Query 039095
Match_columns 492
No_of_seqs 286 out of 2704
Neff 10.6
Searched_HMMs 46136
Date Fri Mar 29 06:14:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039095.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039095hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1074 Transcriptional repres 100.0 1.2E-31 2.5E-36 258.3 8.7 54 13-66 354-407 (958)
2 KOG2462 C2H2-type Zn-finger pr 100.0 6E-31 1.3E-35 223.9 4.9 82 9-94 127-211 (279)
3 KOG3623 Homeobox transcription 99.9 4.2E-27 9.1E-32 223.1 7.4 105 13-117 211-329 (1007)
4 KOG2462 C2H2-type Zn-finger pr 99.9 2.8E-27 6.2E-32 201.5 5.6 106 9-118 158-264 (279)
5 KOG1074 Transcriptional repres 99.9 1.4E-26 3.1E-31 223.5 6.5 93 314-436 603-699 (958)
6 KOG3608 Zn finger proteins [Ge 99.9 1.5E-25 3.1E-30 195.5 1.6 223 13-437 135-384 (467)
7 KOG3608 Zn finger proteins [Ge 99.8 7.6E-22 1.6E-26 172.5 1.3 109 11-120 176-286 (467)
8 KOG3576 Ovo and related transc 99.8 4.9E-20 1.1E-24 148.7 1.3 111 9-121 114-236 (267)
9 KOG3576 Ovo and related transc 99.6 4.7E-17 1E-21 131.6 -0.1 83 36-120 113-196 (267)
10 KOG3623 Homeobox transcription 99.6 7.5E-17 1.6E-21 154.1 0.6 80 10-91 892-971 (1007)
11 PHA00733 hypothetical protein 99.3 1.8E-12 3.9E-17 102.4 2.3 79 10-92 38-121 (128)
12 PHA02768 hypothetical protein; 99.2 6.3E-12 1.4E-16 80.4 1.2 44 343-422 5-48 (55)
13 PHA02768 hypothetical protein; 99.1 1.3E-11 2.8E-16 79.0 1.2 44 40-87 5-48 (55)
14 PLN03086 PRLI-interacting fact 99.1 4.6E-11 1E-15 116.2 4.8 94 8-108 449-552 (567)
15 PLN03086 PRLI-interacting fact 99.1 6.7E-11 1.4E-15 115.1 5.8 87 13-117 408-496 (567)
16 PHA00733 hypothetical protein 99.1 2.7E-11 5.9E-16 95.7 2.0 92 27-121 27-123 (128)
17 KOG3993 Transcription factor ( 99.0 2.1E-10 4.5E-15 104.0 1.7 83 13-95 268-381 (500)
18 KOG3993 Transcription factor ( 98.8 2.5E-09 5.5E-14 97.1 4.4 53 40-96 267-321 (500)
19 PF13465 zf-H2C2_2: Zinc-finge 98.8 8.6E-10 1.9E-14 60.4 0.5 25 55-81 1-25 (26)
20 PF13465 zf-H2C2_2: Zinc-finge 98.8 9.2E-10 2E-14 60.3 0.5 22 396-417 5-26 (26)
21 PHA00732 hypothetical protein 98.7 1E-08 2.2E-13 73.0 2.1 48 40-94 1-48 (79)
22 PHA00732 hypothetical protein 98.6 1.4E-08 3.1E-13 72.2 2.2 47 343-429 1-48 (79)
23 PHA00616 hypothetical protein 98.6 8.6E-09 1.9E-13 62.7 0.1 33 343-375 1-33 (44)
24 PHA00616 hypothetical protein 98.6 1.4E-08 3E-13 61.8 0.8 35 40-76 1-35 (44)
25 PF05605 zf-Di19: Drought indu 98.4 2.6E-07 5.6E-12 61.2 3.1 51 40-94 2-53 (54)
26 PF00096 zf-C2H2: Zinc finger, 98.3 2.6E-07 5.7E-12 49.3 0.9 23 406-428 1-23 (23)
27 PF05605 zf-Di19: Drought indu 98.2 6.6E-07 1.4E-11 59.2 2.3 52 343-430 2-54 (54)
28 PF00096 zf-C2H2: Zinc finger, 98.1 9.1E-07 2E-11 47.1 0.8 22 41-62 1-22 (23)
29 COG5189 SFP1 Putative transcri 98.0 3.6E-06 7.7E-11 74.0 2.7 67 340-426 346-419 (423)
30 PF13894 zf-C2H2_4: C2H2-type 97.9 5.1E-06 1.1E-10 44.8 1.2 24 406-429 1-24 (24)
31 PF13912 zf-C2H2_6: C2H2-type 97.9 6E-06 1.3E-10 45.9 1.1 26 405-430 1-26 (27)
32 PF13912 zf-C2H2_6: C2H2-type 97.8 1.2E-05 2.6E-10 44.7 1.6 25 40-64 1-25 (27)
33 PF13894 zf-C2H2_4: C2H2-type 97.8 9.8E-06 2.1E-10 43.6 1.0 23 41-63 1-23 (24)
34 PF12756 zf-C2H2_2: C2H2 type 97.7 1.4E-05 3E-10 61.3 1.6 74 345-429 1-74 (100)
35 PF12756 zf-C2H2_2: C2H2 type 97.7 1.5E-05 3.2E-10 61.2 1.2 73 14-93 1-73 (100)
36 COG5189 SFP1 Putative transcri 97.7 1.5E-05 3.3E-10 70.2 1.2 55 37-91 346-419 (423)
37 PF09237 GAGA: GAGA factor; I 97.5 4.3E-05 9.4E-10 47.5 1.3 37 57-94 12-48 (54)
38 smart00355 ZnF_C2H2 zinc finge 97.4 9.1E-05 2E-09 40.6 1.6 25 406-430 1-25 (26)
39 PF09237 GAGA: GAGA factor; I 97.3 0.00013 2.9E-09 45.4 1.7 34 33-66 17-50 (54)
40 smart00355 ZnF_C2H2 zinc finge 97.1 0.00021 4.6E-09 39.0 1.3 24 71-94 1-24 (26)
41 PF12874 zf-met: Zinc-finger o 97.1 0.0002 4.4E-09 38.8 0.8 23 406-428 1-23 (25)
42 COG5048 FOG: Zn-finger [Genera 97.1 0.012 2.6E-07 58.8 14.1 63 315-377 288-357 (467)
43 PF12874 zf-met: Zinc-finger o 97.0 0.00035 7.6E-09 37.8 1.0 23 41-63 1-23 (25)
44 PF13909 zf-H2C2_5: C2H2-type 96.9 0.00035 7.5E-09 37.4 0.9 24 406-430 1-24 (24)
45 PF12171 zf-C2H2_jaz: Zinc-fin 96.8 0.00057 1.2E-08 37.7 1.2 22 41-62 2-23 (27)
46 PRK04860 hypothetical protein; 96.8 0.00038 8.3E-09 57.3 0.6 37 40-82 119-155 (160)
47 PRK04860 hypothetical protein; 96.8 0.0005 1.1E-08 56.6 1.3 25 342-370 118-142 (160)
48 PF12171 zf-C2H2_jaz: Zinc-fin 96.7 0.00059 1.3E-08 37.7 0.8 23 406-428 2-24 (27)
49 KOG2231 Predicted E3 ubiquitin 96.7 0.0017 3.7E-08 65.0 4.6 48 41-104 100-147 (669)
50 PF13909 zf-H2C2_5: C2H2-type 96.6 0.00065 1.4E-08 36.3 0.4 21 71-92 1-21 (24)
51 KOG1146 Homeobox protein [Gene 96.5 0.0022 4.7E-08 68.1 3.6 53 314-366 587-641 (1406)
52 COG5048 FOG: Zn-finger [Genera 96.0 0.0044 9.5E-08 61.9 2.6 56 11-66 288-349 (467)
53 KOG1146 Homeobox protein [Gene 95.7 0.0063 1.4E-07 64.8 2.5 103 319-431 439-546 (1406)
54 KOG2893 Zn finger protein [Gen 95.4 0.0042 9.2E-08 52.8 0.2 47 345-429 12-59 (341)
55 PF13913 zf-C2HC_2: zinc-finge 95.3 0.01 2.3E-07 31.8 1.3 21 406-427 3-23 (25)
56 PF13913 zf-C2HC_2: zinc-finge 94.8 0.017 3.6E-07 31.0 1.2 19 42-61 4-22 (25)
57 smart00451 ZnF_U1 U1-like zinc 94.6 0.017 3.7E-07 34.1 1.2 23 405-427 3-25 (35)
58 smart00451 ZnF_U1 U1-like zinc 94.3 0.025 5.5E-07 33.3 1.4 23 40-62 3-25 (35)
59 cd00350 rubredoxin_like Rubred 93.7 0.04 8.7E-07 31.9 1.4 24 13-48 2-25 (33)
60 KOG2893 Zn finger protein [Gen 92.2 0.039 8.5E-07 47.1 -0.2 47 42-94 12-59 (341)
61 KOG4173 Alpha-SNAP protein [In 91.5 0.081 1.8E-06 44.2 1.0 79 10-92 77-168 (253)
62 TIGR00622 ssl1 transcription f 91.1 0.64 1.4E-05 35.4 5.3 27 403-429 79-105 (112)
63 PF09986 DUF2225: Uncharacteri 90.5 0.15 3.3E-06 44.7 1.8 25 341-365 3-27 (214)
64 KOG2482 Predicted C2H2-type Zn 90.3 0.19 4.2E-06 45.6 2.2 110 11-120 143-357 (423)
65 COG5236 Uncharacterized conser 90.3 0.38 8.2E-06 43.8 4.0 104 11-123 178-307 (493)
66 COG4049 Uncharacterized protei 89.2 0.12 2.7E-06 32.9 0.2 23 69-91 16-38 (65)
67 TIGR00622 ssl1 transcription f 88.9 1.4 2.9E-05 33.7 5.5 91 269-367 13-105 (112)
68 cd00729 rubredoxin_SM Rubredox 88.9 0.25 5.5E-06 28.8 1.3 25 12-48 2-26 (34)
69 PF12013 DUF3505: Protein of u 88.8 0.32 6.9E-06 37.6 2.3 25 71-95 81-109 (109)
70 KOG2482 Predicted C2H2-type Zn 88.5 0.25 5.4E-06 44.9 1.6 82 12-93 195-357 (423)
71 KOG2231 Predicted E3 ubiquitin 88.0 0.47 1E-05 48.2 3.3 79 13-94 100-206 (669)
72 PF13717 zinc_ribbon_4: zinc-r 87.7 0.33 7.2E-06 28.7 1.3 34 317-354 3-36 (36)
73 PRK00464 nrdR transcriptional 87.3 0.29 6.4E-06 40.1 1.2 47 317-363 1-48 (154)
74 PF10571 UPF0547: Uncharacteri 86.5 0.49 1.1E-05 25.6 1.4 24 318-354 2-25 (26)
75 PF09538 FYDLN_acid: Protein o 86.3 0.48 1E-05 36.2 1.8 30 41-83 10-39 (108)
76 COG1198 PriA Primosomal protei 86.2 0.54 1.2E-05 48.9 2.8 50 316-414 435-484 (730)
77 COG4049 Uncharacterized protei 85.9 0.36 7.7E-06 30.9 0.8 31 35-65 12-42 (65)
78 PF09986 DUF2225: Uncharacteri 85.4 0.46 1E-05 41.7 1.6 17 11-27 4-20 (214)
79 PF09538 FYDLN_acid: Protein o 84.3 0.72 1.6E-05 35.3 2.0 32 315-356 8-39 (108)
80 PF02892 zf-BED: BED zinc fing 84.2 0.61 1.3E-05 29.2 1.3 25 402-426 13-41 (45)
81 smart00614 ZnF_BED BED zinc fi 83.6 0.67 1.4E-05 29.9 1.4 25 405-429 17-48 (50)
82 PF02892 zf-BED: BED zinc fing 82.3 0.74 1.6E-05 28.8 1.2 27 340-366 13-44 (45)
83 TIGR02098 MJ0042_CXXC MJ0042 f 82.3 0.62 1.3E-05 27.9 0.8 34 317-354 3-36 (38)
84 COG0068 HypF Hydrogenase matur 81.8 0.7 1.5E-05 47.0 1.3 56 317-378 124-180 (750)
85 PF13719 zinc_ribbon_5: zinc-r 81.6 0.79 1.7E-05 27.3 1.0 34 317-354 3-36 (37)
86 smart00734 ZnF_Rad18 Rad18-lik 81.6 0.93 2E-05 24.5 1.2 21 406-427 2-22 (26)
87 smart00531 TFIIE Transcription 81.3 1.1 2.5E-05 36.7 2.2 37 37-80 96-133 (147)
88 PRK00464 nrdR transcriptional 81.1 0.71 1.5E-05 37.9 0.9 17 70-86 28-44 (154)
89 PRK00398 rpoP DNA-directed RNA 80.3 1.3 2.8E-05 27.9 1.7 31 315-354 2-32 (46)
90 smart00834 CxxC_CXXC_SSSS Puta 80.2 0.87 1.9E-05 27.8 0.9 14 13-26 6-19 (41)
91 COG5236 Uncharacterized conser 80.0 1.4 3E-05 40.3 2.5 105 13-119 152-273 (493)
92 PHA00626 hypothetical protein 79.3 1.4 3E-05 28.5 1.6 16 404-419 22-37 (59)
93 KOG2186 Cell growth-regulating 79.1 0.82 1.8E-05 39.9 0.7 46 41-91 4-49 (276)
94 COG1592 Rubrerythrin [Energy p 79.0 1.1 2.3E-05 37.1 1.4 9 343-351 134-142 (166)
95 smart00614 ZnF_BED BED zinc fi 78.9 1.1 2.5E-05 28.8 1.2 20 42-61 20-44 (50)
96 PRK14890 putative Zn-ribbon RN 78.3 1.9 4.2E-05 28.4 2.1 32 40-78 25-56 (59)
97 PRK09678 DNA-binding transcrip 78.0 0.6 1.3E-05 32.5 -0.3 12 97-108 27-40 (72)
98 TIGR02605 CxxC_CxxC_SSSS putat 77.6 1.1 2.4E-05 29.1 0.9 12 13-24 6-17 (52)
99 TIGR02300 FYDLN_acid conserved 77.4 1.8 3.8E-05 33.7 2.0 34 41-87 10-43 (129)
100 PRK09678 DNA-binding transcrip 77.0 1.3 2.8E-05 30.9 1.1 43 317-360 2-46 (72)
101 KOG4173 Alpha-SNAP protein [In 75.9 1.4 3E-05 37.1 1.2 81 39-124 78-173 (253)
102 smart00659 RPOLCX RNA polymera 75.6 1.9 4E-05 26.9 1.4 11 13-23 3-13 (44)
103 COG1997 RPL43A Ribosomal prote 75.6 2 4.4E-05 30.8 1.7 32 315-355 34-65 (89)
104 TIGR02300 FYDLN_acid conserved 75.4 2.2 4.8E-05 33.2 2.0 36 315-360 8-43 (129)
105 TIGR00373 conserved hypothetic 75.0 1.3 2.9E-05 36.7 0.9 34 35-79 104-137 (158)
106 COG2888 Predicted Zn-ribbon RN 74.2 2.2 4.7E-05 28.1 1.5 32 40-78 27-58 (61)
107 PF05443 ROS_MUCR: ROS/MUCR tr 73.9 1.6 3.4E-05 34.7 1.0 28 404-434 71-98 (132)
108 TIGR01384 TFS_arch transcripti 72.6 4.7 0.0001 30.7 3.4 27 318-355 2-28 (104)
109 PRK06266 transcription initiat 72.6 1.6 3.4E-05 37.0 0.8 35 36-81 113-147 (178)
110 PF15269 zf-C2H2_7: Zinc-finge 72.3 2.1 4.5E-05 26.1 1.0 22 41-62 21-42 (54)
111 COG1996 RPC10 DNA-directed RNA 72.1 1.7 3.6E-05 27.6 0.6 11 12-22 6-16 (49)
112 PF09723 Zn-ribbon_8: Zinc rib 72.0 1.9 4.1E-05 26.5 0.8 29 13-48 6-34 (42)
113 KOG4167 Predicted DNA-binding 71.7 0.61 1.3E-05 47.1 -2.1 82 13-94 289-372 (907)
114 cd00730 rubredoxin Rubredoxin; 71.0 5.1 0.00011 25.7 2.6 35 317-351 2-42 (50)
115 PRK14873 primosome assembly pr 70.6 2.8 6.1E-05 43.7 2.2 39 344-414 393-431 (665)
116 TIGR00373 conserved hypothetic 69.7 2.7 5.8E-05 34.9 1.5 31 69-107 108-138 (158)
117 smart00531 TFIIE Transcription 69.7 3.1 6.8E-05 34.1 1.9 34 69-106 98-132 (147)
118 PF14353 CpXC: CpXC protein 69.3 2.5 5.4E-05 33.7 1.2 50 317-366 2-61 (128)
119 PRK06266 transcription initiat 69.0 2.8 6E-05 35.6 1.5 32 69-108 116-147 (178)
120 PF12013 DUF3505: Protein of u 69.0 2.7 5.8E-05 32.4 1.3 25 406-430 81-109 (109)
121 PRK04023 DNA polymerase II lar 67.4 5.3 0.00011 42.6 3.3 37 314-380 624-660 (1121)
122 TIGR00595 priA primosomal prot 66.7 3.8 8.3E-05 41.4 2.2 40 344-414 223-262 (505)
123 PF06524 NOA36: NOA36 protein; 66.7 3.6 7.7E-05 36.2 1.7 72 35-108 137-220 (314)
124 PF00301 Rubredoxin: Rubredoxi 65.7 3.6 7.8E-05 26.0 1.1 35 317-351 2-42 (47)
125 KOG2593 Transcription initiati 65.5 3.1 6.7E-05 39.7 1.2 39 35-78 123-161 (436)
126 COG4530 Uncharacterized protei 65.3 4.6 0.0001 30.2 1.8 12 69-80 25-36 (129)
127 KOG2186 Cell growth-regulating 65.2 3.3 7.1E-05 36.3 1.2 52 12-66 3-54 (276)
128 PF06524 NOA36: NOA36 protein; 65.0 3.8 8.3E-05 36.0 1.6 28 340-367 206-233 (314)
129 PF02176 zf-TRAF: TRAF-type zi 64.8 3.8 8.2E-05 27.4 1.2 39 40-81 9-53 (60)
130 PF03604 DNA_RNApol_7kD: DNA d 63.6 6.3 0.00014 22.6 1.8 11 13-23 1-11 (32)
131 PF07975 C1_4: TFIIH C1-like d 63.3 3.6 7.9E-05 26.5 0.8 27 341-367 19-45 (51)
132 PF04810 zf-Sec23_Sec24: Sec23 63.2 4.2 9.1E-05 24.7 1.1 33 371-415 2-34 (40)
133 KOG2785 C2H2-type Zn-finger pr 63.0 4.8 0.0001 37.7 1.9 75 11-92 165-242 (390)
134 COG1592 Rubrerythrin [Energy p 62.0 4.7 0.0001 33.5 1.5 24 316-351 134-157 (166)
135 COG4530 Uncharacterized protei 61.8 4.3 9.4E-05 30.3 1.1 31 316-356 9-39 (129)
136 KOG4124 Putative transcription 61.2 2.9 6.3E-05 38.4 0.2 23 38-60 347-371 (442)
137 PTZ00255 60S ribosomal protein 61.0 4.9 0.00011 29.4 1.2 32 315-355 35-66 (90)
138 COG4957 Predicted transcriptio 60.5 3.6 7.7E-05 32.2 0.5 26 406-434 77-102 (148)
139 PF05443 ROS_MUCR: ROS/MUCR tr 60.4 4 8.7E-05 32.5 0.8 24 40-66 72-95 (132)
140 PRK04023 DNA polymerase II lar 59.5 7.1 0.00015 41.8 2.6 47 12-106 626-672 (1121)
141 PF08274 PhnA_Zn_Ribbon: PhnA 59.2 4.4 9.5E-05 22.8 0.6 10 95-104 17-26 (30)
142 TIGR00280 L37a ribosomal prote 59.1 4.6 9.9E-05 29.5 0.8 32 315-355 34-65 (91)
143 PF01780 Ribosomal_L37ae: Ribo 59.1 2.9 6.2E-05 30.5 -0.2 32 315-355 34-65 (90)
144 KOG4167 Predicted DNA-binding 58.8 2.3 5.1E-05 43.1 -0.9 29 38-66 790-818 (907)
145 KOG2807 RNA polymerase II tran 57.8 11 0.00023 34.6 3.1 20 40-59 290-309 (378)
146 COG1198 PriA Primosomal protei 57.7 5.5 0.00012 41.8 1.5 9 15-23 438-446 (730)
147 COG1773 Rubredoxin [Energy pro 56.4 11 0.00024 24.6 2.2 35 316-350 3-43 (55)
148 smart00154 ZnF_AN1 AN1-like Zi 55.5 9 0.0002 23.1 1.6 15 405-419 12-26 (39)
149 PF12760 Zn_Tnp_IS1595: Transp 55.3 6.7 0.00015 24.6 1.1 10 69-78 36-45 (46)
150 PF13240 zinc_ribbon_2: zinc-r 55.3 7.7 0.00017 20.2 1.1 7 43-49 16-22 (23)
151 COG5151 SSL1 RNA polymerase II 54.6 19 0.0004 32.8 4.0 52 315-367 361-412 (421)
152 PF05191 ADK_lid: Adenylate ki 54.2 7.4 0.00016 23.0 1.0 32 13-52 2-33 (36)
153 PRK03976 rpl37ae 50S ribosomal 54.1 6 0.00013 28.9 0.8 32 315-355 35-66 (90)
154 PF05290 Baculo_IE-1: Baculovi 53.9 8.2 0.00018 30.3 1.5 18 315-332 79-96 (140)
155 KOG2785 C2H2-type Zn-finger pr 53.7 9.5 0.00021 35.9 2.2 78 41-124 167-247 (390)
156 PF15269 zf-C2H2_7: Zinc-finge 53.6 6.4 0.00014 24.0 0.7 23 70-92 20-42 (54)
157 TIGR01206 lysW lysine biosynth 53.2 4.8 0.0001 26.3 0.1 31 71-108 3-33 (54)
158 PF01363 FYVE: FYVE zinc finge 52.5 12 0.00025 26.0 2.0 32 314-356 7-38 (69)
159 COG3357 Predicted transcriptio 51.9 9.9 0.00021 27.5 1.5 14 342-355 57-70 (97)
160 smart00440 ZnF_C2C2 C2C2 Zinc 51.7 7.7 0.00017 23.6 0.9 11 41-51 29-39 (40)
161 KOG4124 Putative transcription 51.0 8.6 0.00019 35.5 1.4 50 314-363 347-418 (442)
162 COG4957 Predicted transcriptio 51.0 6.3 0.00014 30.9 0.5 26 343-371 76-101 (148)
163 PF01096 TFIIS_C: Transcriptio 50.5 4.7 0.0001 24.3 -0.2 10 41-50 29-38 (39)
164 COG4888 Uncharacterized Zn rib 50.3 6.6 0.00014 29.1 0.5 19 340-358 19-37 (104)
165 PF08271 TF_Zn_Ribbon: TFIIB z 50.0 10 0.00022 23.4 1.3 29 13-50 1-29 (43)
166 COG5151 SSL1 RNA polymerase II 49.9 8.3 0.00018 34.9 1.1 10 12-21 308-317 (421)
167 PF12773 DZR: Double zinc ribb 49.6 28 0.00061 22.1 3.4 10 345-354 14-23 (50)
168 PRK05580 primosome assembly pr 49.2 11 0.00024 39.8 2.1 40 344-414 391-430 (679)
169 PF07754 DUF1610: Domain of un 48.9 14 0.00031 19.5 1.5 9 11-19 15-23 (24)
170 PF04959 ARS2: Arsenite-resist 48.9 6.8 0.00015 34.2 0.4 24 69-92 76-99 (214)
171 smart00661 RPOL9 RNA polymeras 48.4 18 0.00038 23.3 2.3 34 318-358 2-35 (52)
172 TIGR00244 transcriptional regu 47.7 11 0.00025 30.3 1.5 45 318-362 2-47 (147)
173 PF08790 zf-LYAR: LYAR-type C2 47.1 14 0.0003 20.4 1.3 23 344-367 1-23 (28)
174 COG1327 Predicted transcriptio 46.7 12 0.00025 30.3 1.4 45 318-362 2-47 (156)
175 PRK14714 DNA polymerase II lar 45.8 21 0.00044 39.6 3.4 37 315-381 666-702 (1337)
176 PF13878 zf-C2H2_3: zinc-finge 45.6 11 0.00023 23.1 0.8 23 71-93 14-38 (41)
177 PRK00432 30S ribosomal protein 45.1 17 0.00036 23.4 1.7 27 318-354 22-48 (50)
178 PF14446 Prok-RING_1: Prokaryo 44.8 17 0.00036 23.7 1.6 28 315-353 4-31 (54)
179 PF09332 Mcm10: Mcm10 replicat 44.5 4.6 0.0001 38.0 -1.3 57 39-105 251-311 (344)
180 COG3677 Transposase and inacti 44.3 14 0.00031 29.4 1.6 16 341-356 51-66 (129)
181 KOG2807 RNA polymerase II tran 44.0 22 0.00048 32.7 2.9 84 315-430 275-370 (378)
182 COG2331 Uncharacterized protei 43.6 16 0.00035 25.4 1.5 33 69-108 11-44 (82)
183 PF03107 C1_2: C1 domain; Int 43.6 22 0.00047 19.9 1.8 8 405-412 15-22 (30)
184 cd00065 FYVE FYVE domain; Zinc 43.2 11 0.00024 24.8 0.7 12 70-81 18-29 (57)
185 PRK03824 hypA hydrogenase nick 42.6 13 0.00029 29.9 1.2 15 11-25 69-83 (135)
186 PF09332 Mcm10: Mcm10 replicat 39.9 6.3 0.00014 37.1 -1.2 38 341-378 250-292 (344)
187 COG4896 Uncharacterized protei 38.6 12 0.00025 24.8 0.2 12 69-80 30-41 (68)
188 KOG3408 U1-like Zn-finger-cont 38.2 17 0.00037 28.0 1.1 23 70-92 57-79 (129)
189 PF07649 C1_3: C1-like domain; 38.1 17 0.00037 20.3 0.8 11 404-414 14-24 (30)
190 KOG3408 U1-like Zn-finger-cont 38.1 14 0.00031 28.4 0.7 27 339-365 53-79 (129)
191 KOG2593 Transcription initiati 37.5 24 0.00052 34.0 2.2 35 69-105 127-161 (436)
192 PF01428 zf-AN1: AN1-like Zinc 36.9 15 0.00033 22.6 0.6 17 342-358 12-28 (43)
193 PF04959 ARS2: Arsenite-resist 36.3 13 0.00028 32.5 0.2 32 402-433 74-105 (214)
194 PRK14714 DNA polymerase II lar 36.2 27 0.00059 38.7 2.6 35 13-80 668-702 (1337)
195 PF13451 zf-trcl: Probable zin 35.7 14 0.00031 23.5 0.3 20 403-422 2-21 (49)
196 COG1655 Uncharacterized protei 35.7 11 0.00025 32.6 -0.2 29 341-369 17-45 (267)
197 KOG4377 Zn-finger protein [Gen 35.6 47 0.001 31.7 3.7 132 275-431 277-429 (480)
198 cd00924 Cyt_c_Oxidase_Vb Cytoc 35.4 17 0.00037 27.2 0.7 15 402-417 77-91 (97)
199 PRK12380 hydrogenase nickel in 35.2 20 0.00044 27.8 1.2 14 315-328 69-82 (113)
200 smart00064 FYVE Protein presen 35.0 35 0.00077 23.4 2.3 29 316-355 10-38 (68)
201 PF09416 UPF1_Zn_bind: RNA hel 34.8 34 0.00074 27.9 2.4 24 340-363 11-40 (152)
202 TIGR00595 priA primosomal prot 33.9 41 0.00088 34.2 3.4 40 315-378 221-260 (505)
203 TIGR00100 hypA hydrogenase nic 33.9 21 0.00046 27.7 1.1 12 13-24 71-82 (115)
204 COG1655 Uncharacterized protei 33.9 15 0.00034 31.8 0.3 22 40-61 19-40 (267)
205 smart00132 LIM Zinc-binding do 33.7 25 0.00054 20.5 1.2 12 343-354 27-38 (39)
206 KOG1280 Uncharacterized conser 33.7 35 0.00075 31.8 2.5 43 35-77 74-116 (381)
207 PF09963 DUF2197: Uncharacteri 33.6 22 0.00049 23.3 1.0 10 14-23 4-13 (56)
208 PF05495 zf-CHY: CHY zinc fing 33.5 11 0.00023 26.4 -0.6 42 13-54 11-55 (71)
209 KOG0717 Molecular chaperone (D 33.4 19 0.00042 34.9 0.9 21 344-364 461-481 (508)
210 PF07282 OrfB_Zn_ribbon: Putat 33.3 27 0.00059 24.1 1.4 12 69-80 45-56 (69)
211 COG1571 Predicted DNA-binding 33.1 26 0.00056 34.0 1.7 32 318-359 352-383 (421)
212 PF15135 UPF0515: Uncharacteri 33.0 45 0.00097 29.5 2.9 13 404-416 154-166 (278)
213 PF01155 HypA: Hydrogenase exp 33.0 17 0.00036 28.2 0.4 14 70-83 70-83 (113)
214 KOG1813 Predicted E3 ubiquitin 32.4 22 0.00049 32.2 1.1 62 341-430 239-304 (313)
215 PF13453 zf-TFIIB: Transcripti 31.8 35 0.00075 20.7 1.6 18 40-57 19-36 (41)
216 PF03563 Bunya_G2: Bunyavirus 31.7 30 0.00065 30.9 1.7 24 404-427 245-272 (285)
217 KOG1280 Uncharacterized conser 31.4 35 0.00077 31.7 2.2 63 34-104 47-116 (381)
218 PF10013 DUF2256: Uncharacteri 31.0 23 0.0005 21.6 0.7 17 406-422 9-25 (42)
219 KOG0696 Serine/threonine prote 30.4 16 0.00036 35.0 -0.1 56 38-104 71-128 (683)
220 PF13824 zf-Mss51: Zinc-finger 30.3 37 0.0008 22.3 1.5 9 70-78 14-22 (55)
221 KOG2636 Splicing factor 3a, su 30.1 31 0.00067 33.3 1.6 23 69-91 400-423 (497)
222 PF09845 DUF2072: Zn-ribbon co 29.8 23 0.00051 27.9 0.7 15 343-357 1-15 (131)
223 PF11494 Ta0938: Ta0938; Inte 29.6 34 0.00073 25.2 1.4 18 402-419 33-51 (105)
224 TIGR00143 hypF [NiFe] hydrogen 29.5 28 0.0006 36.9 1.4 56 317-378 91-147 (711)
225 COG1656 Uncharacterized conser 29.4 29 0.00063 28.7 1.2 39 42-84 99-144 (165)
226 PF04780 DUF629: Protein of un 29.1 26 0.00056 34.6 1.0 31 404-434 56-87 (466)
227 PF13248 zf-ribbon_3: zinc-rib 29.1 39 0.00084 18.1 1.3 9 317-325 3-11 (26)
228 PRK00564 hypA hydrogenase nick 28.8 28 0.00061 27.2 1.0 12 13-24 72-83 (117)
229 PF11789 zf-Nse: Zinc-finger o 28.5 45 0.00098 22.1 1.8 46 9-75 8-53 (57)
230 PF06220 zf-U1: U1 zinc finger 28.3 40 0.00087 20.2 1.4 10 41-50 4-13 (38)
231 PF09082 DUF1922: Domain of un 28.3 20 0.00043 24.6 0.1 26 317-353 4-29 (68)
232 KOG2071 mRNA cleavage and poly 28.3 33 0.0007 34.6 1.5 28 402-429 415-442 (579)
233 PF01286 XPA_N: XPA protein N- 27.5 23 0.0005 20.6 0.2 16 14-29 5-20 (34)
234 COG3091 SprT Zn-dependent meta 27.2 29 0.00063 28.2 0.8 34 340-378 114-147 (156)
235 PF07295 DUF1451: Protein of u 27.0 36 0.00078 27.8 1.3 9 406-414 131-139 (146)
236 PF10276 zf-CHCC: Zinc-finger 26.8 32 0.0007 20.9 0.8 13 342-354 28-40 (40)
237 PF04423 Rad50_zn_hook: Rad50 26.7 23 0.0005 23.1 0.2 13 407-419 22-34 (54)
238 KOG2071 mRNA cleavage and poly 26.5 34 0.00075 34.5 1.3 27 38-64 416-442 (579)
239 PF10263 SprT-like: SprT-like 26.4 20 0.00043 29.6 -0.2 11 70-80 123-133 (157)
240 PRK14559 putative protein seri 26.0 72 0.0016 33.4 3.6 53 317-418 2-54 (645)
241 PRK03681 hypA hydrogenase nick 26.0 36 0.00077 26.5 1.1 13 315-327 69-81 (114)
242 PF05129 Elf1: Transcription e 25.9 16 0.00035 26.3 -0.7 41 314-357 20-60 (81)
243 COG3364 Zn-ribbon containing p 25.8 38 0.00082 25.2 1.1 28 70-106 2-29 (112)
244 KOG0717 Molecular chaperone (D 25.5 30 0.00065 33.7 0.7 22 71-92 293-314 (508)
245 PLN02294 cytochrome c oxidase 25.2 26 0.00056 29.0 0.2 19 90-108 134-152 (174)
246 smart00731 SprT SprT homologue 24.7 51 0.0011 26.9 1.9 12 342-353 132-143 (146)
247 PF03811 Zn_Tnp_IS1: InsA N-te 24.0 45 0.00097 19.7 1.0 14 6-19 23-36 (36)
248 PF14311 DUF4379: Domain of un 23.9 47 0.001 21.7 1.2 13 41-53 29-41 (55)
249 PRK03564 formate dehydrogenase 23.8 48 0.001 30.9 1.7 37 315-353 186-222 (309)
250 COG5188 PRP9 Splicing factor 3 23.6 46 0.00099 31.0 1.5 28 62-91 368-396 (470)
251 COG0068 HypF Hydrogenase matur 22.8 34 0.00073 35.4 0.5 55 15-78 126-181 (750)
252 PRK12496 hypothetical protein; 22.7 52 0.0011 27.5 1.6 27 315-352 126-152 (164)
253 PF12907 zf-met2: Zinc-binding 22.7 46 0.001 20.2 0.9 9 72-80 3-11 (40)
254 PF11672 DUF3268: Protein of u 22.7 86 0.0019 23.8 2.5 9 316-324 2-10 (102)
255 COG4391 Uncharacterized protei 22.5 60 0.0013 21.8 1.4 38 315-355 23-60 (62)
256 PHA02998 RNA polymerase subuni 22.2 42 0.00092 28.0 0.9 11 71-81 172-182 (195)
257 COG5152 Uncharacterized conser 22.0 61 0.0013 27.5 1.8 18 9-26 193-210 (259)
258 KOG3362 Predicted BBOX Zn-fing 21.9 36 0.00078 27.2 0.4 23 404-426 128-150 (156)
259 PF07503 zf-HYPF: HypF finger; 21.9 12 0.00026 22.0 -1.7 11 70-80 21-31 (35)
260 KOG2636 Splicing factor 3a, su 21.9 46 0.001 32.2 1.2 25 36-60 397-422 (497)
261 TIGR00310 ZPR1_znf ZPR1 zinc f 21.6 41 0.00088 29.0 0.7 12 70-81 30-41 (192)
262 KOG3214 Uncharacterized Zn rib 21.0 46 0.001 24.7 0.8 42 314-358 21-62 (109)
263 PTZ00303 phosphatidylinositol 20.9 59 0.0013 34.0 1.7 13 13-25 461-473 (1374)
264 COG1594 RPB9 DNA-directed RNA 20.7 49 0.0011 25.6 0.9 11 41-51 101-111 (113)
265 TIGR01562 FdhE formate dehydro 20.6 67 0.0014 30.0 1.9 37 316-353 184-220 (305)
266 KOG2461 Transcription factor B 20.1 68 0.0015 31.3 1.9 81 20-102 311-392 (396)
No 1
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.97 E-value=1.2e-31 Score=258.33 Aligned_cols=54 Identities=22% Similarity=0.294 Sum_probs=51.5
Q ss_pred cccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcc
Q 039095 13 YDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRR 66 (492)
Q Consensus 13 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~ 66 (492)
.+|.+|.|+|...+.|+.|.|.|++++||+|.+||.+|.++.+|+.|...|+..
T Consensus 354 hkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~ 407 (958)
T KOG1074|consen 354 HKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREK 407 (958)
T ss_pred chhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeecccc
Confidence 679999999999999999999999999999999999999999999999888765
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.96 E-value=6e-31 Score=223.87 Aligned_cols=82 Identities=32% Similarity=0.485 Sum_probs=63.2
Q ss_pred CCCccccCCCCcccccccchhhhhhccCC---CCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhh
Q 039095 9 GHISYDLRENPKKSWKFSSFNHAASASAS---TQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKS 85 (492)
Q Consensus 9 ~~~~~~C~~C~k~f~~~~~l~~H~~~H~~---~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~ 85 (492)
....|+|++|+|.|.+.+.|.+|.+.|-. .+.|.|++|+|+|.+-..|++|+|+|+ .+++|.+|||.|+..+-
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~----l~c~C~iCGKaFSRPWL 202 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT----LPCECGICGKAFSRPWL 202 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC----CCcccccccccccchHH
Confidence 45558888888888888888888887743 456788888888888888888888887 47888888888888888
Q ss_pred Hhhhhhhcc
Q 039095 86 LSNHMRVHS 94 (492)
Q Consensus 86 L~~H~~~H~ 94 (492)
|+-|+|+|+
T Consensus 203 LQGHiRTHT 211 (279)
T KOG2462|consen 203 LQGHIRTHT 211 (279)
T ss_pred hhccccccc
Confidence 888888774
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.94 E-value=4.2e-27 Score=223.08 Aligned_cols=105 Identities=21% Similarity=0.308 Sum_probs=90.5
Q ss_pred cccCCCCcccccccchhhhhh-cc-CCCCccccccccccccChhHHHhhhhccCccc-----------ccccccccchhh
Q 039095 13 YDLRENPKKSWKFSSFNHAAS-AS-ASTQESQCKVCGKDFESLKALYGHMRHHSRRE-----------RERIQCKECGKA 79 (492)
Q Consensus 13 ~~C~~C~k~f~~~~~l~~H~~-~H-~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~-----------~k~y~C~~C~k~ 79 (492)
..|++|++.|.....|+.|+. .| ..+..|.|.+|.++|..+..|.+||.+|..-. -|.|+|+.|||+
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 689999999999999988865 34 34556999999999999999999999986542 167999999999
Q ss_pred hcChhhHhhhhhhccc-CcccccccCchhhhHHhhhhhc
Q 039095 80 LLSAKSLSNHMRVHSQ-KLRACNESGAVKSLVLKKKRSK 117 (492)
Q Consensus 80 F~~~~~L~~H~~~H~~-k~~~C~~C~~~f~~~~~~~~h~ 117 (492)
|..+..|+.|+|+|.| |||.|+.|++.|+..-...-|+
T Consensus 291 FKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHm 329 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHM 329 (1007)
T ss_pred hhhHHHHHhhheeecCCCCcCCcccccccccCCcccccc
Confidence 9999999999999997 9999999999999665555554
No 4
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.94 E-value=2.8e-27 Score=201.51 Aligned_cols=106 Identities=24% Similarity=0.449 Sum_probs=101.9
Q ss_pred CCCccccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhh
Q 039095 9 GHISYDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSN 88 (492)
Q Consensus 9 ~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~ 88 (492)
..+.|.|++|+|+|.+...|+.|+++|+ .++.|.+|||.|.+.+-|+-|+|+|||| |||.|+.|+|+|.+++||+.
T Consensus 158 s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGE--KPF~C~hC~kAFADRSNLRA 233 (279)
T KOG2462|consen 158 SKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGE--KPFSCPHCGKAFADRSNLRA 233 (279)
T ss_pred ccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCC--CCccCCcccchhcchHHHHH
Confidence 3677999999999999999999999997 7999999999999999999999999999 99999999999999999999
Q ss_pred hhhhccc-CcccccccCchhhhHHhhhhhcc
Q 039095 89 HMRVHSQ-KLRACNESGAVKSLVLKKKRSKR 118 (492)
Q Consensus 89 H~~~H~~-k~~~C~~C~~~f~~~~~~~~h~~ 118 (492)
||++|.+ |+|+|..|++.|+..+.|.+|..
T Consensus 234 HmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 234 HMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred HHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 9999997 99999999999999999999975
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.93 E-value=1.4e-26 Score=223.45 Aligned_cols=93 Identities=23% Similarity=0.406 Sum_probs=80.0
Q ss_pred cccccCCcccccccCCCCCcc-ccCCCCCCceecccCccccccchhhhhhcccCCCCCCCCCCcCCCCCCCCcccchhhh
Q 039095 314 YAEYGGDSSSKAMCNASDYDV-FDDPQKESEIRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFTETEPHSKLVKL 392 (492)
Q Consensus 314 ~~~~~C~~C~~~f~~~~~l~~-h~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~~~~~~~~~~~~ 392 (492)
..+.+|-+|.+....++.|+. ++.|+|++||+|++||+.|.++.+|+.||.+|...
T Consensus 603 TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~----------------------- 659 (958)
T KOG1074|consen 603 TDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAK----------------------- 659 (958)
T ss_pred CCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccC-----------------------
Confidence 367889999999999999998 45899999999999999999999999999999732
Q ss_pred hhhhccccCCCCcccCC---ccccccCCchhhhhhhhhcccCCCCCC
Q 039095 393 ECIEDLMQRGNKEHTCR---ICLKVFATGQALGGHKRAHLVKNLDNI 436 (492)
Q Consensus 393 ~~~h~~~H~~~kpf~C~---~C~k~F~~~~~L~~H~r~H~~~~~~~~ 436 (492)
+.-.-+|.|+ ||.+.|+..-.|..|+|+|.+...++.
T Consensus 660 -------p~~R~q~ScP~~~ic~~kftn~V~lpQhIriH~~~~~s~g 699 (958)
T KOG1074|consen 660 -------PPARVQFSCPSTFICQKKFTNAVTLPQHIRIHLGGQISNG 699 (958)
T ss_pred -------ccccccccCCchhhhcccccccccccceEEeecCCCCCCC
Confidence 2233679999 999999999999999999997776655
No 6
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.91 E-value=1.5e-25 Score=195.54 Aligned_cols=223 Identities=17% Similarity=0.261 Sum_probs=183.7
Q ss_pred ccc--CCCCcccccccchhhhhhccCC------------CCc-ccc--ccccccccChhHHHhhhhccCccccccccccc
Q 039095 13 YDL--RENPKKSWKFSSFNHAASASAS------------TQE-SQC--KVCGKDFESLKALYGHMRHHSRRERERIQCKE 75 (492)
Q Consensus 13 ~~C--~~C~k~f~~~~~l~~H~~~H~~------------~~~-~~C--~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~ 75 (492)
|.| ..|+..|.+...|..|.-.|.. ++| +.| .-|.+.|.+++.|.+|+|+|+++ |...|+.
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~e--KvvACp~ 212 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNE--KVVACPH 212 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCC--eEEecch
Confidence 556 5899999999999988887742 223 566 46999999999999999999999 9999999
Q ss_pred chhhhcChhhHhhhhhhcc---cCcccccccCchhhhHHhhhhhcccccccCCCCCcccccccCccccccchhhhhhhhh
Q 039095 76 CGKALLSAKSLSNHMRVHS---QKLRACNESGAVKSLVLKKKRSKRKRYNFIGSSSISTLNESLSSVTEIDQEVVQTAIS 152 (492)
Q Consensus 76 C~k~F~~~~~L~~H~~~H~---~k~~~C~~C~~~f~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (492)
||..|+++..|-.|++.-+ ..+|.|..|.+.|++...|..|+..|.
T Consensus 213 Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv------------------------------- 261 (467)
T KOG3608|consen 213 CGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV------------------------------- 261 (467)
T ss_pred HHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh-------------------------------
Confidence 9999999999999998766 378999999999999988888887552
Q ss_pred hhcccCCCCCCCccccCCcccccCceeeeecccccccceeeccCCcccccCCccccCcccccccccccccccCccccccc
Q 039095 153 LMMLSRGVQDWGKFCSSSEFSCNDSVTIEVKSFGKKKRLLTNRAGCFVSNGNGCLLKKPRLEKLDSIVLYEKEEDECHEV 232 (492)
Q Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~c 232 (492)
T Consensus 262 -------------------------------------------------------------------------------- 261 (467)
T KOG3608|consen 262 -------------------------------------------------------------------------------- 261 (467)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCccceeeeeeeccccccccCccCCcccCCCCCccchhhhccccchhhhhhhcchhhcccceeeecCCcccccCC
Q 039095 233 GSGAESDEGKKVKLEVFIEKFYEEGEFEMPKLDVKPGSVASDDEIGKESSEDLMEEDGLDAEAGKRIITSTSSKKVGFNA 312 (492)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ 312 (492)
T Consensus 262 -------------------------------------------------------------------------------- 261 (467)
T KOG3608|consen 262 -------------------------------------------------------------------------------- 261 (467)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CcccccCCcccccccCCCCCcccc--CCCCCCceecccCccccccchhhhhhcccCCCCCCCCCCc--CCCCCCCCcccc
Q 039095 313 CYAEYGGDSSSKAMCNASDYDVFD--DPQKESEIRCQACNKIFCSRRALGGHQRMHSAKRSSLPVK--TTMFTETEPHSK 388 (492)
Q Consensus 313 ~~~~~~C~~C~~~f~~~~~l~~h~--~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~--C~~~~~~~~~~~ 388 (492)
.-|+|+.|+.+....+.|..|. .|...|||+|+.|.+.|.+.+.|.+|..+|+ +..|.|+. |.++++....+.
T Consensus 262 --n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~ 338 (467)
T KOG3608|consen 262 --NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMR 338 (467)
T ss_pred --hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHH
Confidence 3488999999999999998866 7888999999999999999999999999998 77899999 777765444332
Q ss_pred hhhhhhhhccc-cCC--CCcccCCccccccCCchhhhhhhhhcccCCCCCCc
Q 039095 389 LVKLECIEDLM-QRG--NKEHTCRICLKVFATGQALGGHKRAHLVKNLDNIL 437 (492)
Q Consensus 389 ~~~~~~~h~~~-H~~--~kpf~C~~C~k~F~~~~~L~~H~r~H~~~~~~~~~ 437 (492)
. |++. |-| +-+|+|..|++.|++..+|.+|++.-++=+.+++-
T Consensus 339 ~------H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsGh 384 (467)
T KOG3608|consen 339 R------HFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSGH 384 (467)
T ss_pred H------HHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCCCCC
Confidence 2 3343 323 46799999999999999999997765566655543
No 7
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.83 E-value=7.6e-22 Score=172.47 Aligned_cols=109 Identities=18% Similarity=0.254 Sum_probs=98.1
Q ss_pred Ccccc--CCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhh
Q 039095 11 ISYDL--RENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSN 88 (492)
Q Consensus 11 ~~~~C--~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~ 88 (492)
..+-| .-|-+.|.+++.|++|++.|++++.-.|+.||.-|.++..|-.|+|.-+.-...+|+|..|.|.|.+...|+.
T Consensus 176 pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~ 255 (467)
T KOG3608|consen 176 PVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKS 255 (467)
T ss_pred ceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHH
Confidence 34556 4699999999999999999999999999999999999999999988776655479999999999999999999
Q ss_pred hhhhcccCcccccccCchhhhHHhhhhhcccc
Q 039095 89 HMRVHSQKLRACNESGAVKSLVLKKKRSKRKR 120 (492)
Q Consensus 89 H~~~H~~k~~~C~~C~~~f~~~~~~~~h~~~~ 120 (492)
|++.|. .-|+|+.|+......+.|.+|++.+
T Consensus 256 Hv~rHv-n~ykCplCdmtc~~~ssL~~H~r~r 286 (467)
T KOG3608|consen 256 HVVRHV-NCYKCPLCDMTCSSASSLTTHIRYR 286 (467)
T ss_pred HHHHhh-hcccccccccCCCChHHHHHHHHhh
Confidence 999885 5699999999999999999998765
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.77 E-value=4.9e-20 Score=148.69 Aligned_cols=111 Identities=24% Similarity=0.340 Sum_probs=99.7
Q ss_pred CCCccccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhh
Q 039095 9 GHISYDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSN 88 (492)
Q Consensus 9 ~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~ 88 (492)
+...|.|.+|+|.|.-...|.+|+.-|...+.|-|..|||.|+...+|++|+|+|+|. +||+|..|+++|+++-.|..
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgv--rpykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGV--RPYKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCc--cccchhhhhHHHHhhccHHH
Confidence 4667999999999999999999999999999999999999999999999999999999 99999999999999999999
Q ss_pred hhh-hcc-----------cCcccccccCchhhhHHhhhhhccccc
Q 039095 89 HMR-VHS-----------QKLRACNESGAVKSLVLKKKRSKRKRY 121 (492)
Q Consensus 89 H~~-~H~-----------~k~~~C~~C~~~f~~~~~~~~h~~~~~ 121 (492)
|++ +|. .|.|.|+.||.+-.....+..|...++
T Consensus 192 hl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 192 HLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHH 236 (267)
T ss_pred HHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcC
Confidence 986 453 267999999977666666777776654
No 9
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.62 E-value=4.7e-17 Score=131.61 Aligned_cols=83 Identities=25% Similarity=0.450 Sum_probs=76.1
Q ss_pred CCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhhhhccc-CcccccccCchhhhHHhhh
Q 039095 36 ASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHMRVHSQ-KLRACNESGAVKSLVLKKK 114 (492)
Q Consensus 36 ~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H~~-k~~~C~~C~~~f~~~~~~~ 114 (492)
.+...|.|.+|+|.|.-+-.|++||+.|... +.|-|..||+.|.....|++|+|+|+| +||+|..|++.|+..-.|.
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~v--kr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsle 190 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDV--KRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLE 190 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHH--HHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHH
Confidence 4456799999999999999999999999999 999999999999999999999999998 9999999999999877777
Q ss_pred hhcccc
Q 039095 115 RSKRKR 120 (492)
Q Consensus 115 ~h~~~~ 120 (492)
-|.++.
T Consensus 191 shl~kv 196 (267)
T KOG3576|consen 191 SHLKKV 196 (267)
T ss_pred HHHHHH
Confidence 776543
No 10
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.61 E-value=7.5e-17 Score=154.10 Aligned_cols=80 Identities=29% Similarity=0.393 Sum_probs=70.9
Q ss_pred CCccccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhh
Q 039095 10 HISYDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNH 89 (492)
Q Consensus 10 ~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H 89 (492)
+-.|.|+.|+|+|...++|.+|..-|+|.+||+|.+|.|.|+.+.+|..|+|.|.|| |||+|..|+|+|+..+..-.|
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGE--KPfQCdKClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGE--KPFQCDKCLKRFSHSGSYSQH 969 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCC--CcchhhhhhhhcccccchHhh
Confidence 456889999999999999999988899999999999999999999999999999998 899999999999988888888
Q ss_pred hh
Q 039095 90 MR 91 (492)
Q Consensus 90 ~~ 91 (492)
|.
T Consensus 970 MN 971 (1007)
T KOG3623|consen 970 MN 971 (1007)
T ss_pred hc
Confidence 86
No 11
>PHA00733 hypothetical protein
Probab=99.26 E-value=1.8e-12 Score=102.41 Aligned_cols=79 Identities=18% Similarity=0.234 Sum_probs=39.5
Q ss_pred CCccccCCCCcccccccchhhh--h---hccCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChh
Q 039095 10 HISYDLRENPKKSWKFSSFNHA--A---SASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAK 84 (492)
Q Consensus 10 ~~~~~C~~C~k~f~~~~~l~~H--~---~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~ 84 (492)
.+++.|.+|.+.|.....|..+ + ..+.+.+||.|+.|++.|.+...|..|+++| + .+|.|++|++.|....
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~--~~~~C~~CgK~F~~~~ 113 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--E--HSKVCPVCGKEFRNTD 113 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--C--cCccCCCCCCccCCHH
Confidence 3445555555555555444333 1 1122345555555555555555555555554 1 3455555555555555
Q ss_pred hHhhhhhh
Q 039095 85 SLSNHMRV 92 (492)
Q Consensus 85 ~L~~H~~~ 92 (492)
.|..|+..
T Consensus 114 sL~~H~~~ 121 (128)
T PHA00733 114 STLDHVCK 121 (128)
T ss_pred HHHHHHHH
Confidence 55555543
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.18 E-value=6.3e-12 Score=80.45 Aligned_cols=44 Identities=18% Similarity=0.380 Sum_probs=39.3
Q ss_pred ceecccCccccccchhhhhhcccCCCCCCCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCCccccccCCchhhh
Q 039095 343 EIRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICLKVFATGQALG 422 (492)
Q Consensus 343 ~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k~F~~~~~L~ 422 (492)
-|.|+.||+.|+..++|..|+++|+ +||+|..|++.|.+++.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~------------------------------------k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN------------------------------------TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC------------------------------------CcccCCcccceecccceeE
Confidence 3899999999999999999999998 6888888989888887764
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.13 E-value=1.3e-11 Score=79.01 Aligned_cols=44 Identities=20% Similarity=0.539 Sum_probs=33.2
Q ss_pred ccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHh
Q 039095 40 ESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLS 87 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~ 87 (492)
.|.|+.||+.|...++|.+||++|+ ++|+|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~----k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN----TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC----CcccCCcccceecccceeE
Confidence 4778888888888888888888877 4777888888777776653
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.12 E-value=4.6e-11 Score=116.18 Aligned_cols=94 Identities=14% Similarity=0.281 Sum_probs=80.6
Q ss_pred CCCCccccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhc------
Q 039095 8 DGHISYDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALL------ 81 (492)
Q Consensus 8 ~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~------ 81 (492)
+....|.|+.|++.|. ...|..|+..|. .||.|+ |++.| .+..|..|+++|.++ +++.|++|++.|.
T Consensus 449 el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~--Kpi~C~fC~~~v~~g~~~~ 521 (567)
T PLN03086 449 EAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPL--RLITCRFCGDMVQAGGSAM 521 (567)
T ss_pred ccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCC--CceeCCCCCCccccCcccc
Confidence 3456689999999996 577999999874 899999 99765 678999999999999 9999999999994
Q ss_pred ----ChhhHhhhhhhcccCcccccccCchhh
Q 039095 82 ----SAKSLSNHMRVHSQKLRACNESGAVKS 108 (492)
Q Consensus 82 ----~~~~L~~H~~~H~~k~~~C~~C~~~f~ 108 (492)
....|..|+.++..+++.|..||+.+.
T Consensus 522 d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vr 552 (567)
T PLN03086 522 DVRDRLRGMSEHESICGSRTAPCDSCGRSVM 552 (567)
T ss_pred chhhhhhhHHHHHHhcCCcceEccccCCeee
Confidence 245899999998669999999998766
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.12 E-value=6.7e-11 Score=115.07 Aligned_cols=87 Identities=17% Similarity=0.319 Sum_probs=55.8
Q ss_pred cccCCCCcccccccchhhhhhccCCCCcccccc--ccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhh
Q 039095 13 YDLRENPKKSWKFSSFNHAASASASTQESQCKV--CGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHM 90 (492)
Q Consensus 13 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~--C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~ 90 (492)
-.|+.|......... ..|...-. -..-.|+. |+..|. +..|. +.+.|+.|++.|. ...|..|+
T Consensus 408 V~C~NC~~~i~l~~l-~lHe~~C~-r~~V~Cp~~~Cg~v~~-r~el~-----------~H~~C~~Cgk~f~-~s~LekH~ 472 (567)
T PLN03086 408 VECRNCKHYIPSRSI-ALHEAYCS-RHNVVCPHDGCGIVLR-VEEAK-----------NHVHCEKCGQAFQ-QGEMEKHM 472 (567)
T ss_pred EECCCCCCccchhHH-HHHHhhCC-CcceeCCcccccceee-ccccc-----------cCccCCCCCCccc-hHHHHHHH
Confidence 469999887765543 35554221 12336874 999883 33333 3468999999996 68899999
Q ss_pred hhcccCcccccccCchhhhHHhhhhhc
Q 039095 91 RVHSQKLRACNESGAVKSLVLKKKRSK 117 (492)
Q Consensus 91 ~~H~~k~~~C~~C~~~f~~~~~~~~h~ 117 (492)
++|+ +++.|+ |+..+ ....+..|.
T Consensus 473 ~~~H-kpv~Cp-Cg~~~-~R~~L~~H~ 496 (567)
T PLN03086 473 KVFH-EPLQCP-CGVVL-EKEQMVQHQ 496 (567)
T ss_pred HhcC-CCccCC-CCCCc-chhHHHhhh
Confidence 9875 778887 87533 333444443
No 16
>PHA00733 hypothetical protein
Probab=99.10 E-value=2.7e-11 Score=95.73 Aligned_cols=92 Identities=14% Similarity=0.101 Sum_probs=74.4
Q ss_pred chhhhhhccCCCCccccccccccccChhHHHhh--hh---ccCcccccccccccchhhhcChhhHhhhhhhcccCccccc
Q 039095 27 SFNHAASASASTQESQCKVCGKDFESLKALYGH--MR---HHSRRERERIQCKECGKALLSAKSLSNHMRVHSQKLRACN 101 (492)
Q Consensus 27 ~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H--~r---~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H~~k~~~C~ 101 (492)
.|..+-..-...+++.|.+|.+.|.....|..| ++ .++++ +||.|+.||+.|....+|..|++.| ..+|.|.
T Consensus 27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~--kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~ 103 (128)
T PHA00733 27 ELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAV--SPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCP 103 (128)
T ss_pred HhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCC--CCccCCCCCCcCCCHHHHHHHHhcC-CcCccCC
Confidence 444444444567889999999999988877766 21 23335 8999999999999999999999987 5679999
Q ss_pred ccCchhhhHHhhhhhccccc
Q 039095 102 ESGAVKSLVLKKKRSKRKRY 121 (492)
Q Consensus 102 ~C~~~f~~~~~~~~h~~~~~ 121 (492)
+|++.|.....+..|+.+.+
T Consensus 104 ~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 104 VCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCCccCCHHHHHHHHHHhc
Confidence 99999999999999887654
No 17
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.96 E-value=2.1e-10 Score=104.01 Aligned_cols=83 Identities=23% Similarity=0.334 Sum_probs=67.7
Q ss_pred cccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCccc-------------------------
Q 039095 13 YDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRE------------------------- 67 (492)
Q Consensus 13 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~------------------------- 67 (492)
|.|..|...|.+.-.|..|.-.----..|+|+.|+|+|+...+|..|.|+|....
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 9999999999999999888653333346999999999999999999999995431
Q ss_pred ------ccccccccchhhhcChhhHhhhhhhccc
Q 039095 68 ------RERIQCKECGKALLSAKSLSNHMRVHSQ 95 (492)
Q Consensus 68 ------~k~y~C~~C~k~F~~~~~L~~H~~~H~~ 95 (492)
.-.|.|.+|+|.|.++.-|+.|+.+|+.
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 0238899999999999999999888873
No 18
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.84 E-value=2.5e-09 Score=97.12 Aligned_cols=53 Identities=28% Similarity=0.559 Sum_probs=47.1
Q ss_pred ccccccccccccChhHHHhhh--hccCcccccccccccchhhhcChhhHhhhhhhcccC
Q 039095 40 ESQCKVCGKDFESLKALYGHM--RHHSRRERERIQCKECGKALLSAKSLSNHMRVHSQK 96 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~--r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H~~k 96 (492)
.|.|.+|...|.....|.+|. |+-+ .-|+|+.|+|.|+-..||..|.|+|.-+
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~----vEYrCPEC~KVFsCPANLASHRRWHKPR 321 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVH----VEYRCPECDKVFSCPANLASHRRWHKPR 321 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEE----eeecCCcccccccCchhhhhhhcccCCc
Confidence 499999999999999999995 5554 3599999999999999999999999643
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.82 E-value=8.6e-10 Score=60.43 Aligned_cols=25 Identities=36% Similarity=0.721 Sum_probs=17.6
Q ss_pred HHHhhhhccCcccccccccccchhhhc
Q 039095 55 ALYGHMRHHSRRERERIQCKECGKALL 81 (492)
Q Consensus 55 ~L~~H~r~H~~~~~k~y~C~~C~k~F~ 81 (492)
+|.+||++|+++ +||+|++|+++|.
T Consensus 1 ~l~~H~~~H~~~--k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGE--KPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSS--SSEEESSSSEEES
T ss_pred CHHHHhhhcCCC--CCCCCCCCcCeeC
Confidence 466777777777 6777777777765
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=98.82 E-value=9.2e-10 Score=60.32 Aligned_cols=22 Identities=27% Similarity=0.478 Sum_probs=17.0
Q ss_pred hccccCCCCcccCCccccccCC
Q 039095 396 EDLMQRGNKEHTCRICLKVFAT 417 (492)
Q Consensus 396 h~~~H~~~kpf~C~~C~k~F~~ 417 (492)
|+++|+|+|||.|++|+++|.+
T Consensus 5 H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 5 HMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHSSSSSEEESSSSEEESS
T ss_pred HhhhcCCCCCCCCCCCcCeeCc
Confidence 3344448999999999999974
No 21
>PHA00732 hypothetical protein
Probab=98.66 E-value=1e-08 Score=72.98 Aligned_cols=48 Identities=27% Similarity=0.484 Sum_probs=34.8
Q ss_pred ccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhhhhcc
Q 039095 40 ESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHMRVHS 94 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H~ 94 (492)
||.|..|++.|.+...|+.|++.++ .++.|+.||+.|. +|..|++++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H----~~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNH----TLTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhccc----CCCccCCCCCEeC---ChhhhhcccC
Confidence 5778888888888888888887432 2457888888886 5777776654
No 22
>PHA00732 hypothetical protein
Probab=98.64 E-value=1.4e-08 Score=72.23 Aligned_cols=47 Identities=26% Similarity=0.473 Sum_probs=39.4
Q ss_pred ceecccCccccccchhhhhhccc-CCCCCCCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCCccccccCCchhh
Q 039095 343 EIRCQACNKIFCSRRALGGHQRM-HSAKRSSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICLKVFATGQAL 421 (492)
Q Consensus 343 ~~~C~~C~k~F~~~~~L~~H~~~-H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k~F~~~~~L 421 (492)
||.|+.||+.|.+..+|+.|++. |+ ++.|+.|+++|. .|
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~-------------------------------------~~~C~~CgKsF~---~l 40 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT-------------------------------------LTKCPVCNKSYR---RL 40 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC-------------------------------------CCccCCCCCEeC---Ch
Confidence 58999999999999999999985 54 357999999998 58
Q ss_pred hhhhhhcc
Q 039095 422 GGHKRAHL 429 (492)
Q Consensus 422 ~~H~r~H~ 429 (492)
..|++++.
T Consensus 41 ~~H~~~~~ 48 (79)
T PHA00732 41 NQHFYSQY 48 (79)
T ss_pred hhhhcccC
Confidence 88885543
No 23
>PHA00616 hypothetical protein
Probab=98.60 E-value=8.6e-09 Score=62.73 Aligned_cols=33 Identities=15% Similarity=0.226 Sum_probs=29.0
Q ss_pred ceecccCccccccchhhhhhcccCCCCCCCCCC
Q 039095 343 EIRCQACNKIFCSRRALGGHQRMHSAKRSSLPV 375 (492)
Q Consensus 343 ~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~ 375 (492)
||+|..||+.|..++.|..|++.|+|++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 689999999999999999999999966655554
No 24
>PHA00616 hypothetical protein
Probab=98.59 E-value=1.4e-08 Score=61.85 Aligned_cols=35 Identities=20% Similarity=0.376 Sum_probs=23.6
Q ss_pred ccccccccccccChhHHHhhhhccCcccccccccccc
Q 039095 40 ESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKEC 76 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C 76 (492)
||+|..||+.|...+.|.+|++.|+++ ++|.|++=
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~--~~~~~~~~ 35 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQ--NKLTLEYF 35 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCC--CccceeEE
Confidence 566777777777777777777777776 66666543
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.39 E-value=2.6e-07 Score=61.16 Aligned_cols=51 Identities=24% Similarity=0.461 Sum_probs=37.0
Q ss_pred ccccccccccccChhHHHhhhhc-cCcccccccccccchhhhcChhhHhhhhhhcc
Q 039095 40 ESQCKVCGKDFESLKALYGHMRH-HSRRERERIQCKECGKALLSAKSLSNHMRVHS 94 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r~-H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H~ 94 (492)
.|.|++|++ -.+...|..|... |..+. +.+.||+|...++ .+|..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~-~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSES-KNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCC-CCccCCCchhhhh--hHHHHHHHHhc
Confidence 488888888 4556788888654 44443 6788999988655 38888888654
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.27 E-value=2.6e-07 Score=49.27 Aligned_cols=23 Identities=39% Similarity=0.678 Sum_probs=21.9
Q ss_pred ccCCccccccCCchhhhhhhhhc
Q 039095 406 HTCRICLKVFATGQALGGHKRAH 428 (492)
Q Consensus 406 f~C~~C~k~F~~~~~L~~H~r~H 428 (492)
|.|++|++.|.++..|.+||++|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 78999999999999999999986
No 27
>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=98.23 E-value=6.6e-07 Score=59.22 Aligned_cols=52 Identities=25% Similarity=0.374 Sum_probs=41.2
Q ss_pred ceecccCccccccchhhhhhcc-cCCCCCCCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCCccccccCCchhh
Q 039095 343 EIRCQACNKIFCSRRALGGHQR-MHSAKRSSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICLKVFATGQAL 421 (492)
Q Consensus 343 ~~~C~~C~k~F~~~~~L~~H~~-~H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k~F~~~~~L 421 (492)
.|+|++|++ ..+...|..|.. .|.+ +.+.+.|++|...++ .+|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~---------------------------------~~~~v~CPiC~~~~~--~~l 45 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRS---------------------------------ESKNVVCPICSSRVT--DNL 45 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcC---------------------------------CCCCccCCCchhhhh--hHH
Confidence 489999999 566789999975 5663 346799999998766 499
Q ss_pred hhhhhhccc
Q 039095 422 GGHKRAHLV 430 (492)
Q Consensus 422 ~~H~r~H~~ 430 (492)
.+||+.+++
T Consensus 46 ~~Hl~~~H~ 54 (54)
T PF05605_consen 46 IRHLNSQHR 54 (54)
T ss_pred HHHHHHhcC
Confidence 999987653
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=98.11 E-value=9.1e-07 Score=47.13 Aligned_cols=22 Identities=45% Similarity=0.893 Sum_probs=11.7
Q ss_pred cccccccccccChhHHHhhhhc
Q 039095 41 SQCKVCGKDFESLKALYGHMRH 62 (492)
Q Consensus 41 ~~C~~C~k~F~~~~~L~~H~r~ 62 (492)
|+|+.|++.|.++..|++||+.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4455555555555555555544
No 29
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.99 E-value=3.6e-06 Score=74.03 Aligned_cols=67 Identities=19% Similarity=0.346 Sum_probs=50.0
Q ss_pred CCCceeccc--Cccccccchhhhhhcc-cCCCCCCCCCC----cCCCCCCCCcccchhhhhhhhccccCCCCcccCCccc
Q 039095 340 KESEIRCQA--CNKIFCSRRALGGHQR-MHSAKRSSLPV----KTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICL 412 (492)
Q Consensus 340 ~~~~~~C~~--C~k~F~~~~~L~~H~~-~H~~~k~~~C~----~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~ 412 (492)
+.|||+|++ |.|.|.....|+.|+. -|-..+...=+ .=.|. ...|||.|++|+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~--------------------~~~KPYrCevC~ 405 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFS--------------------AKDKPYRCEVCD 405 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCcccccccc--------------------ccCCceeccccc
Confidence 469999987 9999999999999975 46332211111 01111 167999999999
Q ss_pred cccCCchhhhhhhh
Q 039095 413 KVFATGQALGGHKR 426 (492)
Q Consensus 413 k~F~~~~~L~~H~r 426 (492)
|+|+....|+.|++
T Consensus 406 KRYKNlNGLKYHr~ 419 (423)
T COG5189 406 KRYKNLNGLKYHRK 419 (423)
T ss_pred hhhccCccceeccc
Confidence 99999999999976
No 30
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.89 E-value=5.1e-06 Score=44.77 Aligned_cols=24 Identities=38% Similarity=0.650 Sum_probs=20.5
Q ss_pred ccCCccccccCCchhhhhhhhhcc
Q 039095 406 HTCRICLKVFATGQALGGHKRAHL 429 (492)
Q Consensus 406 f~C~~C~k~F~~~~~L~~H~r~H~ 429 (492)
|.|++|++.|.+...|..|+++|+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999999874
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.85 E-value=6e-06 Score=45.91 Aligned_cols=26 Identities=38% Similarity=0.598 Sum_probs=24.4
Q ss_pred cccCCccccccCCchhhhhhhhhccc
Q 039095 405 EHTCRICLKVFATGQALGGHKRAHLV 430 (492)
Q Consensus 405 pf~C~~C~k~F~~~~~L~~H~r~H~~ 430 (492)
||.|.+|++.|.+...|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 69999999999999999999999864
No 32
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.78 E-value=1.2e-05 Score=44.69 Aligned_cols=25 Identities=48% Similarity=0.830 Sum_probs=16.4
Q ss_pred ccccccccccccChhHHHhhhhccC
Q 039095 40 ESQCKVCGKDFESLKALYGHMRHHS 64 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r~H~ 64 (492)
||.|..|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 4666666666666666666666664
No 33
>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=97.76 E-value=9.8e-06 Score=43.62 Aligned_cols=23 Identities=52% Similarity=0.944 Sum_probs=10.4
Q ss_pred cccccccccccChhHHHhhhhcc
Q 039095 41 SQCKVCGKDFESLKALYGHMRHH 63 (492)
Q Consensus 41 ~~C~~C~k~F~~~~~L~~H~r~H 63 (492)
|.|++|++.|.+...|..|+++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 34555555555555555554443
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.71 E-value=1.4e-05 Score=61.28 Aligned_cols=74 Identities=20% Similarity=0.334 Sum_probs=22.5
Q ss_pred ecccCccccccchhhhhhcccCCCCCCCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCCccccccCCchhhhhh
Q 039095 345 RCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICLKVFATGQALGGH 424 (492)
Q Consensus 345 ~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k~F~~~~~L~~H 424 (492)
+|..|+..|.+...|..|+...++...-...... ... .+..+ .+ ..-...|.|.+|++.|.+...|..|
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~---~~~---~~~~~----~~-~~~~~~~~C~~C~~~f~s~~~l~~H 69 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLV---DPN---RLLNY----LR-KKVKESFRCPYCNKTFRSREALQEH 69 (100)
T ss_dssp -----------------------------------------------------------SSEEBSSSS-EESSHHHHHHH
T ss_pred Cccccccccccccccccccccccccccccccccc---ccc---ccccc----cc-cccCCCCCCCccCCCCcCHHHHHHH
Confidence 5999999999999999999654332111000000 000 00000 00 0012379999999999999999999
Q ss_pred hhhcc
Q 039095 425 KRAHL 429 (492)
Q Consensus 425 ~r~H~ 429 (492)
|+.+.
T Consensus 70 m~~~~ 74 (100)
T PF12756_consen 70 MRSKH 74 (100)
T ss_dssp HHHTT
T ss_pred HcCcc
Confidence 99753
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.68 E-value=1.5e-05 Score=61.19 Aligned_cols=73 Identities=16% Similarity=0.197 Sum_probs=20.2
Q ss_pred ccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhhhhc
Q 039095 14 DLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHMRVH 93 (492)
Q Consensus 14 ~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H 93 (492)
+|.+|+..|.+...|..|+....+-. -. ....+.....|..+++.-.. ..+.|.+|++.|.+...|..||+.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~---~~-~~~~l~~~~~~~~~~~~~~~---~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFD---IP-DQKYLVDPNRLLNYLRKKVK---ESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccc---cc-cccccccccccccccccccC---CCCCCCccCCCCcCHHHHHHHHcCc
Confidence 58888888888888888875433221 11 22333355555566554332 3688999999999999999998864
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.67 E-value=1.5e-05 Score=70.18 Aligned_cols=55 Identities=24% Similarity=0.515 Sum_probs=36.4
Q ss_pred CCCcccccc--ccccccChhHHHhhhh-ccCcc----------------cccccccccchhhhcChhhHhhhhh
Q 039095 37 STQESQCKV--CGKDFESLKALYGHMR-HHSRR----------------ERERIQCKECGKALLSAKSLSNHMR 91 (492)
Q Consensus 37 ~~~~~~C~~--C~k~F~~~~~L~~H~r-~H~~~----------------~~k~y~C~~C~k~F~~~~~L~~H~~ 91 (492)
+++||+|++ |.|.++.+..|+-||. -|... +.|||.|++|+|+|.....|+-|..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 358888876 8888888888888865 23111 1166677777777766666666654
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.51 E-value=4.3e-05 Score=47.54 Aligned_cols=37 Identities=19% Similarity=0.485 Sum_probs=14.9
Q ss_pred HhhhhccCcccccccccccchhhhcChhhHhhhhhhcc
Q 039095 57 YGHMRHHSRRERERIQCKECGKALLSAKSLSNHMRVHS 94 (492)
Q Consensus 57 ~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H~ 94 (492)
..+.+.|.... .|-.|++|+..++...+|++|+.+++
T Consensus 12 ~~~~k~~~~S~-~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 12 TKKPKSKSQSE-QPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp ----CCCCTTS---EE-TTT--EESSHHHHHHHHHHHT
T ss_pred hhHHHHhhccC-CCCCCCcchhhccchhhHHHHHHHHh
Confidence 33444443333 55566666666666666666665544
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.39 E-value=9.1e-05 Score=40.56 Aligned_cols=25 Identities=40% Similarity=0.622 Sum_probs=22.9
Q ss_pred ccCCccccccCCchhhhhhhhhccc
Q 039095 406 HTCRICLKVFATGQALGGHKRAHLV 430 (492)
Q Consensus 406 f~C~~C~k~F~~~~~L~~H~r~H~~ 430 (492)
|.|+.|++.|.+...|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999998753
No 39
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.31 E-value=0.00013 Score=45.42 Aligned_cols=34 Identities=26% Similarity=0.471 Sum_probs=25.1
Q ss_pred hccCCCCccccccccccccChhHHHhhhhccCcc
Q 039095 33 SASASTQESQCKVCGKDFESLKALYGHMRHHSRR 66 (492)
Q Consensus 33 ~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~ 66 (492)
..+..+.|-.|++|+..+....+|++|+.++++.
T Consensus 17 ~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 17 SKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp CCCTTS--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred HhhccCCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 3455678999999999999999999999888876
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.14 E-value=0.00021 Score=39.02 Aligned_cols=24 Identities=46% Similarity=0.919 Sum_probs=16.9
Q ss_pred cccccchhhhcChhhHhhhhhhcc
Q 039095 71 IQCKECGKALLSAKSLSNHMRVHS 94 (492)
Q Consensus 71 y~C~~C~k~F~~~~~L~~H~~~H~ 94 (492)
|+|+.|+++|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 567777777777777777777553
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.07 E-value=0.0002 Score=38.78 Aligned_cols=23 Identities=35% Similarity=0.678 Sum_probs=21.4
Q ss_pred ccCCccccccCCchhhhhhhhhc
Q 039095 406 HTCRICLKVFATGQALGGHKRAH 428 (492)
Q Consensus 406 f~C~~C~k~F~~~~~L~~H~r~H 428 (492)
|.|++|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 78999999999999999999865
No 42
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=97.07 E-value=0.012 Score=58.76 Aligned_cols=63 Identities=16% Similarity=0.223 Sum_probs=57.6
Q ss_pred ccccCCcccccccCCCCCccccC---CCCC--Cceecc--cCccccccchhhhhhcccCCCCCCCCCCcC
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDD---PQKE--SEIRCQ--ACNKIFCSRRALGGHQRMHSAKRSSLPVKT 377 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~---~~~~--~~~~C~--~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C 377 (492)
.++.|..|...|.....|..|.. |.++ +++.|+ .|++.|.....|..|..+|++.+++.+..-
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 357 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLL 357 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccc
Confidence 47999999999999999999665 8888 999999 899999999999999999999988887774
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.96 E-value=0.00035 Score=37.82 Aligned_cols=23 Identities=35% Similarity=0.722 Sum_probs=13.6
Q ss_pred cccccccccccChhHHHhhhhcc
Q 039095 41 SQCKVCGKDFESLKALYGHMRHH 63 (492)
Q Consensus 41 ~~C~~C~k~F~~~~~L~~H~r~H 63 (492)
|.|.+|++.|.+...|+.|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 45666666666666666665543
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.93 E-value=0.00035 Score=37.40 Aligned_cols=24 Identities=21% Similarity=0.286 Sum_probs=19.6
Q ss_pred ccCCccccccCCchhhhhhhhhccc
Q 039095 406 HTCRICLKVFATGQALGGHKRAHLV 430 (492)
Q Consensus 406 f~C~~C~k~F~~~~~L~~H~r~H~~ 430 (492)
|+|+.|+.... +..|.+|+++|++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 78999999998 9999999998764
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.82 E-value=0.00057 Score=37.73 Aligned_cols=22 Identities=36% Similarity=0.614 Sum_probs=15.6
Q ss_pred cccccccccccChhHHHhhhhc
Q 039095 41 SQCKVCGKDFESLKALYGHMRH 62 (492)
Q Consensus 41 ~~C~~C~k~F~~~~~L~~H~r~ 62 (492)
|.|..|++.|.+...|..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5677777777777777777665
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.81 E-value=0.00038 Score=57.28 Aligned_cols=37 Identities=24% Similarity=0.552 Sum_probs=21.0
Q ss_pred ccccccccccccChhHHHhhhhccCcccccccccccchhhhcC
Q 039095 40 ESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLS 82 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~ 82 (492)
+|.|. |++ ....+.+|.++|+++ ++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~--~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGE--AVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCC--ccEECCCCCceeEE
Confidence 45665 555 455556666666655 55666666555543
No 47
>PRK04860 hypothetical protein; Provisional
Probab=96.81 E-value=0.0005 Score=56.59 Aligned_cols=25 Identities=20% Similarity=0.514 Sum_probs=20.9
Q ss_pred CceecccCccccccchhhhhhcccCCCCC
Q 039095 342 SEIRCQACNKIFCSRRALGGHQRMHSAKR 370 (492)
Q Consensus 342 ~~~~C~~C~k~F~~~~~L~~H~~~H~~~k 370 (492)
-+|.|. |++ ....+.+|.++|+|++
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~ 142 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEA 142 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCc
Confidence 479998 998 8888999999999433
No 48
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.74 E-value=0.00059 Score=37.69 Aligned_cols=23 Identities=26% Similarity=0.554 Sum_probs=21.3
Q ss_pred ccCCccccccCCchhhhhhhhhc
Q 039095 406 HTCRICLKVFATGQALGGHKRAH 428 (492)
Q Consensus 406 f~C~~C~k~F~~~~~L~~H~r~H 428 (492)
|.|.+|++.|.+...|..|++..
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 88999999999999999999853
No 49
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.74 E-value=0.0017 Score=64.99 Aligned_cols=48 Identities=31% Similarity=0.704 Sum_probs=30.6
Q ss_pred cccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhhhhcccCcccccccC
Q 039095 41 SQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHMRVHSQKLRACNESG 104 (492)
Q Consensus 41 ~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H~~k~~~C~~C~ 104 (492)
+.|.+|++.|.-.. ..-.|..| -.|.+..+|+.||+.-+ +.+.|..|-
T Consensus 100 ~~C~~C~~~~~~~~--------------~~~~~~~c-~~~~s~~~Lk~H~~~~H-~~~~c~lC~ 147 (669)
T KOG2231|consen 100 HSCHICDRRFRALY--------------NKKECLHC-TEFKSVENLKNHMRDQH-KLHLCSLCL 147 (669)
T ss_pred hhcCccccchhhhc--------------ccCCCccc-cchhHHHHHHHHHHHhh-hhhcccccc
Confidence 68999988875332 23457777 67777788888875322 334555553
No 50
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.61 E-value=0.00065 Score=36.30 Aligned_cols=21 Identities=19% Similarity=0.542 Sum_probs=8.3
Q ss_pred cccccchhhhcChhhHhhhhhh
Q 039095 71 IQCKECGKALLSAKSLSNHMRV 92 (492)
Q Consensus 71 y~C~~C~k~F~~~~~L~~H~~~ 92 (492)
|+|+.|+.... ...|.+|++.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 34444444443 4444444444
No 51
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.48 E-value=0.0022 Score=68.13 Aligned_cols=53 Identities=15% Similarity=0.117 Sum_probs=46.2
Q ss_pred cccccCCcccccccCCCCCccccC--CCCCCceecccCccccccchhhhhhcccC
Q 039095 314 YAEYGGDSSSKAMCNASDYDVFDD--PQKESEIRCQACNKIFCSRRALGGHQRMH 366 (492)
Q Consensus 314 ~~~~~C~~C~~~f~~~~~l~~h~~--~~~~~~~~C~~C~k~F~~~~~L~~H~~~H 366 (492)
...+.|..|++...-..+|+.|+. ++...|..|..|+-.+.....|..+.+.+
T Consensus 587 kP~~~C~vc~yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~~~~~~~~~lp 641 (1406)
T KOG1146|consen 587 KPSWRCEVCSYETNIARNLRIHMTASPSSSPPSLVLQQNITSSLASLLGGQGRLP 641 (1406)
T ss_pred CCCcchhhhcchhhhhhccccccccCCCCCChHHHhhhcchhhccccccCcCCCC
Confidence 367999999999999999999773 45555699999999999999999999988
No 52
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.95 E-value=0.0044 Score=61.89 Aligned_cols=56 Identities=18% Similarity=0.265 Sum_probs=53.6
Q ss_pred CccccCCCCcccccccchhhhhh--ccCCC--Cccccc--cccccccChhHHHhhhhccCcc
Q 039095 11 ISYDLRENPKKSWKFSSFNHAAS--ASAST--QESQCK--VCGKDFESLKALYGHMRHHSRR 66 (492)
Q Consensus 11 ~~~~C~~C~k~f~~~~~l~~H~~--~H~~~--~~~~C~--~C~k~F~~~~~L~~H~r~H~~~ 66 (492)
.++.|..|...|.....|..|.+ .|.++ +|+.|+ .|++.|.....|.+|..+|++.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCC
Confidence 47999999999999999999999 89999 999999 8999999999999999999887
No 53
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=95.70 E-value=0.0063 Score=64.83 Aligned_cols=103 Identities=17% Similarity=0.185 Sum_probs=66.9
Q ss_pred CCcccccccCCCCCcccc--CCCCCCceecccCccccccchhhhhhccc-CCCCCCCCCCcCCCCCCCCcccchhhhhhh
Q 039095 319 GDSSSKAMCNASDYDVFD--DPQKESEIRCQACNKIFCSRRALGGHQRM-HSAKRSSLPVKTTMFTETEPHSKLVKLECI 395 (492)
Q Consensus 319 C~~C~~~f~~~~~l~~h~--~~~~~~~~~C~~C~k~F~~~~~L~~H~~~-H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~ 395 (492)
|..|...+.....+..+. .+.-.+.|+|+.|+..|+....|..|||+ |..-+. ..|-+.........
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~~gq~~~~~ar------- 508 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCKAGQNHPRLAR------- 508 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch---hHhHhccccccccc-------
Confidence 445555555555555422 45556889999999999999999999996 544333 33322111111000
Q ss_pred hccccCCCCcccCCccccccCCchhhhhhhh--hcccC
Q 039095 396 EDLMQRGNKEHTCRICLKVFATGQALGGHKR--AHLVK 431 (492)
Q Consensus 396 h~~~H~~~kpf~C~~C~k~F~~~~~L~~H~r--~H~~~ 431 (492)
....--+.+||.|..|..+|+++.+|.+||. .|..+
T Consensus 509 g~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~ 546 (1406)
T KOG1146|consen 509 GEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNE 546 (1406)
T ss_pred cccccCCCCcccceeeeeeeecchHHHHHHHHHhhHHH
Confidence 0000116799999999999999999999987 45443
No 54
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=95.44 E-value=0.0042 Score=52.75 Aligned_cols=47 Identities=34% Similarity=0.603 Sum_probs=41.0
Q ss_pred ecccCccccccchhhhhhcccCCCCCCCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCCccccccCCchhhhhh
Q 039095 345 RCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICLKVFATGQALGGH 424 (492)
Q Consensus 345 ~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k~F~~~~~L~~H 424 (492)
=|-+|++-|.....|.+|++. |-|+|.||.|...+.-.|..|
T Consensus 12 wcwycnrefddekiliqhqka--------------------------------------khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA--------------------------------------KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhh--------------------------------------ccceeeeehhhhccCCCceee
Confidence 389999999999999999853 349999999999999999999
Q ss_pred -hhhcc
Q 039095 425 -KRAHL 429 (492)
Q Consensus 425 -~r~H~ 429 (492)
|++|.
T Consensus 54 cmqvhk 59 (341)
T KOG2893|consen 54 CMQVHK 59 (341)
T ss_pred hhhhhh
Confidence 88884
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.27 E-value=0.01 Score=31.84 Aligned_cols=21 Identities=29% Similarity=0.607 Sum_probs=18.3
Q ss_pred ccCCccccccCCchhhhhhhhh
Q 039095 406 HTCRICLKVFATGQALGGHKRA 427 (492)
Q Consensus 406 f~C~~C~k~F~~~~~L~~H~r~ 427 (492)
..|++||+.| ....|.+|++.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 78889999864
No 56
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.77 E-value=0.017 Score=31.04 Aligned_cols=19 Identities=32% Similarity=0.833 Sum_probs=11.1
Q ss_pred ccccccccccChhHHHhhhh
Q 039095 42 QCKVCGKDFESLKALYGHMR 61 (492)
Q Consensus 42 ~C~~C~k~F~~~~~L~~H~r 61 (492)
+|+.|++.| ....|.+|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 566666666 4555666654
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=94.64 E-value=0.017 Score=34.06 Aligned_cols=23 Identities=17% Similarity=0.517 Sum_probs=21.0
Q ss_pred cccCCccccccCCchhhhhhhhh
Q 039095 405 EHTCRICLKVFATGQALGGHKRA 427 (492)
Q Consensus 405 pf~C~~C~k~F~~~~~L~~H~r~ 427 (492)
+|.|++|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 68999999999999999999863
No 58
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.28 E-value=0.025 Score=33.32 Aligned_cols=23 Identities=22% Similarity=0.504 Sum_probs=15.3
Q ss_pred ccccccccccccChhHHHhhhhc
Q 039095 40 ESQCKVCGKDFESLKALYGHMRH 62 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r~ 62 (492)
+|.|++|++.|.+...+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46677777777766667666653
No 59
>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=93.67 E-value=0.04 Score=31.92 Aligned_cols=24 Identities=21% Similarity=0.108 Sum_probs=14.3
Q ss_pred cccCCCCcccccccchhhhhhccCCCCccccccccc
Q 039095 13 YDLRENPKKSWKFSSFNHAASASASTQESQCKVCGK 48 (492)
Q Consensus 13 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k 48 (492)
|+|.+||..+.... .++.|++|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 66777776654332 4566666654
No 60
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=92.15 E-value=0.039 Score=47.07 Aligned_cols=47 Identities=36% Similarity=0.711 Sum_probs=35.1
Q ss_pred ccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhh-hhhcc
Q 039095 42 QCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNH-MRVHS 94 (492)
Q Consensus 42 ~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H-~~~H~ 94 (492)
=|=+|++.|....-|..|++. |-|+|.+|.|..-+--.|..| |.+|.
T Consensus 12 wcwycnrefddekiliqhqka------khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA------KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhhhhhh------ccceeeeehhhhccCCCceeehhhhhh
Confidence 377888888888888887653 568888888777777777777 66675
No 61
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.51 E-value=0.081 Score=44.18 Aligned_cols=79 Identities=14% Similarity=0.289 Sum_probs=53.8
Q ss_pred CCccccCC--CCcccccccchhhhhhc-cCCCCccccccccccccChhHHHhhhhccCcc--------ccccccccc--c
Q 039095 10 HISYDLRE--NPKKSWKFSSFNHAASA-SASTQESQCKVCGKDFESLKALYGHMRHHSRR--------ERERIQCKE--C 76 (492)
Q Consensus 10 ~~~~~C~~--C~k~f~~~~~l~~H~~~-H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~--------~~k~y~C~~--C 76 (492)
.+.|.|++ |...|.....+.+|... |.+ .|.+|.+.|.+..-|..|+.-.+.- +..-|+|-+ |
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY~~~h~~----sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgC 152 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHYHTLHGN----SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGC 152 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhhhhcccc----hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhh
Confidence 34477776 67778887777777543 332 7888888888888888886532211 114588865 8
Q ss_pred hhhhcChhhHhhhhhh
Q 039095 77 GKALLSAKSLSNHMRV 92 (492)
Q Consensus 77 ~k~F~~~~~L~~H~~~ 92 (492)
+..|.+...-+.||-.
T Consensus 153 t~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 153 TEKFKTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhhhhhHHHH
Confidence 8888888888888653
No 62
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.07 E-value=0.64 Score=35.44 Aligned_cols=27 Identities=22% Similarity=0.443 Sum_probs=22.1
Q ss_pred CCcccCCccccccCCchhhhhhhhhcc
Q 039095 403 NKEHTCRICLKVFATGQALGGHKRAHL 429 (492)
Q Consensus 403 ~kpf~C~~C~k~F~~~~~L~~H~r~H~ 429 (492)
...|.|+.|...|=-.-..-.|..+|.
T Consensus 79 ~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 79 SHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ccceeCCCCCCccccccchhhhhhccC
Confidence 456889999998888888888888775
No 63
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.51 E-value=0.15 Score=44.75 Aligned_cols=25 Identities=28% Similarity=0.702 Sum_probs=21.1
Q ss_pred CCceecccCccccccchhhhhhccc
Q 039095 341 ESEIRCQACNKIFCSRRALGGHQRM 365 (492)
Q Consensus 341 ~~~~~C~~C~k~F~~~~~L~~H~~~ 365 (492)
++.++|++|++.|.+..-+....|+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 3568999999999999888888764
No 64
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=90.30 E-value=0.19 Score=45.61 Aligned_cols=110 Identities=19% Similarity=0.191 Sum_probs=73.3
Q ss_pred CccccCCCCcccc-cccchhhhhh-ccC-----C----------------CCccccccccccccChhHHHhhhhc--cCc
Q 039095 11 ISYDLRENPKKSW-KFSSFNHAAS-ASA-----S----------------TQESQCKVCGKDFESLKALYGHMRH--HSR 65 (492)
Q Consensus 11 ~~~~C~~C~k~f~-~~~~l~~H~~-~H~-----~----------------~~~~~C~~C~k~F~~~~~L~~H~r~--H~~ 65 (492)
..-+|-+|...+. ..+..-+|+. .|. . -..++|-.|.|.|..+..|+.|||. |..
T Consensus 143 fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrr 222 (423)
T KOG2482|consen 143 FSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRR 222 (423)
T ss_pred eeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCcc
Confidence 3457889988866 4455555543 231 1 1137999999999999999999974 433
Q ss_pred ccc----------------------------------------------------cccccccchhhhcChhhHhhhhhh-
Q 039095 66 RER----------------------------------------------------ERIQCKECGKALLSAKSLSNHMRV- 92 (492)
Q Consensus 66 ~~~----------------------------------------------------k~y~C~~C~k~F~~~~~L~~H~~~- 92 (492)
..+ -...|-.|.....+...|..||++
T Consensus 223 inPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~v 302 (423)
T KOG2482|consen 223 INPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKIV 302 (423)
T ss_pred cCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHHH
Confidence 210 115899999999999999999985
Q ss_pred cc-c--C------------------------cccccccCchhhhHHhhhhhcccc
Q 039095 93 HS-Q--K------------------------LRACNESGAVKSLVLKKKRSKRKR 120 (492)
Q Consensus 93 H~-~--k------------------------~~~C~~C~~~f~~~~~~~~h~~~~ 120 (492)
|. . | .-.|-.|+-.|-....+..|+-..
T Consensus 303 He~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 303 HEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred HHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 42 1 1 125677776666666666666443
No 65
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.26 E-value=0.38 Score=43.79 Aligned_cols=104 Identities=16% Similarity=0.164 Sum_probs=66.9
Q ss_pred CccccCCCC---ccccccc------chhhhhhccCCCCcc----ccccccccccChhHHHhhhhccCcccccccccccch
Q 039095 11 ISYDLRENP---KKSWKFS------SFNHAASASASTQES----QCKVCGKDFESLKALYGHMRHHSRRERERIQCKECG 77 (492)
Q Consensus 11 ~~~~C~~C~---k~f~~~~------~l~~H~~~H~~~~~~----~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~ 77 (492)
..+.|.+|- +.|+... .|+.|...=..+..| .|.+|.+.|-....|.+|+|.-+. + |.+|+
T Consensus 178 ~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~HE---~---ChICD 251 (493)
T COG5236 178 GFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRHE---A---CHICD 251 (493)
T ss_pred CcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccceecChHHHHHHHHhhhh---h---hhhhh
Confidence 346677774 3466543 445554432222233 799999999999999999997665 3 55554
Q ss_pred -------hhhcChhhHhhhhhhcccCcccccc--cC----chhhhHHhhhhhccccccc
Q 039095 78 -------KALLSAKSLSNHMRVHSQKLRACNE--SG----AVKSLVLKKKRSKRKRYNF 123 (492)
Q Consensus 78 -------k~F~~~~~L~~H~~~H~~k~~~C~~--C~----~~f~~~~~~~~h~~~~~~~ 123 (492)
.-|..-.+|..|.+.-+ |.|.+ |- .+|.....|+.|...-+..
T Consensus 252 ~v~p~~~QYFK~Y~~Le~HF~~~h---y~ct~qtc~~~k~~vf~~~~el~~h~~~~h~~ 307 (493)
T COG5236 252 MVGPIRYQYFKSYEDLEAHFRNAH---YCCTFQTCRVGKCYVFPYHTELLEHLTRFHKV 307 (493)
T ss_pred ccCccchhhhhCHHHHHHHhhcCc---eEEEEEEEecCcEEEeccHHHHHHHHHHHhhc
Confidence 46888899999987321 55544 21 3577777777777554433
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.24 E-value=0.12 Score=32.95 Aligned_cols=23 Identities=26% Similarity=0.608 Sum_probs=12.3
Q ss_pred cccccccchhhhcChhhHhhhhh
Q 039095 69 ERIQCKECGKALLSAKSLSNHMR 91 (492)
Q Consensus 69 k~y~C~~C~k~F~~~~~L~~H~~ 91 (492)
.-+.||-||+.|..+....+|+.
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhh
Confidence 45555555555555555555544
No 67
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.95 E-value=1.4 Score=33.72 Aligned_cols=91 Identities=8% Similarity=0.035 Sum_probs=50.9
Q ss_pred CCccchhhhccccchhhhhhhcchh--hcccceeeecCCcccccCCCcccccCCcccccccCCCCCccccCCCCCCceec
Q 039095 269 GSVASDDEIGKESSEDLMEEDGLDA--EAGKRIITSTSSKKVGFNACYAEYGGDSSSKAMCNASDYDVFDDPQKESEIRC 346 (492)
Q Consensus 269 ~~~~~c~~c~~~~~~~~~~~~h~~~--~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C 346 (492)
..|..|..|+-......+|.+.+.- .... .....++.......|-.|...|........- .-.....|+|
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~-------f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~-~~~~~~~y~C 84 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKA-------FQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD-ELKDSHRYVC 84 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcc-------cccccccccCCCCcccCcCCCCCCccccccc-ccccccceeC
Confidence 4556688888776666555432211 1110 0000111111223588888888765422110 1223457899
Q ss_pred ccCccccccchhhhhhcccCC
Q 039095 347 QACNKIFCSRRALGGHQRMHS 367 (492)
Q Consensus 347 ~~C~k~F~~~~~L~~H~~~H~ 367 (492)
+.|...|=-.-.+-.|...|.
T Consensus 85 ~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 85 AVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred CCCCCccccccchhhhhhccC
Confidence 999999988888888888886
No 68
>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=88.85 E-value=0.25 Score=28.76 Aligned_cols=25 Identities=12% Similarity=0.158 Sum_probs=14.2
Q ss_pred ccccCCCCcccccccchhhhhhccCCCCccccccccc
Q 039095 12 SYDLRENPKKSWKFSSFNHAASASASTQESQCKVCGK 48 (492)
Q Consensus 12 ~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k 48 (492)
.|+|.+||..+.... .|..|++|+.
T Consensus 2 ~~~C~~CG~i~~g~~------------~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGEE------------APEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECCc------------CCCcCcCCCC
Confidence 366777776654321 3456766664
No 69
>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=88.83 E-value=0.32 Score=37.60 Aligned_cols=25 Identities=28% Similarity=0.546 Sum_probs=21.3
Q ss_pred ccc----ccchhhhcChhhHhhhhhhccc
Q 039095 71 IQC----KECGKALLSAKSLSNHMRVHSQ 95 (492)
Q Consensus 71 y~C----~~C~k~F~~~~~L~~H~~~H~~ 95 (492)
|.| ..|+..+.+...|++|++.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 8899999999999999887654
No 70
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=88.54 E-value=0.25 Score=44.92 Aligned_cols=82 Identities=16% Similarity=0.254 Sum_probs=64.0
Q ss_pred ccccCCCCcccccccchhhhhhc--cCC----------------------------------------------------
Q 039095 12 SYDLRENPKKSWKFSSFNHAASA--SAS---------------------------------------------------- 37 (492)
Q Consensus 12 ~~~C~~C~k~f~~~~~l~~H~~~--H~~---------------------------------------------------- 37 (492)
.+.|-.|.|.|+.+..|+.||+. |..
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 47899999999999999999983 211
Q ss_pred CCc--cccccccccccChhHHHhhhhccCccc-------------------------ccccccccchhhhcChhhHhhhh
Q 039095 38 TQE--SQCKVCGKDFESLKALYGHMRHHSRRE-------------------------RERIQCKECGKALLSAKSLSNHM 90 (492)
Q Consensus 38 ~~~--~~C~~C~k~F~~~~~L~~H~r~H~~~~-------------------------~k~y~C~~C~k~F~~~~~L~~H~ 90 (492)
..+ -.|-+|....-+...|..||.+-+.=. .+.-.|-.|.-.|.....|..||
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm 354 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHM 354 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhc
Confidence 111 389999999999999999998643210 02246888999999999999999
Q ss_pred hhc
Q 039095 91 RVH 93 (492)
Q Consensus 91 ~~H 93 (492)
.-+
T Consensus 355 ~e~ 357 (423)
T KOG2482|consen 355 VED 357 (423)
T ss_pred ccc
Confidence 854
No 71
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.98 E-value=0.47 Score=48.21 Aligned_cols=79 Identities=16% Similarity=0.275 Sum_probs=45.4
Q ss_pred cccCCCCcccc---------------cccchhhhhh-ccCCCCcccccccc---------ccccChhHHHhhhhccCc-c
Q 039095 13 YDLRENPKKSW---------------KFSSFNHAAS-ASASTQESQCKVCG---------KDFESLKALYGHMRHHSR-R 66 (492)
Q Consensus 13 ~~C~~C~k~f~---------------~~~~l~~H~~-~H~~~~~~~C~~C~---------k~F~~~~~L~~H~r~H~~-~ 66 (492)
+.|.+|+..|. +...|+.|++ .|. .+.|.+|- ...-++..|..|++.=.. +
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~---~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~ 176 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHK---LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDD 176 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhh---hhccccccccceeeeeeeehehHHHHHHHHhcCCCcc
Confidence 56777777773 5667888874 453 23444433 223345567777654222 1
Q ss_pred c--ccccccccchhhhcChhhHhhhhhhcc
Q 039095 67 E--RERIQCKECGKALLSAKSLSNHMRVHS 94 (492)
Q Consensus 67 ~--~k~y~C~~C~k~F~~~~~L~~H~~~H~ 94 (492)
. .---.|..|...|-....|.+||+.++
T Consensus 177 ~s~rGhp~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 177 ESCRGHPLCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred ccccCCccchhhhhhhccHHHHHHhhccce
Confidence 0 012457777777777777777777554
No 72
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=87.66 E-value=0.33 Score=28.73 Aligned_cols=34 Identities=18% Similarity=0.380 Sum_probs=25.3
Q ss_pred ccCCcccccccCCCCCccccCCCCCCceecccCccccc
Q 039095 317 YGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFC 354 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~ 354 (492)
..|+.|+..|.-..+. ........+|+.|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~----ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK----IPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHH----CCCCCcEEECCCCCCEeC
Confidence 5789999888766653 345556789999999884
No 73
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=87.26 E-value=0.29 Score=40.07 Aligned_cols=47 Identities=15% Similarity=0.109 Sum_probs=28.9
Q ss_pred ccCCcccccccCCCCCccccC-CCCCCceecccCccccccchhhhhhc
Q 039095 317 YGGDSSSKAMCNASDYDVFDD-PQKESEIRCQACNKIFCSRRALGGHQ 363 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~-~~~~~~~~C~~C~k~F~~~~~L~~H~ 363 (492)
++||.|+-.+..-..-..+.. -.-.+.++|+-||++|.+...+..=+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 479999976533333222221 11223499999999999887765543
No 74
>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=86.48 E-value=0.49 Score=25.59 Aligned_cols=24 Identities=13% Similarity=0.187 Sum_probs=15.6
Q ss_pred cCCcccccccCCCCCccccCCCCCCceecccCccccc
Q 039095 318 GGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFC 354 (492)
Q Consensus 318 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~ 354 (492)
.|+.|+....... -.|+.||..|.
T Consensus 2 ~CP~C~~~V~~~~-------------~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESA-------------KFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhc-------------CcCCCCCCCCc
Confidence 4677776653333 47888888875
No 75
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=86.25 E-value=0.48 Score=36.20 Aligned_cols=30 Identities=30% Similarity=0.832 Sum_probs=18.5
Q ss_pred cccccccccccChhHHHhhhhccCcccccccccccchhhhcCh
Q 039095 41 SQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSA 83 (492)
Q Consensus 41 ~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~ 83 (492)
..|+.||+.|-.-+ . .|..||.||..|.-.
T Consensus 10 R~Cp~CG~kFYDLn-----------k--~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN-----------K--DPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCC-----------C--CCccCCCCCCccCcc
Confidence 36777777765432 1 466777777777654
No 76
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=86.24 E-value=0.54 Score=48.91 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=35.6
Q ss_pred cccCCcccccccCCCCCccccCCCCCCceecccCccccccchhhhhhcccCCCCCCCCCCcCCCCCCCCcccchhhhhhh
Q 039095 316 EYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFTETEPHSKLVKLECI 395 (492)
Q Consensus 316 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~ 395 (492)
-.-|..|+..+ +|+.|+-. | ..|...+-.+|..|++.
T Consensus 435 ~l~C~~Cg~v~------------------~Cp~Cd~~------l----t~H~~~~~L~CH~Cg~~--------------- 471 (730)
T COG1198 435 LLLCRDCGYIA------------------ECPNCDSP------L----TLHKATGQLRCHYCGYQ--------------- 471 (730)
T ss_pred eeecccCCCcc------------------cCCCCCcc------e----EEecCCCeeEeCCCCCC---------------
Confidence 45677777754 78888764 3 34555566888888855
Q ss_pred hccccCCCCcccCCccccc
Q 039095 396 EDLMQRGNKEHTCRICLKV 414 (492)
Q Consensus 396 h~~~H~~~kpf~C~~C~k~ 414 (492)
...|+.|+.||-.
T Consensus 472 ------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 ------EPIPQSCPECGSE 484 (730)
T ss_pred ------CCCCCCCCCCCCC
Confidence 5689999999765
No 77
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=85.88 E-value=0.36 Score=30.92 Aligned_cols=31 Identities=19% Similarity=0.350 Sum_probs=25.0
Q ss_pred cCCCCccccccccccccChhHHHhhhhccCc
Q 039095 35 SASTQESQCKVCGKDFESLKALYGHMRHHSR 65 (492)
Q Consensus 35 H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~ 65 (492)
-.|+.-++|+.|++.|....++.+|+..-++
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 4567778999999999999999999765444
No 78
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.38 E-value=0.46 Score=41.74 Aligned_cols=17 Identities=6% Similarity=-0.318 Sum_probs=9.2
Q ss_pred CccccCCCCcccccccc
Q 039095 11 ISYDLRENPKKSWKFSS 27 (492)
Q Consensus 11 ~~~~C~~C~k~f~~~~~ 27 (492)
+.+.||+|++.|++...
T Consensus 4 k~~~CPvC~~~F~~~~v 20 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKV 20 (214)
T ss_pred CceECCCCCCeeeeeEE
Confidence 34556666666655543
No 79
>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=84.25 E-value=0.72 Score=35.26 Aligned_cols=32 Identities=16% Similarity=0.306 Sum_probs=22.2
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCccccccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSR 356 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~ 356 (492)
....|+.||..|+... ..|..|++||..|.-.
T Consensus 8 tKR~Cp~CG~kFYDLn----------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLN----------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCC----------CCCccCCCCCCccCcc
Confidence 3456888888886544 2567788888877766
No 80
>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=84.21 E-value=0.61 Score=29.20 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=16.9
Q ss_pred CCCcccCCccccccCCc----hhhhhhhh
Q 039095 402 GNKEHTCRICLKVFATG----QALGGHKR 426 (492)
Q Consensus 402 ~~kpf~C~~C~k~F~~~----~~L~~H~r 426 (492)
+..-.+|.+|++.+... ++|.+|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 45667999999999885 78999984
No 81
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=83.60 E-value=0.67 Score=29.86 Aligned_cols=25 Identities=28% Similarity=0.555 Sum_probs=20.4
Q ss_pred cc-cCCccccccCCc-----hhhhhhhh-hcc
Q 039095 405 EH-TCRICLKVFATG-----QALGGHKR-AHL 429 (492)
Q Consensus 405 pf-~C~~C~k~F~~~-----~~L~~H~r-~H~ 429 (492)
++ .|..|++.+... ++|.+|++ +|.
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 44 799999999776 58999998 664
No 82
>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=82.27 E-value=0.74 Score=28.81 Aligned_cols=27 Identities=22% Similarity=0.533 Sum_probs=17.9
Q ss_pred CCCceecccCccccccc----hhhhhhc-ccC
Q 039095 340 KESEIRCQACNKIFCSR----RALGGHQ-RMH 366 (492)
Q Consensus 340 ~~~~~~C~~C~k~F~~~----~~L~~H~-~~H 366 (492)
+....+|.+|++.+... ++|.+|+ +.|
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 45668999999999885 8999998 444
No 83
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=82.25 E-value=0.62 Score=27.94 Aligned_cols=34 Identities=9% Similarity=0.265 Sum_probs=21.8
Q ss_pred ccCCcccccccCCCCCccccCCCCCCceecccCccccc
Q 039095 317 YGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFC 354 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~ 354 (492)
+.|+.|+..|.-..+.. ........|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~----~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL----GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc----CCCCCEEECCCCCCEEE
Confidence 57888888776554321 12223678999988774
No 84
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=81.80 E-value=0.7 Score=46.95 Aligned_cols=56 Identities=11% Similarity=0.147 Sum_probs=43.4
Q ss_pred ccCCcccccccCCCCCccccCCCCCCce-ecccCccccccchhhhhhcccCCCCCCCCCCcCC
Q 039095 317 YGGDSSSKAMCNASDYDVFDDPQKESEI-RCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTT 378 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~-~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~ 378 (492)
..|..||-.|+-...|..-+..+..+.| .|+.|.+-|..+-+ .|-|. +|.-|+.|+
T Consensus 124 ~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~n----RRfHA--Qp~aCp~CG 180 (750)
T COG0068 124 INCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLN----RRFHA--QPIACPKCG 180 (750)
T ss_pred cccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccc----ccccc--ccccCcccC
Confidence 3599999999999998888888888887 49999999988887 34555 444555555
No 85
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=81.62 E-value=0.79 Score=27.31 Aligned_cols=34 Identities=18% Similarity=0.378 Sum_probs=24.1
Q ss_pred ccCCcccccccCCCCCccccCCCCCCceecccCccccc
Q 039095 317 YGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFC 354 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~ 354 (492)
..|+.|+..|.=..+. ...+.+..+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH----cccCCcEEECCCCCcEee
Confidence 4688898888655542 234556789999998884
No 86
>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=81.57 E-value=0.93 Score=24.53 Aligned_cols=21 Identities=14% Similarity=0.528 Sum_probs=17.2
Q ss_pred ccCCccccccCCchhhhhhhhh
Q 039095 406 HTCRICLKVFATGQALGGHKRA 427 (492)
Q Consensus 406 f~C~~C~k~F~~~~~L~~H~r~ 427 (492)
..|++|++.+ ....++.|+..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3699999999 66789999863
No 87
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=81.28 E-value=1.1 Score=36.68 Aligned_cols=37 Identities=22% Similarity=0.468 Sum_probs=19.1
Q ss_pred CCCccccccccccccChhHHHh-hhhccCcccccccccccchhhh
Q 039095 37 STQESQCKVCGKDFESLKALYG-HMRHHSRRERERIQCKECGKAL 80 (492)
Q Consensus 37 ~~~~~~C~~C~k~F~~~~~L~~-H~r~H~~~~~k~y~C~~C~k~F 80 (492)
+..-|.|+.|+..|.....+.. + . . ..|.||.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d----~-~--~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLD----M-D--GTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcC----C-C--CcEECCCCCCEE
Confidence 3345666666666665443332 1 1 2 246666666543
No 88
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.11 E-value=0.71 Score=37.89 Aligned_cols=17 Identities=29% Similarity=0.722 Sum_probs=10.6
Q ss_pred ccccccchhhhcChhhH
Q 039095 70 RIQCKECGKALLSAKSL 86 (492)
Q Consensus 70 ~y~C~~C~k~F~~~~~L 86 (492)
.|+|+.||++|.+.-.+
T Consensus 28 ~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 28 RRECLACGKRFTTFERV 44 (154)
T ss_pred eeeccccCCcceEeEec
Confidence 46677777777655444
No 89
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=80.28 E-value=1.3 Score=27.95 Aligned_cols=31 Identities=19% Similarity=0.288 Sum_probs=19.3
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCccccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFC 354 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~ 354 (492)
..|.|+.|+..|.-.... ..++|+.||..+.
T Consensus 2 ~~y~C~~CG~~~~~~~~~---------~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEYG---------TGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCCC---------CceECCCCCCeEE
Confidence 357788887776554431 1577888876544
No 90
>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=80.22 E-value=0.87 Score=27.76 Aligned_cols=14 Identities=7% Similarity=-0.002 Sum_probs=8.0
Q ss_pred cccCCCCccccccc
Q 039095 13 YDLRENPKKSWKFS 26 (492)
Q Consensus 13 ~~C~~C~k~f~~~~ 26 (492)
|.|+.|++.|.-..
T Consensus 6 y~C~~Cg~~fe~~~ 19 (41)
T smart00834 6 YRCEDCGHTFEVLQ 19 (41)
T ss_pred EEcCCCCCEEEEEE
Confidence 56666666665443
No 91
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.97 E-value=1.4 Score=40.26 Aligned_cols=105 Identities=15% Similarity=0.212 Sum_probs=60.2
Q ss_pred cccCC--CCcccccccchhhhhhccCCCCcccccccc---ccc------cChhHHHhhhhccCcc-c-ccccccccchhh
Q 039095 13 YDLRE--NPKKSWKFSSFNHAASASASTQESQCKVCG---KDF------ESLKALYGHMRHHSRR-E-RERIQCKECGKA 79 (492)
Q Consensus 13 ~~C~~--C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~---k~F------~~~~~L~~H~r~H~~~-~-~k~y~C~~C~k~ 79 (492)
|.|+. |..+...+..|+.|.....+ .+.|.+|- +.| -+++.|..|...=..+ + ..--.|..|...
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~--~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 55553 55555555666666553222 34555553 222 2334455554332222 0 012459999999
Q ss_pred hcChhhHhhhhhhcccCcccccccC----chhhhHHhhhhhccc
Q 039095 80 LLSAKSLSNHMRVHSQKLRACNESG----AVKSLVLKKKRSKRK 119 (492)
Q Consensus 80 F~~~~~L~~H~~~H~~k~~~C~~C~----~~f~~~~~~~~h~~~ 119 (492)
|-.-..|.+|+|.-+++-|.|+.-+ ..|.+...|..|-+.
T Consensus 230 FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~ 273 (493)
T COG5236 230 FYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRN 273 (493)
T ss_pred ecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhc
Confidence 9999999999997666655554433 336677777777654
No 92
>PHA00626 hypothetical protein
Probab=79.27 E-value=1.4 Score=28.50 Aligned_cols=16 Identities=13% Similarity=0.125 Sum_probs=12.4
Q ss_pred CcccCCccccccCCch
Q 039095 404 KEHTCRICLKVFATGQ 419 (492)
Q Consensus 404 kpf~C~~C~k~F~~~~ 419 (492)
..|+|+.||+.|+.-.
T Consensus 22 nrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 22 DDYVCCDCGYNDSKDA 37 (59)
T ss_pred cceEcCCCCCeechhh
Confidence 5688999988887644
No 93
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=79.11 E-value=0.82 Score=39.94 Aligned_cols=46 Identities=28% Similarity=0.605 Sum_probs=22.8
Q ss_pred cccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhhh
Q 039095 41 SQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHMR 91 (492)
Q Consensus 41 ~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~ 91 (492)
|.|.+||-....+ .|.+||-.-++. -|.|-.|++.|.. ...+.|..
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn~---~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRNA---YFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccCC---eeEEeeccccccc-chhhhhhh
Confidence 4555555554433 244455444442 4555555555554 44444544
No 94
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=79.04 E-value=1.1 Score=37.15 Aligned_cols=9 Identities=22% Similarity=0.575 Sum_probs=6.4
Q ss_pred ceecccCcc
Q 039095 343 EIRCQACNK 351 (492)
Q Consensus 343 ~~~C~~C~k 351 (492)
.|.|++||.
T Consensus 134 ~~vC~vCGy 142 (166)
T COG1592 134 VWVCPVCGY 142 (166)
T ss_pred EEEcCCCCC
Confidence 578888863
No 95
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=78.92 E-value=1.1 Score=28.77 Aligned_cols=20 Identities=40% Similarity=0.855 Sum_probs=12.8
Q ss_pred ccccccccccCh-----hHHHhhhh
Q 039095 42 QCKVCGKDFESL-----KALYGHMR 61 (492)
Q Consensus 42 ~C~~C~k~F~~~-----~~L~~H~r 61 (492)
.|..|++.+... ++|.+|++
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 566666666554 46777766
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=78.26 E-value=1.9 Score=28.42 Aligned_cols=32 Identities=25% Similarity=0.500 Sum_probs=16.8
Q ss_pred ccccccccccccChhHHHhhhhccCcccccccccccchh
Q 039095 40 ESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGK 78 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k 78 (492)
.|.|+.||+.-..+-. .-|... .+|.|+.||.
T Consensus 25 ~F~CPnCG~~~I~RC~---~CRk~~----~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRCE---KCRKQS----NPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeech---hHHhcC----CceECCCCCC
Confidence 4777777766333221 111121 4788887774
No 97
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=77.98 E-value=0.6 Score=32.55 Aligned_cols=12 Identities=17% Similarity=0.315 Sum_probs=5.4
Q ss_pred ccccc--ccCchhh
Q 039095 97 LRACN--ESGAVKS 108 (492)
Q Consensus 97 ~~~C~--~C~~~f~ 108 (492)
-+.|. .||..|.
T Consensus 27 Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 27 YHQCQNVNCSATFI 40 (72)
T ss_pred eeecCCCCCCCEEE
Confidence 34444 4444444
No 98
>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=77.64 E-value=1.1 Score=29.06 Aligned_cols=12 Identities=8% Similarity=-0.083 Sum_probs=6.5
Q ss_pred cccCCCCccccc
Q 039095 13 YDLRENPKKSWK 24 (492)
Q Consensus 13 ~~C~~C~k~f~~ 24 (492)
|.|..|+..|.-
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 555555555553
No 99
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=77.44 E-value=1.8 Score=33.68 Aligned_cols=34 Identities=21% Similarity=0.346 Sum_probs=21.1
Q ss_pred cccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHh
Q 039095 41 SQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLS 87 (492)
Q Consensus 41 ~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~ 87 (492)
..|+.||+.|-..+ . .|..|+.||..|.-...++
T Consensus 10 r~Cp~cg~kFYDLn-----------k--~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 10 RICPNTGSKFYDLN-----------R--RPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred ccCCCcCccccccC-----------C--CCccCCCcCCccCcchhhc
Confidence 46777777775432 1 5777777777776553333
No 100
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=76.97 E-value=1.3 Score=30.90 Aligned_cols=43 Identities=19% Similarity=0.301 Sum_probs=28.6
Q ss_pred ccCCcccccccCCCCCccccCCCCCCceecc--cCccccccchhhh
Q 039095 317 YGGDSSSKAMCNASDYDVFDDPQKESEIRCQ--ACNKIFCSRRALG 360 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~--~C~k~F~~~~~L~ 360 (492)
+.|+.|+....-...-..... ..+.-+.|. .||.+|.+...+.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~-~~~~Y~qC~N~eCg~tF~t~es~s 46 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT-TKERYHQCQNVNCSATFITYESVQ 46 (72)
T ss_pred ccCCCCCCccEEEEChhcChh-hheeeeecCCCCCCCEEEEEEEEE
Confidence 679999877633322222222 556778998 9999999887654
No 101
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=75.85 E-value=1.4 Score=37.11 Aligned_cols=81 Identities=17% Similarity=0.310 Sum_probs=63.1
Q ss_pred Ccccccc--ccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhhhh-cc---------c-Ccccccc--c
Q 039095 39 QESQCKV--CGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHMRV-HS---------Q-KLRACNE--S 103 (492)
Q Consensus 39 ~~~~C~~--C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~-H~---------~-k~~~C~~--C 103 (492)
..|.|.+ |-.+|..-.++..|..+-++. .|.+|.+.|.+..-|..|+.- |- | .-|.|-+ |
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~-----sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgC 152 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGN-----SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGC 152 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccc-----hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhh
Confidence 4588987 899999999999998765543 599999999999999999863 32 3 3588854 8
Q ss_pred CchhhhHHhhhhhcccccccC
Q 039095 104 GAVKSLVLKKKRSKRKRYNFI 124 (492)
Q Consensus 104 ~~~f~~~~~~~~h~~~~~~~~ 124 (492)
+..|.+....+.|....+.+.
T Consensus 153 t~KFkT~r~RkdH~I~~Hk~P 173 (253)
T KOG4173|consen 153 TEKFKTSRDRKDHMIRMHKYP 173 (253)
T ss_pred hhhhhhhhhhhhHHHHhccCC
Confidence 888888888888875544443
No 102
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=75.61 E-value=1.9 Score=26.87 Aligned_cols=11 Identities=18% Similarity=0.069 Sum_probs=5.5
Q ss_pred cccCCCCcccc
Q 039095 13 YDLRENPKKSW 23 (492)
Q Consensus 13 ~~C~~C~k~f~ 23 (492)
|.|..|+..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 45555555444
No 103
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=75.58 E-value=2 Score=30.78 Aligned_cols=32 Identities=13% Similarity=0.232 Sum_probs=21.9
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCcccccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCS 355 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~ 355 (492)
..|.|+.|++.-... .....+.|..||..|.-
T Consensus 34 ~~~~Cp~C~~~~VkR---------~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRTTVKR---------IATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCcceee---------eccCeEEcCCCCCeecc
Confidence 568888888763221 24566888888888864
No 104
>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=75.36 E-value=2.2 Score=33.18 Aligned_cols=36 Identities=8% Similarity=0.026 Sum_probs=25.8
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCccccccchhhh
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRALG 360 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~L~ 360 (492)
....|+.|++.|+... ..|..|++||..|.-...++
T Consensus 8 tKr~Cp~cg~kFYDLn----------k~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 8 TKRICPNTGSKFYDLN----------RRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred ccccCCCcCccccccC----------CCCccCCCcCCccCcchhhc
Confidence 3567888888886553 35788999998887664444
No 105
>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=74.99 E-value=1.3 Score=36.74 Aligned_cols=34 Identities=18% Similarity=0.276 Sum_probs=21.0
Q ss_pred cCCCCccccccccccccChhHHHhhhhccCcccccccccccchhh
Q 039095 35 SASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKA 79 (492)
Q Consensus 35 H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~ 79 (492)
..+..-|.|+.|+..|+.-..+. .-|.||.||..
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~-----------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME-----------LNFTCPRCGAM 137 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH-----------cCCcCCCCCCE
Confidence 34445567777777776666663 24777777654
No 106
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=74.17 E-value=2.2 Score=28.07 Aligned_cols=32 Identities=25% Similarity=0.415 Sum_probs=18.7
Q ss_pred ccccccccccccChhHHHhhhhccCcccccccccccchh
Q 039095 40 ESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGK 78 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k 78 (492)
.|.|+.||..-..+..-- |.+ + .+|.|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~~C---Rk~-g---~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCAKC---RKL-G---NPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhhhH---HHc-C---CceECCCcCc
Confidence 477888886655443221 112 2 5788888874
No 107
>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=73.89 E-value=1.6 Score=34.74 Aligned_cols=28 Identities=32% Similarity=0.358 Sum_probs=18.3
Q ss_pred CcccCCccccccCCchhhhhhhhhcccCCCC
Q 039095 404 KEHTCRICLKVFATGQALGGHKRAHLVKNLD 434 (492)
Q Consensus 404 kpf~C~~C~k~F~~~~~L~~H~r~H~~~~~~ 434 (492)
.--.|-+||+.|++ |++|++.|+|-.+.
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp~ 98 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTPE 98 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-HH
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCHH
Confidence 44689999999986 59999999887654
No 108
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=72.65 E-value=4.7 Score=30.72 Aligned_cols=27 Identities=11% Similarity=0.053 Sum_probs=18.2
Q ss_pred cCCcccccccCCCCCccccCCCCCCceecccCcccccc
Q 039095 318 GGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCS 355 (492)
Q Consensus 318 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~ 355 (492)
-|+.|+..+.... ..+.|+.|+..+..
T Consensus 2 fC~~Cg~~l~~~~-----------~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPKN-----------GVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccCC-----------CeEECcCCCCcccc
Confidence 4778877774321 25888888877664
No 109
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=72.60 E-value=1.6 Score=37.04 Aligned_cols=35 Identities=23% Similarity=0.406 Sum_probs=22.9
Q ss_pred CCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhc
Q 039095 36 ASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALL 81 (492)
Q Consensus 36 ~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~ 81 (492)
....-|.|+.|++.|+.-..+. .-|.|+.||-...
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~-----------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME-----------YGFRCPQCGEMLE 147 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh-----------cCCcCCCCCCCCe
Confidence 3345577877877777776652 3577888875443
No 110
>PF15269 zf-C2H2_7: Zinc-finger
Probab=72.32 E-value=2.1 Score=26.11 Aligned_cols=22 Identities=23% Similarity=0.466 Sum_probs=19.3
Q ss_pred cccccccccccChhHHHhhhhc
Q 039095 41 SQCKVCGKDFESLKALYGHMRH 62 (492)
Q Consensus 41 ~~C~~C~k~F~~~~~L~~H~r~ 62 (492)
|+|-.|..+...+++|-.||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 6899999999999999999864
No 111
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=72.07 E-value=1.7 Score=27.62 Aligned_cols=11 Identities=9% Similarity=0.193 Sum_probs=5.6
Q ss_pred ccccCCCCccc
Q 039095 12 SYDLRENPKKS 22 (492)
Q Consensus 12 ~~~C~~C~k~f 22 (492)
.|.|..|++.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 35555555554
No 112
>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=71.97 E-value=1.9 Score=26.54 Aligned_cols=29 Identities=21% Similarity=0.377 Sum_probs=15.4
Q ss_pred cccCCCCcccccccchhhhhhccCCCCccccccccc
Q 039095 13 YDLRENPKKSWKFSSFNHAASASASTQESQCKVCGK 48 (492)
Q Consensus 13 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k 48 (492)
|.|..|+..|........ ..+-.|+.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-------~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-------DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-------CCCCcCCCCCC
Confidence 566666666655443221 23446666664
No 113
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=71.67 E-value=0.61 Score=47.07 Aligned_cols=82 Identities=6% Similarity=-0.046 Sum_probs=58.2
Q ss_pred cccCCCCcccccccchhhhhhccCCCCc--cccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhh
Q 039095 13 YDLRENPKKSWKFSSFNHAASASASTQE--SQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHM 90 (492)
Q Consensus 13 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~--~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~ 90 (492)
+.|+-|.-.|.....+..|+.+++.--+ +.|..|+++|.....--.|+..|--..+.--.|.+|+..|...-.+.-++
T Consensus 289 ~p~k~~St~p~~e~G~~s~~~~psa~wpqhlP~g~~~~~~p~s~g~s~~a~~~Qv~~P~g~~~si~~~~~~llP~a~~pI 368 (907)
T KOG4167|consen 289 RPLKSPSTIPLNEMGPQSQQLSPSAMWPQHLPDGRAQPGSPESSGQSKGAFGEQVDAPNGLTCSICLKEFKLLPAANGPI 368 (907)
T ss_pred ccccccccchhhhcCCccccccchhhccccCcccccCCCCCCcccccccchHhhhcCCCCCccccccCCCCcCcCCCCce
Confidence 6788888888888788888877776666 78888887777776666666655444223456788888887766666666
Q ss_pred hhcc
Q 039095 91 RVHS 94 (492)
Q Consensus 91 ~~H~ 94 (492)
+.+.
T Consensus 369 ~aP~ 372 (907)
T KOG4167|consen 369 RAPG 372 (907)
T ss_pred ecCC
Confidence 6665
No 114
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=71.00 E-value=5.1 Score=25.74 Aligned_cols=35 Identities=14% Similarity=0.126 Sum_probs=18.7
Q ss_pred ccCCcccccccCCCCCccccCCCC------CCceecccCcc
Q 039095 317 YGGDSSSKAMCNASDYDVFDDPQK------ESEIRCQACNK 351 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~~~~------~~~~~C~~C~k 351 (492)
|.|..|+..+.....-.......+ ...|.|++|+.
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence 677777777765443322222111 22367777774
No 115
>PRK14873 primosome assembly protein PriA; Provisional
Probab=70.59 E-value=2.8 Score=43.73 Aligned_cols=39 Identities=18% Similarity=0.222 Sum_probs=25.2
Q ss_pred eecccCccccccchhhhhhcccCCCCCCCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCCccccc
Q 039095 344 IRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICLKV 414 (492)
Q Consensus 344 ~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k~ 414 (492)
.+|+.|+-. +..|......+|..|++.. .|+.|+.||-.
T Consensus 393 ~~C~~C~~~----------L~~h~~~~~l~Ch~CG~~~----------------------~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGP----------LGLPSAGGTPRCRWCGRAA----------------------PDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCc----------eeEecCCCeeECCCCcCCC----------------------cCccCCCCcCC
Confidence 467777643 2334555667788888642 47888888764
No 116
>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=69.74 E-value=2.7 Score=34.92 Aligned_cols=31 Identities=13% Similarity=0.166 Sum_probs=23.4
Q ss_pred cccccccchhhhcChhhHhhhhhhcccCcccccccCchh
Q 039095 69 ERIQCKECGKALLSAKSLSNHMRVHSQKLRACNESGAVK 107 (492)
Q Consensus 69 k~y~C~~C~k~F~~~~~L~~H~~~H~~k~~~C~~C~~~f 107 (492)
.-|.|+.|+..|+.-..+. .-|.|+.||...
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME--------LNFTCPRCGAML 138 (158)
T ss_pred CeEECCCCCcEeeHHHHHH--------cCCcCCCCCCEe
Confidence 5688888888888777774 258888888653
No 117
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=69.70 E-value=3.1 Score=34.09 Aligned_cols=34 Identities=12% Similarity=0.226 Sum_probs=21.0
Q ss_pred cccccccchhhhcChhhHhh-hhhhcccCcccccccCch
Q 039095 69 ERIQCKECGKALLSAKSLSN-HMRVHSQKLRACNESGAV 106 (492)
Q Consensus 69 k~y~C~~C~k~F~~~~~L~~-H~~~H~~k~~~C~~C~~~ 106 (492)
.-|.|+.|+..|+....+.. + ....|.|+.||..
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d----~~~~f~Cp~Cg~~ 132 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLD----MDGTFTCPRCGEE 132 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcC----CCCcEECCCCCCE
Confidence 56788888877775544332 2 1233788888754
No 118
>PF14353 CpXC: CpXC protein
Probab=69.32 E-value=2.5 Score=33.74 Aligned_cols=50 Identities=10% Similarity=0.037 Sum_probs=33.9
Q ss_pred ccCCcccccccCCCCCcccc-C---------CCCCCceecccCccccccchhhhhhcccC
Q 039095 317 YGGDSSSKAMCNASDYDVFD-D---------PQKESEIRCQACNKIFCSRRALGGHQRMH 366 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~-~---------~~~~~~~~C~~C~k~F~~~~~L~~H~~~H 366 (492)
.+|+.|+..|.......... . -..-..|+|+.||..|.-...+..|-..+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCCC
Confidence 57999998876554433211 1 12344689999999999888887776554
No 119
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=69.02 E-value=2.8 Score=35.58 Aligned_cols=32 Identities=13% Similarity=0.249 Sum_probs=25.0
Q ss_pred cccccccchhhhcChhhHhhhhhhcccCcccccccCchhh
Q 039095 69 ERIQCKECGKALLSAKSLSNHMRVHSQKLRACNESGAVKS 108 (492)
Q Consensus 69 k~y~C~~C~k~F~~~~~L~~H~~~H~~k~~~C~~C~~~f~ 108 (492)
.-|.|+.|+..|+.-..+. .-|.|+.||....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCe
Confidence 5799999999998877663 3699999996543
No 120
>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=68.96 E-value=2.7 Score=32.44 Aligned_cols=25 Identities=16% Similarity=0.222 Sum_probs=23.4
Q ss_pred ccC----CccccccCCchhhhhhhhhccc
Q 039095 406 HTC----RICLKVFATGQALGGHKRAHLV 430 (492)
Q Consensus 406 f~C----~~C~k~F~~~~~L~~H~r~H~~ 430 (492)
|.| ..|++.+.+...+.+|++.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999998775
No 121
>PRK04023 DNA polymerase II large subunit; Validated
Probab=67.37 E-value=5.3 Score=42.65 Aligned_cols=37 Identities=14% Similarity=0.057 Sum_probs=24.5
Q ss_pred cccccCCcccccccCCCCCccccCCCCCCceecccCccccccchhhhhhcccCCCCCCCCCCcCCCC
Q 039095 314 YAEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMF 380 (492)
Q Consensus 314 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~ 380 (492)
.....|+.|+... -.+.|+.||.. .+..|.|+.|+..
T Consensus 624 Vg~RfCpsCG~~t---------------~~frCP~CG~~---------------Te~i~fCP~CG~~ 660 (1121)
T PRK04023 624 IGRRKCPSCGKET---------------FYRRCPFCGTH---------------TEPVYRCPRCGIE 660 (1121)
T ss_pred ccCccCCCCCCcC---------------CcccCCCCCCC---------------CCcceeCccccCc
Confidence 3567888888763 23788888875 3455777777533
No 122
>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=66.75 E-value=3.8 Score=41.42 Aligned_cols=40 Identities=15% Similarity=0.210 Sum_probs=27.7
Q ss_pred eecccCccccccchhhhhhcccCCCCCCCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCCccccc
Q 039095 344 IRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICLKV 414 (492)
Q Consensus 344 ~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k~ 414 (492)
.+|+.|+- .+..|.......|..|++.. .-|..|+.|+-.
T Consensus 223 ~~C~~C~~----------~l~~h~~~~~l~Ch~Cg~~~---------------------~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDV----------SLTYHKKEGKLRCHYCGYQE---------------------PIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCC----------ceEEecCCCeEEcCCCcCcC---------------------CCCCCCCCCCCC
Confidence 37777753 34555666678888888663 567889999763
No 123
>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=66.69 E-value=3.6 Score=36.21 Aligned_cols=72 Identities=21% Similarity=0.412 Sum_probs=37.7
Q ss_pred cCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhH-------hhhhhh-----cccCcccccc
Q 039095 35 SASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSL-------SNHMRV-----HSQKLRACNE 102 (492)
Q Consensus 35 H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L-------~~H~~~-----H~~k~~~C~~ 102 (492)
..|.+.|+|.+|.. |-....-..|+.+--.-..-.|+|.-|.+ +-+-+-| ..|++. -.++++.|+.
T Consensus 137 ~hGGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNr-lGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPK 214 (314)
T PF06524_consen 137 DHGGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNR-LGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPK 214 (314)
T ss_pred cCCCeEEEeecCCC-eeeccchhhhhhhhhhhhccccccccccc-ccchhhhheeeeehhhhhhhcccccccCCCCCCCC
Confidence 34667788888764 44444555565432111013566666653 2222222 234443 2258899999
Q ss_pred cCchhh
Q 039095 103 SGAVKS 108 (492)
Q Consensus 103 C~~~f~ 108 (492)
|+..-.
T Consensus 215 Cg~et~ 220 (314)
T PF06524_consen 215 CGYETQ 220 (314)
T ss_pred CCCccc
Confidence 994444
No 124
>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=65.66 E-value=3.6 Score=26.03 Aligned_cols=35 Identities=11% Similarity=0.130 Sum_probs=16.0
Q ss_pred ccCCcccccccCCCCCccccCCCC------CCceecccCcc
Q 039095 317 YGGDSSSKAMCNASDYDVFDDPQK------ESEIRCQACNK 351 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~~~~------~~~~~C~~C~k 351 (492)
|.|..|+..+.....-.......+ ..-|.|++|+-
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGA 42 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSS
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCC
Confidence 566667666655554333222221 22367777764
No 125
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=65.53 E-value=3.1 Score=39.73 Aligned_cols=39 Identities=26% Similarity=0.558 Sum_probs=25.5
Q ss_pred cCCCCccccccccccccChhHHHhhhhccCcccccccccccchh
Q 039095 35 SASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGK 78 (492)
Q Consensus 35 H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k 78 (492)
-+....|.|+.|.+.|+.-..|+.= --.. -.|.|..|+-
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L~---~~~~--~~F~C~~C~g 161 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQLL---DNET--GEFHCENCGG 161 (436)
T ss_pred ccccccccCCccccchhhhHHHHhh---cccC--ceEEEecCCC
Confidence 3455678888888888776665432 2112 4688888873
No 126
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.31 E-value=4.6 Score=30.21 Aligned_cols=12 Identities=25% Similarity=0.321 Sum_probs=8.3
Q ss_pred cccccccchhhh
Q 039095 69 ERIQCKECGKAL 80 (492)
Q Consensus 69 k~y~C~~C~k~F 80 (492)
.|..||+||++|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 566777777776
No 127
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=65.21 E-value=3.3 Score=36.34 Aligned_cols=52 Identities=17% Similarity=0.162 Sum_probs=41.6
Q ss_pred ccccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcc
Q 039095 12 SYDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRR 66 (492)
Q Consensus 12 ~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~ 66 (492)
.|.|.+||.+.+.+..=+ |+..=.+ .-|.|--|++.|-. .++..|..--+..
T Consensus 3 ~FtCnvCgEsvKKp~vek-H~srCrn-~~fSCIDC~k~F~~-~sYknH~kCITEa 54 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQVEK-HMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCITEA 54 (276)
T ss_pred EEehhhhhhhccccchHH-HHHhccC-CeeEEeeccccccc-chhhhhhhhcchH
Confidence 589999999998877555 6555444 67999999999999 7789998766554
No 128
>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=65.04 E-value=3.8 Score=36.02 Aligned_cols=28 Identities=25% Similarity=0.370 Sum_probs=20.7
Q ss_pred CCCceecccCccccccchhhhhhcccCC
Q 039095 340 KESEIRCQACNKIFCSRRALGGHQRMHS 367 (492)
Q Consensus 340 ~~~~~~C~~C~k~F~~~~~L~~H~~~H~ 367 (492)
..++++|+.||.-...-..|..-.|+|.
T Consensus 206 k~k~~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 206 KGKPIPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred cCCCCCCCCCCCcccccccceeeeecch
Confidence 3467788888877777777777777775
No 129
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=64.77 E-value=3.8 Score=27.41 Aligned_cols=39 Identities=18% Similarity=0.460 Sum_probs=16.0
Q ss_pred cccccc--ccccccChhHHHhhhhccCccccccccccc----chhhhc
Q 039095 40 ESQCKV--CGKDFESLKALYGHMRHHSRRERERIQCKE----CGKALL 81 (492)
Q Consensus 40 ~~~C~~--C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~----C~k~F~ 81 (492)
+-.|+. |...+. +..|..|+..--.. ++..|++ |+..+.
T Consensus 9 ~v~C~~~cc~~~i~-r~~l~~H~~~~C~~--~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 9 PVPCPNGCCNEMIP-RKELDDHLENECPK--RPVPCPYSPYGCKERVP 53 (60)
T ss_dssp EEE-TT--S-BEEE-CCCHHHHHHTTSTT--SEEE-SS----S--EEE
T ss_pred EeeCCCCCccccee-HHHHHHHHHccCCC--CcEECCCCCCCCCCccc
Confidence 344554 333333 33455555544444 4555555 555443
No 130
>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=63.56 E-value=6.3 Score=22.56 Aligned_cols=11 Identities=18% Similarity=-0.082 Sum_probs=5.2
Q ss_pred cccCCCCcccc
Q 039095 13 YDLRENPKKSW 23 (492)
Q Consensus 13 ~~C~~C~k~f~ 23 (492)
|.|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 44555555544
No 131
>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=63.33 E-value=3.6 Score=26.46 Aligned_cols=27 Identities=30% Similarity=0.640 Sum_probs=17.5
Q ss_pred CCceecccCccccccchhhhhhcccCC
Q 039095 341 ESEIRCQACNKIFCSRRALGGHQRMHS 367 (492)
Q Consensus 341 ~~~~~C~~C~k~F~~~~~L~~H~~~H~ 367 (492)
...|+|+.|+..|=--=.+-.|...|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CCeEECCCCCCccccCcChhhhccccC
Confidence 467999999999999989888888886
No 132
>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=63.24 E-value=4.2 Score=24.69 Aligned_cols=33 Identities=12% Similarity=0.103 Sum_probs=15.7
Q ss_pred CCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCCcccccc
Q 039095 371 SSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICLKVF 415 (492)
Q Consensus 371 ~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k~F 415 (492)
|.+|..|....+....... +.+.+.|.+|+..-
T Consensus 2 p~rC~~C~aylNp~~~~~~------------~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDD------------GGKTWICNFCGTKN 34 (40)
T ss_dssp S-B-TTT--BS-TTSEEET------------TTTEEEETTT--EE
T ss_pred ccccCCCCCEECCcceEcC------------CCCEEECcCCCCcC
Confidence 4456666644443333322 66889999998643
No 133
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=63.00 E-value=4.8 Score=37.74 Aligned_cols=75 Identities=17% Similarity=0.084 Sum_probs=40.9
Q ss_pred CccccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcccccccccccch---hhhcChhhHh
Q 039095 11 ISYDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECG---KALLSAKSLS 87 (492)
Q Consensus 11 ~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~---k~F~~~~~L~ 87 (492)
.|=.|..|++.|.+...-..||-.+.+= |.=++ .-......|..=+..--+ .-|.|-.|. +.|.+....+
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~Hgf--fIPdr--eYL~D~~GLl~YLgeKV~---~~~~CL~CN~~~~~f~sleavr 237 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGF--FIPDR--EYLTDEKGLLKYLGEKVG---IGFICLFCNELGRPFSSLEAVR 237 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCC--cCCch--HhhhchhHHHHHHHHHhc---cCceEEEeccccCcccccHHHH
Confidence 3466888888877776666666655431 11000 001112222222222222 357777787 8888888888
Q ss_pred hhhhh
Q 039095 88 NHMRV 92 (492)
Q Consensus 88 ~H~~~ 92 (492)
.||..
T Consensus 238 ~HM~~ 242 (390)
T KOG2785|consen 238 AHMRD 242 (390)
T ss_pred HHHhh
Confidence 88863
No 134
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=61.95 E-value=4.7 Score=33.47 Aligned_cols=24 Identities=13% Similarity=0.210 Sum_probs=20.0
Q ss_pred cccCCcccccccCCCCCccccCCCCCCceecccCcc
Q 039095 316 EYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNK 351 (492)
Q Consensus 316 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k 351 (492)
.|.|+.||.++ .++.|-+|++||-
T Consensus 134 ~~vC~vCGy~~------------~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH------------EGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc------------cCCCCCcCCCCCC
Confidence 69999999966 4566899999993
No 135
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.85 E-value=4.3 Score=30.34 Aligned_cols=31 Identities=10% Similarity=0.058 Sum_probs=23.7
Q ss_pred cccCCcccccccCCCCCccccCCCCCCceecccCccccccc
Q 039095 316 EYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSR 356 (492)
Q Consensus 316 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~ 356 (492)
.-.|+.|+++|.... ..|..|++||++|+..
T Consensus 9 KridPetg~KFYDLN----------rdPiVsPytG~s~P~s 39 (129)
T COG4530 9 KRIDPETGKKFYDLN----------RDPIVSPYTGKSYPRS 39 (129)
T ss_pred cccCccccchhhccC----------CCccccCcccccchHH
Confidence 346889999986543 4688999999999543
No 136
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=61.25 E-value=2.9 Score=38.40 Aligned_cols=23 Identities=26% Similarity=0.563 Sum_probs=14.0
Q ss_pred CCcccccc--ccccccChhHHHhhh
Q 039095 38 TQESQCKV--CGKDFESLKALYGHM 60 (492)
Q Consensus 38 ~~~~~C~~--C~k~F~~~~~L~~H~ 60 (492)
.++|+|.+ |.+.++....|+.|.
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~ 371 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHK 371 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeecc
Confidence 34566644 666666666666663
No 137
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=61.04 E-value=4.9 Score=29.38 Aligned_cols=32 Identities=25% Similarity=0.350 Sum_probs=22.3
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCcccccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCS 355 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~ 355 (492)
..|.|+.|++.-... .....+.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vkR---------~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVKR---------QAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCceee---------eeeEEEEcCCCCCEEeC
Confidence 678999998643222 23467899999998864
No 138
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=60.46 E-value=3.6 Score=32.20 Aligned_cols=26 Identities=27% Similarity=0.201 Sum_probs=22.0
Q ss_pred ccCCccccccCCchhhhhhhhhcccCCCC
Q 039095 406 HTCRICLKVFATGQALGGHKRAHLVKNLD 434 (492)
Q Consensus 406 f~C~~C~k~F~~~~~L~~H~r~H~~~~~~ 434 (492)
..|-.+||.|++ |++|+.+|.|-.+.
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTPd 102 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTPD 102 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCHH
Confidence 479999999974 99999999986654
No 139
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=60.40 E-value=4 Score=32.47 Aligned_cols=24 Identities=38% Similarity=0.685 Sum_probs=15.4
Q ss_pred ccccccccccccChhHHHhhhhccCcc
Q 039095 40 ESQCKVCGKDFESLKALYGHMRHHSRR 66 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r~H~~~ 66 (492)
--.|-+|||.|+. |++|++.|+|-
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S
T ss_pred eeEEccCCcccch---HHHHHHHccCC
Confidence 3589999998876 58999988775
No 140
>PRK04023 DNA polymerase II large subunit; Validated
Probab=59.45 E-value=7.1 Score=41.76 Aligned_cols=47 Identities=19% Similarity=0.494 Sum_probs=32.5
Q ss_pred ccccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhhh
Q 039095 12 SYDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHMR 91 (492)
Q Consensus 12 ~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~ 91 (492)
...|+.||... -.+.|+.||.. +. ..|.|+.|+...
T Consensus 626 ~RfCpsCG~~t----------------~~frCP~CG~~--------------Te---~i~fCP~CG~~~----------- 661 (1121)
T PRK04023 626 RRKCPSCGKET----------------FYRRCPFCGTH--------------TE---PVYRCPRCGIEV----------- 661 (1121)
T ss_pred CccCCCCCCcC----------------CcccCCCCCCC--------------CC---cceeCccccCcC-----------
Confidence 36799998873 23789999876 32 478888884322
Q ss_pred hcccCcccccccCch
Q 039095 92 VHSQKLRACNESGAV 106 (492)
Q Consensus 92 ~H~~k~~~C~~C~~~ 106 (492)
.++.|+.|+..
T Consensus 662 ----~~y~CPKCG~E 672 (1121)
T PRK04023 662 ----EEDECEKCGRE 672 (1121)
T ss_pred ----CCCcCCCCCCC
Confidence 34679999844
No 141
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=59.23 E-value=4.4 Score=22.80 Aligned_cols=10 Identities=40% Similarity=0.767 Sum_probs=4.8
Q ss_pred cCcccccccC
Q 039095 95 QKLRACNESG 104 (492)
Q Consensus 95 ~k~~~C~~C~ 104 (492)
+..|.|+.|+
T Consensus 17 ~~~~vCp~C~ 26 (30)
T PF08274_consen 17 GELLVCPECG 26 (30)
T ss_dssp SSSEEETTTT
T ss_pred CCEEeCCccc
Confidence 3445555554
No 142
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=59.12 E-value=4.6 Score=29.55 Aligned_cols=32 Identities=19% Similarity=0.315 Sum_probs=22.2
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCcccccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCS 355 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~ 355 (492)
..|.|+.|++.-... .....+.|..|++.|.-
T Consensus 34 a~y~CpfCgk~~vkR---------~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKTVKR---------GSTGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCceEE---------EeeEEEEcCCCCCEEeC
Confidence 678999998643221 23456899999998864
No 143
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=59.06 E-value=2.9 Score=30.53 Aligned_cols=32 Identities=22% Similarity=0.402 Sum_probs=21.6
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCcccccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCS 355 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~ 355 (492)
..|.|+.|++.-.... ....+.|..|++.|.-
T Consensus 34 ~ky~Cp~Cgk~~vkR~---------a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRV---------ATGIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEEEE---------ETTEEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeEEe---------eeEEeecCCCCCEEeC
Confidence 6789999988643222 3446899999998863
No 144
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=58.83 E-value=2.3 Score=43.13 Aligned_cols=29 Identities=34% Similarity=0.635 Sum_probs=25.9
Q ss_pred CCccccccccccccChhHHHhhhhccCcc
Q 039095 38 TQESQCKVCGKDFESLKALYGHMRHHSRR 66 (492)
Q Consensus 38 ~~~~~C~~C~k~F~~~~~L~~H~r~H~~~ 66 (492)
..-|.|..|+|+|-.-.+++.||++|...
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 45699999999999999999999999764
No 145
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=57.77 E-value=11 Score=34.61 Aligned_cols=20 Identities=20% Similarity=0.378 Sum_probs=12.9
Q ss_pred ccccccccccccChhHHHhh
Q 039095 40 ESQCKVCGKDFESLKALYGH 59 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H 59 (492)
|-.|++|+-+.....+|.+=
T Consensus 290 P~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 290 PIECPICSLTLVSSPHLARS 309 (378)
T ss_pred CccCCccceeEecchHHHHH
Confidence 55677777776666666553
No 146
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=57.72 E-value=5.5 Score=41.76 Aligned_cols=9 Identities=11% Similarity=-0.178 Sum_probs=5.2
Q ss_pred cCCCCcccc
Q 039095 15 LRENPKKSW 23 (492)
Q Consensus 15 C~~C~k~f~ 23 (492)
|..||..+.
T Consensus 438 C~~Cg~v~~ 446 (730)
T COG1198 438 CRDCGYIAE 446 (730)
T ss_pred cccCCCccc
Confidence 666665543
No 147
>COG1773 Rubredoxin [Energy production and conversion]
Probab=56.42 E-value=11 Score=24.62 Aligned_cols=35 Identities=6% Similarity=0.067 Sum_probs=17.7
Q ss_pred cccCCcccccccCCCCCccccCCCCCC------ceecccCc
Q 039095 316 EYGGDSSSKAMCNASDYDVFDDPQKES------EIRCQACN 350 (492)
Q Consensus 316 ~~~C~~C~~~f~~~~~l~~h~~~~~~~------~~~C~~C~ 350 (492)
.|+|..|+..|.....-...-...+.+ -+.|+.||
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg 43 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECG 43 (55)
T ss_pred ceEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCC
Confidence 466666766665554443333222211 25666666
No 148
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=55.51 E-value=9 Score=23.10 Aligned_cols=15 Identities=27% Similarity=0.660 Sum_probs=11.3
Q ss_pred cccCCccccccCCch
Q 039095 405 EHTCRICLKVFATGQ 419 (492)
Q Consensus 405 pf~C~~C~k~F~~~~ 419 (492)
||+|..|++.|=.+.
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 888888888886543
No 149
>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=55.35 E-value=6.7 Score=24.65 Aligned_cols=10 Identities=50% Similarity=1.102 Sum_probs=5.6
Q ss_pred cccccccchh
Q 039095 69 ERIQCKECGK 78 (492)
Q Consensus 69 k~y~C~~C~k 78 (492)
..|+|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 4566666553
No 150
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=55.31 E-value=7.7 Score=20.24 Aligned_cols=7 Identities=43% Similarity=1.246 Sum_probs=4.0
Q ss_pred ccccccc
Q 039095 43 CKVCGKD 49 (492)
Q Consensus 43 C~~C~k~ 49 (492)
|+.||..
T Consensus 16 C~~CG~~ 22 (23)
T PF13240_consen 16 CPNCGTP 22 (23)
T ss_pred hhhhCCc
Confidence 6666543
No 151
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=54.61 E-value=19 Score=32.78 Aligned_cols=52 Identities=13% Similarity=0.200 Sum_probs=38.9
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCccccccchhhhhhcccCC
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRALGGHQRMHS 367 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~ 367 (492)
+.-.|..|...|..+..-..- ..+....|+|+.|...|-..-+.-.|...|-
T Consensus 361 ks~~Cf~CQ~~fp~~~~~~~~-~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 361 KSTHCFVCQGPFPKPPVSPFD-ESTSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred CCccceeccCCCCCCCCCccc-ccccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 445688888888766543221 2345667999999999999999999988885
No 152
>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=54.16 E-value=7.4 Score=23.00 Aligned_cols=32 Identities=13% Similarity=0.121 Sum_probs=17.2
Q ss_pred cccCCCCcccccccchhhhhhccCCCCccccccccccccC
Q 039095 13 YDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFES 52 (492)
Q Consensus 13 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~ 52 (492)
+.|+.|+++|.-.. -....+-.|+.||-.+..
T Consensus 2 r~C~~Cg~~Yh~~~--------~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHIEF--------NPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEETTT--------B--SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCcccccc--------CCCCCCCccCCCCCeeEe
Confidence 46777777765332 123334577777765443
No 153
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=54.07 E-value=6 Score=28.91 Aligned_cols=32 Identities=13% Similarity=0.212 Sum_probs=22.1
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCcccccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCS 355 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~ 355 (492)
..|.|+.|++.-... .....+.|..|++.|.-
T Consensus 35 a~y~CpfCgk~~vkR---------~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVKR---------VGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceEE---------EEEEEEEcCCCCCEEeC
Confidence 678999997643222 23456899999998864
No 154
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=53.91 E-value=8.2 Score=30.33 Aligned_cols=18 Identities=6% Similarity=-0.007 Sum_probs=12.1
Q ss_pred ccccCCcccccccCCCCC
Q 039095 315 AEYGGDSSSKAMCNASDY 332 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l 332 (492)
+.|+|++|..+.....-|
T Consensus 79 ~lYeCnIC~etS~ee~FL 96 (140)
T PF05290_consen 79 KLYECNICKETSAEERFL 96 (140)
T ss_pred CceeccCcccccchhhcC
Confidence 667777777766555544
No 155
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=53.70 E-value=9.5 Score=35.87 Aligned_cols=78 Identities=17% Similarity=0.103 Sum_probs=51.6
Q ss_pred cccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhhhhcccCcccccccC---chhhhHHhhhhhc
Q 039095 41 SQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHMRVHSQKLRACNESG---AVKSLVLKKKRSK 117 (492)
Q Consensus 41 ~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H~~k~~~C~~C~---~~f~~~~~~~~h~ 117 (492)
=.|-+|++.|++-..-..||-.+||= |.= . -...+....|-.=+..-.+.-|.|-.|. ..|..+...+.|+
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~Hgf----fIP-d-reYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM 240 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGF----FIP-D-REYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHM 240 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCC----cCC-c-hHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHH
Confidence 46788888888888888888877762 110 0 0112344445555555556678899998 8899999999988
Q ss_pred ccccccC
Q 039095 118 RKRYNFI 124 (492)
Q Consensus 118 ~~~~~~~ 124 (492)
...-++.
T Consensus 241 ~~K~HCk 247 (390)
T KOG2785|consen 241 RDKGHCK 247 (390)
T ss_pred hhccCcc
Confidence 6654443
No 156
>PF15269 zf-C2H2_7: Zinc-finger
Probab=53.59 E-value=6.4 Score=24.05 Aligned_cols=23 Identities=26% Similarity=0.475 Sum_probs=20.3
Q ss_pred ccccccchhhhcChhhHhhhhhh
Q 039095 70 RIQCKECGKALLSAKSLSNHMRV 92 (492)
Q Consensus 70 ~y~C~~C~k~F~~~~~L~~H~~~ 92 (492)
.|+|=.|..+..-++.|-.||+-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 37899999999999999999984
No 157
>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=53.16 E-value=4.8 Score=26.34 Aligned_cols=31 Identities=26% Similarity=0.562 Sum_probs=17.0
Q ss_pred cccccchhhhcChhhHhhhhhhcccCcccccccCchhh
Q 039095 71 IQCKECGKALLSAKSLSNHMRVHSQKLRACNESGAVKS 108 (492)
Q Consensus 71 y~C~~C~k~F~~~~~L~~H~~~H~~k~~~C~~C~~~f~ 108 (492)
|+|+.||..+.-.... .|....|+.||..+-
T Consensus 3 ~~CP~CG~~iev~~~~-------~GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENPE-------LGELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCCc-------cCCEEeCCCCCCEEE
Confidence 5677777655432221 144567777775443
No 158
>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=52.47 E-value=12 Score=25.95 Aligned_cols=32 Identities=16% Similarity=0.330 Sum_probs=14.3
Q ss_pred cccccCCcccccccCCCCCccccCCCCCCceecccCccccccc
Q 039095 314 YAEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSR 356 (492)
Q Consensus 314 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~ 356 (492)
...-.|..|++.|.- -.+.+.|..||..|=..
T Consensus 7 ~~~~~C~~C~~~F~~-----------~~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 7 SEASNCMICGKKFSL-----------FRRRHHCRNCGRVVCSS 38 (69)
T ss_dssp GG-SB-TTT--B-BS-----------SS-EEE-TTT--EEECC
T ss_pred CCCCcCcCcCCcCCC-----------ceeeEccCCCCCEECCc
Confidence 355678888888842 13567888888877543
No 159
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=51.89 E-value=9.9 Score=27.52 Aligned_cols=14 Identities=29% Similarity=0.643 Sum_probs=8.9
Q ss_pred CceecccCcccccc
Q 039095 342 SEIRCQACNKIFCS 355 (492)
Q Consensus 342 ~~~~C~~C~k~F~~ 355 (492)
+|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 45567777776654
No 160
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=51.71 E-value=7.7 Score=23.55 Aligned_cols=11 Identities=27% Similarity=0.875 Sum_probs=7.0
Q ss_pred ccccccccccc
Q 039095 41 SQCKVCGKDFE 51 (492)
Q Consensus 41 ~~C~~C~k~F~ 51 (492)
|.|..|+..|.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 66766766553
No 161
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=51.00 E-value=8.6 Score=35.49 Aligned_cols=50 Identities=20% Similarity=0.286 Sum_probs=35.1
Q ss_pred cccccCC--cccccccCCCCCccccCC--------------------CCCCceecccCccccccchhhhhhc
Q 039095 314 YAEYGGD--SSSKAMCNASDYDVFDDP--------------------QKESEIRCQACNKIFCSRRALGGHQ 363 (492)
Q Consensus 314 ~~~~~C~--~C~~~f~~~~~l~~h~~~--------------------~~~~~~~C~~C~k~F~~~~~L~~H~ 363 (492)
.++|+|+ .|.+...+...|+.|..| ...|+|+|++|.+.+..-..|.-|.
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 4778884 688888888888876644 1356677777777777666666653
No 162
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=50.95 E-value=6.3 Score=30.89 Aligned_cols=26 Identities=27% Similarity=0.266 Sum_probs=21.8
Q ss_pred ceecccCccccccchhhhhhcccCCCCCC
Q 039095 343 EIRCQACNKIFCSRRALGGHQRMHSAKRS 371 (492)
Q Consensus 343 ~~~C~~C~k~F~~~~~L~~H~~~H~~~k~ 371 (492)
-..|-.+||.|. .|++|+.+|.|.-|
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred eEEEeccCcchH---HHHHHHhcccCCCH
Confidence 368999999997 49999999987644
No 163
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=50.47 E-value=4.7 Score=24.31 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=6.3
Q ss_pred cccccccccc
Q 039095 41 SQCKVCGKDF 50 (492)
Q Consensus 41 ~~C~~C~k~F 50 (492)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 6666666654
No 164
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=50.30 E-value=6.6 Score=29.05 Aligned_cols=19 Identities=16% Similarity=0.279 Sum_probs=12.6
Q ss_pred CCCceecccCccccccchh
Q 039095 340 KESEIRCQACNKIFCSRRA 358 (492)
Q Consensus 340 ~~~~~~C~~C~k~F~~~~~ 358 (492)
-.+.|.|+.||..-.+.-.
T Consensus 19 L~k~FtCp~Cghe~vs~ct 37 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCT 37 (104)
T ss_pred CCceEecCccCCeeeeEEE
Confidence 3566888888875555444
No 165
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=50.02 E-value=10 Score=23.39 Aligned_cols=29 Identities=17% Similarity=0.214 Sum_probs=14.9
Q ss_pred cccCCCCcccccccchhhhhhccCCCCccccccccccc
Q 039095 13 YDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDF 50 (492)
Q Consensus 13 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F 50 (492)
|.|+.|+.... . .-.....+.|..||.+.
T Consensus 1 m~Cp~Cg~~~~-~--------~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEI-V--------FDPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEE-E--------EETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCce-E--------EcCCCCeEECCCCCCEe
Confidence 56777776541 1 11233456777777654
No 166
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=49.87 E-value=8.3 Score=34.92 Aligned_cols=10 Identities=20% Similarity=0.252 Sum_probs=7.1
Q ss_pred ccccCCCCcc
Q 039095 12 SYDLRENPKK 21 (492)
Q Consensus 12 ~~~C~~C~k~ 21 (492)
.|.|+.|...
T Consensus 308 Gy~CP~Cktk 317 (421)
T COG5151 308 GYECPVCKTK 317 (421)
T ss_pred ceeCCcccce
Confidence 4888888654
No 167
>PF12773 DZR: Double zinc ribbon
Probab=49.61 E-value=28 Score=22.11 Aligned_cols=10 Identities=20% Similarity=0.521 Sum_probs=4.8
Q ss_pred ecccCccccc
Q 039095 345 RCQACNKIFC 354 (492)
Q Consensus 345 ~C~~C~k~F~ 354 (492)
-|+.||....
T Consensus 14 fC~~CG~~l~ 23 (50)
T PF12773_consen 14 FCPHCGTPLP 23 (50)
T ss_pred CChhhcCChh
Confidence 3555554444
No 168
>PRK05580 primosome assembly protein PriA; Validated
Probab=49.24 E-value=11 Score=39.80 Aligned_cols=40 Identities=15% Similarity=0.289 Sum_probs=24.0
Q ss_pred eecccCccccccchhhhhhcccCCCCCCCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCCccccc
Q 039095 344 IRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICLKV 414 (492)
Q Consensus 344 ~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k~ 414 (492)
.+|+.|+-.. ..|.......|..|++. ...|..|+.||..
T Consensus 391 ~~C~~C~~~l----------~~h~~~~~l~Ch~Cg~~---------------------~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASL----------TLHRFQRRLRCHHCGYQ---------------------EPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCce----------eEECCCCeEECCCCcCC---------------------CCCCCCCCCCcCC
Confidence 3666666432 33344555677777755 3456778888654
No 169
>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=48.87 E-value=14 Score=19.51 Aligned_cols=9 Identities=0% Similarity=0.113 Sum_probs=4.7
Q ss_pred CccccCCCC
Q 039095 11 ISYDLRENP 19 (492)
Q Consensus 11 ~~~~C~~C~ 19 (492)
.+|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 345555555
No 170
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=48.87 E-value=6.8 Score=34.18 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=14.2
Q ss_pred cccccccchhhhcChhhHhhhhhh
Q 039095 69 ERIQCKECGKALLSAKSLSNHMRV 92 (492)
Q Consensus 69 k~y~C~~C~k~F~~~~~L~~H~~~ 92 (492)
..|.|++|+|.|.-..-.+.|+..
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHH
T ss_pred CEECCCCCCcccCChHHHHHHHhh
Confidence 456666666666666666666654
No 171
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=48.43 E-value=18 Score=23.25 Aligned_cols=34 Identities=6% Similarity=0.090 Sum_probs=20.9
Q ss_pred cCCcccccccCCCCCccccCCCCCCceecccCccccccchh
Q 039095 318 GGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRA 358 (492)
Q Consensus 318 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~ 358 (492)
-|+.|+........ .+...|.|+.||..+.-...
T Consensus 2 FCp~Cg~~l~~~~~-------~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNMLIPKEG-------KEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCccccccC-------CCCCEEECCcCCCeEECCCc
Confidence 37778775433321 11236889999988776555
No 172
>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=47.67 E-value=11 Score=30.34 Aligned_cols=45 Identities=9% Similarity=0.078 Sum_probs=27.5
Q ss_pred cCCcccccccCCCCCcccc-CCCCCCceecccCccccccchhhhhh
Q 039095 318 GGDSSSKAMCNASDYDVFD-DPQKESEIRCQACNKIFCSRRALGGH 362 (492)
Q Consensus 318 ~C~~C~~~f~~~~~l~~h~-~~~~~~~~~C~~C~k~F~~~~~L~~H 362 (492)
+||.|+..=..-.+-+... ...-.+.=.|..||+.|++...+..-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~ 47 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELL 47 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecccc
Confidence 6888876433322222111 11223456899999999999887765
No 173
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=47.15 E-value=14 Score=20.41 Aligned_cols=23 Identities=22% Similarity=0.475 Sum_probs=13.3
Q ss_pred eecccCccccccchhhhhhcccCC
Q 039095 344 IRCQACNKIFCSRRALGGHQRMHS 367 (492)
Q Consensus 344 ~~C~~C~k~F~~~~~L~~H~~~H~ 367 (492)
|.|-.|++.| .....+.|..--+
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~CIt 23 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTSCIT 23 (28)
T ss_dssp EEETTTTEEE-EGGGTTT-----S
T ss_pred CeeecCCCCc-CcCCcCCCCcccC
Confidence 5788889988 5666677755333
No 174
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=46.71 E-value=12 Score=30.28 Aligned_cols=45 Identities=9% Similarity=0.048 Sum_probs=28.0
Q ss_pred cCCcccccccCCCCCccc-cCCCCCCceecccCccccccchhhhhh
Q 039095 318 GGDSSSKAMCNASDYDVF-DDPQKESEIRCQACNKIFCSRRALGGH 362 (492)
Q Consensus 318 ~C~~C~~~f~~~~~l~~h-~~~~~~~~~~C~~C~k~F~~~~~L~~H 362 (492)
.||.|+..-+.-.+-+.. ...+-.+.-.|..||+.|++......=
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~ 47 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELR 47 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeec
Confidence 588887654443333321 122334557899999999998766554
No 175
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=45.77 E-value=21 Score=39.59 Aligned_cols=37 Identities=14% Similarity=0.091 Sum_probs=24.0
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCccccccchhhhhhcccCCCCCCCCCCcCCCCC
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFT 381 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~ 381 (492)
..++|+.|+.... ...|+.||... +.+|.|+.|+...
T Consensus 666 ~~rkCPkCG~~t~---------------~~fCP~CGs~t---------------e~vy~CPsCGaev 702 (1337)
T PRK14714 666 GRRRCPSCGTETY---------------ENRCPDCGTHT---------------EPVYVCPDCGAEV 702 (1337)
T ss_pred EEEECCCCCCccc---------------cccCcccCCcC---------------CCceeCccCCCcc
Confidence 3578888887321 13788888753 2357888888653
No 176
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=45.56 E-value=11 Score=23.10 Aligned_cols=23 Identities=26% Similarity=0.498 Sum_probs=11.7
Q ss_pred cccccchhhhc--ChhhHhhhhhhc
Q 039095 71 IQCKECGKALL--SAKSLSNHMRVH 93 (492)
Q Consensus 71 y~C~~C~k~F~--~~~~L~~H~~~H 93 (492)
-.|+.||..|. ....-+.|.+-|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 45666666655 233344444444
No 177
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=45.06 E-value=17 Score=23.39 Aligned_cols=27 Identities=7% Similarity=0.070 Sum_probs=16.6
Q ss_pred cCCcccccccCCCCCccccCCCCCCceecccCccccc
Q 039095 318 GGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFC 354 (492)
Q Consensus 318 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~ 354 (492)
.||.|+..|... ....+.|..||.++-
T Consensus 22 fCP~Cg~~~m~~----------~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 22 FCPRCGSGFMAE----------HLDRWHCGKCGYTEF 48 (50)
T ss_pred cCcCCCcchhec----------cCCcEECCCcCCEEe
Confidence 688887532111 125688999987653
No 178
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=44.75 E-value=17 Score=23.74 Aligned_cols=28 Identities=14% Similarity=0.354 Sum_probs=19.7
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCcccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIF 353 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F 353 (492)
..-+|+.|++.|....+. -.|+.||..+
T Consensus 4 ~~~~C~~Cg~~~~~~dDi-----------VvCp~Cgapy 31 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDI-----------VVCPECGAPY 31 (54)
T ss_pred cCccChhhCCcccCCCCE-----------EECCCCCCcc
Confidence 346788888888665553 5788887654
No 179
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=44.48 E-value=4.6 Score=37.98 Aligned_cols=57 Identities=25% Similarity=0.551 Sum_probs=27.8
Q ss_pred CccccccccccccChhHH---Hhh-hhccCcccccccccccchhhhcChhhHhhhhhhcccCcccccccCc
Q 039095 39 QESQCKVCGKDFESLKAL---YGH-MRHHSRRERERIQCKECGKALLSAKSLSNHMRVHSQKLRACNESGA 105 (492)
Q Consensus 39 ~~~~C~~C~k~F~~~~~L---~~H-~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H~~k~~~C~~C~~ 105 (492)
+.+.|..|.++.-..+.. ..| +..|...+ +-|+|..|++...+...| -.-.|..||.
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~K-RFFkC~~C~~Rt~sl~r~---------P~~~C~~Cg~ 311 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVK-RFFKCKDCGNRTISLERL---------PKKHCSNCGS 311 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE--EEEE-T-TS-EEEESSSS-----------S--TTT-S
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeee-eeEECCCCCCeeeecccC---------CCCCCCcCCc
Confidence 457888888887777765 456 45666665 778888888775543222 1126777873
No 180
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.25 E-value=14 Score=29.41 Aligned_cols=16 Identities=19% Similarity=0.717 Sum_probs=9.3
Q ss_pred CCceecccCccccccc
Q 039095 341 ESEIRCQACNKIFCSR 356 (492)
Q Consensus 341 ~~~~~C~~C~k~F~~~ 356 (492)
...|+|+.|+++|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4446666666666543
No 181
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=44.05 E-value=22 Score=32.70 Aligned_cols=84 Identities=15% Similarity=0.178 Sum_probs=54.6
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCccccccchhhhhhcccCCCCCCC------------CCCcCCCCCC
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRALGGHQRMHSAKRSS------------LPVKTTMFTE 382 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~------------~C~~C~~~~~ 382 (492)
.-|.|+.|....- .-|-.|++|+-+....-+|.+=.+-=-..+|| .|-.|+-.
T Consensus 275 ~Gy~CP~CkakvC-------------sLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~-- 339 (378)
T KOG2807|consen 275 GGYFCPQCKAKVC-------------SLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGE-- 339 (378)
T ss_pred CceeCCcccCeee-------------cCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccc--
Confidence 4577888776542 34578999999999888887654311111111 14444100
Q ss_pred CCcccchhhhhhhhccccCCCCcccCCccccccCCchhhhhhhhhccc
Q 039095 383 TEPHSKLVKLECIEDLMQRGNKEHTCRICLKVFATGQALGGHKRAHLV 430 (492)
Q Consensus 383 ~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k~F~~~~~L~~H~r~H~~ 430 (492)
. .+.-.|.|..|.-.|=.--..-.|...|.-
T Consensus 340 -----~------------~~~~~y~C~~Ck~~FCldCDv~iHesLh~C 370 (378)
T KOG2807|consen 340 -----L------------LSSGRYRCESCKNVFCLDCDVFIHESLHNC 370 (378)
T ss_pred -----c------------CCCCcEEchhccceeeccchHHHHhhhhcC
Confidence 0 144569999999999888888888888753
No 182
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.62 E-value=16 Score=25.45 Aligned_cols=33 Identities=27% Similarity=0.556 Sum_probs=22.0
Q ss_pred cccccccchhhhcChhhHhhhhhhcccCc-ccccccCchhh
Q 039095 69 ERIQCKECGKALLSAKSLSNHMRVHSQKL-RACNESGAVKS 108 (492)
Q Consensus 69 k~y~C~~C~k~F~~~~~L~~H~~~H~~k~-~~C~~C~~~f~ 108 (492)
-.|+|..||..|. +..||. +.| -.|+.|+..+.
T Consensus 11 Y~Y~c~~cg~~~d----vvq~~~---ddplt~ce~c~a~~k 44 (82)
T COG2331 11 YSYECTECGNRFD----VVQAMT---DDPLTTCEECGARLK 44 (82)
T ss_pred eEEeecccchHHH----HHHhcc---cCccccChhhChHHH
Confidence 3589999998885 444444 333 36899987554
No 183
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=43.58 E-value=22 Score=19.88 Aligned_cols=8 Identities=25% Similarity=0.509 Sum_probs=6.2
Q ss_pred cccCCccc
Q 039095 405 EHTCRICL 412 (492)
Q Consensus 405 pf~C~~C~ 412 (492)
-|.|..|+
T Consensus 15 ~Y~C~~c~ 22 (30)
T PF03107_consen 15 FYHCSECC 22 (30)
T ss_pred eEEeCCCC
Confidence 67888877
No 184
>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=43.25 E-value=11 Score=24.80 Aligned_cols=12 Identities=33% Similarity=1.090 Sum_probs=5.4
Q ss_pred ccccccchhhhc
Q 039095 70 RIQCKECGKALL 81 (492)
Q Consensus 70 ~y~C~~C~k~F~ 81 (492)
.+.|..||+.|-
T Consensus 18 k~~Cr~Cg~~~C 29 (57)
T cd00065 18 RHHCRNCGRIFC 29 (57)
T ss_pred ccccCcCcCCcC
Confidence 444444444443
No 185
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.64 E-value=13 Score=29.86 Aligned_cols=15 Identities=7% Similarity=-0.232 Sum_probs=9.2
Q ss_pred CccccCCCCcccccc
Q 039095 11 ISYDLRENPKKSWKF 25 (492)
Q Consensus 11 ~~~~C~~C~k~f~~~ 25 (492)
..|.|..|++.|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 346677777666543
No 186
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=39.93 E-value=6.3 Score=37.09 Aligned_cols=38 Identities=16% Similarity=0.235 Sum_probs=17.5
Q ss_pred CCceecccCccccccchhh---hhh-cccCCCCCC-CCCCcCC
Q 039095 341 ESEIRCQACNKIFCSRRAL---GGH-QRMHSAKRS-SLPVKTT 378 (492)
Q Consensus 341 ~~~~~C~~C~k~F~~~~~L---~~H-~~~H~~~k~-~~C~~C~ 378 (492)
-+.+.|..|.+++-....+ ..| +..|.+.|. |+|..|+
T Consensus 250 ~kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~ 292 (344)
T PF09332_consen 250 CKAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCG 292 (344)
T ss_dssp EEEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS
T ss_pred EEEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCC
Confidence 4568888888777666655 345 345554443 3455554
No 187
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.64 E-value=12 Score=24.80 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=6.2
Q ss_pred cccccccchhhh
Q 039095 69 ERIQCKECGKAL 80 (492)
Q Consensus 69 k~y~C~~C~k~F 80 (492)
+.|.|+.|.-..
T Consensus 30 rtymC~eC~~Rv 41 (68)
T COG4896 30 RTYMCPECEHRV 41 (68)
T ss_pred eeEechhhHhhh
Confidence 445565555433
No 188
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=38.18 E-value=17 Score=28.00 Aligned_cols=23 Identities=30% Similarity=0.771 Sum_probs=16.0
Q ss_pred ccccccchhhhcChhhHhhhhhh
Q 039095 70 RIQCKECGKALLSAKSLSNHMRV 92 (492)
Q Consensus 70 ~y~C~~C~k~F~~~~~L~~H~~~ 92 (492)
-|.|-.|.+-|.+...|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 56677777777777777777664
No 189
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=38.11 E-value=17 Score=20.28 Aligned_cols=11 Identities=18% Similarity=0.005 Sum_probs=4.5
Q ss_pred CcccCCccccc
Q 039095 404 KEHTCRICLKV 414 (492)
Q Consensus 404 kpf~C~~C~k~ 414 (492)
-.|.|.+|+..
T Consensus 14 ~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 14 WFYRCSECDFD 24 (30)
T ss_dssp -EEE-TTT---
T ss_pred ceEECccCCCc
Confidence 56777777644
No 190
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=38.10 E-value=14 Score=28.39 Aligned_cols=27 Identities=22% Similarity=0.497 Sum_probs=24.6
Q ss_pred CCCCceecccCccccccchhhhhhccc
Q 039095 339 QKESEIRCQACNKIFCSRRALGGHQRM 365 (492)
Q Consensus 339 ~~~~~~~C~~C~k~F~~~~~L~~H~~~ 365 (492)
.|...|-|-.|.+-|.+...|+.|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 567789999999999999999999875
No 191
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=37.48 E-value=24 Score=33.99 Aligned_cols=35 Identities=20% Similarity=0.325 Sum_probs=25.5
Q ss_pred cccccccchhhhcChhhHhhhhhhcccCcccccccCc
Q 039095 69 ERIQCKECGKALLSAKSLSNHMRVHSQKLRACNESGA 105 (492)
Q Consensus 69 k~y~C~~C~k~F~~~~~L~~H~~~H~~k~~~C~~C~~ 105 (492)
.-|.|+.|.+.|+....|+. -.--.-.|.|..|+-
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L--~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQL--LDNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHh--hcccCceEEEecCCC
Confidence 56999999999997776642 111135699999983
No 192
>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=36.87 E-value=15 Score=22.60 Aligned_cols=17 Identities=29% Similarity=0.895 Sum_probs=10.8
Q ss_pred CceecccCccccccchh
Q 039095 342 SEIRCQACNKIFCSRRA 358 (492)
Q Consensus 342 ~~~~C~~C~k~F~~~~~ 358 (492)
-+|.|+.|++.|=....
T Consensus 12 ~~~~C~~C~~~FC~~Hr 28 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHR 28 (43)
T ss_dssp SHEE-TTTS-EE-TTTH
T ss_pred CCeECCCCCcccCcccc
Confidence 47999999999976543
No 193
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=36.35 E-value=13 Score=32.53 Aligned_cols=32 Identities=16% Similarity=0.327 Sum_probs=23.9
Q ss_pred CCCcccCCccccccCCchhhhhhhhhcccCCC
Q 039095 402 GNKEHTCRICLKVFATGQALGGHKRAHLVKNL 433 (492)
Q Consensus 402 ~~kpf~C~~C~k~F~~~~~L~~H~r~H~~~~~ 433 (492)
++--|.|.+|+|.|+-......|+..-|.+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~v 105 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEKV 105 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHHH
Confidence 45569999999999999999999886555544
No 194
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=36.24 E-value=27 Score=38.72 Aligned_cols=35 Identities=17% Similarity=0.534 Sum_probs=22.6
Q ss_pred cccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhh
Q 039095 13 YDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKAL 80 (492)
Q Consensus 13 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F 80 (492)
+.|+.|+..-.. ..|+.||... + .+|.|+.||...
T Consensus 668 rkCPkCG~~t~~----------------~fCP~CGs~t---------------e--~vy~CPsCGaev 702 (1337)
T PRK14714 668 RRCPSCGTETYE----------------NRCPDCGTHT---------------E--PVYVCPDCGAEV 702 (1337)
T ss_pred EECCCCCCcccc----------------ccCcccCCcC---------------C--CceeCccCCCcc
Confidence 789999874211 1677777653 2 467888888653
No 195
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=35.74 E-value=14 Score=23.52 Aligned_cols=20 Identities=25% Similarity=0.358 Sum_probs=15.7
Q ss_pred CCcccCCccccccCCchhhh
Q 039095 403 NKEHTCRICLKVFATGQALG 422 (492)
Q Consensus 403 ~kpf~C~~C~k~F~~~~~L~ 422 (492)
++.+.|..||..|.....=+
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ 21 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQ 21 (49)
T ss_pred CeeEEcccCCCeEEEehhHH
Confidence 57899999999998665433
No 196
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.71 E-value=11 Score=32.62 Aligned_cols=29 Identities=24% Similarity=0.505 Sum_probs=21.7
Q ss_pred CCceecccCccccccchhhhhhcccCCCC
Q 039095 341 ESEIRCQACNKIFCSRRALGGHQRMHSAK 369 (492)
Q Consensus 341 ~~~~~C~~C~k~F~~~~~L~~H~~~H~~~ 369 (492)
.+.+.|++|+..|....-+..-.|+-.|+
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagD 45 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGD 45 (267)
T ss_pred hceeccCcccchhhhhheeccceeEeccc
Confidence 45678999999888887777777766554
No 197
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=35.55 E-value=47 Score=31.71 Aligned_cols=132 Identities=11% Similarity=0.061 Sum_probs=71.9
Q ss_pred hhhccccchhhhhhhcchhhcccceeeecCCcccccCCCcccccC--CcccccccCCCCCccccC-CC-----CC--Cce
Q 039095 275 DEIGKESSEDLMEEDGLDAEAGKRIITSTSSKKVGFNACYAEYGG--DSSSKAMCNASDYDVFDD-PQ-----KE--SEI 344 (492)
Q Consensus 275 ~~c~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~C--~~C~~~f~~~~~l~~h~~-~~-----~~--~~~ 344 (492)
+.|+-.+-.+.....|+..|.....+......+.+ ..|.| ..|.+ +.++...|.. |+ |- .-|
T Consensus 277 e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs-----~syhC~~~~C~k---sTsdV~~h~nFht~~~n~Gfrrthf 348 (480)
T KOG4377|consen 277 EYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFS-----NSYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRTHF 348 (480)
T ss_pred ccccccccchhhhHHHHHHHhhcccccccchhhcC-----ccchhhhcccCc---ccccccccCccccccccCceeccee
Confidence 56776666677777888877766554444333322 22677 46877 2233333321 21 11 237
Q ss_pred ecccCccccccchhhhhhcccC----CCC-----CCCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCC--cccc
Q 039095 345 RCQACNKIFCSRRALGGHQRMH----SAK-----RSSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCR--ICLK 413 (492)
Q Consensus 345 ~C~~C~k~F~~~~~L~~H~~~H----~~~-----k~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~--~C~k 413 (492)
.|..||=++..+ ...|...| .++ |-|+=..|.|....... .---|-|. -|+.
T Consensus 349 hC~r~gCTdtfK--~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~---------------~cnhfhc~r~Gc~~ 411 (480)
T KOG4377|consen 349 HCQRIGCTDTFK--DSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSG---------------ICNHFHCDRLGCEA 411 (480)
T ss_pred EEeccCCccccc--cccccccccCcchhhhhhhhhhhccccCCccCccccc---------------ceeeeeecccCCce
Confidence 888888444444 45554444 222 12333334332211110 11225565 4999
Q ss_pred ccCCchhhhhhhhhcccC
Q 039095 414 VFATGQALGGHKRAHLVK 431 (492)
Q Consensus 414 ~F~~~~~L~~H~r~H~~~ 431 (492)
.|...+.+..|.|.|...
T Consensus 412 tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 412 TLYSVSQMASHKRKHERQ 429 (480)
T ss_pred EEEehhhhhhhhhhhhhh
Confidence 999999999999999765
No 198
>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=35.36 E-value=17 Score=27.23 Aligned_cols=15 Identities=40% Similarity=0.755 Sum_probs=11.8
Q ss_pred CCCcccCCccccccCC
Q 039095 402 GNKEHTCRICLKVFAT 417 (492)
Q Consensus 402 ~~kpf~C~~C~k~F~~ 417 (492)
| +|+.|+.||..|.-
T Consensus 77 g-~~~rC~eCG~~fkL 91 (97)
T cd00924 77 G-KPKRCPECGHVFKL 91 (97)
T ss_pred C-CceeCCCCCcEEEE
Confidence 5 78888888888864
No 199
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=35.17 E-value=20 Score=27.76 Aligned_cols=14 Identities=14% Similarity=-0.213 Sum_probs=8.3
Q ss_pred ccccCCcccccccC
Q 039095 315 AEYGGDSSSKAMCN 328 (492)
Q Consensus 315 ~~~~C~~C~~~f~~ 328 (492)
....|..|+..|..
T Consensus 69 ~~~~C~~Cg~~~~~ 82 (113)
T PRK12380 69 AQAWCWDCSQVVEI 82 (113)
T ss_pred cEEEcccCCCEEec
Confidence 45667777665543
No 200
>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 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=34.83 E-value=34 Score=27.93 Aligned_cols=24 Identities=33% Similarity=0.779 Sum_probs=15.9
Q ss_pred CCCceecccCccccc------cchhhhhhc
Q 039095 340 KESEIRCQACNKIFC------SRRALGGHQ 363 (492)
Q Consensus 340 ~~~~~~C~~C~k~F~------~~~~L~~H~ 363 (492)
..-..+|..|+|.|= +.+.+..|+
T Consensus 11 p~~vv~C~~c~kWFCNg~~~~s~SHIv~HL 40 (152)
T PF09416_consen 11 PSCVVKCNTCNKWFCNGRGNTSGSHIVNHL 40 (152)
T ss_dssp CCCEEEETTTTEEEES--TTSSS-HHHHHH
T ss_pred cccEeEcCCCCcEeecCCCCCcccHHHHHH
Confidence 445578999999884 445556664
No 202
>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=33.89 E-value=41 Score=34.17 Aligned_cols=40 Identities=13% Similarity=0.145 Sum_probs=24.8
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCccccccchhhhhhcccCCCCCCCCCCcCC
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTT 378 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~ 378 (492)
....|+.|+-.. . -|.......|.+||.. ..-|..|+.|+
T Consensus 221 ~~~~C~~C~~~l------~---~h~~~~~l~Ch~Cg~~---------------~~~~~~Cp~C~ 260 (505)
T TIGR00595 221 YILCCPNCDVSL------T---YHKKEGKLRCHYCGYQ---------------EPIPKTCPQCG 260 (505)
T ss_pred CccCCCCCCCce------E---EecCCCeEEcCCCcCc---------------CCCCCCCCCCC
Confidence 566677665432 2 2334556789999853 34567888887
No 203
>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=33.88 E-value=21 Score=27.74 Aligned_cols=12 Identities=0% Similarity=-0.000 Sum_probs=6.5
Q ss_pred cccCCCCccccc
Q 039095 13 YDLRENPKKSWK 24 (492)
Q Consensus 13 ~~C~~C~k~f~~ 24 (492)
+.|..|++.|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 556666655543
No 204
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.86 E-value=15 Score=31.84 Aligned_cols=22 Identities=27% Similarity=0.652 Sum_probs=10.2
Q ss_pred ccccccccccccChhHHHhhhh
Q 039095 40 ESQCKVCGKDFESLKALYGHMR 61 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~~H~r 61 (492)
.+.|++|+-.|....-+..=.|
T Consensus 19 ~ieCPvC~tkFkkeev~tgsiR 40 (267)
T COG1655 19 TIECPVCNTKFKKEEVKTGSIR 40 (267)
T ss_pred eeccCcccchhhhhheecccee
Confidence 3455555555554443333333
No 205
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=33.69 E-value=25 Score=20.46 Aligned_cols=12 Identities=25% Similarity=0.681 Sum_probs=8.3
Q ss_pred ceecccCccccc
Q 039095 343 EIRCQACNKIFC 354 (492)
Q Consensus 343 ~~~C~~C~k~F~ 354 (492)
=|.|..|++.+.
T Consensus 27 Cf~C~~C~~~L~ 38 (39)
T smart00132 27 CFKCSKCGKPLG 38 (39)
T ss_pred CCCCcccCCcCc
Confidence 377888877653
No 206
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=33.68 E-value=35 Score=31.78 Aligned_cols=43 Identities=16% Similarity=0.285 Sum_probs=24.9
Q ss_pred cCCCCccccccccccccChhHHHhhhhccCcccccccccccch
Q 039095 35 SASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECG 77 (492)
Q Consensus 35 H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~ 77 (492)
|...+-|.|++|++.=-+...|..|+..-+.+..-.-.|++|+
T Consensus 74 ~y~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 74 HYDPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3344567777777777777777777655444421223344443
No 207
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=33.59 E-value=22 Score=23.35 Aligned_cols=10 Identities=20% Similarity=-0.210 Sum_probs=4.8
Q ss_pred ccCCCCcccc
Q 039095 14 DLRENPKKSW 23 (492)
Q Consensus 14 ~C~~C~k~f~ 23 (492)
+|-.|++.+.
T Consensus 4 kC~lCdk~~~ 13 (56)
T PF09963_consen 4 KCILCDKKEE 13 (56)
T ss_pred EEEecCCEEE
Confidence 3555555543
No 208
>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=33.50 E-value=11 Score=26.44 Aligned_cols=42 Identities=7% Similarity=-0.085 Sum_probs=14.2
Q ss_pred cccCCCCccccccc---chhhhhhccCCCCccccccccccccChh
Q 039095 13 YDLRENPKKSWKFS---SFNHAASASASTQESQCKVCGKDFESLK 54 (492)
Q Consensus 13 ~~C~~C~k~f~~~~---~l~~H~~~H~~~~~~~C~~C~k~F~~~~ 54 (492)
++|+-|++.|+=.. .+..|...........|..|+..+.-..
T Consensus 11 ~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~~~~~ 55 (71)
T PF05495_consen 11 IRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQPIDE 55 (71)
T ss_dssp EEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EEES-S
T ss_pred EECCcccCeecHHHHHHHhccCccccccccCeECCCCCCccChhh
Confidence 44455555444221 2223333233333445555554444433
No 209
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=33.40 E-value=19 Score=34.93 Aligned_cols=21 Identities=38% Similarity=0.700 Sum_probs=18.5
Q ss_pred eecccCccccccchhhhhhcc
Q 039095 344 IRCQACNKIFCSRRALGGHQR 364 (492)
Q Consensus 344 ~~C~~C~k~F~~~~~L~~H~~ 364 (492)
..|..|+..|.++..|..|+.
T Consensus 461 ~~C~tCr~~FdSRnkLF~Hlk 481 (508)
T KOG0717|consen 461 ISCTTCRESFDSRNKLFAHLK 481 (508)
T ss_pred HhhhhhhhhccchhHHHHHhh
Confidence 689999999999999999975
No 210
>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=33.25 E-value=27 Score=24.06 Aligned_cols=12 Identities=25% Similarity=0.800 Sum_probs=6.8
Q ss_pred cccccccchhhh
Q 039095 69 ERIQCKECGKAL 80 (492)
Q Consensus 69 k~y~C~~C~k~F 80 (492)
+.|.|+.||..+
T Consensus 45 r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 45 RVFTCPNCGFEM 56 (69)
T ss_pred ceEEcCCCCCEE
Confidence 456666666543
No 211
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.10 E-value=26 Score=33.97 Aligned_cols=32 Identities=13% Similarity=0.127 Sum_probs=19.6
Q ss_pred cCCcccccccCCCCCccccCCCCCCceecccCccccccchhh
Q 039095 318 GGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRAL 359 (492)
Q Consensus 318 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~L 359 (492)
.|+.|+..+. ..|.+-|+|+.||..+.+....
T Consensus 352 ~Cp~Cg~~m~----------S~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGRMK----------SAGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCchh----------hcCCCCcccccccccCCccccc
Confidence 5777776552 2333467777777777665543
No 212
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=32.99 E-value=45 Score=29.49 Aligned_cols=13 Identities=31% Similarity=0.651 Sum_probs=6.6
Q ss_pred CcccCCccccccC
Q 039095 404 KEHTCRICLKVFA 416 (492)
Q Consensus 404 kpf~C~~C~k~F~ 416 (492)
--|.|+.|+..|+
T Consensus 154 aef~C~~C~h~F~ 166 (278)
T PF15135_consen 154 AEFHCPKCRHNFR 166 (278)
T ss_pred eeeecccccccch
Confidence 3355555555554
No 213
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=32.99 E-value=17 Score=28.23 Aligned_cols=14 Identities=29% Similarity=0.959 Sum_probs=7.1
Q ss_pred ccccccchhhhcCh
Q 039095 70 RIQCKECGKALLSA 83 (492)
Q Consensus 70 ~y~C~~C~k~F~~~ 83 (492)
.+.|..||..|...
T Consensus 70 ~~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 70 RARCRDCGHEFEPD 83 (113)
T ss_dssp EEEETTTS-EEECH
T ss_pred cEECCCCCCEEecC
Confidence 35566666666543
No 214
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.37 E-value=22 Score=32.23 Aligned_cols=62 Identities=15% Similarity=0.197 Sum_probs=38.3
Q ss_pred CCceecccCccccccchhhhhhcccCCCCCCCCCCcCCCCCCCCcccchhhhhhhhccccCCCCcccCCcccc----ccC
Q 039095 341 ESEIRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFTETEPHSKLVKLECIEDLMQRGNKEHTCRICLK----VFA 416 (492)
Q Consensus 341 ~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~h~~~H~~~kpf~C~~C~k----~F~ 416 (492)
.-||.|.+|.+.|.++- -+.-+-|.|..|.... -.|.=+|-+|++ .|.
T Consensus 239 ~~Pf~c~icr~~f~~pV--------vt~c~h~fc~~ca~~~--------------------~qk~~~c~vC~~~t~g~~~ 290 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRPV--------VTKCGHYFCEVCALKP--------------------YQKGEKCYVCSQQTHGSFN 290 (313)
T ss_pred cCCccccccccccccch--------hhcCCceeehhhhccc--------------------cccCCcceecccccccccc
Confidence 45789999999887653 3334456777776432 123346777766 466
Q ss_pred Cchhhhhhhhhccc
Q 039095 417 TGQALGGHKRAHLV 430 (492)
Q Consensus 417 ~~~~L~~H~r~H~~ 430 (492)
....|..=|..+-.
T Consensus 291 ~akeL~~~L~~kks 304 (313)
T KOG1813|consen 291 VAKELLVSLKLKKS 304 (313)
T ss_pred hHHHHHHHHHhhhh
Confidence 66667666665543
No 215
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=31.76 E-value=35 Score=20.72 Aligned_cols=18 Identities=22% Similarity=0.346 Sum_probs=9.1
Q ss_pred ccccccccccccChhHHH
Q 039095 40 ESQCKVCGKDFESLKALY 57 (492)
Q Consensus 40 ~~~C~~C~k~F~~~~~L~ 57 (492)
.+.|+.|+=.|-....|.
T Consensus 19 id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 19 IDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEECCCCCeEEccHHHHH
Confidence 345555555555544443
No 216
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=31.72 E-value=30 Score=30.86 Aligned_cols=24 Identities=21% Similarity=0.510 Sum_probs=19.9
Q ss_pred Ccc-cCC---ccccccCCchhhhhhhhh
Q 039095 404 KEH-TCR---ICLKVFATGQALGGHKRA 427 (492)
Q Consensus 404 kpf-~C~---~C~k~F~~~~~L~~H~r~ 427 (492)
-|| .|+ +||..|.+...|+.|...
T Consensus 245 HPFtnC~s~CvCG~~f~~sd~mk~HR~~ 272 (285)
T PF03563_consen 245 HPFTNCGSHCVCGMKFETSDRMKMHRES 272 (285)
T ss_pred cCCCCCCCeeeccccccchHHHHHHHhc
Confidence 567 476 799999999999999763
No 217
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=31.43 E-value=35 Score=31.73 Aligned_cols=63 Identities=14% Similarity=0.247 Sum_probs=40.7
Q ss_pred ccCCCCccccccccccccChhHHHhh----hhccCcccccccccccchhhhcChhhHhhhhhh-ccc--CcccccccC
Q 039095 34 ASASTQESQCKVCGKDFESLKALYGH----MRHHSRRERERIQCKECGKALLSAKSLSNHMRV-HSQ--KLRACNESG 104 (492)
Q Consensus 34 ~H~~~~~~~C~~C~k~F~~~~~L~~H----~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~-H~~--k~~~C~~C~ 104 (492)
+|..+-|-+|- |.++ ++..+ ...|-.. ..|.|++|++.=.+...|..|+.. |.+ -...|++|+
T Consensus 47 ~H~~dHPmqci-l~~~-----dfeL~f~Ge~i~~y~~--qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 47 IHDEDHPMQCI-LSRV-----DFELYFGGEPISHYDP--QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccCCCCceeEE-eecc-----ceeeEecCcccccccc--ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 56667776663 3322 22222 1234455 789999999998899999999764 654 234566665
No 218
>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=31.05 E-value=23 Score=21.61 Aligned_cols=17 Identities=18% Similarity=0.505 Sum_probs=13.3
Q ss_pred ccCCccccccCCchhhh
Q 039095 406 HTCRICLKVFATGQALG 422 (492)
Q Consensus 406 f~C~~C~k~F~~~~~L~ 422 (492)
=.|.+||+.|+.+.-..
T Consensus 9 K~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWA 25 (42)
T ss_pred CcCcccCCcchHHHHHH
Confidence 36999999999876543
No 219
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=30.38 E-value=16 Score=35.03 Aligned_cols=56 Identities=27% Similarity=0.481 Sum_probs=28.3
Q ss_pred CCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhh-hhcc-cCcccccccC
Q 039095 38 TQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHM-RVHS-QKLRACNESG 104 (492)
Q Consensus 38 ~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~-~~H~-~k~~~C~~C~ 104 (492)
.+.|+|.+|. +..|.|.|.-. .|.|+-=++.+.+-.--..|- ++|+ ..|--|+.||
T Consensus 71 KQGfQCqvC~--------fvvHkrChefV---tF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCG 128 (683)
T KOG0696|consen 71 KQGFQCQVCC--------FVVHKRCHEFV---TFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCG 128 (683)
T ss_pred cCceeeeEEe--------ehhhhhhcceE---EEECCCCCCCCCCCCcccccceeeeecCCCchhhhHH
Confidence 3445555554 34555555443 555655555555555444452 3444 3444455555
No 220
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=30.32 E-value=37 Score=22.29 Aligned_cols=9 Identities=33% Similarity=1.206 Sum_probs=4.3
Q ss_pred ccccccchh
Q 039095 70 RIQCKECGK 78 (492)
Q Consensus 70 ~y~C~~C~k 78 (492)
.|.|+.||.
T Consensus 14 ~~~Cp~cGi 22 (55)
T PF13824_consen 14 NFECPDCGI 22 (55)
T ss_pred CCcCCCCCC
Confidence 444444443
No 221
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=30.14 E-value=31 Score=33.32 Aligned_cols=23 Identities=22% Similarity=0.530 Sum_probs=14.3
Q ss_pred cccccccch-hhhcChhhHhhhhh
Q 039095 69 ERIQCKECG-KALLSAKSLSNHMR 91 (492)
Q Consensus 69 k~y~C~~C~-k~F~~~~~L~~H~~ 91 (492)
+.|.|.+|| +++.-+..+.+|..
T Consensus 400 ~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 400 IEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cccceeeccCccccCcHHHHHHhH
Confidence 566666666 56666666666643
No 222
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=29.81 E-value=23 Score=27.93 Aligned_cols=15 Identities=20% Similarity=0.687 Sum_probs=10.7
Q ss_pred ceecccCccccccch
Q 039095 343 EIRCQACNKIFCSRR 357 (492)
Q Consensus 343 ~~~C~~C~k~F~~~~ 357 (492)
|++|..||+.|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 567778888777654
No 223
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=29.62 E-value=34 Score=25.18 Aligned_cols=18 Identities=28% Similarity=0.510 Sum_probs=8.9
Q ss_pred CCCc-ccCCccccccCCch
Q 039095 402 GNKE-HTCRICLKVFATGQ 419 (492)
Q Consensus 402 ~~kp-f~C~~C~k~F~~~~ 419 (492)
|+|- |.|++|-+.|.+--
T Consensus 33 G~rLfFCCd~ca~EF~nmi 51 (105)
T PF11494_consen 33 GERLFFCCDDCAKEFKNMI 51 (105)
T ss_dssp T--BSSS--SSSS-TTS-T
T ss_pred CCEEEEEcHHHHHHHHHHH
Confidence 4454 58899999998644
No 224
>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=29.53 E-value=28 Score=36.94 Aligned_cols=56 Identities=9% Similarity=0.112 Sum_probs=37.3
Q ss_pred ccCCcccccccCCCCCccccCCCCCCce-ecccCccccccchhhhhhcccCCCCCCCCCCcCC
Q 039095 317 YGGDSSSKAMCNASDYDVFDDPQKESEI-RCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTT 378 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~-~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~ 378 (492)
..|..||-.|+=...|..-+..+....| .|+.|-+-+.+..+- |-|. .+.-|..|+
T Consensus 91 ~nCt~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p~~r----r~h~--~~~~C~~Cg 147 (711)
T TIGR00143 91 ISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLDR----RFHA--QPIACPRCG 147 (711)
T ss_pred ccccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCCccc----cCCC--CCccCCCCC
Confidence 3588898888877777665555555555 588888888777553 3343 445566666
No 225
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=29.44 E-value=29 Score=28.69 Aligned_cols=39 Identities=23% Similarity=0.513 Sum_probs=20.9
Q ss_pred ccccccccccChhHHH-------hhhhccCcccccccccccchhhhcChh
Q 039095 42 QCKVCGKDFESLKALY-------GHMRHHSRRERERIQCKECGKALLSAK 84 (492)
Q Consensus 42 ~C~~C~k~F~~~~~L~-------~H~r~H~~~~~k~y~C~~C~k~F~~~~ 84 (492)
.|+.|+-.....+.=. .|.+.+. .-|.|+.||+.|=--+
T Consensus 99 RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~----~f~~C~~CgkiYW~Gs 144 (165)
T COG1656 99 RCPECNGELEKVSREEVKEKVPEKVYRNYE----EFYRCPKCGKIYWKGS 144 (165)
T ss_pred cCcccCCEeccCcHHHHhhccchhhhhccc----ceeECCCCcccccCch
Confidence 6777776554433211 2333333 4566777777764333
No 226
>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=29.08 E-value=26 Score=34.57 Aligned_cols=31 Identities=19% Similarity=0.263 Sum_probs=25.2
Q ss_pred CcccCCccccccCCchhhhhhhh-hcccCCCC
Q 039095 404 KEHTCRICLKVFATGQALGGHKR-AHLVKNLD 434 (492)
Q Consensus 404 kpf~C~~C~k~F~~~~~L~~H~r-~H~~~~~~ 434 (492)
+-..|++|.+.|.....+..||. .|.++-.+
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P 87 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGLKP 87 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhcCh
Confidence 34589999999999999999987 67665443
No 227
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=29.07 E-value=39 Score=18.12 Aligned_cols=9 Identities=0% Similarity=-0.260 Sum_probs=5.9
Q ss_pred ccCCccccc
Q 039095 317 YGGDSSSKA 325 (492)
Q Consensus 317 ~~C~~C~~~ 325 (492)
..|+.|+..
T Consensus 3 ~~Cp~Cg~~ 11 (26)
T PF13248_consen 3 MFCPNCGAE 11 (26)
T ss_pred CCCcccCCc
Confidence 457777773
No 228
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.76 E-value=28 Score=27.19 Aligned_cols=12 Identities=0% Similarity=-0.075 Sum_probs=6.5
Q ss_pred cccCCCCccccc
Q 039095 13 YDLRENPKKSWK 24 (492)
Q Consensus 13 ~~C~~C~k~f~~ 24 (492)
+.|..|+..|..
T Consensus 72 ~~C~~Cg~~~~~ 83 (117)
T PRK00564 72 LECKDCSHVFKP 83 (117)
T ss_pred EEhhhCCCcccc
Confidence 556666655443
No 229
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=28.49 E-value=45 Score=22.11 Aligned_cols=46 Identities=22% Similarity=0.325 Sum_probs=18.8
Q ss_pred CCCccccCCCCcccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCccccccccccc
Q 039095 9 GHISYDLRENPKKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKE 75 (492)
Q Consensus 9 ~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~ 75 (492)
+...+.|++..+.|. .|.+...|+-+|.... +...++ .. +..+||+
T Consensus 8 ~~~~~~CPiT~~~~~---------------~PV~s~~C~H~fek~a-I~~~i~---~~--~~~~CPv 53 (57)
T PF11789_consen 8 GTISLKCPITLQPFE---------------DPVKSKKCGHTFEKEA-ILQYIQ---RN--GSKRCPV 53 (57)
T ss_dssp SB--SB-TTTSSB-S---------------SEEEESSS--EEEHHH-HHHHCT---TT--S-EE-SC
T ss_pred cEeccCCCCcCChhh---------------CCcCcCCCCCeecHHH-HHHHHH---hc--CCCCCCC
Confidence 445566666655443 3445556666665544 333331 12 4566666
No 230
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=28.28 E-value=40 Score=20.17 Aligned_cols=10 Identities=30% Similarity=0.670 Sum_probs=2.6
Q ss_pred cccccccccc
Q 039095 41 SQCKVCGKDF 50 (492)
Q Consensus 41 ~~C~~C~k~F 50 (492)
|-|++|..-|
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 4455555555
No 231
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=28.27 E-value=20 Score=24.60 Aligned_cols=26 Identities=12% Similarity=0.424 Sum_probs=13.4
Q ss_pred ccCCcccccccCCCCCccccCCCCCCceecccCcccc
Q 039095 317 YGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIF 353 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F 353 (492)
|.| .|+....... +.+.-+| +||++-
T Consensus 4 frC-~Cgr~lya~e---------~~kTkkC-~CG~~l 29 (68)
T PF09082_consen 4 FRC-DCGRYLYAKE---------GAKTKKC-VCGKTL 29 (68)
T ss_dssp EEE-TTS--EEEET---------T-SEEEE-TTTEEE
T ss_pred EEe-cCCCEEEecC---------CcceeEe-cCCCee
Confidence 556 4666544433 3455677 787753
No 232
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=28.25 E-value=33 Score=34.64 Aligned_cols=28 Identities=18% Similarity=0.343 Sum_probs=22.6
Q ss_pred CCCcccCCccccccCCchhhhhhhhhcc
Q 039095 402 GNKEHTCRICLKVFATGQALGGHKRAHL 429 (492)
Q Consensus 402 ~~kpf~C~~C~k~F~~~~~L~~H~r~H~ 429 (492)
..+|-.|..||.+|........||-.|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 4567899999999999988777776553
No 233
>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=27.49 E-value=23 Score=20.62 Aligned_cols=16 Identities=19% Similarity=-0.056 Sum_probs=8.7
Q ss_pred ccCCCCcccccccchh
Q 039095 14 DLRENPKKSWKFSSFN 29 (492)
Q Consensus 14 ~C~~C~k~f~~~~~l~ 29 (492)
.|.+|++.|.....+.
T Consensus 5 ~C~eC~~~f~dSyL~~ 20 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLN 20 (34)
T ss_dssp E-TTT--EES-SSCCC
T ss_pred hHhHhCCHHHHHHHHH
Confidence 5888888888776654
No 234
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=27.22 E-value=29 Score=28.16 Aligned_cols=34 Identities=18% Similarity=0.262 Sum_probs=18.6
Q ss_pred CCCceecccCccccccchhhhhhcccCCCCCCCCCCcCC
Q 039095 340 KESEIRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTT 378 (492)
Q Consensus 340 ~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~ 378 (492)
..-+|.|. |+..|-+. ++|-.+-.|+ .|.|..|+
T Consensus 114 ~~~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~ 147 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCG 147 (156)
T ss_pred cceeEEee-cCCccchh---hhcccccccc-eEEeccCC
Confidence 34468888 88775543 3344444444 45555554
No 235
>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=26.96 E-value=36 Score=27.77 Aligned_cols=9 Identities=22% Similarity=0.563 Sum_probs=4.8
Q ss_pred ccCCccccc
Q 039095 406 HTCRICLKV 414 (492)
Q Consensus 406 f~C~~C~k~ 414 (492)
=.|+.||..
T Consensus 131 ~~Cp~C~~~ 139 (146)
T PF07295_consen 131 PPCPKCGHT 139 (146)
T ss_pred CCCCCCCCC
Confidence 356666543
No 236
>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=26.79 E-value=32 Score=20.90 Aligned_cols=13 Identities=15% Similarity=0.636 Sum_probs=9.6
Q ss_pred CceecccCccccc
Q 039095 342 SEIRCQACNKIFC 354 (492)
Q Consensus 342 ~~~~C~~C~k~F~ 354 (492)
++-.|++||..|.
T Consensus 28 ~~~~CpYCg~~yv 40 (40)
T PF10276_consen 28 GPVVCPYCGTRYV 40 (40)
T ss_dssp CEEEETTTTEEEE
T ss_pred CeEECCCCCCEEC
Confidence 4678888888773
No 237
>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=26.74 E-value=23 Score=23.08 Aligned_cols=13 Identities=15% Similarity=0.588 Sum_probs=7.1
Q ss_pred cCCccccccCCch
Q 039095 407 TCRICLKVFATGQ 419 (492)
Q Consensus 407 ~C~~C~k~F~~~~ 419 (492)
.|++|++.|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 9999999998543
No 238
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=26.45 E-value=34 Score=34.47 Aligned_cols=27 Identities=33% Similarity=0.631 Sum_probs=14.3
Q ss_pred CCccccccccccccChhHHHhhhhccC
Q 039095 38 TQESQCKVCGKDFESLKALYGHMRHHS 64 (492)
Q Consensus 38 ~~~~~C~~C~k~F~~~~~L~~H~r~H~ 64 (492)
..|.+|..||.+|.......+||-.|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 334555555555555555555555553
No 239
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=26.43 E-value=20 Score=29.64 Aligned_cols=11 Identities=27% Similarity=0.930 Sum_probs=5.5
Q ss_pred ccccccchhhh
Q 039095 70 RIQCKECGKAL 80 (492)
Q Consensus 70 ~y~C~~C~k~F 80 (492)
.|.|+.|+..+
T Consensus 123 ~~~C~~C~~~~ 133 (157)
T PF10263_consen 123 VYRCPSCGREY 133 (157)
T ss_pred EEEcCCCCCEe
Confidence 45555555444
No 240
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.00 E-value=72 Score=33.37 Aligned_cols=53 Identities=15% Similarity=0.035 Sum_probs=34.6
Q ss_pred ccCCcccccccCCCCCccccCCCCCCceecccCccccccchhhhhhcccCCCCCCCCCCcCCCCCCCCcccchhhhhhhh
Q 039095 317 YGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRALGGHQRMHSAKRSSLPVKTTMFTETEPHSKLVKLECIE 396 (492)
Q Consensus 317 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~~~~~~~~~~~~~~~~~~h 396 (492)
..|+.|+....... --|+.||..+.. -.|..|+...
T Consensus 2 ~~Cp~Cg~~n~~~a-------------kFC~~CG~~l~~----------------~~Cp~CG~~~--------------- 37 (645)
T PRK14559 2 LICPQCQFENPNNN-------------RFCQKCGTSLTH----------------KPCPQCGTEV--------------- 37 (645)
T ss_pred CcCCCCCCcCCCCC-------------ccccccCCCCCC----------------CcCCCCCCCC---------------
Confidence 36888887643322 369999987741 1488888553
Q ss_pred ccccCCCCcccCCccccccCCc
Q 039095 397 DLMQRGNKEHTCRICLKVFATG 418 (492)
Q Consensus 397 ~~~H~~~kpf~C~~C~k~F~~~ 418 (492)
....--|+.||....+.
T Consensus 38 -----~~~~~fC~~CG~~~~~~ 54 (645)
T PRK14559 38 -----PVDEAHCPNCGAETGTI 54 (645)
T ss_pred -----CcccccccccCCcccch
Confidence 23334799999887665
No 241
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.97 E-value=36 Score=26.47 Aligned_cols=13 Identities=15% Similarity=0.115 Sum_probs=7.9
Q ss_pred ccccCCccccccc
Q 039095 315 AEYGGDSSSKAMC 327 (492)
Q Consensus 315 ~~~~C~~C~~~f~ 327 (492)
....|..|+..|.
T Consensus 69 ~~~~C~~Cg~~~~ 81 (114)
T PRK03681 69 AECWCETCQQYVT 81 (114)
T ss_pred cEEEcccCCCeee
Confidence 4566777776553
No 242
>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=25.87 E-value=16 Score=26.31 Aligned_cols=41 Identities=10% Similarity=0.212 Sum_probs=17.7
Q ss_pred cccccCCcccccccCCCCCccccCCCCCCceecccCccccccch
Q 039095 314 YAEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRR 357 (492)
Q Consensus 314 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~ 357 (492)
.+.|.|+.|+-.-+=...+ ....+...-.|.+||..|.+.-
T Consensus 20 ~~~F~CPfC~~~~sV~v~i---dkk~~~~~~~C~~Cg~~~~~~i 60 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKI---DKKEGIGILSCRVCGESFQTKI 60 (81)
T ss_dssp SS----TTT--SS-EEEEE---ETTTTEEEEEESSS--EEEEE-
T ss_pred CceEcCCcCCCCCeEEEEE---EccCCEEEEEecCCCCeEEEcc
Confidence 4789999998322111111 1223445678999999887653
No 243
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=25.83 E-value=38 Score=25.22 Aligned_cols=28 Identities=21% Similarity=0.488 Sum_probs=17.9
Q ss_pred ccccccchhhhcChhhHhhhhhhcccCcccccccCch
Q 039095 70 RIQCKECGKALLSAKSLSNHMRVHSQKLRACNESGAV 106 (492)
Q Consensus 70 ~y~C~~C~k~F~~~~~L~~H~~~H~~k~~~C~~C~~~ 106 (492)
|++|.-||..|.+-+.+. - --|+.||..
T Consensus 2 pH~CtrCG~vf~~g~~~i-----l----~GCp~CG~n 29 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEI-----L----SGCPKCGCN 29 (112)
T ss_pred CceecccccccccccHHH-----H----ccCccccch
Confidence 677888888888754321 1 257778744
No 244
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=25.48 E-value=30 Score=33.67 Aligned_cols=22 Identities=36% Similarity=0.635 Sum_probs=20.4
Q ss_pred cccccchhhhcChhhHhhhhhh
Q 039095 71 IQCKECGKALLSAKSLSNHMRV 92 (492)
Q Consensus 71 y~C~~C~k~F~~~~~L~~H~~~ 92 (492)
+.|.+|.++|.+..+|+.|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8899999999999999999874
No 245
>PLN02294 cytochrome c oxidase subunit Vb
Probab=25.19 E-value=26 Score=29.05 Aligned_cols=19 Identities=11% Similarity=0.046 Sum_probs=16.3
Q ss_pred hhhcccCcccccccCchhh
Q 039095 90 MRVHSQKLRACNESGAVKS 108 (492)
Q Consensus 90 ~~~H~~k~~~C~~C~~~f~ 108 (492)
|..+.|+++.|+.||..|.
T Consensus 134 f~L~kGkp~RCpeCG~~fk 152 (174)
T PLN02294 134 FWLEKGKSFECPVCTQYFE 152 (174)
T ss_pred EEecCCCceeCCCCCCEEE
Confidence 5677789999999998876
No 246
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=24.74 E-value=51 Score=26.92 Aligned_cols=12 Identities=33% Similarity=0.761 Sum_probs=6.3
Q ss_pred CceecccCcccc
Q 039095 342 SEIRCQACNKIF 353 (492)
Q Consensus 342 ~~~~C~~C~k~F 353 (492)
..|.|..|+-.|
T Consensus 132 ~~y~C~~C~g~l 143 (146)
T smart00731 132 SRYRCGKCGGKL 143 (146)
T ss_pred ceEEcCCCCCEE
Confidence 445555555443
No 247
>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=24.01 E-value=45 Score=19.72 Aligned_cols=14 Identities=21% Similarity=0.463 Sum_probs=10.5
Q ss_pred CCCCCCccccCCCC
Q 039095 6 GDDGHISYDLRENP 19 (492)
Q Consensus 6 ~~~~~~~~~C~~C~ 19 (492)
+.+|...|.|..|.
T Consensus 23 ~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 23 SPSGHQRYRCKDCR 36 (36)
T ss_pred CCCCCEeEecCcCC
Confidence 45678889998883
No 248
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=23.88 E-value=47 Score=21.71 Aligned_cols=13 Identities=23% Similarity=0.835 Sum_probs=6.1
Q ss_pred cccccccccccCh
Q 039095 41 SQCKVCGKDFESL 53 (492)
Q Consensus 41 ~~C~~C~k~F~~~ 53 (492)
++|+.|+..|...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 4555554444433
No 249
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=23.76 E-value=48 Score=30.92 Aligned_cols=37 Identities=8% Similarity=0.079 Sum_probs=21.0
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCcccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIF 353 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F 353 (492)
..-.|+.||..-.-. +.......|.+-..|..|+-.+
T Consensus 186 ~~~~CPvCGs~P~~s--~v~~~~~~G~RyL~CslC~teW 222 (309)
T PRK03564 186 QRQFCPVCGSMPVSS--VVQIGTTQGLRYLHCNLCESEW 222 (309)
T ss_pred CCCCCCCCCCcchhh--eeeccCCCCceEEEcCCCCCcc
Confidence 346788888754322 1111223566777888888643
No 250
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=23.62 E-value=46 Score=31.01 Aligned_cols=28 Identities=18% Similarity=0.470 Sum_probs=16.2
Q ss_pred ccCcccccccccccch-hhhcChhhHhhhhh
Q 039095 62 HHSRRERERIQCKECG-KALLSAKSLSNHMR 91 (492)
Q Consensus 62 ~H~~~~~k~y~C~~C~-k~F~~~~~L~~H~~ 91 (492)
.|.-. +-|.|.+|| +.+.-+..+.+|..
T Consensus 368 lhgLd--~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 368 LHGLD--IEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hcCCC--cceeeeecccccccchHHHHhhhh
Confidence 34444 566666666 55555666666643
No 251
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=22.81 E-value=34 Score=35.44 Aligned_cols=55 Identities=16% Similarity=0.349 Sum_probs=33.7
Q ss_pred cCCCCcccccccchhhhhhccCCCCcc-ccccccccccChhHHHhhhhccCcccccccccccchh
Q 039095 15 LRENPKKSWKFSSFNHAASASASTQES-QCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGK 78 (492)
Q Consensus 15 C~~C~k~f~~~~~l~~H~~~H~~~~~~-~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k 78 (492)
|..||-.|+-...|--=.. .+.-+.| .|+.|.+.+..+.+-+ -| . .|..|+.||-
T Consensus 126 CT~CGPRfTIi~alPYDR~-nTsM~~F~lC~~C~~EY~dP~nRR----fH-A---Qp~aCp~CGP 181 (750)
T COG0068 126 CTNCGPRFTIIEALPYDRE-NTSMADFPLCPFCDKEYKDPLNRR----FH-A---QPIACPKCGP 181 (750)
T ss_pred cCCCCcceeeeccCCCCcc-cCccccCcCCHHHHHHhcCccccc----cc-c---ccccCcccCC
Confidence 8888888887766621111 1222233 6888888877776533 23 2 4788888885
No 252
>PRK12496 hypothetical protein; Provisional
Probab=22.72 E-value=52 Score=27.53 Aligned_cols=27 Identities=11% Similarity=0.017 Sum_probs=16.3
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKI 352 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~ 352 (492)
..|.|..|++.|...... -.|++||-.
T Consensus 126 w~~~C~gC~~~~~~~~~~-----------~~C~~CG~~ 152 (164)
T PRK12496 126 WRKVCKGCKKKYPEDYPD-----------DVCEICGSP 152 (164)
T ss_pred eeEECCCCCccccCCCCC-----------CcCCCCCCh
Confidence 346788888777433211 258888754
No 253
>PF12907 zf-met2: Zinc-binding
Probab=22.69 E-value=46 Score=20.22 Aligned_cols=9 Identities=33% Similarity=0.914 Sum_probs=3.9
Q ss_pred ccccchhhh
Q 039095 72 QCKECGKAL 80 (492)
Q Consensus 72 ~C~~C~k~F 80 (492)
.|.+|-.+|
T Consensus 3 ~C~iC~qtF 11 (40)
T PF12907_consen 3 ICKICRQTF 11 (40)
T ss_pred CcHHhhHHH
Confidence 444444333
No 254
>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=22.66 E-value=86 Score=23.76 Aligned_cols=9 Identities=0% Similarity=-0.400 Sum_probs=4.4
Q ss_pred cccCCcccc
Q 039095 316 EYGGDSSSK 324 (492)
Q Consensus 316 ~~~C~~C~~ 324 (492)
|..|+.|+.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 344555554
No 255
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.53 E-value=60 Score=21.76 Aligned_cols=38 Identities=11% Similarity=0.123 Sum_probs=23.1
Q ss_pred ccccCCcccccccCCCCCccccCCCCCCceecccCcccccc
Q 039095 315 AEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCS 355 (492)
Q Consensus 315 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~ 355 (492)
.++.|+--+-.|..+.-+..+ ..+.--.|++|++.|+-
T Consensus 23 ~~l~C~g~~~p~~HPrV~L~m---g~~gev~CPYC~t~y~l 60 (62)
T COG4391 23 LPLMCPGPEPPNDHPRVFLDM---GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred eeEEcCCCCCCCCCCEEEEEc---CCCCcEecCccccEEEe
Confidence 667776555544444333333 34556789999998863
No 256
>PHA02998 RNA polymerase subunit; Provisional
Probab=22.22 E-value=42 Score=27.96 Aligned_cols=11 Identities=27% Similarity=0.824 Sum_probs=5.2
Q ss_pred cccccchhhhc
Q 039095 71 IQCKECGKALL 81 (492)
Q Consensus 71 y~C~~C~k~F~ 81 (492)
|.|..||+.|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 44555554443
No 257
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=22.04 E-value=61 Score=27.48 Aligned_cols=18 Identities=11% Similarity=-0.173 Sum_probs=14.0
Q ss_pred CCCccccCCCCccccccc
Q 039095 9 GHISYDLRENPKKSWKFS 26 (492)
Q Consensus 9 ~~~~~~C~~C~k~f~~~~ 26 (492)
...||.|.+|.+.|.++-
T Consensus 193 e~IPF~C~iCKkdy~spv 210 (259)
T COG5152 193 EKIPFLCGICKKDYESPV 210 (259)
T ss_pred CCCceeehhchhhccchh
Confidence 357888999988887764
No 258
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=21.95 E-value=36 Score=27.20 Aligned_cols=23 Identities=17% Similarity=0.401 Sum_probs=18.6
Q ss_pred CcccCCccccccCCchhhhhhhh
Q 039095 404 KEHTCRICLKVFATGQALGGHKR 426 (492)
Q Consensus 404 kpf~C~~C~k~F~~~~~L~~H~r 426 (492)
-+|.|.-||-++=+..-|..|--
T Consensus 128 S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 128 SKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred chhHHHhcCCceeechhhhhccc
Confidence 46889999998888888888853
No 259
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=21.93 E-value=12 Score=21.99 Aligned_cols=11 Identities=36% Similarity=0.920 Sum_probs=4.1
Q ss_pred ccccccchhhh
Q 039095 70 RIQCKECGKAL 80 (492)
Q Consensus 70 ~y~C~~C~k~F 80 (492)
+..|+.||-.|
T Consensus 21 ~isC~~CGPr~ 31 (35)
T PF07503_consen 21 FISCTNCGPRY 31 (35)
T ss_dssp T--BTTCC-SC
T ss_pred CccCCCCCCCE
Confidence 45555555443
No 260
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=21.88 E-value=46 Score=32.21 Aligned_cols=25 Identities=28% Similarity=0.583 Sum_probs=11.4
Q ss_pred CCCCcccccccc-ccccChhHHHhhh
Q 039095 36 ASTQESQCKVCG-KDFESLKALYGHM 60 (492)
Q Consensus 36 ~~~~~~~C~~C~-k~F~~~~~L~~H~ 60 (492)
.-...|.|.+|| +++.-+..+.+|-
T Consensus 397 GL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 397 GLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred CCCcccceeeccCccccCcHHHHHHh
Confidence 334444455554 4444444444444
No 261
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=21.58 E-value=41 Score=28.96 Aligned_cols=12 Identities=25% Similarity=0.576 Sum_probs=6.2
Q ss_pred ccccccchhhhc
Q 039095 70 RIQCKECGKALL 81 (492)
Q Consensus 70 ~y~C~~C~k~F~ 81 (492)
.|.|+.||+..+
T Consensus 30 sf~C~~CGyr~~ 41 (192)
T TIGR00310 30 STICEHCGYRSN 41 (192)
T ss_pred EEECCCCCCccc
Confidence 355555554443
No 262
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=21.03 E-value=46 Score=24.66 Aligned_cols=42 Identities=10% Similarity=0.225 Sum_probs=24.8
Q ss_pred cccccCCcccccccCCCCCccccCCCCCCceecccCccccccchh
Q 039095 314 YAEYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIFCSRRA 358 (492)
Q Consensus 314 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F~~~~~ 358 (492)
...|.|+.|.---.-...|. .........|.+|+.+|.+.-+
T Consensus 21 dt~FnClfcnHek~v~~~~D---k~~~iG~~sC~iC~esFqt~it 62 (109)
T KOG3214|consen 21 DTQFNCLFCNHEKSVSCTLD---KKHNIGKASCRICEESFQTTIT 62 (109)
T ss_pred heeeccCccccccceeeeeh---hhcCcceeeeeehhhhhccchH
Confidence 36788888864433222222 2223445688888888877543
No 263
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=20.87 E-value=59 Score=33.98 Aligned_cols=13 Identities=0% Similarity=-0.204 Sum_probs=10.7
Q ss_pred cccCCCCcccccc
Q 039095 13 YDLRENPKKSWKF 25 (492)
Q Consensus 13 ~~C~~C~k~f~~~ 25 (492)
-.|..|++.|...
T Consensus 461 dtC~~C~kkFfSl 473 (1374)
T PTZ00303 461 DSCPSCGRAFISL 473 (1374)
T ss_pred CcccCcCCccccc
Confidence 4699999999765
No 264
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=20.65 E-value=49 Score=25.65 Aligned_cols=11 Identities=27% Similarity=0.875 Sum_probs=6.9
Q ss_pred ccccccccccc
Q 039095 41 SQCKVCGKDFE 51 (492)
Q Consensus 41 ~~C~~C~k~F~ 51 (492)
|.|..||.+|.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 66666666654
No 265
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.60 E-value=67 Score=29.97 Aligned_cols=37 Identities=5% Similarity=0.011 Sum_probs=20.0
Q ss_pred cccCCcccccccCCCCCccccCCCCCCceecccCcccc
Q 039095 316 EYGGDSSSKAMCNASDYDVFDDPQKESEIRCQACNKIF 353 (492)
Q Consensus 316 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~C~~C~k~F 353 (492)
.-.|+.||..-.-.. +..-....|.+-..|..|+-.+
T Consensus 184 ~~~CPvCGs~P~~s~-~~~~~~~~G~RyL~CslC~teW 220 (305)
T TIGR01562 184 RTLCPACGSPPVASM-VRQGGKETGLRYLSCSLCATEW 220 (305)
T ss_pred CCcCCCCCChhhhhh-hcccCCCCCceEEEcCCCCCcc
Confidence 347888886542111 1100123566777888888643
No 266
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=20.07 E-value=68 Score=31.25 Aligned_cols=81 Identities=2% Similarity=-0.179 Sum_probs=50.1
Q ss_pred cccccccchhhhhhccCCCCccccccccccccChhHHHhhhhccCcccccccccccchhhhcChhhHhhhhhhccc-Ccc
Q 039095 20 KKSWKFSSFNHAASASASTQESQCKVCGKDFESLKALYGHMRHHSRRERERIQCKECGKALLSAKSLSNHMRVHSQ-KLR 98 (492)
Q Consensus 20 k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~F~~~~~L~~H~r~H~~~~~k~y~C~~C~k~F~~~~~L~~H~~~H~~-k~~ 98 (492)
..+.....+.-+...++...+..+.++.+.+.....+..|...+.++ .++.++.+...+....-+..+..+|.. +.+
T Consensus 311 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 388 (396)
T KOG2461|consen 311 LSLPKQLVLDQSEVPATVSVWTGETIPVRTPAGQLIYTQSHSMEVAE--PTDMAPNQIWKIYHTGVLGFLIITTDESECN 388 (396)
T ss_pred cccccccccccccccccccccCcCcccccccccccchhhhhhcccCC--CCcccccccccceeccccceeeeeccccccc
Confidence 33444445556666677777777888888888888888887777777 566666555555545555555555542 334
Q ss_pred cccc
Q 039095 99 ACNE 102 (492)
Q Consensus 99 ~C~~ 102 (492)
.+..
T Consensus 389 ~~~~ 392 (396)
T KOG2461|consen 389 NMSF 392 (396)
T ss_pred cccc
Confidence 3333
Done!