRAIP 20 (203)
Q Consensus 8 k~y~C~~C~~~f~ 20 (203)
+.|+|..|+..+.
T Consensus 5 ~~YkC~~CGniVe 17 (36)
T PF06397_consen 5 EFYKCEHCGNIVE 17 (36)
T ss_dssp EEEE-TTT--EEE
T ss_pred cEEEccCCCCEEE
Confidence 4688888887653
No 222
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=27.82 E-value=48 Score=26.21 Aligned_cols=32 Identities=28% Similarity=0.643 Sum_probs=17.4
Q ss_pred cccccccccccccccHHHHHHcCCCCccCccChhhhhH
Q 028830 35 LERCKVCGDMVPRKYAEEHFLNTHAPVACSQCSETMER 72 (203)
Q Consensus 35 ~~~C~~C~~~f~~~~~~~~~~~~h~~~~C~~C~~~f~~ 72 (203)
..+|+.|+.....+.+.. ..+.|+.|+..|.-
T Consensus 27 ~~~c~~c~~~~~~~~l~~------~~~vc~~c~~h~rl 58 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEA------NLNVCPKCGHHMRI 58 (292)
T ss_pred eeECCCccchhhHHHHHh------cCCCCCCCCCCeeC
Confidence 356777776654443221 13567777766643
No 223
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=27.79 E-value=31 Score=19.68 Aligned_cols=10 Identities=20% Similarity=0.640 Sum_probs=5.4
Q ss_pred cCccCCCCCC
Q 028830 89 TCDFCEFPLP 98 (203)
Q Consensus 89 ~C~~C~~~f~ 98 (203)
.|+.|++.|.
T Consensus 7 ~C~~Cg~~~~ 16 (54)
T PF14446_consen 7 KCPVCGKKFK 16 (54)
T ss_pred cChhhCCccc
Confidence 4555555553
No 224
>PF14369 zf-RING_3: zinc-finger
Probab=27.69 E-value=29 Score=17.72 Aligned_cols=30 Identities=17% Similarity=0.418 Sum_probs=15.3
Q ss_pred cccCccCCCcCc-cccHHHHHhhcCCCcccccccccccc
Q 028830 9 TKICSHCDRAIP-SSNIDLHFAHCSRNLERCKVCGDMVP 46 (203)
Q Consensus 9 ~y~C~~C~~~f~-~~~l~~H~~h~~~~~~~C~~C~~~f~ 46 (203)
.|-|-.|.+.+. ... ......|+.|+..|.
T Consensus 2 ~ywCh~C~~~V~~~~~--------~~~~~~CP~C~~gFv 32 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPS--------PDSDVACPRCHGGFV 32 (35)
T ss_pred CEeCccCCCEeEeCcC--------CCCCcCCcCCCCcEe
Confidence 466667766553 111 011124777777664
No 225
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=27.59 E-value=54 Score=18.80 Aligned_cols=9 Identities=33% Similarity=0.586 Sum_probs=3.8
Q ss_pred ccccccccc
Q 028830 35 LERCKVCGD 43 (203)
Q Consensus 35 ~~~C~~C~~ 43 (203)
.|.|+.||.
T Consensus 14 ~~~Cp~cGi 22 (55)
T PF13824_consen 14 NFECPDCGI 22 (55)
T ss_pred CCcCCCCCC
Confidence 344444443
No 226
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.36 E-value=50 Score=17.74 Aligned_cols=15 Identities=27% Similarity=0.609 Sum_probs=11.3
Q ss_pred cCccCCCCCC-hhhHH
Q 028830 89 TCDFCEFPLP-AVDLA 103 (203)
Q Consensus 89 ~C~~C~~~f~-~~~l~ 103 (203)
.|..|++.|+ .....
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 6889999998 65544
No 227
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=27.04 E-value=33 Score=19.30 Aligned_cols=11 Identities=18% Similarity=0.419 Sum_probs=5.7
Q ss_pred ccCccCCCCCC
Q 028830 88 VTCDFCEFPLP 98 (203)
Q Consensus 88 ~~C~~C~~~f~ 98 (203)
++|+.||..|.
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 45555555543
No 228
>PLN02294 cytochrome c oxidase subunit Vb
Probab=26.83 E-value=27 Score=25.06 Aligned_cols=16 Identities=19% Similarity=0.598 Sum_probs=13.2
Q ss_pred hCCcceecccchhhcc
Q 028830 109 CGNRTELCHLCNRYIR 124 (203)
Q Consensus 109 ~~~~~~~C~~C~~~f~ 124 (203)
+..++++|++||..|.
T Consensus 137 ~kGkp~RCpeCG~~fk 152 (174)
T PLN02294 137 EKGKSFECPVCTQYFE 152 (174)
T ss_pred cCCCceeCCCCCCEEE
Confidence 4567999999999885
No 229
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=26.51 E-value=55 Score=17.33 Aligned_cols=6 Identities=33% Similarity=1.110 Sum_probs=1.5
Q ss_pred ccCccC
Q 028830 88 VTCDFC 93 (203)
Q Consensus 88 ~~C~~C 93 (203)
+.|+.|
T Consensus 37 ~~CP~C 42 (42)
T PF15227_consen 37 FSCPEC 42 (42)
T ss_dssp ---SSS
T ss_pred CCCcCC
Confidence 555544
No 230
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=25.85 E-value=41 Score=28.34 Aligned_cols=21 Identities=19% Similarity=0.490 Sum_probs=18.6
Q ss_pred ccCccCCCCCC-hhhHHHHHHH
Q 028830 88 VTCDFCEFPLP-AVDLAEHQEV 108 (203)
Q Consensus 88 ~~C~~C~~~f~-~~~l~~H~~~ 108 (203)
+.|.+|++.|. ...|..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 78999999998 8899999876
No 231
>PRK04351 hypothetical protein; Provisional
Probab=25.76 E-value=24 Score=24.87 Aligned_cols=31 Identities=13% Similarity=0.357 Sum_probs=19.1
Q ss_pred cccCccCCCCCChhhHHHHHHHhCCcceecccchhhc
Q 028830 87 IVTCDFCEFPLPAVDLAEHQEVCGNRTELCHLCNRYI 123 (203)
Q Consensus 87 ~~~C~~C~~~f~~~~l~~H~~~~~~~~~~C~~C~~~f 123 (203)
.|.|..||..+. ++ +.+....|.|..|+..+
T Consensus 112 ~Y~C~~Cg~~~~-----r~-Rr~n~~~yrCg~C~g~L 142 (149)
T PRK04351 112 LYECQSCGQQYL-----RK-RRINTKRYRCGKCRGKL 142 (149)
T ss_pred EEECCCCCCEee-----ee-eecCCCcEEeCCCCcEe
Confidence 577877886553 11 12355678888887544
No 232
>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=25.75 E-value=28 Score=20.57 Aligned_cols=11 Identities=45% Similarity=1.069 Sum_probs=4.9
Q ss_pred CcccCccCCCC
Q 028830 86 RIVTCDFCEFP 96 (203)
Q Consensus 86 ~~~~C~~C~~~ 96 (203)
+.|.|+.||..
T Consensus 45 r~~~C~~Cg~~ 55 (69)
T PF07282_consen 45 RVFTCPNCGFE 55 (69)
T ss_pred ceEEcCCCCCE
Confidence 34444444443
No 233
>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=24.94 E-value=17 Score=19.18 Aligned_cols=9 Identities=33% Similarity=1.121 Sum_probs=3.4
Q ss_pred CcccCccCC
Q 028830 86 RIVTCDFCE 94 (203)
Q Consensus 86 ~~~~C~~C~ 94 (203)
+.+.|..|+
T Consensus 23 ~~w~C~~C~ 31 (40)
T PF04810_consen 23 KTWICNFCG 31 (40)
T ss_dssp TEEEETTT-
T ss_pred CEEECcCCC
Confidence 344444443
No 234
>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=24.72 E-value=32 Score=22.29 Aligned_cols=14 Identities=14% Similarity=0.593 Sum_probs=9.4
Q ss_pred Ccceecccchhhcc
Q 028830 111 NRTELCHLCNRYIR 124 (203)
Q Consensus 111 ~~~~~C~~C~~~f~ 124 (203)
.++++|+.||..|.
T Consensus 77 g~~~rC~eCG~~fk 90 (97)
T cd00924 77 GKPKRCPECGHVFK 90 (97)
T ss_pred CCceeCCCCCcEEE
Confidence 35777777776664
No 235
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=24.70 E-value=50 Score=23.33 Aligned_cols=10 Identities=20% Similarity=0.408 Sum_probs=3.1
Q ss_pred cceecccchh
Q 028830 112 RTELCHLCNR 121 (203)
Q Consensus 112 ~~~~C~~C~~ 121 (203)
...+|-.||.
T Consensus 59 t~leCy~Cg~ 68 (152)
T PF09416_consen 59 TVLECYNCGS 68 (152)
T ss_dssp -B---TTT--
T ss_pred cEEEEEecCC
Confidence 4578888874
No 236
>COG1773 Rubredoxin [Energy production and conversion]
Probab=24.12 E-value=28 Score=19.92 Aligned_cols=12 Identities=25% Similarity=0.393 Sum_probs=7.6
Q ss_pred cccCccCCCcCc
Q 028830 9 TKICSHCDRAIP 20 (203)
Q Consensus 9 ~y~C~~C~~~f~ 20 (203)
.|+|..|+..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 466666666664
No 237
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=24.09 E-value=35 Score=26.92 Aligned_cols=7 Identities=57% Similarity=1.369 Sum_probs=3.4
Q ss_pred ccccccc
Q 028830 37 RCKVCGD 43 (203)
Q Consensus 37 ~C~~C~~ 43 (203)
.|..|+.
T Consensus 170 ~C~~C~~ 176 (288)
T KOG1729|consen 170 ECMVCGC 176 (288)
T ss_pred ecccCCC
Confidence 4444544
No 238
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=23.90 E-value=1.7 Score=35.55 Aligned_cols=10 Identities=30% Similarity=1.172 Sum_probs=6.6
Q ss_pred cCccCCCcCc
Q 028830 11 ICSHCDRAIP 20 (203)
Q Consensus 11 ~C~~C~~~f~ 20 (203)
.|-.|++...
T Consensus 276 iC~~C~K~V~ 285 (468)
T KOG1701|consen 276 ICAFCHKTVS 285 (468)
T ss_pred hhhhcCCccc
Confidence 5667777664
No 239
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=23.70 E-value=24 Score=23.39 Aligned_cols=18 Identities=17% Similarity=0.289 Sum_probs=13.2
Q ss_pred cCCCcCc--cccHHHH-Hhhc
Q 028830 14 HCDRAIP--SSNIDLH-FAHC 31 (203)
Q Consensus 14 ~C~~~f~--~~~l~~H-~~h~ 31 (203)
.||..|- +.|.+.| ..+-
T Consensus 28 ~CGh~f~d~r~NwK~~alv~v 48 (112)
T PF08882_consen 28 DCGHEFCDARENWKLGALVYV 48 (112)
T ss_pred cCCCeecChhcChhhCcEEEe
Confidence 4999984 8888888 5543
No 240
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=23.53 E-value=36 Score=26.17 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=9.6
Q ss_pred CCcccCccCCCCCC
Q 028830 85 QRIVTCDFCEFPLP 98 (203)
Q Consensus 85 ~~~~~C~~C~~~f~ 98 (203)
...|.|..|.+-|.
T Consensus 219 veHFvCa~CekPFl 232 (332)
T KOG2272|consen 219 VEHFVCAKCEKPFL 232 (332)
T ss_pred hhheeehhcCCccc
Confidence 35677777777764
No 241
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=23.35 E-value=40 Score=22.44 Aligned_cols=36 Identities=14% Similarity=0.156 Sum_probs=19.8
Q ss_pred cccCccCCCCCC-hhhHHHHHHHhCC---cceecccchhhcc
Q 028830 87 IVTCDFCEFPLP-AVDLAEHQEVCGN---RTELCHLCNRYIR 124 (203)
Q Consensus 87 ~~~C~~C~~~f~-~~~l~~H~~~~~~---~~~~C~~C~~~f~ 124 (203)
..+|+.||..=. ...|+ +|...| --|.|+.|+..|+
T Consensus 74 ~~kCpkCghe~m~Y~T~Q--lRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQ--LRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred hccCcccCCchhhhhhhh--cccccCCceEEEEcCccceeee
Confidence 357888885522 22222 122222 3488998987765
No 242
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=22.76 E-value=60 Score=27.22 Aligned_cols=28 Identities=25% Similarity=0.445 Sum_probs=22.9
Q ss_pred CcccCccCCCCCC-hhhHHHHHHH-hCCcc
Q 028830 86 RIVTCDFCEFPLP-AVDLAEHQEV-CGNRT 113 (203)
Q Consensus 86 ~~~~C~~C~~~f~-~~~l~~H~~~-~~~~~ 113 (203)
..|.|+.|..-|. ...|..|... |++.-
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 4688999999998 8889999888 86643
No 243
>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=22.45 E-value=21 Score=24.96 Aligned_cols=32 Identities=16% Similarity=0.387 Sum_probs=18.7
Q ss_pred CcccCccCCCCCChhhHHHHHHHhCCcceecccchhhc
Q 028830 86 RIVTCDFCEFPLPAVDLAEHQEVCGNRTELCHLCNRYI 123 (203)
Q Consensus 86 ~~~~C~~C~~~f~~~~l~~H~~~~~~~~~~C~~C~~~f 123 (203)
-.|.|..|+..+. +|.+. ....|.|+.|+..+
T Consensus 122 ~~~~C~~C~~~~~-----r~~~~-~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 122 YVYRCPSCGREYK-----RHRRS-KRKRYRCGRCGGPL 153 (157)
T ss_pred eEEEcCCCCCEee-----eeccc-chhhEECCCCCCEE
Confidence 3677888887763 11111 22347888887544
No 244
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=22.05 E-value=11 Score=23.45 Aligned_cols=13 Identities=38% Similarity=0.946 Sum_probs=5.7
Q ss_pred ccccccccccccc
Q 028830 36 ERCKVCGDMVPRK 48 (203)
Q Consensus 36 ~~C~~C~~~f~~~ 48 (203)
..|..|+..|...
T Consensus 47 ~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 47 LSCRVCGESFQTK 59 (81)
T ss_dssp EEESSS--EEEEE
T ss_pred EEecCCCCeEEEc
Confidence 3455565555544
No 245
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=22.02 E-value=47 Score=27.82 Aligned_cols=24 Identities=17% Similarity=0.263 Sum_probs=20.2
Q ss_pred CCccCccChhhhhH-HHHHhhHhcc
Q 028830 59 APVACSQCSETMER-EILAIHKGEN 82 (203)
Q Consensus 59 ~~~~C~~C~~~f~~-~~l~~H~~~h 82 (203)
.-|.|++|...|.. ..|..|....
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~e 38 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVE 38 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhh
Confidence 47899999999988 8899998763
No 246
>PRK12496 hypothetical protein; Provisional
Probab=21.86 E-value=43 Score=23.97 Aligned_cols=26 Identities=19% Similarity=0.554 Sum_probs=17.2
Q ss_pred CcccCccCCCCCC-hhhHHHHHHHhCCcceecccchhh
Q 028830 86 RIVTCDFCEFPLP-AVDLAEHQEVCGNRTELCHLCNRY 122 (203)
Q Consensus 86 ~~~~C~~C~~~f~-~~~l~~H~~~~~~~~~~C~~C~~~ 122 (203)
+.|.|.-|++.|. ... .-.|+.||..
T Consensus 126 w~~~C~gC~~~~~~~~~-----------~~~C~~CG~~ 152 (164)
T PRK12496 126 WRKVCKGCKKKYPEDYP-----------DDVCEICGSP 152 (164)
T ss_pred eeEECCCCCccccCCCC-----------CCcCCCCCCh
Confidence 4578999998885 211 1259999863
No 247
>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=21.01 E-value=29 Score=18.96 Aligned_cols=37 Identities=19% Similarity=0.403 Sum_probs=17.8
Q ss_pred cCccCCCcCc-cccHHHHHhhcCCCcccccc--cccccccc
Q 028830 11 ICSHCDRAIP-SSNIDLHFAHCSRNLERCKV--CGDMVPRK 48 (203)
Q Consensus 11 ~C~~C~~~f~-~~~l~~H~~h~~~~~~~C~~--C~~~f~~~ 48 (203)
.||.||.... +.....+. -..+.-|.|.. ||..|...
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~-~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSP-LTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhhCc-ceEEEEEEECCCcCCCEEEEE
Confidence 3677776655 44433330 11122345544 77666543
No 248
>KOG4118 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.95 E-value=46 Score=19.73 Aligned_cols=21 Identities=24% Similarity=0.575 Sum_probs=10.4
Q ss_pred ccCccCCCCCC-hhhHHHHHHH
Q 028830 88 VTCDFCEFPLP-AVDLAEHQEV 108 (203)
Q Consensus 88 ~~C~~C~~~f~-~~~l~~H~~~ 108 (203)
|+|.+|--... ...+..|...
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~ 60 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFEN 60 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhh
Confidence 45555554444 4445555444
No 249
>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=20.25 E-value=31 Score=18.29 Aligned_cols=12 Identities=25% Similarity=0.537 Sum_probs=8.9
Q ss_pred Cccccccccccc
Q 028830 34 NLERCKVCGDMV 45 (203)
Q Consensus 34 ~~~~C~~C~~~f 45 (203)
.+..|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 356788888776
No 250
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=20.24 E-value=58 Score=24.84 Aligned_cols=11 Identities=18% Similarity=0.501 Sum_probs=6.7
Q ss_pred cccCccCCCcC
Q 028830 9 TKICSHCDRAI 19 (203)
Q Consensus 9 ~y~C~~C~~~f 19 (203)
||+|+.|...|
T Consensus 23 Pf~Cd~C~~~F 33 (250)
T KOG3183|consen 23 PFKCDGCSGIF 33 (250)
T ss_pred ceeeCCccchh
Confidence 55666666665
No 251
>PRK12722 transcriptional activator FlhC; Provisional
Probab=20.24 E-value=68 Score=23.57 Aligned_cols=30 Identities=17% Similarity=0.466 Sum_probs=18.6
Q ss_pred CCccCccChhhhhHHHHHhhHhccCCCCcccCccCCC
Q 028830 59 APVACSQCSETMEREILAIHKGENCPQRIVTCDFCEF 95 (203)
Q Consensus 59 ~~~~C~~C~~~f~~~~l~~H~~~h~~~~~~~C~~C~~ 95 (203)
....|..|+-.|.... +.....|.|+.|.-
T Consensus 133 ~l~~C~~Cgg~fv~~~-------~e~~~~f~CplC~~ 162 (187)
T PRK12722 133 QLSSCNCCGGHFVTHA-------HDPVGSFVCGLCQP 162 (187)
T ss_pred eeccCCCCCCCeeccc-------cccCCCCcCCCCCC
Confidence 3667888887775421 11235788888864
Done!