Query 037179
Match_columns 266
No_of_seqs 309 out of 2797
Neff 10.0
Searched_HMMs 46136
Date Fri Mar 29 09:29:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037179.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037179hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 100.0 7E-31 1.5E-35 206.2 9.4 133 77-239 127-265 (279)
2 KOG2462 C2H2-type Zn-finger pr 100.0 3.1E-30 6.7E-35 202.6 3.9 132 106-265 128-262 (279)
3 KOG1074 Transcriptional repres 99.9 1.2E-26 2.6E-31 205.1 7.3 57 79-135 352-408 (958)
4 KOG3608 Zn finger proteins [Ge 99.9 3.6E-24 7.7E-29 172.9 0.9 174 62-265 189-371 (467)
5 KOG1074 Transcriptional repres 99.8 8.6E-21 1.9E-25 168.4 3.7 112 77-212 602-729 (958)
6 KOG3608 Zn finger proteins [Ge 99.8 4.6E-20 1E-24 149.3 -0.1 155 81-265 180-340 (467)
7 KOG3576 Ovo and related transc 99.7 1.3E-17 2.8E-22 125.4 8.1 111 105-243 114-238 (267)
8 KOG3576 Ovo and related transc 99.6 2.4E-16 5.3E-21 118.6 4.1 114 74-215 111-235 (267)
9 KOG3623 Homeobox transcription 99.6 1.7E-16 3.7E-21 139.4 2.4 101 153-266 211-329 (1007)
10 KOG3623 Homeobox transcription 99.5 2E-15 4.3E-20 132.8 0.3 120 79-213 209-330 (1007)
11 PLN03086 PRLI-interacting fact 99.4 9.3E-13 2E-17 116.4 6.8 133 81-260 408-555 (567)
12 PLN03086 PRLI-interacting fact 99.3 5.7E-12 1.2E-16 111.5 8.7 120 80-243 433-566 (567)
13 PHA00733 hypothetical protein 99.2 4E-12 8.6E-17 92.3 3.2 64 178-242 60-124 (128)
14 PHA02768 hypothetical protein; 99.2 1.4E-11 2.9E-16 74.0 2.4 42 218-262 5-47 (55)
15 PHA00733 hypothetical protein 99.1 9.1E-12 2E-16 90.4 0.2 87 176-265 24-118 (128)
16 PHA02768 hypothetical protein; 99.1 2.6E-11 5.7E-16 72.7 1.6 43 152-208 5-47 (55)
17 PF13465 zf-H2C2_2: Zinc-finge 99.0 1.7E-10 3.7E-15 59.3 1.6 26 232-258 1-26 (26)
18 PF13465 zf-H2C2_2: Zinc-finge 98.9 9.7E-10 2.1E-14 56.5 2.2 26 179-204 1-26 (26)
19 KOG3993 Transcription factor ( 98.8 4.2E-10 9E-15 94.1 -0.9 54 79-132 266-319 (500)
20 PHA00616 hypothetical protein 98.5 2E-08 4.3E-13 57.4 0.7 38 218-256 1-39 (44)
21 PHA00732 hypothetical protein 98.5 6.5E-08 1.4E-12 63.8 1.9 29 172-203 9-38 (79)
22 PHA00732 hypothetical protein 98.5 7.4E-08 1.6E-12 63.6 2.1 45 192-239 1-46 (79)
23 KOG3993 Transcription factor ( 98.4 2.7E-08 5.8E-13 83.5 -0.7 84 148-243 263-382 (500)
24 PHA00616 hypothetical protein 98.0 3.2E-06 6.9E-11 48.4 1.3 34 153-198 2-35 (44)
25 COG5189 SFP1 Putative transcri 97.9 3.1E-06 6.7E-11 68.8 0.7 50 189-238 346-419 (423)
26 PF00096 zf-C2H2: Zinc finger, 97.9 9.3E-06 2E-10 40.3 1.9 21 219-239 1-22 (23)
27 PF00096 zf-C2H2: Zinc finger, 97.8 1.4E-05 3.1E-10 39.5 2.0 23 193-215 1-23 (23)
28 PF13894 zf-C2H2_4: C2H2-type 97.7 2.2E-05 4.7E-10 39.2 2.0 23 219-241 1-24 (24)
29 PF05605 zf-Di19: Drought indu 97.7 4.3E-05 9.3E-10 46.7 3.4 46 193-241 3-53 (54)
30 PF13912 zf-C2H2_6: C2H2-type 97.7 2.2E-05 4.8E-10 40.6 1.6 23 218-240 1-24 (27)
31 COG5189 SFP1 Putative transcri 97.5 5.4E-05 1.2E-09 61.8 1.9 50 215-264 346-416 (423)
32 PRK04860 hypothetical protein; 97.4 0.00014 3.1E-09 54.8 2.7 40 218-261 119-158 (160)
33 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00015 3.3E-09 50.3 2.6 72 154-241 1-74 (100)
34 PF13912 zf-C2H2_6: C2H2-type 97.3 0.00015 3.3E-09 37.3 1.9 25 108-132 1-25 (27)
35 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00017 3.7E-09 50.0 2.5 73 110-215 1-73 (100)
36 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00022 4.9E-09 35.3 2.1 23 193-215 1-23 (24)
37 PF05605 zf-Di19: Drought indu 97.2 0.00014 3.1E-09 44.4 1.1 40 218-258 2-43 (54)
38 COG5048 FOG: Zn-finger [Genera 97.0 0.0016 3.5E-08 57.4 6.3 152 79-257 288-457 (467)
39 smart00355 ZnF_C2H2 zinc finge 96.6 0.0015 3.3E-08 32.8 1.9 20 220-239 2-22 (26)
40 smart00355 ZnF_C2H2 zinc finge 96.6 0.0011 2.3E-08 33.3 1.3 23 193-215 1-23 (26)
41 PRK04860 hypothetical protein; 96.5 0.00072 1.6E-08 51.1 0.3 39 80-122 119-157 (160)
42 KOG2231 Predicted E3 ubiquitin 96.3 0.0073 1.6E-07 55.2 5.7 129 81-250 100-240 (669)
43 PF12874 zf-met: Zinc-finger o 96.2 0.0032 6.9E-08 31.6 1.5 21 219-239 1-22 (25)
44 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0035 7.5E-08 31.1 1.5 22 219-241 1-23 (24)
45 PF12874 zf-met: Zinc-finger o 95.9 0.0048 1E-07 30.9 1.5 23 109-131 1-23 (25)
46 PF09237 GAGA: GAGA factor; I 95.8 0.0072 1.6E-07 35.5 2.0 29 106-134 22-50 (54)
47 PF09237 GAGA: GAGA factor; I 95.7 0.0072 1.6E-07 35.5 1.8 25 189-213 21-45 (54)
48 KOG1146 Homeobox protein [Gene 95.6 0.0042 9.1E-08 60.2 0.7 149 81-260 437-632 (1406)
49 PF12171 zf-C2H2_jaz: Zinc-fin 95.3 0.011 2.3E-07 30.3 1.3 22 109-130 2-23 (27)
50 PF13909 zf-H2C2_5: C2H2-type 94.7 0.014 3.1E-07 28.8 0.9 22 109-131 1-22 (24)
51 PF12171 zf-C2H2_jaz: Zinc-fin 94.4 0.0092 2E-07 30.5 -0.4 21 193-213 2-22 (27)
52 KOG2482 Predicted C2H2-type Zn 93.8 0.13 2.8E-06 43.0 4.9 75 192-266 195-354 (423)
53 COG5048 FOG: Zn-finger [Genera 93.5 0.023 5.1E-07 50.0 0.3 132 107-265 288-437 (467)
54 KOG2893 Zn finger protein [Gen 93.5 0.025 5.4E-07 44.7 0.4 24 107-131 10-33 (341)
55 PF13913 zf-C2HC_2: zinc-finge 93.5 0.065 1.4E-06 26.8 1.8 19 194-213 4-22 (25)
56 KOG1146 Homeobox protein [Gene 93.3 0.034 7.4E-07 54.3 1.0 66 174-239 446-540 (1406)
57 smart00451 ZnF_U1 U1-like zinc 93.0 0.076 1.7E-06 28.8 1.8 21 218-238 3-24 (35)
58 smart00451 ZnF_U1 U1-like zinc 92.4 0.086 1.9E-06 28.6 1.5 23 192-214 3-25 (35)
59 KOG2893 Zn finger protein [Gen 92.0 0.059 1.3E-06 42.6 0.7 40 195-236 13-53 (341)
60 cd00350 rubredoxin_like Rubred 90.6 0.17 3.7E-06 27.2 1.4 10 245-254 16-25 (33)
61 KOG2231 Predicted E3 ubiquitin 90.5 0.37 8E-06 44.5 4.3 136 82-250 117-275 (669)
62 COG5236 Uncharacterized conser 89.8 0.22 4.8E-06 41.7 2.1 25 109-133 152-178 (493)
63 KOG2482 Predicted C2H2-type Zn 88.9 0.54 1.2E-05 39.5 3.6 23 109-131 196-218 (423)
64 KOG4173 Alpha-SNAP protein [In 88.1 0.16 3.5E-06 39.4 0.1 77 153-242 80-171 (253)
65 COG4049 Uncharacterized protei 85.9 0.37 8E-06 28.9 0.8 28 186-213 11-38 (65)
66 KOG2186 Cell growth-regulating 85.6 0.82 1.8E-05 36.8 2.9 46 153-213 4-49 (276)
67 PF09986 DUF2225: Uncharacteri 84.3 0.49 1.1E-05 37.8 1.1 44 78-121 3-61 (214)
68 KOG2785 C2H2-type Zn-finger pr 83.1 2.5 5.4E-05 36.2 4.8 49 191-239 165-242 (390)
69 PF09416 UPF1_Zn_bind: RNA hel 80.1 2.2 4.8E-05 31.8 3.1 53 104-161 10-69 (152)
70 smart00659 RPOLCX RNA polymera 79.9 1.2 2.6E-05 25.7 1.4 10 219-228 3-13 (44)
71 PF09538 FYDLN_acid: Protein o 79.8 1.4 3E-05 31.0 1.9 31 80-121 9-39 (108)
72 COG4049 Uncharacterized protei 79.0 0.85 1.8E-05 27.4 0.6 28 103-130 12-39 (65)
73 PF06524 NOA36: NOA36 protein; 78.6 1.3 2.8E-05 35.8 1.6 76 187-264 137-227 (314)
74 COG1996 RPC10 DNA-directed RNA 78.5 1.2 2.6E-05 26.2 1.1 10 218-227 6-16 (49)
75 PF15269 zf-C2H2_7: Zinc-finge 77.7 1.8 3.9E-05 24.7 1.6 21 219-239 21-42 (54)
76 PRK00398 rpoP DNA-directed RNA 77.4 1.6 3.5E-05 25.3 1.5 30 80-119 3-32 (46)
77 PF02892 zf-BED: BED zinc fing 77.1 2.3 5E-05 24.3 2.1 15 190-204 14-28 (45)
78 COG5236 Uncharacterized conser 77.1 3.5 7.5E-05 34.9 3.8 128 81-242 152-306 (493)
79 TIGR01384 TFS_arch transcripti 76.6 1.2 2.5E-05 31.1 0.8 28 82-121 2-29 (104)
80 PF10571 UPF0547: Uncharacteri 76.5 1.9 4.1E-05 21.8 1.3 10 110-119 16-25 (26)
81 KOG2071 mRNA cleavage and poly 76.1 1.9 4E-05 39.2 2.1 27 189-215 415-441 (579)
82 PF13719 zinc_ribbon_5: zinc-r 75.9 2 4.3E-05 23.7 1.5 34 81-119 3-36 (37)
83 smart00614 ZnF_BED BED zinc fi 75.7 2.7 5.8E-05 24.9 2.1 11 194-204 20-30 (50)
84 PF09538 FYDLN_acid: Protein o 75.0 2.6 5.6E-05 29.6 2.2 30 153-205 10-39 (108)
85 PRK00464 nrdR transcriptional 74.6 1.3 2.8E-05 33.3 0.6 43 81-125 1-45 (154)
86 TIGR02098 MJ0042_CXXC MJ0042 f 74.1 2.5 5.4E-05 23.3 1.6 34 81-119 3-36 (38)
87 PF13717 zinc_ribbon_4: zinc-r 72.5 2.7 5.9E-05 23.0 1.5 34 81-119 3-36 (36)
88 TIGR00622 ssl1 transcription f 72.3 4.5 9.7E-05 28.5 2.8 16 172-187 89-104 (112)
89 TIGR00622 ssl1 transcription f 72.2 5.6 0.00012 28.0 3.3 45 195-239 58-103 (112)
90 COG1198 PriA Primosomal protei 70.7 1.9 4.1E-05 40.8 0.9 13 189-201 472-484 (730)
91 PF12013 DUF3505: Protein of u 70.7 13 0.00027 26.1 5.0 21 193-213 81-105 (109)
92 PRK09678 DNA-binding transcrip 69.4 1.5 3.3E-05 28.3 -0.0 16 190-205 25-42 (72)
93 PRK14890 putative Zn-ribbon RN 69.4 6.4 0.00014 24.2 2.7 7 153-159 49-55 (59)
94 PF05290 Baculo_IE-1: Baculovi 69.1 2.8 6.2E-05 30.3 1.3 61 186-263 74-138 (140)
95 COG1592 Rubrerythrin [Energy p 69.1 2.3 5.1E-05 32.3 0.9 24 80-116 134-157 (166)
96 KOG2186 Cell growth-regulating 67.6 2.4 5.3E-05 34.2 0.8 46 81-129 4-49 (276)
97 TIGR02605 CxxC_CxxC_SSSS putat 67.2 2.5 5.5E-05 25.1 0.7 29 81-116 6-34 (52)
98 TIGR02300 FYDLN_acid conserved 66.1 4.9 0.00011 28.9 2.0 35 80-125 9-43 (129)
99 PRK06266 transcription initiat 65.1 3.4 7.3E-05 32.0 1.1 30 217-256 116-146 (178)
100 TIGR00373 conserved hypothetic 64.8 3.9 8.4E-05 31.0 1.4 30 217-256 108-138 (158)
101 COG1592 Rubrerythrin [Energy p 64.6 3.6 7.7E-05 31.3 1.1 13 187-199 144-156 (166)
102 PF05443 ROS_MUCR: ROS/MUCR tr 63.7 4.1 8.9E-05 29.7 1.3 23 216-241 70-93 (132)
103 KOG4124 Putative transcription 62.5 2 4.2E-05 36.4 -0.6 50 216-265 347-417 (442)
104 COG1997 RPL43A Ribosomal prote 62.3 6.3 0.00014 26.3 1.8 32 79-120 34-65 (89)
105 PF14353 CpXC: CpXC protein 62.0 1.1 2.3E-05 32.6 -2.0 48 81-128 2-58 (128)
106 PF13451 zf-trcl: Probable zin 61.9 5.2 0.00011 23.6 1.3 15 217-231 3-18 (49)
107 KOG4173 Alpha-SNAP protein [In 61.2 4 8.7E-05 31.9 0.9 42 172-213 114-167 (253)
108 PF07754 DUF1610: Domain of un 60.6 4 8.7E-05 20.1 0.5 10 245-254 15-24 (24)
109 smart00531 TFIIE Transcription 60.1 5.2 0.00011 29.8 1.4 18 107-124 98-115 (147)
110 COG4957 Predicted transcriptio 59.4 7 0.00015 28.3 1.8 23 219-245 77-100 (148)
111 COG2888 Predicted Zn-ribbon RN 59.0 7.1 0.00015 23.9 1.5 14 109-122 28-41 (61)
112 PF04606 Ogr_Delta: Ogr/Delta- 57.3 2.7 5.8E-05 24.6 -0.5 34 195-228 2-38 (47)
113 TIGR02300 FYDLN_acid conserved 57.2 8.8 0.00019 27.6 2.0 17 189-205 23-39 (129)
114 PRK06266 transcription initiat 55.5 7.1 0.00015 30.2 1.4 20 106-125 115-134 (178)
115 smart00531 TFIIE Transcription 54.4 9.4 0.0002 28.4 1.9 11 247-257 124-134 (147)
116 COG3091 SprT Zn-dependent meta 54.4 7.4 0.00016 29.0 1.3 33 217-254 116-148 (156)
117 PF05443 ROS_MUCR: ROS/MUCR tr 53.3 4.6 9.9E-05 29.5 0.1 29 77-108 69-97 (132)
118 PHA00626 hypothetical protein 52.6 6.4 0.00014 23.8 0.6 12 246-257 23-34 (59)
119 PF03604 DNA_RNApol_7kD: DNA d 52.5 8.6 0.00019 20.4 1.0 26 81-117 1-26 (32)
120 smart00154 ZnF_AN1 AN1-like Zi 51.4 7.1 0.00015 21.8 0.6 15 246-260 12-26 (39)
121 KOG2785 C2H2-type Zn-finger pr 51.1 15 0.00032 31.7 2.7 25 215-239 65-90 (390)
122 smart00834 CxxC_CXXC_SSSS Puta 51.0 7.2 0.00016 21.6 0.7 13 247-259 6-18 (41)
123 TIGR00595 priA primosomal prot 50.4 8.8 0.00019 35.0 1.4 12 190-201 251-262 (505)
124 PF12907 zf-met2: Zinc-binding 50.4 3.9 8.4E-05 23.0 -0.5 31 219-249 2-36 (40)
125 TIGR00373 conserved hypothetic 50.4 15 0.00033 27.7 2.5 36 186-228 103-139 (158)
126 PF08274 PhnA_Zn_Ribbon: PhnA 50.0 11 0.00024 19.7 1.2 25 82-117 4-28 (30)
127 PF09986 DUF2225: Uncharacteri 49.9 8.6 0.00019 30.7 1.1 55 106-161 3-57 (214)
128 KOG4167 Predicted DNA-binding 49.4 5.5 0.00012 37.2 -0.0 24 192-215 792-815 (907)
129 PF01363 FYVE: FYVE zinc finge 49.2 7 0.00015 24.7 0.5 12 191-202 24-35 (69)
130 KOG2906 RNA polymerase III sub 49.0 3.4 7.4E-05 28.1 -1.1 33 82-122 3-35 (105)
131 PF09723 Zn-ribbon_8: Zinc rib 48.8 7.6 0.00016 22.0 0.5 16 247-262 6-21 (42)
132 KOG4167 Predicted DNA-binding 48.6 4.2 9.1E-05 38.0 -0.9 25 108-132 792-816 (907)
133 smart00734 ZnF_Rad18 Rad18-lik 48.4 15 0.00033 18.4 1.5 19 194-213 3-21 (26)
134 PF04959 ARS2: Arsenite-resist 48.1 14 0.00031 29.4 2.1 27 216-242 75-102 (214)
135 PF01428 zf-AN1: AN1-like Zinc 47.4 6.5 0.00014 22.4 0.1 15 245-259 12-26 (43)
136 PF12760 Zn_Tnp_IS1595: Transp 47.3 13 0.00029 21.4 1.4 27 81-116 19-45 (46)
137 smart00440 ZnF_C2C2 C2C2 Zinc 47.2 7.2 0.00016 21.9 0.2 11 109-119 29-39 (40)
138 PF08790 zf-LYAR: LYAR-type C2 47.0 4.6 0.0001 20.7 -0.5 18 219-237 1-19 (28)
139 PF13240 zinc_ribbon_2: zinc-r 46.4 13 0.00029 18.0 1.1 8 83-90 2-9 (23)
140 PRK04023 DNA polymerase II lar 46.1 17 0.00037 35.6 2.6 10 80-89 626-635 (1121)
141 KOG2807 RNA polymerase II tran 46.1 32 0.0007 29.1 3.9 35 79-127 275-309 (378)
142 PRK14873 primosome assembly pr 45.7 13 0.00028 35.1 1.8 9 82-90 385-393 (665)
143 PF01780 Ribosomal_L37ae: Ribo 45.3 7.8 0.00017 26.1 0.2 31 79-119 34-64 (90)
144 COG5152 Uncharacterized conser 45.2 9.2 0.0002 29.7 0.6 16 190-205 194-209 (259)
145 KOG2593 Transcription initiati 44.2 14 0.00031 32.4 1.7 42 74-118 122-163 (436)
146 cd00065 FYVE FYVE domain; Zinc 44.1 11 0.00025 22.6 0.8 10 193-202 19-28 (57)
147 PF01096 TFIIS_C: Transcriptio 44.1 3.8 8.3E-05 22.8 -1.2 10 109-118 29-38 (39)
148 COG3357 Predicted transcriptio 44.1 8.9 0.00019 25.7 0.3 12 217-228 57-69 (97)
149 PTZ00255 60S ribosomal protein 43.3 14 0.0003 25.0 1.2 32 79-120 35-66 (90)
150 PF04959 ARS2: Arsenite-resist 42.9 15 0.00033 29.3 1.5 26 189-214 74-99 (214)
151 TIGR00595 priA primosomal prot 42.8 16 0.00035 33.3 1.9 35 82-117 215-249 (505)
152 PRK00432 30S ribosomal protein 42.6 15 0.00033 21.8 1.1 12 191-202 36-47 (50)
153 PF01286 XPA_N: XPA protein N- 41.0 14 0.0003 20.0 0.7 16 81-96 4-19 (34)
154 TIGR00280 L37a ribosomal prote 40.8 14 0.0003 25.0 0.8 31 79-119 34-64 (91)
155 PRK03824 hypA hydrogenase nick 40.0 13 0.00029 27.3 0.7 39 79-117 69-116 (135)
156 smart00064 FYVE Protein presen 39.7 15 0.00033 23.0 0.9 11 192-202 26-36 (68)
157 PRK04023 DNA polymerase II lar 38.9 35 0.00077 33.6 3.5 10 246-255 663-672 (1121)
158 PF10013 DUF2256: Uncharacteri 38.5 17 0.00036 20.7 0.8 15 111-125 11-25 (42)
159 PF02176 zf-TRAF: TRAF-type zi 38.1 17 0.00038 22.0 1.0 28 230-258 23-54 (60)
160 KOG3408 U1-like Zn-finger-cont 37.7 17 0.00036 26.0 0.9 22 218-239 57-79 (129)
161 PF09963 DUF2197: Uncharacteri 37.3 22 0.00048 21.7 1.3 11 244-254 29-39 (56)
162 PF04423 Rad50_zn_hook: Rad50 36.0 14 0.0003 22.1 0.3 13 248-260 22-34 (54)
163 PRK14714 DNA polymerase II lar 35.7 40 0.00087 34.1 3.4 27 217-255 691-718 (1337)
164 PRK12380 hydrogenase nickel in 35.7 24 0.00051 25.0 1.5 10 219-228 71-81 (113)
165 PF04810 zf-Sec23_Sec24: Sec23 35.5 16 0.00035 20.4 0.5 32 80-117 2-33 (40)
166 PF12013 DUF3505: Protein of u 35.3 25 0.00054 24.6 1.5 24 109-132 81-108 (109)
167 COG1998 RPS31 Ribosomal protei 35.2 26 0.00055 20.7 1.3 9 192-200 37-45 (51)
168 PF09845 DUF2072: Zn-ribbon co 34.4 17 0.00037 26.4 0.6 15 192-206 1-15 (131)
169 COG1655 Uncharacterized protei 34.3 14 0.00029 29.6 0.1 40 78-117 17-71 (267)
170 PF04216 FdhE: Protein involve 34.0 5.7 0.00012 33.3 -2.2 35 81-118 173-207 (290)
171 PRK03976 rpl37ae 50S ribosomal 33.6 20 0.00044 24.2 0.8 31 79-119 35-65 (90)
172 KOG0978 E3 ubiquitin ligase in 33.3 26 0.00057 33.1 1.7 35 223-263 661-695 (698)
173 KOG3362 Predicted BBOX Zn-fing 32.7 13 0.00028 27.4 -0.3 23 217-239 128-151 (156)
174 COG3677 Transposase and inacti 32.3 27 0.00059 25.4 1.3 16 244-259 51-66 (129)
175 PF06220 zf-U1: U1 zinc finger 31.7 25 0.00054 19.5 0.8 16 245-260 2-17 (38)
176 TIGR00100 hypA hydrogenase nic 31.5 27 0.00058 24.8 1.2 11 219-229 71-82 (115)
177 PRK05580 primosome assembly pr 31.4 25 0.00054 33.5 1.3 13 189-201 418-430 (679)
178 KOG2807 RNA polymerase II tran 31.2 96 0.0021 26.4 4.4 49 191-239 289-367 (378)
179 KOG1813 Predicted E3 ubiquitin 30.4 17 0.00037 30.3 0.0 16 190-205 239-254 (313)
180 PF05191 ADK_lid: Adenylate ki 30.2 28 0.0006 19.0 0.8 32 81-120 2-33 (36)
181 COG1773 Rubredoxin [Energy pro 29.7 25 0.00053 21.4 0.6 13 192-204 3-15 (55)
182 KOG2593 Transcription initiati 29.6 17 0.00036 32.0 -0.1 22 244-265 126-147 (436)
183 PF14787 zf-CCHC_5: GAG-polypr 29.6 31 0.00066 18.9 0.9 18 246-263 2-19 (36)
184 COG5151 SSL1 RNA polymerase II 29.5 24 0.00053 29.6 0.8 106 79-216 307-412 (421)
185 PF13248 zf-ribbon_3: zinc-rib 29.5 38 0.00081 16.8 1.2 8 81-88 3-10 (26)
186 COG4530 Uncharacterized protei 29.3 44 0.00095 23.4 1.8 15 189-203 23-37 (129)
187 cd00924 Cyt_c_Oxidase_Vb Cytoc 28.9 21 0.00046 24.5 0.3 20 184-204 72-91 (97)
188 PF13453 zf-TFIIB: Transcripti 28.8 37 0.00081 18.9 1.3 37 82-126 1-37 (41)
189 smart00504 Ubox Modified RING 28.7 47 0.001 20.1 1.9 30 222-258 18-47 (63)
190 PF07975 C1_4: TFIIH C1-like d 28.6 27 0.00058 20.9 0.6 25 107-131 20-44 (51)
191 PF14446 Prok-RING_1: Prokaryo 27.8 28 0.0006 21.1 0.6 14 247-260 6-19 (54)
192 COG4896 Uncharacterized protei 27.3 26 0.00056 21.6 0.4 41 153-204 3-43 (68)
193 PF10263 SprT-like: SprT-like 27.2 16 0.00034 27.3 -0.7 10 247-256 144-153 (157)
194 COG1198 PriA Primosomal protei 27.1 43 0.00094 32.1 2.1 32 81-116 436-470 (730)
195 smart00731 SprT SprT homologue 27.1 24 0.00051 26.2 0.3 12 245-256 132-143 (146)
196 KOG0782 Predicted diacylglycer 26.7 28 0.00062 31.8 0.7 32 177-208 238-269 (1004)
197 PF10276 zf-CHCC: Zinc-finger 26.1 24 0.00051 19.9 0.1 12 245-256 28-39 (40)
198 COG3364 Zn-ribbon containing p 25.9 35 0.00076 23.5 0.9 13 192-204 2-14 (112)
199 smart00661 RPOL9 RNA polymeras 25.6 49 0.0011 19.3 1.4 15 108-122 20-34 (52)
200 TIGR00244 transcriptional regu 25.3 29 0.00063 25.8 0.5 16 109-124 29-44 (147)
201 COG1327 Predicted transcriptio 25.1 32 0.00069 25.7 0.6 15 109-123 29-43 (156)
202 PF10083 DUF2321: Uncharacteri 25.1 28 0.0006 26.1 0.3 42 82-123 41-83 (158)
203 PF11789 zf-Nse: Zinc-finger o 25.1 58 0.0013 19.8 1.7 31 216-251 22-53 (57)
204 PF07282 OrfB_Zn_ribbon: Putat 24.9 52 0.0011 20.6 1.6 29 82-120 30-58 (69)
205 PF03811 Zn_Tnp_IS1: InsA N-te 24.9 21 0.00046 19.5 -0.2 19 180-198 17-35 (36)
206 TIGR01206 lysW lysine biosynth 24.3 46 0.001 20.1 1.1 15 247-261 3-17 (54)
207 COG1571 Predicted DNA-binding 24.2 47 0.001 29.4 1.6 31 81-122 351-381 (421)
208 KOG3408 U1-like Zn-finger-cont 24.2 48 0.001 23.7 1.3 24 191-214 56-79 (129)
209 PF04641 Rtf2: Rtf2 RING-finge 24.1 84 0.0018 25.9 3.0 52 189-259 110-163 (260)
210 PF15227 zf-C3HC4_4: zinc fing 23.8 38 0.00083 19.1 0.7 27 223-252 16-42 (42)
211 PF14447 Prok-RING_4: Prokaryo 23.6 42 0.00092 20.3 0.9 12 248-259 41-52 (55)
212 KOG2461 Transcription factor B 23.6 1.7E+02 0.0038 25.8 4.9 80 174-254 313-395 (396)
213 PF14803 Nudix_N_2: Nudix N-te 23.4 17 0.00037 19.6 -0.8 11 191-201 21-31 (34)
214 KOG0717 Molecular chaperone (D 23.2 59 0.0013 29.1 2.0 21 219-239 293-314 (508)
215 KOG0696 Serine/threonine prote 23.1 23 0.00049 31.4 -0.5 44 210-253 83-128 (683)
216 COG4888 Uncharacterized Zn rib 22.6 25 0.00055 24.1 -0.2 39 78-120 20-58 (104)
217 PF06397 Desulfoferrod_N: Desu 22.6 33 0.00072 18.8 0.3 12 245-256 5-16 (36)
218 PRK04351 hypothetical protein; 22.2 44 0.00096 25.0 0.9 34 80-121 112-145 (149)
219 PF01155 HypA: Hydrogenase exp 22.1 33 0.00072 24.2 0.3 10 219-228 71-81 (113)
220 PRK05978 hypothetical protein; 21.8 48 0.001 24.8 1.0 31 81-120 34-64 (148)
221 PF08209 Sgf11: Sgf11 (transcr 21.3 41 0.00089 18.0 0.4 12 246-257 4-15 (33)
222 COG4391 Uncharacterized protei 21.2 42 0.00091 20.8 0.5 15 183-197 15-29 (62)
223 KOG4377 Zn-finger protein [Gen 21.0 54 0.0012 28.7 1.3 23 218-240 401-426 (480)
224 PF07295 DUF1451: Protein of u 20.8 34 0.00073 25.5 0.1 10 151-160 111-120 (146)
225 PRK01343 zinc-binding protein; 20.0 64 0.0014 19.8 1.1 12 247-258 10-21 (57)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.97 E-value=7e-31 Score=206.24 Aligned_cols=133 Identities=27% Similarity=0.453 Sum_probs=121.8
Q ss_pred CCCCCCCCcccccccccCCCchhhhhhcC---CCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCc
Q 037179 77 SNNPSAKGNANVAAAKQYWIPTPEQILIG---FTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGI 153 (266)
Q Consensus 77 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~---~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~ 153 (266)
....|.|+.||+.+...++|.+|.++|-. .+.+.|++|||.|.....|.+|+|+|+ ...
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~------------------l~c 188 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT------------------LPC 188 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC------------------CCc
Confidence 45669999999999999999999999865 567999999999999999999999995 228
Q ss_pred CCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHHHh--CCCEEe-EcCccccCc
Q 037179 154 PCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEKNC--GKRWLC-VCGSDFKHK 230 (266)
Q Consensus 154 ~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~--~k~~~C-~C~k~F~~~ 230 (266)
+|.+|| |.|.....|+.|+|+|||||||.|..|+|+|..+++|+.|++|| .|+|+| .|+|+|...
T Consensus 189 ~C~iCG------------KaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~ 256 (279)
T KOG2462|consen 189 ECGICG------------KAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALK 256 (279)
T ss_pred cccccc------------ccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHH
Confidence 899999 99999999999999999999999999999999999999999987 799999 999999999
Q ss_pred hHHHHHHHh
Q 037179 231 RSLKDHIKA 239 (266)
Q Consensus 231 ~~L~~H~~~ 239 (266)
+.|.+|...
T Consensus 257 SyLnKH~ES 265 (279)
T KOG2462|consen 257 SYLNKHSES 265 (279)
T ss_pred HHHHHhhhh
Confidence 999999875
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.96 E-value=3.1e-30 Score=202.62 Aligned_cols=132 Identities=22% Similarity=0.389 Sum_probs=119.0
Q ss_pred CCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCCCCCCCccCCCCCCCCCCCCChhhHHHHhh
Q 037179 106 FTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYK 185 (266)
Q Consensus 106 ~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~ 185 (266)
...|+|..||+.+.+.++|.+|..+|..- . ....+.|..|+ |.|.....|..|+|
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~--------~-----s~ka~~C~~C~------------K~YvSmpALkMHir 182 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSL--------D-----SKKAFSCKYCG------------KVYVSMPALKMHIR 182 (279)
T ss_pred CCceeccccccccccccccchhhcccccc--------c-----ccccccCCCCC------------ceeeehHHHhhHhh
Confidence 44599999999999999999999999531 1 12238999999 99999999999999
Q ss_pred hhcCCCCeecccccccccchhhHHHHHHHh--CCCEEe-EcCccccCchHHHHHHHhhCCCCCCccCCCCCccccccccc
Q 037179 186 RKHGLKPFMCRKCGKFLAVKGDWRTHEKNC--GKRWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEVLDDASS 262 (266)
Q Consensus 186 ~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~--~k~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f~~~~~~ 262 (266)
+|+ -|++|.+|||.|.+..-|+.|+|+| ||||.| .|+|+|..+++|+.||++ |.+.|+|+|..|+|+|++++-|
T Consensus 183 TH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQT-HS~~K~~qC~~C~KsFsl~SyL 259 (279)
T KOG2462|consen 183 THT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQT-HSDVKKHQCPRCGKSFALKSYL 259 (279)
T ss_pred ccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHh-hcCCccccCcchhhHHHHHHHH
Confidence 997 6899999999999999999999964 999999 999999999999999999 8999999999999999998876
Q ss_pred ccC
Q 037179 263 SLL 265 (266)
Q Consensus 263 ~~~ 265 (266)
.-|
T Consensus 260 nKH 262 (279)
T KOG2462|consen 260 NKH 262 (279)
T ss_pred HHh
Confidence 543
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.93 E-value=1.2e-26 Score=205.11 Aligned_cols=57 Identities=19% Similarity=0.255 Sum_probs=52.0
Q ss_pred CCCCCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHHhhhhhcCCCC
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQMHMWGHGSQY 135 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~ 135 (266)
-.++|.+|.++|...+.|+.|+|.|+|++||+|++||..|+++.+|+.|...|+..|
T Consensus 352 ~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~ 408 (958)
T KOG1074|consen 352 FKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREKY 408 (958)
T ss_pred ccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeeccccC
Confidence 346899999999999999999999999999999999999999999999987774443
No 4
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.88 E-value=3.6e-24 Score=172.93 Aligned_cols=174 Identities=18% Similarity=0.250 Sum_probs=152.5
Q ss_pred chhccccCCCccCCCCCCCCCCCcccccccccCCCchhhhhh--cCCCceecccccccccChhhHHhhhhhcCCCCCCCC
Q 037179 62 VAVALHIGLPNYSHSSNNPSAKGNANVAAAKQYWIPTPEQIL--IGFTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGP 139 (266)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h--~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~ 139 (266)
+.....+.++.+.|++++...|+.||.-|.....|-.|.+.. ....+|.|..|.|.|.++..|..|++.|-.
T Consensus 189 ~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn------ 262 (467)
T KOG3608|consen 189 MGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN------ 262 (467)
T ss_pred hccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh------
Confidence 334566788888999999999999999999999999998644 456789999999999999999999998842
Q ss_pred CCcCCCCCCccCCcCCCCCCCCccCCCCCCCCCCCCChhhHHHHhh-hhcCCCCeecccccccccchhhHHHHHHHh-CC
Q 037179 140 ESLKGTQPRAILGIPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYK-RKHGLKPFMCRKCGKFLAVKGDWRTHEKNC-GK 217 (266)
Q Consensus 140 ~~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~-~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~-~k 217 (266)
.|+|+.|+ -+....+.|..|++ .|...|||+|+.|++.|.+.++|.+|..+| +-
T Consensus 263 ------------~ykCplCd------------mtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~ 318 (467)
T KOG3608|consen 263 ------------CYKCPLCD------------MTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKT 318 (467)
T ss_pred ------------cccccccc------------cCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcccc
Confidence 28999999 56677899999998 688999999999999999999999999998 55
Q ss_pred CEEe-E--cCccccCchHHHHHHHhhCCCCC--CccCCCCCcccccccccccC
Q 037179 218 RWLC-V--CGSDFKHKRSLKDHIKAFGSGHG--PFSRPFDGVEVLDDASSSLL 265 (266)
Q Consensus 218 ~~~C-~--C~k~F~~~~~L~~H~~~~H~~~~--p~~C~~C~k~f~~~~~~~~~ 265 (266)
-|+| . |..+|.+...|.+|++.||.|.. +|.|-.|++.|++..++.-|
T Consensus 319 ~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~H 371 (467)
T KOG3608|consen 319 VYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAH 371 (467)
T ss_pred ceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHH
Confidence 6999 4 99999999999999999998765 59999999999998887654
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.81 E-value=8.6e-21 Score=168.42 Aligned_cols=112 Identities=21% Similarity=0.306 Sum_probs=90.7
Q ss_pred CCCCCCCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCC
Q 037179 77 SNNPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCY 156 (266)
Q Consensus 77 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~ 156 (266)
...+..|-+|-++...++.|+.|+|+|+|++||+|.+||++|+++.+|+.|+.+|. .+|.....+.|+
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHk------------a~p~~R~q~ScP 669 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHK------------AKPPARVQFSCP 669 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccc------------cCccccccccCC
Confidence 34678999999999999999999999999999999999999999999999999994 223333568899
Q ss_pred ---CCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCC-CC------------eecccccccccchhhHHHHH
Q 037179 157 ---CCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGL-KP------------FMCRKCGKFLAVKGDWRTHE 212 (266)
Q Consensus 157 ---~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~-kp------------~~C~~C~k~f~~~~~L~~H~ 212 (266)
+|. +.|.....|..|+++|++. .+ -+|..|.+.|.....+..++
T Consensus 670 ~~~ic~------------~kftn~V~lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~ 729 (958)
T KOG1074|consen 670 STFICQ------------KKFTNAVTLPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQI 729 (958)
T ss_pred chhhhc------------ccccccccccceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhh
Confidence 999 7888888888888888732 22 35777777776555555554
No 6
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.76 E-value=4.6e-20 Score=149.28 Aligned_cols=155 Identities=15% Similarity=0.209 Sum_probs=138.7
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCCCCCC
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCYCCAE 160 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~~C~~ 160 (266)
..+..|-+.|..++.|.+|.+.|+++|...|+.||.-|.++..|..|.+..+.- ....|.|..|.
T Consensus 180 C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l--------------~~n~fqC~~C~- 244 (467)
T KOG3608|consen 180 CNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTEL--------------NTNSFQCAQCF- 244 (467)
T ss_pred ccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhh--------------cCCchHHHHHH-
Confidence 345689999999999999999999999999999999999999999999876421 11139999999
Q ss_pred CccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHHH-h--CCCEEe-EcCccccCchHHHHH
Q 037179 161 GCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEKN-C--GKRWLC-VCGSDFKHKRSLKDH 236 (266)
Q Consensus 161 ~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~-~--~k~~~C-~C~k~F~~~~~L~~H 236 (266)
|.|.+...|..|++.|.. -|+|+.|+.+....+.|..|++. | .|||+| .|++.|.+.+.|.+|
T Consensus 245 -----------KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 245 -----------KRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKH 311 (467)
T ss_pred -----------HHHhHHHHHHHHHHHhhh--cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHH
Confidence 999999999999999975 59999999999999999999995 3 899999 999999999999999
Q ss_pred HHhhCCCCCCccCCC--CCcccccccccccC
Q 037179 237 IKAFGSGHGPFSRPF--DGVEVLDDASSSLL 265 (266)
Q Consensus 237 ~~~~H~~~~p~~C~~--C~k~f~~~~~~~~~ 265 (266)
..+ |+ +..|.|+. |..+|.+...|+.|
T Consensus 312 ~~~-HS-~~~y~C~h~~C~~s~r~~~q~~~H 340 (467)
T KOG3608|consen 312 VQV-HS-KTVYQCEHPDCHYSVRTYTQMRRH 340 (467)
T ss_pred HHh-cc-ccceecCCCCCcHHHHHHHHHHHH
Confidence 997 67 77899999 99999998887654
No 7
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.73 E-value=1.3e-17 Score=125.41 Aligned_cols=111 Identities=25% Similarity=0.464 Sum_probs=97.2
Q ss_pred CCCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCCCCCCCccCCCCCCCCCCCCChhhHHHHh
Q 037179 105 GFTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCYCCAEGCKNSINHPKAKPLKDFRTLQTHY 184 (266)
Q Consensus 105 ~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~ 184 (266)
+...|.|.+|+|.|....-|++|++-|..- ..+-|..|| |.|.+.-.|++|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~v----------------kr~lct~cg------------kgfndtfdlkrh~ 165 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDV----------------KRHLCTFCG------------KGFNDTFDLKRHT 165 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHH----------------HHHHHhhcc------------Ccccchhhhhhhh
Confidence 345689999999999999999999999433 338899999 7888888999999
Q ss_pred hhhcCCCCeecccccccccchhhHHHHHHH-h------------CCCEEe-EcCccccCchHHHHHHHhhCCC
Q 037179 185 KRKHGLKPFMCRKCGKFLAVKGDWRTHEKN-C------------GKRWLC-VCGSDFKHKRSLKDHIKAFGSG 243 (266)
Q Consensus 185 ~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~-~------------~k~~~C-~C~k~F~~~~~L~~H~~~~H~~ 243 (266)
|+|+|.+||+|..|+|+|.+.-.|..|.+. | .|.|.| .||.+-.....+..|++.||..
T Consensus 166 rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 166 RTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred ccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 999999999999999999999999999872 2 578999 9999999999999999997654
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.62 E-value=2.4e-16 Score=118.63 Aligned_cols=114 Identities=22% Similarity=0.297 Sum_probs=102.0
Q ss_pred CCCCCCCCCCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCc
Q 037179 74 SHSSNNPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGI 153 (266)
Q Consensus 74 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~ 153 (266)
...+...+.|.+|+|.|.....|.+|++.|...+.|-|..||+.|...-.|++|+|+|+|-.+ |
T Consensus 111 sssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrp----------------y 174 (267)
T KOG3576|consen 111 SSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRP----------------Y 174 (267)
T ss_pred CCCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccc----------------c
Confidence 344567799999999999999999999999999999999999999999999999999976443 9
Q ss_pred CCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcC-----------CCCeecccccccccchhhHHHHHHHh
Q 037179 154 PCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHG-----------LKPFMCRKCGKFLAVKGDWRTHEKNC 215 (266)
Q Consensus 154 ~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~-----------~kp~~C~~C~k~f~~~~~L~~H~~~~ 215 (266)
+|..|+ |.|.+...|..|.+.-+| +|-|.|..||.+-.....+..|++.+
T Consensus 175 kc~~c~------------kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~ 235 (267)
T KOG3576|consen 175 KCSLCE------------KAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLH 235 (267)
T ss_pred chhhhh------------HHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhc
Confidence 999999 999999999999876544 46799999999999999999999865
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.61 E-value=1.7e-16 Score=139.41 Aligned_cols=101 Identities=28% Similarity=0.514 Sum_probs=89.5
Q ss_pred cCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhc--CCCCeecccccccccchhhHHHHHHHh---------------
Q 037179 153 IPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKH--GLKPFMCRKCGKFLAVKGDWRTHEKNC--------------- 215 (266)
Q Consensus 153 ~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~--~~kp~~C~~C~k~f~~~~~L~~H~~~~--------------- 215 (266)
..|..|. +.+.....|+.|++..+ .+--|.|..|..+|.+...|.+|+.+|
T Consensus 211 ltcpycd------------rgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~ 278 (1007)
T KOG3623|consen 211 LTCPYCD------------RGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSAL 278 (1007)
T ss_pred hcchhHH------------HHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhh
Confidence 6799999 77888899999988543 345699999999999999999999965
Q ss_pred CCCEEe-EcCccccCchHHHHHHHhhCCCCCCccCCCCCcccccccccccCC
Q 037179 216 GKRWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEVLDDASSSLLV 266 (266)
Q Consensus 216 ~k~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f~~~~~~~~~~ 266 (266)
.+.|+| .|||+|..+..|+.|+|+ |.|||||.|+.|+|+|....+-+.||
T Consensus 279 lRKFKCtECgKAFKfKHHLKEHlRI-HSGEKPfeCpnCkKRFSHSGSySSHm 329 (1007)
T KOG3623|consen 279 LRKFKCTECGKAFKFKHHLKEHLRI-HSGEKPFECPNCKKRFSHSGSYSSHM 329 (1007)
T ss_pred hccccccccchhhhhHHHHHhhhee-ecCCCCcCCcccccccccCCcccccc
Confidence 267999 999999999999999999 89999999999999999988877765
No 10
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.51 E-value=2e-15 Score=132.78 Aligned_cols=120 Identities=23% Similarity=0.324 Sum_probs=96.4
Q ss_pred CCCCCCcccccccccCCCchhhhhhc--CCCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCC
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQILI--GFTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCY 156 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~~h~--~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~ 156 (266)
....|+.|.+.+.....|+.|++.-. .+..|.|..|..+|..+..|.+|+.+|..... .............|+|.
T Consensus 209 qlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~d---qa~sltqsa~lRKFKCt 285 (1007)
T KOG3623|consen 209 QLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGD---QAISLTQSALLRKFKCT 285 (1007)
T ss_pred hhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCc---ccccccchhhhcccccc
Confidence 34689999999999999999986533 34569999999999999999999999943211 11111122334569999
Q ss_pred CCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHH
Q 037179 157 CCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEK 213 (266)
Q Consensus 157 ~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~ 213 (266)
.|+ |+|..+-.|+.|+|+|.|||||.|..|+|.|.....+-.|+.
T Consensus 286 ECg------------KAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 286 ECG------------KAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred ccc------------hhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 999 899999999999999999999999999999999998888886
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.37 E-value=9.3e-13 Score=116.36 Aligned_cols=133 Identities=20% Similarity=0.325 Sum_probs=97.4
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceeccc--ccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCCCC
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHV--CFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCYCC 158 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~--C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~~C 158 (266)
-.|+.|....... .|..|.... .-..-.|+. |+..|. +..+..| +.|..|
T Consensus 408 V~C~NC~~~i~l~-~l~lHe~~C-~r~~V~Cp~~~Cg~v~~-r~el~~H-------------------------~~C~~C 459 (567)
T PLN03086 408 VECRNCKHYIPSR-SIALHEAYC-SRHNVVCPHDGCGIVLR-VEEAKNH-------------------------VHCEKC 459 (567)
T ss_pred EECCCCCCccchh-HHHHHHhhC-CCcceeCCcccccceee-ccccccC-------------------------ccCCCC
Confidence 4688888776653 344555322 122235764 888772 2333333 569999
Q ss_pred CCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHHHh--CCCEEe-EcCccccC------
Q 037179 159 AEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEKNC--GKRWLC-VCGSDFKH------ 229 (266)
Q Consensus 159 ~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~--~k~~~C-~C~k~F~~------ 229 (266)
+ +.|. ...|..|+.+|+ +|+.|. ||+.+ ....|..|+.++ ++|+.| .|++.|..
T Consensus 460 g------------k~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d 522 (567)
T PLN03086 460 G------------QAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMD 522 (567)
T ss_pred C------------Cccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccc
Confidence 9 7775 578999999985 789999 99755 668999999875 899999 99999952
Q ss_pred ----chHHHHHHHhhCCCCCCccCCCCCccccccc
Q 037179 230 ----KRSLKDHIKAFGSGHGPFSRPFDGVEVLDDA 260 (266)
Q Consensus 230 ----~~~L~~H~~~~H~~~~p~~C~~C~k~f~~~~ 260 (266)
.+.|..|+.+ + |.+++.|..||+.|..+.
T Consensus 523 ~~d~~s~Lt~HE~~-C-G~rt~~C~~Cgk~Vrlrd 555 (567)
T PLN03086 523 VRDRLRGMSEHESI-C-GSRTAPCDSCGRSVMLKE 555 (567)
T ss_pred hhhhhhhHHHHHHh-c-CCcceEccccCCeeeehh
Confidence 4589999997 3 999999999999987654
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.32 E-value=5.7e-12 Score=111.46 Aligned_cols=120 Identities=19% Similarity=0.338 Sum_probs=96.8
Q ss_pred CCCCCc--ccccccccCCCchhhhhhcCCCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCCC
Q 037179 80 PSAKGN--ANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCYC 157 (266)
Q Consensus 80 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~~ 157 (266)
.-.|+. |+..|.. ..+..| +.|+.|++.|. ...|..|+.+|+. .+.|.
T Consensus 433 ~V~Cp~~~Cg~v~~r-~el~~H---------~~C~~Cgk~f~-~s~LekH~~~~Hk------------------pv~Cp- 482 (567)
T PLN03086 433 NVVCPHDGCGIVLRV-EEAKNH---------VHCEKCGQAFQ-QGEMEKHMKVFHE------------------PLQCP- 482 (567)
T ss_pred ceeCCcccccceeec-cccccC---------ccCCCCCCccc-hHHHHHHHHhcCC------------------CccCC-
Confidence 346874 9998843 344555 58999999996 6889999998752 18898
Q ss_pred CCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeeccccccccc----------chhhHHHHHHHh-CCCEEe-EcCc
Q 037179 158 CAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLA----------VKGDWRTHEKNC-GKRWLC-VCGS 225 (266)
Q Consensus 158 C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~----------~~~~L~~H~~~~-~k~~~C-~C~k 225 (266)
|+ +.+ .+..|..|+.+|.+.+|+.|..|++.|. ..+.|..|+.++ .+++.| .||+
T Consensus 483 Cg------------~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk 549 (567)
T PLN03086 483 CG------------VVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGR 549 (567)
T ss_pred CC------------CCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCC
Confidence 98 545 5689999999999999999999999995 245899999975 899999 9999
Q ss_pred cccCchHHHHHHHhhCCC
Q 037179 226 DFKHKRSLKDHIKAFGSG 243 (266)
Q Consensus 226 ~F~~~~~L~~H~~~~H~~ 243 (266)
.|..+ .|..|+..+|..
T Consensus 550 ~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 550 SVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred eeeeh-hHHHHHHHhhcC
Confidence 99776 588998887753
No 13
>PHA00733 hypothetical protein
Probab=99.25 E-value=4e-12 Score=92.32 Aligned_cols=64 Identities=22% Similarity=0.439 Sum_probs=53.6
Q ss_pred hhHHHHhhhhcCCCCeecccccccccchhhHHHHHHHhCCCEEe-EcCccccCchHHHHHHHhhCC
Q 037179 178 RTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEKNCGKRWLC-VCGSDFKHKRSLKDHIKAFGS 242 (266)
Q Consensus 178 ~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~~k~~~C-~C~k~F~~~~~L~~H~~~~H~ 242 (266)
+.|.+|+..+ +++||.|..||+.|.....|..|++.++.+|.| .|++.|.....|..|+...|.
T Consensus 60 ~~l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 60 SYLYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HHHHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3455565444 478999999999999999999999987788999 999999999999999988664
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.17 E-value=1.4e-11 Score=73.99 Aligned_cols=42 Identities=14% Similarity=0.316 Sum_probs=32.9
Q ss_pred CEEe-EcCccccCchHHHHHHHhhCCCCCCccCCCCCccccccccc
Q 037179 218 RWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEVLDDASS 262 (266)
Q Consensus 218 ~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f~~~~~~ 262 (266)
.|+| .||+.|.+.++|..|+++ |+ +||+|..|++.|.+.+.+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~-H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK-HN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh-cC--CcccCCcccceeccccee
Confidence 4778 888888888888888888 55 688888888888877654
No 15
>PHA00733 hypothetical protein
Probab=99.13 E-value=9.1e-12 Score=90.45 Aligned_cols=87 Identities=16% Similarity=0.137 Sum_probs=69.7
Q ss_pred ChhhHHHHhhhhcCCCCeecccccccccchhhHHHH--HH----H-hCCCEEe-EcCccccCchHHHHHHHhhCCCCCCc
Q 037179 176 DFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTH--EK----N-CGKRWLC-VCGSDFKHKRSLKDHIKAFGSGHGPF 247 (266)
Q Consensus 176 ~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H--~~----~-~~k~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~ 247 (266)
+...|..+-..-...+++.|.+|++.|.....|..| ++ + .++||.| .||+.|.....|..|+++ | +.+|
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~-h--~~~~ 100 (128)
T PHA00733 24 TLEELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRY-T--EHSK 100 (128)
T ss_pred CHHHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhc-C--CcCc
Confidence 345555554444457889999999999888777766 22 2 3789999 999999999999999997 4 4689
Q ss_pred cCCCCCcccccccccccC
Q 037179 248 SRPFDGVEVLDDASSSLL 265 (266)
Q Consensus 248 ~C~~C~k~f~~~~~~~~~ 265 (266)
.|++|++.|.+..++..|
T Consensus 101 ~C~~CgK~F~~~~sL~~H 118 (128)
T PHA00733 101 VCPVCGKEFRNTDSTLDH 118 (128)
T ss_pred cCCCCCCccCCHHHHHHH
Confidence 999999999999888765
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.11 E-value=2.6e-11 Score=72.75 Aligned_cols=43 Identities=16% Similarity=0.470 Sum_probs=27.5
Q ss_pred CcCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhH
Q 037179 152 GIPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDW 208 (266)
Q Consensus 152 ~~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L 208 (266)
+|+|+.|| +.|...++|..|+++|+ +||+|..|++.|.+.+.|
T Consensus 5 ~y~C~~CG------------K~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICG------------EIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhC------------CeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 36666666 66666666666666666 566666666666655544
No 17
>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=98.99 E-value=1.7e-10 Score=59.34 Aligned_cols=26 Identities=23% Similarity=0.648 Sum_probs=24.0
Q ss_pred HHHHHHHhhCCCCCCccCCCCCccccc
Q 037179 232 SLKDHIKAFGSGHGPFSRPFDGVEVLD 258 (266)
Q Consensus 232 ~L~~H~~~~H~~~~p~~C~~C~k~f~~ 258 (266)
+|.+|+++ |+|++||.|++|+++|.+
T Consensus 1 ~l~~H~~~-H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRT-HTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHH-HSSSSSEEESSSSEEESS
T ss_pred CHHHHhhh-cCCCCCCCCCCCcCeeCc
Confidence 58999998 899999999999999974
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.89 E-value=9.7e-10 Score=56.50 Aligned_cols=26 Identities=35% Similarity=0.777 Sum_probs=23.8
Q ss_pred hHHHHhhhhcCCCCeecccccccccc
Q 037179 179 TLQTHYKRKHGLKPFMCRKCGKFLAV 204 (266)
Q Consensus 179 ~l~~H~~~h~~~kp~~C~~C~k~f~~ 204 (266)
+|.+|+++|+|+|||.|++|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 48899999999999999999999964
No 19
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.83 E-value=4.2e-10 Score=94.08 Aligned_cols=54 Identities=17% Similarity=0.130 Sum_probs=46.3
Q ss_pred CCCCCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHHhhhhhcC
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQMHMWGHG 132 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~ 132 (266)
.-|.|..|...|...+.|.+|.-.-+-...|+|++|+|.|+-..+|..|.|-|.
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccC
Confidence 348999999999999999999743333345999999999999999999999883
No 20
>PHA00616 hypothetical protein
Probab=98.55 E-value=2e-08 Score=57.39 Aligned_cols=38 Identities=16% Similarity=0.404 Sum_probs=32.2
Q ss_pred CEEe-EcCccccCchHHHHHHHhhCCCCCCccCCCCCccc
Q 037179 218 RWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEV 256 (266)
Q Consensus 218 ~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f 256 (266)
||+| .||+.|.+++.|.+|++. |+|++|+.|+.=-..|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~-~hg~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS-VHKQNKLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH-hcCCCccceeEEEEEE
Confidence 6899 999999999999999998 7899999988644333
No 21
>PHA00732 hypothetical protein
Probab=98.48 E-value=6.5e-08 Score=63.81 Aligned_cols=29 Identities=21% Similarity=0.288 Sum_probs=13.7
Q ss_pred CCCCChhhHHHHhhh-hcCCCCeeccccccccc
Q 037179 172 KPLKDFRTLQTHYKR-KHGLKPFMCRKCGKFLA 203 (266)
Q Consensus 172 k~f~~~~~l~~H~~~-h~~~kp~~C~~C~k~f~ 203 (266)
+.|.....|..|++. |. ++.|+.||+.|.
T Consensus 9 k~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~ 38 (79)
T PHA00732 9 FTTVTLFALKQHARRNHT---LTKCPVCNKSYR 38 (79)
T ss_pred CccCCHHHHHHHhhcccC---CCccCCCCCEeC
Confidence 445555555555542 32 234555555554
No 22
>PHA00732 hypothetical protein
Probab=98.48 E-value=7.4e-08 Score=63.56 Aligned_cols=45 Identities=22% Similarity=0.462 Sum_probs=32.4
Q ss_pred CeecccccccccchhhHHHHHHHhCCCEEe-EcCccccCchHHHHHHHh
Q 037179 192 PFMCRKCGKFLAVKGDWRTHEKNCGKRWLC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 192 p~~C~~C~k~f~~~~~L~~H~~~~~k~~~C-~C~k~F~~~~~L~~H~~~ 239 (266)
||.|..||+.|.....|..|++.+..++.| .||+.|. .|..|+++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---Chhhhhcc
Confidence 577888888888888888887753345678 7888876 46777765
No 23
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.44 E-value=2.7e-08 Score=83.50 Aligned_cols=84 Identities=19% Similarity=0.401 Sum_probs=68.6
Q ss_pred CccCCcCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHHHhC----------C
Q 037179 148 RAILGIPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEKNCG----------K 217 (266)
Q Consensus 148 ~~~~~~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~~----------k 217 (266)
...+.|.|..|. ..|.+.-.|.+|.-.-...--|+|.+|+|+|.-..+|..|.|+|. .
T Consensus 263 n~iGdyiCqLCK------------~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~ 330 (500)
T KOG3993|consen 263 NVIGDYICQLCK------------EKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSP 330 (500)
T ss_pred ccHHHHHHHHHH------------HhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCC
Confidence 444569999999 667777889999754333345999999999999999999999651 1
Q ss_pred -------------------------CEEe-EcCccccCchHHHHHHHhhCCC
Q 037179 218 -------------------------RWLC-VCGSDFKHKRSLKDHIKAFGSG 243 (266)
Q Consensus 218 -------------------------~~~C-~C~k~F~~~~~L~~H~~~~H~~ 243 (266)
-|.| .|+|.|.+...|++|+.+||..
T Consensus 331 P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 331 PPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred ChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhcc
Confidence 2899 9999999999999999997754
No 24
>PHA00616 hypothetical protein
Probab=97.97 E-value=3.2e-06 Score=48.42 Aligned_cols=34 Identities=12% Similarity=0.236 Sum_probs=27.6
Q ss_pred cCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccc
Q 037179 153 IPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKC 198 (266)
Q Consensus 153 ~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C 198 (266)
|+|..|| +.|...+.|..|++.|+|++++.|+.-
T Consensus 2 YqC~~CG------------~~F~~~s~l~~H~r~~hg~~~~~~~~~ 35 (44)
T PHA00616 2 YQCLRCG------------GIFRKKKEVIEHLLSVHKQNKLTLEYF 35 (44)
T ss_pred Cccchhh------------HHHhhHHHHHHHHHHhcCCCccceeEE
Confidence 7788888 788888888888888888888887653
No 25
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.91 E-value=3.1e-06 Score=68.81 Aligned_cols=50 Identities=30% Similarity=0.543 Sum_probs=37.5
Q ss_pred CCCCeeccc--ccccccchhhHHHHHHHh---------------------CCCEEe-EcCccccCchHHHHHHH
Q 037179 189 GLKPFMCRK--CGKFLAVKGDWRTHEKNC---------------------GKRWLC-VCGSDFKHKRSLKDHIK 238 (266)
Q Consensus 189 ~~kp~~C~~--C~k~f~~~~~L~~H~~~~---------------------~k~~~C-~C~k~F~~~~~L~~H~~ 238 (266)
++|||+|++ |.|.|.....|+.|+.-+ .|||+| +|+|+|.....|+-|..
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 458888876 888888888888887621 377777 77777777777777753
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=97.88 E-value=9.3e-06 Score=40.25 Aligned_cols=21 Identities=38% Similarity=1.009 Sum_probs=13.3
Q ss_pred EEe-EcCccccCchHHHHHHHh
Q 037179 219 WLC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 219 ~~C-~C~k~F~~~~~L~~H~~~ 239 (266)
|.| .|++.|..+..|..|+++
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 456 666666666666666665
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.81 E-value=1.4e-05 Score=39.54 Aligned_cols=23 Identities=26% Similarity=0.668 Sum_probs=18.9
Q ss_pred eecccccccccchhhHHHHHHHh
Q 037179 193 FMCRKCGKFLAVKGDWRTHEKNC 215 (266)
Q Consensus 193 ~~C~~C~k~f~~~~~L~~H~~~~ 215 (266)
|.|..|++.|..+..|..|+++|
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 67888888888888888888753
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.74 E-value=2.2e-05 Score=39.15 Aligned_cols=23 Identities=30% Similarity=0.954 Sum_probs=14.4
Q ss_pred EEe-EcCccccCchHHHHHHHhhC
Q 037179 219 WLC-VCGSDFKHKRSLKDHIKAFG 241 (266)
Q Consensus 219 ~~C-~C~k~F~~~~~L~~H~~~~H 241 (266)
|.| .|++.|.+...|..|++++|
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 566 77777777777777777654
No 29
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.71 E-value=4.3e-05 Score=46.73 Aligned_cols=46 Identities=26% Similarity=0.533 Sum_probs=22.0
Q ss_pred eecccccccccchhhHHHHHHH-h---CCCEEe-EcCccccCchHHHHHHHhhC
Q 037179 193 FMCRKCGKFLAVKGDWRTHEKN-C---GKRWLC-VCGSDFKHKRSLKDHIKAFG 241 (266)
Q Consensus 193 ~~C~~C~k~f~~~~~L~~H~~~-~---~k~~~C-~C~k~F~~~~~L~~H~~~~H 241 (266)
|.|++|++ ......|..|... | .+.+.| +|...+. .+|..|+..+|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 45555555 2333445555442 1 234555 5555433 25556655543
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.69 E-value=2.2e-05 Score=40.57 Aligned_cols=23 Identities=26% Similarity=0.730 Sum_probs=17.3
Q ss_pred CEEe-EcCccccCchHHHHHHHhh
Q 037179 218 RWLC-VCGSDFKHKRSLKDHIKAF 240 (266)
Q Consensus 218 ~~~C-~C~k~F~~~~~L~~H~~~~ 240 (266)
||.| .|++.|.....|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 5777 7777777777777777764
No 31
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.48 E-value=5.4e-05 Score=61.76 Aligned_cols=50 Identities=18% Similarity=0.278 Sum_probs=41.2
Q ss_pred hCCCEEe---EcCccccCchHHHHHHHhhC------------------CCCCCccCCCCCccccccccccc
Q 037179 215 CGKRWLC---VCGSDFKHKRSLKDHIKAFG------------------SGHGPFSRPFDGVEVLDDASSSL 264 (266)
Q Consensus 215 ~~k~~~C---~C~k~F~~~~~L~~H~~~~H------------------~~~~p~~C~~C~k~f~~~~~~~~ 264 (266)
.+|||+| -|.|.|.....|+-|+.--| ...|||+|++|+|+|..---|+-
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCcccee
Confidence 3699999 49999999999999987434 13599999999999987666554
No 32
>PRK04860 hypothetical protein; Provisional
Probab=97.35 E-value=0.00014 Score=54.79 Aligned_cols=40 Identities=15% Similarity=0.343 Sum_probs=33.6
Q ss_pred CEEeEcCccccCchHHHHHHHhhCCCCCCccCCCCCcccccccc
Q 037179 218 RWLCVCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEVLDDAS 261 (266)
Q Consensus 218 ~~~C~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f~~~~~ 261 (266)
+|.|.|++ ....+.+|.++ |+|+++|.|..|++.|.....
T Consensus 119 ~Y~C~C~~---~~~~~rrH~ri-~~g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 119 PYRCKCQE---HQLTVRRHNRV-VRGEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEcCCCC---eeCHHHHHHHH-hcCCccEECCCCCceeEEecc
Confidence 57888877 67788999998 899999999999999876544
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.34 E-value=0.00015 Score=50.26 Aligned_cols=72 Identities=21% Similarity=0.478 Sum_probs=21.6
Q ss_pred CCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHHHh-CCCEEe-EcCccccCch
Q 037179 154 PCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEKNC-GKRWLC-VCGSDFKHKR 231 (266)
Q Consensus 154 ~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~-~k~~~C-~C~k~F~~~~ 231 (266)
+|..|+ ..|.....|..|+...++-..- ....+.....+..+.+.. ...+.| .|++.|....
T Consensus 1 ~C~~C~------------~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~ 64 (100)
T PF12756_consen 1 QCLFCD------------ESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSRE 64 (100)
T ss_dssp ----------------------------------------------------------------SSEEBSSSS-EESSHH
T ss_pred Cccccc------------cccccccccccccccccccccc----cccccccccccccccccccCCCCCCCccCCCCcCHH
Confidence 488888 7888889999999755443211 122223444444554433 347999 9999999999
Q ss_pred HHHHHHHhhC
Q 037179 232 SLKDHIKAFG 241 (266)
Q Consensus 232 ~L~~H~~~~H 241 (266)
.|..||+.++
T Consensus 65 ~l~~Hm~~~~ 74 (100)
T PF12756_consen 65 ALQEHMRSKH 74 (100)
T ss_dssp HHHHHHHHTT
T ss_pred HHHHHHcCcc
Confidence 9999999753
No 34
>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=97.33 E-value=0.00015 Score=37.30 Aligned_cols=25 Identities=36% Similarity=0.631 Sum_probs=22.5
Q ss_pred ceecccccccccChhhHHhhhhhcC
Q 037179 108 HFSCHVCFKTFNRYNNLQMHMWGHG 132 (266)
Q Consensus 108 ~~~C~~C~k~F~~~~~L~~H~~~h~ 132 (266)
||.|..|++.|.....|..|++.|.
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 5889999999999999999998874
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.30 E-value=0.00017 Score=50.00 Aligned_cols=73 Identities=22% Similarity=0.315 Sum_probs=20.9
Q ss_pred ecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcC
Q 037179 110 SCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHG 189 (266)
Q Consensus 110 ~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~ 189 (266)
+|..|+..|.....|..|+...++-. .. .. ..+.....+..+.+.-.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~-------------------~~-~~------------~~l~~~~~~~~~~~~~~- 47 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFD-------------------IP-DQ------------KYLVDPNRLLNYLRKKV- 47 (100)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred Cccccccccccccccccccccccccc-------------------cc-cc------------ccccccccccccccccc-
Confidence 48889999999999999986554311 01 00 11222233333333222
Q ss_pred CCCeecccccccccchhhHHHHHHHh
Q 037179 190 LKPFMCRKCGKFLAVKGDWRTHEKNC 215 (266)
Q Consensus 190 ~kp~~C~~C~k~f~~~~~L~~H~~~~ 215 (266)
...+.|..|++.|.....|..|++.+
T Consensus 48 ~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 48 KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 23689999999999999999999953
No 36
>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=97.27 E-value=0.00022 Score=35.31 Aligned_cols=23 Identities=35% Similarity=0.719 Sum_probs=17.3
Q ss_pred eecccccccccchhhHHHHHHHh
Q 037179 193 FMCRKCGKFLAVKGDWRTHEKNC 215 (266)
Q Consensus 193 ~~C~~C~k~f~~~~~L~~H~~~~ 215 (266)
|.|++|++.|.+...|..|++++
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 67888888888888888888753
No 37
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.20 E-value=0.00014 Score=44.41 Aligned_cols=40 Identities=25% Similarity=0.449 Sum_probs=32.6
Q ss_pred CEEe-EcCccccCchHHHHHHHhhCCCC-CCccCCCCCccccc
Q 037179 218 RWLC-VCGSDFKHKRSLKDHIKAFGSGH-GPFSRPFDGVEVLD 258 (266)
Q Consensus 218 ~~~C-~C~k~F~~~~~L~~H~~~~H~~~-~p~~C~~C~k~f~~ 258 (266)
.|.| .|++.| ....|..|....|..+ +.+.|++|...+..
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~ 43 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCEDEHRSESKNVVCPICSSRVTD 43 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHhHCcCCCCCccCCCchhhhhh
Confidence 4889 999955 5678999998888875 57999999987653
No 38
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=97.00 E-value=0.0016 Score=57.38 Aligned_cols=152 Identities=17% Similarity=0.154 Sum_probs=99.1
Q ss_pred CCCCCCcccccccccCCCchhhh--hhcCC--Cceecc--cccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCC
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQ--ILIGF--THFSCH--VCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILG 152 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~--~h~~~--k~~~C~--~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~ 152 (266)
.++.|..|...|.....|.+|.+ .|.++ +++.|. .|++.|.+...+..|...|.+...
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~---------------- 351 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP---------------- 351 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc----------------
Confidence 57999999999999999999999 89999 999999 799999999999999999975432
Q ss_pred cCCCCCCCCccCCCCCCCCCCCCChh-----hHHHHhhhhcCCCCeecc--cccccccchhhHHHHHHHh--CC--CEEe
Q 037179 153 IPCYCCAEGCKNSINHPKAKPLKDFR-----TLQTHYKRKHGLKPFMCR--KCGKFLAVKGDWRTHEKNC--GK--RWLC 221 (266)
Q Consensus 153 ~~C~~C~~~~~~~~~~~~~k~f~~~~-----~l~~H~~~h~~~kp~~C~--~C~k~f~~~~~L~~H~~~~--~k--~~~C 221 (266)
..+..-... +.+.... ........-...+.+.+. .|-..+.....+..|...+ .. .+.+
T Consensus 352 ~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 421 (467)
T COG5048 352 AKEKLLNSS----------SKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKN 421 (467)
T ss_pred cccccccCc----------cccccccCCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCC
Confidence 111111100 1111000 011111112223344443 3555666666666665543 23 4445
Q ss_pred -EcCccccCchHHHHHHHhhCCCCCCccCCCCCcccc
Q 037179 222 -VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEVL 257 (266)
Q Consensus 222 -~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f~ 257 (266)
.|.+.|.....|..|++. |....++.|..++..+.
T Consensus 422 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 457 (467)
T COG5048 422 PPCSKSFNRHYNLIPHKKI-HTNHAPLLCSILKSFRR 457 (467)
T ss_pred CcchhhccCcccccccccc-cccCCceeeccccccch
Confidence 788888888888888887 66666666666554443
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.62 E-value=0.0015 Score=32.76 Aligned_cols=20 Identities=45% Similarity=0.974 Sum_probs=11.8
Q ss_pred Ee-EcCccccCchHHHHHHHh
Q 037179 220 LC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 220 ~C-~C~k~F~~~~~L~~H~~~ 239 (266)
.| .|++.|.....|..|++.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHH
Confidence 45 566666666666666554
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.62 E-value=0.0011 Score=33.33 Aligned_cols=23 Identities=26% Similarity=0.700 Sum_probs=20.8
Q ss_pred eecccccccccchhhHHHHHHHh
Q 037179 193 FMCRKCGKFLAVKGDWRTHEKNC 215 (266)
Q Consensus 193 ~~C~~C~k~f~~~~~L~~H~~~~ 215 (266)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 57999999999999999999865
No 41
>PRK04860 hypothetical protein; Provisional
Probab=96.53 E-value=0.00072 Score=51.06 Aligned_cols=39 Identities=15% Similarity=0.235 Sum_probs=33.9
Q ss_pred CCCCCcccccccccCCCchhhhhhcCCCceecccccccccChh
Q 037179 80 PSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYN 122 (266)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~ 122 (266)
+|.|. |+. ....+.+|.++|.++++|.|..|+..|....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 59998 997 5666899999999999999999999986543
No 42
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.35 E-value=0.0073 Score=55.23 Aligned_cols=129 Identities=19% Similarity=0.286 Sum_probs=73.6
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCCCCCC
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCYCCAE 160 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~~C~~ 160 (266)
+.|.+|++.|..... .-.|..| -.|.....|..|++..++. +-|..|-.
T Consensus 100 ~~C~~C~~~~~~~~~------------~~~~~~c-~~~~s~~~Lk~H~~~~H~~------------------~~c~lC~~ 148 (669)
T KOG2231|consen 100 HSCHICDRRFRALYN------------KKECLHC-TEFKSVENLKNHMRDQHKL------------------HLCSLCLQ 148 (669)
T ss_pred hhcCccccchhhhcc------------cCCCccc-cchhHHHHHHHHHHHhhhh------------------hccccccc
Confidence 567777766643211 1236666 5566778888888533221 45666653
Q ss_pred CccCCCCCCCCCCCCChhhHHHHhhhhc-CCCC----eecccccccccchhhHHHHHHHhCCCEEe-Ec------Ccccc
Q 037179 161 GCKNSINHPKAKPLKDFRTLQTHYKRKH-GLKP----FMCRKCGKFLAVKGDWRTHEKNCGKRWLC-VC------GSDFK 228 (266)
Q Consensus 161 ~~~~~~~~~~~k~f~~~~~l~~H~~~h~-~~kp----~~C~~C~k~f~~~~~L~~H~~~~~k~~~C-~C------~k~F~ 228 (266)
.-+-.++- ....+...|..|+..-. +++. -.|..|...|.....|.+|++. ..|.| .| +.-|.
T Consensus 149 ~~kif~~e---~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~--~h~~chfC~~~~~~neyy~ 223 (669)
T KOG2231|consen 149 NLKIFINE---RKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRF--DHEFCHFCDYKTGQNEYYN 223 (669)
T ss_pred cceeeeee---eehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhcc--ceeheeecCcccccchhcc
Confidence 21100000 11234566777766421 1222 3688888888888888888883 33456 55 34466
Q ss_pred CchHHHHHHHhhCCCCCCccCC
Q 037179 229 HKRSLKDHIKAFGSGHGPFSRP 250 (266)
Q Consensus 229 ~~~~L~~H~~~~H~~~~p~~C~ 250 (266)
....|..|-|..| |.|+
T Consensus 224 ~~~dLe~HfR~~H-----flCE 240 (669)
T KOG2231|consen 224 DYDDLEEHFRKGH-----FLCE 240 (669)
T ss_pred cchHHHHHhhhcC-----cccc
Confidence 7778888888755 5666
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.18 E-value=0.0032 Score=31.56 Aligned_cols=21 Identities=29% Similarity=0.975 Sum_probs=13.8
Q ss_pred EEe-EcCccccCchHHHHHHHh
Q 037179 219 WLC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 219 ~~C-~C~k~F~~~~~L~~H~~~ 239 (266)
|.| +|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 456 666666666666666654
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.16 E-value=0.0035 Score=31.13 Aligned_cols=22 Identities=32% Similarity=0.615 Sum_probs=14.0
Q ss_pred EEe-EcCccccCchHHHHHHHhhC
Q 037179 219 WLC-VCGSDFKHKRSLKDHIKAFG 241 (266)
Q Consensus 219 ~~C-~C~k~F~~~~~L~~H~~~~H 241 (266)
|+| .|+.... ...|.+|++++|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 567 7777666 667777777754
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.93 E-value=0.0048 Score=30.87 Aligned_cols=23 Identities=35% Similarity=0.806 Sum_probs=19.8
Q ss_pred eecccccccccChhhHHhhhhhc
Q 037179 109 FSCHVCFKTFNRYNNLQMHMWGH 131 (266)
Q Consensus 109 ~~C~~C~k~F~~~~~L~~H~~~h 131 (266)
|.|..|++.|.....|..|++.+
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 67999999999999999998754
No 46
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.80 E-value=0.0072 Score=35.53 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=17.7
Q ss_pred CCceecccccccccChhhHHhhhhhcCCC
Q 037179 106 FTHFSCHVCFKTFNRYNNLQMHMWGHGSQ 134 (266)
Q Consensus 106 ~k~~~C~~C~k~F~~~~~L~~H~~~h~~~ 134 (266)
+.|-.|++|+..+.+..+|.+|+.++++.
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 45677888888888888888888766544
No 47
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.74 E-value=0.0072 Score=35.52 Aligned_cols=25 Identities=24% Similarity=0.538 Sum_probs=12.4
Q ss_pred CCCCeecccccccccchhhHHHHHH
Q 037179 189 GLKPFMCRKCGKFLAVKGDWRTHEK 213 (266)
Q Consensus 189 ~~kp~~C~~C~k~f~~~~~L~~H~~ 213 (266)
.+.|-.|++|+..+.+..+|++|+.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHH
T ss_pred cCCCCCCCcchhhccchhhHHHHHH
Confidence 3556666666666666666666664
No 48
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=95.58 E-value=0.0042 Score=60.20 Aligned_cols=149 Identities=17% Similarity=0.258 Sum_probs=95.8
Q ss_pred CCCCcccccccccCCCchhhh-hhcCCCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCCCCC
Q 037179 81 SAKGNANVAAAKQYWIPTPEQ-ILIGFTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCYCCA 159 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~-~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~~C~ 159 (266)
-.|.-|+..+.....+..|+. ++...+.|.|+.|+..|+....|..|+|.-+-+.. -.+|.
T Consensus 437 ~e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~------------------~~~c~ 498 (1406)
T KOG1146|consen 437 VELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQ------------------SAYCK 498 (1406)
T ss_pred ccccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccc------------------hhHhH
Confidence 356667777777777777763 56667889999999999999999999997432211 01111
Q ss_pred CCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHHH--h----------------------
Q 037179 160 EGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEKN--C---------------------- 215 (266)
Q Consensus 160 ~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~--~---------------------- 215 (266)
.+.....+.+-...--+.+||.|..|..++..+..|.+|+.. |
T Consensus 499 -------------~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v 565 (1406)
T KOG1146|consen 499 -------------AGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASV 565 (1406)
T ss_pred -------------hccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhh
Confidence 000000011111112245678888888888888888888751 0
Q ss_pred ---------------------CCCEEe-EcCccccCchHHHHHHHhhCCCCCCccCCCCCccccccc
Q 037179 216 ---------------------GKRWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEVLDDA 260 (266)
Q Consensus 216 ---------------------~k~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f~~~~ 260 (266)
.-++.| +|+..-+-..+|+.||..-+.-..|.-|..|+-.+...+
T Consensus 566 ~s~~P~~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~~ 632 (1406)
T KOG1146|consen 566 TSAVPEEAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTASPSSSPPSLVLQQNITSSLAS 632 (1406)
T ss_pred cccCcccccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccCCCCCChHHHhhhcchhhccc
Confidence 123789 999998888889999886444444566766666665544
No 49
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.27 E-value=0.011 Score=30.31 Aligned_cols=22 Identities=41% Similarity=0.706 Sum_probs=18.8
Q ss_pred eecccccccccChhhHHhhhhh
Q 037179 109 FSCHVCFKTFNRYNNLQMHMWG 130 (266)
Q Consensus 109 ~~C~~C~k~F~~~~~L~~H~~~ 130 (266)
|.|..|++.|.....|..|++.
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 6789999999999999988864
No 50
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.73 E-value=0.014 Score=28.82 Aligned_cols=22 Identities=27% Similarity=0.563 Sum_probs=16.0
Q ss_pred eecccccccccChhhHHhhhhhc
Q 037179 109 FSCHVCFKTFNRYNNLQMHMWGH 131 (266)
Q Consensus 109 ~~C~~C~k~F~~~~~L~~H~~~h 131 (266)
|.|+.|+.... ...|.+|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 67888888777 78888888775
No 51
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.36 E-value=0.0092 Score=30.54 Aligned_cols=21 Identities=29% Similarity=0.814 Sum_probs=11.4
Q ss_pred eecccccccccchhhHHHHHH
Q 037179 193 FMCRKCGKFLAVKGDWRTHEK 213 (266)
Q Consensus 193 ~~C~~C~k~f~~~~~L~~H~~ 213 (266)
|-|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 445555555555555555543
No 52
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=93.75 E-value=0.13 Score=42.98 Aligned_cols=75 Identities=13% Similarity=0.241 Sum_probs=58.0
Q ss_pred CeecccccccccchhhHHHHHHH--hC-----------------------------------------------------
Q 037179 192 PFMCRKCGKFLAVKGDWRTHEKN--CG----------------------------------------------------- 216 (266)
Q Consensus 192 p~~C~~C~k~f~~~~~L~~H~~~--~~----------------------------------------------------- 216 (266)
.++|-.|.|.|+.+..|+.||+. |.
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 37999999999999999999982 10
Q ss_pred -CC--EEe-EcCccccCchHHHHHHHhhCC--------------------------CCCCccCCCCCcccccccccccCC
Q 037179 217 -KR--WLC-VCGSDFKHKRSLKDHIKAFGS--------------------------GHGPFSRPFDGVEVLDDASSSLLV 266 (266)
Q Consensus 217 -k~--~~C-~C~k~F~~~~~L~~H~~~~H~--------------------------~~~p~~C~~C~k~f~~~~~~~~~~ 266 (266)
.+ -+| .|....-....|..||+++|. ..+.-.|-.|.-.|-.+..+.-||
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 01 479 999999889999999999884 122345888888888877665443
No 53
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.51 E-value=0.023 Score=49.96 Aligned_cols=132 Identities=15% Similarity=0.164 Sum_probs=95.6
Q ss_pred CceecccccccccChhhHHhhhh--hcCCCCCCCCCCcCCCCCCccCCcCCC--CCCCCccCCCCCCCCCCCCChhhHHH
Q 037179 107 THFSCHVCFKTFNRYNNLQMHMW--GHGSQYRKGPESLKGTQPRAILGIPCY--CCAEGCKNSINHPKAKPLKDFRTLQT 182 (266)
Q Consensus 107 k~~~C~~C~k~F~~~~~L~~H~~--~h~~~~~~~~~~~~~~~~~~~~~~~C~--~C~~~~~~~~~~~~~k~f~~~~~l~~ 182 (266)
.++.|..|...|.....|..|.+ .|.++. ...+.|. .|+ +.|.....+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~--------------~~~~~~p~~~~~------------~~~~~~~~~~~ 341 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGES--------------LKPFSCPYSLCG------------KLFSRNDALKR 341 (467)
T ss_pred cCCCCccccCCcccccccccccccccccccc--------------CCceeeeccCCC------------ccccccccccC
Confidence 46889999999999999999999 786541 1227777 788 88999999999
Q ss_pred HhhhhcCCCCeeccc--ccccccchhhHHHHHH-------HhCCCEEe---EcCccccCchHHHHHHHhhCCCCC--Ccc
Q 037179 183 HYKRKHGLKPFMCRK--CGKFLAVKGDWRTHEK-------NCGKRWLC---VCGSDFKHKRSLKDHIKAFGSGHG--PFS 248 (266)
Q Consensus 183 H~~~h~~~kp~~C~~--C~k~f~~~~~L~~H~~-------~~~k~~~C---~C~k~F~~~~~L~~H~~~~H~~~~--p~~ 248 (266)
|..+|++.+++.+.. +.+.+.....-..++. ...+.+.+ .|-..+.....+..|... |...+ .+.
T Consensus 342 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 420 (467)
T COG5048 342 HILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIIT-HLSFRPYNCK 420 (467)
T ss_pred CcccccCCCccccccccCccccccccCCCCccchhhccCccCCccccccccchhhhhcccccccccccc-ccccCCcCCC
Confidence 999999988887754 5555544433111111 12566777 588899999999998876 66655 567
Q ss_pred CCCCCcccccccccccC
Q 037179 249 RPFDGVEVLDDASSSLL 265 (266)
Q Consensus 249 C~~C~k~f~~~~~~~~~ 265 (266)
+..|.+.|.....+..+
T Consensus 421 ~~~~~~~~~~~~~~~~~ 437 (467)
T COG5048 421 NPPCSKSFNRHYNLIPH 437 (467)
T ss_pred CCcchhhccCccccccc
Confidence 78899888877665543
No 54
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=93.49 E-value=0.025 Score=44.67 Aligned_cols=24 Identities=21% Similarity=0.433 Sum_probs=15.1
Q ss_pred CceecccccccccChhhHHhhhhhc
Q 037179 107 THFSCHVCFKTFNRYNNLQMHMWGH 131 (266)
Q Consensus 107 k~~~C~~C~k~F~~~~~L~~H~~~h 131 (266)
|+| |-+|.+.|....-|.+|++..
T Consensus 10 kpw-cwycnrefddekiliqhqkak 33 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEKILIQHQKAK 33 (341)
T ss_pred Cce-eeecccccchhhhhhhhhhhc
Confidence 444 666666666666666666543
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.47 E-value=0.065 Score=26.85 Aligned_cols=19 Identities=32% Similarity=0.618 Sum_probs=10.2
Q ss_pred ecccccccccchhhHHHHHH
Q 037179 194 MCRKCGKFLAVKGDWRTHEK 213 (266)
Q Consensus 194 ~C~~C~k~f~~~~~L~~H~~ 213 (266)
.|..||+.| ....|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 455566666 4445555554
No 56
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=93.28 E-value=0.034 Score=54.26 Aligned_cols=66 Identities=21% Similarity=0.392 Sum_probs=52.2
Q ss_pred CCChhhHHHHhh-hhcCCCCeecccccccccchhhHHHHHHH---------------------------hCCCEEe-EcC
Q 037179 174 LKDFRTLQTHYK-RKHGLKPFMCRKCGKFLAVKGDWRTHEKN---------------------------CGKRWLC-VCG 224 (266)
Q Consensus 174 f~~~~~l~~H~~-~h~~~kp~~C~~C~k~f~~~~~L~~H~~~---------------------------~~k~~~C-~C~ 224 (266)
+.....+..|+. .|.-.|.|+|..|+..|.....|-.|+|+ ..+||.| .|.
T Consensus 446 ~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~ 525 (1406)
T KOG1146|consen 446 LESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACN 525 (1406)
T ss_pred hhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeee
Confidence 333334444433 45556889999999999999999999984 1378999 999
Q ss_pred ccccCchHHHHHHHh
Q 037179 225 SDFKHKRSLKDHIKA 239 (266)
Q Consensus 225 k~F~~~~~L~~H~~~ 239 (266)
.++..+..|.+|+..
T Consensus 526 ~stttng~LsihlqS 540 (1406)
T KOG1146|consen 526 YSTTTNGNLSIHLQS 540 (1406)
T ss_pred eeeecchHHHHHHHH
Confidence 999999999999874
No 57
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.01 E-value=0.076 Score=28.78 Aligned_cols=21 Identities=29% Similarity=0.793 Sum_probs=13.8
Q ss_pred CEEe-EcCccccCchHHHHHHH
Q 037179 218 RWLC-VCGSDFKHKRSLKDHIK 238 (266)
Q Consensus 218 ~~~C-~C~k~F~~~~~L~~H~~ 238 (266)
+|.| .|++.|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4666 67777776666666654
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=92.45 E-value=0.086 Score=28.58 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=20.1
Q ss_pred CeecccccccccchhhHHHHHHH
Q 037179 192 PFMCRKCGKFLAVKGDWRTHEKN 214 (266)
Q Consensus 192 p~~C~~C~k~f~~~~~L~~H~~~ 214 (266)
+|.|.+|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999873
No 59
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=92.01 E-value=0.059 Score=42.63 Aligned_cols=40 Identities=23% Similarity=0.465 Sum_probs=21.9
Q ss_pred cccccccccchhhHHHHHHHhCCCEEe-EcCccccCchHHHHH
Q 037179 195 CRKCGKFLAVKGDWRTHEKNCGKRWLC-VCGSDFKHKRSLKDH 236 (266)
Q Consensus 195 C~~C~k~f~~~~~L~~H~~~~~k~~~C-~C~k~F~~~~~L~~H 236 (266)
|=+|++.|....-|++|++ .|.|+| +|-|...+--.|..|
T Consensus 13 cwycnrefddekiliqhqk--akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK--AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhh--hccceeeeehhhhccCCCceee
Confidence 4455555655555555555 455556 565554444445444
No 60
>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=90.62 E-value=0.17 Score=27.20 Aligned_cols=10 Identities=30% Similarity=0.657 Sum_probs=6.1
Q ss_pred CCccCCCCCc
Q 037179 245 GPFSRPFDGV 254 (266)
Q Consensus 245 ~p~~C~~C~k 254 (266)
.|..|++||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 5566666663
No 61
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.55 E-value=0.37 Score=44.52 Aligned_cols=136 Identities=19% Similarity=0.295 Sum_probs=82.1
Q ss_pred CCCcccccccccCCCchhh-hhhcCCCceecccccc---cc------cChhhHHhhhhhcCCCCCCCCCCcCCCCCCccC
Q 037179 82 AKGNANVAAAKQYWIPTPE-QILIGFTHFSCHVCFK---TF------NRYNNLQMHMWGHGSQYRKGPESLKGTQPRAIL 151 (266)
Q Consensus 82 ~C~~C~~~f~~~~~l~~H~-~~h~~~k~~~C~~C~k---~F------~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~ 151 (266)
.|..| -.|.....|..|+ ..|-. +.|..|-. .| -+...|..|+..-.. +..+..+
T Consensus 117 ~~~~c-~~~~s~~~Lk~H~~~~H~~---~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~----d~~s~rG------- 181 (669)
T KOG2231|consen 117 ECLHC-TEFKSVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDP----DDESCRG------- 181 (669)
T ss_pred CCccc-cchhHHHHHHHHHHHhhhh---hccccccccceeeeeeeehehHHHHHHHHhcCCC----ccccccC-------
Confidence 69999 7888888899999 44533 44555432 12 344667777754321 0001111
Q ss_pred CcCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccc------cccccchhhHHHHHHHhCCCEEe---E
Q 037179 152 GIPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKC------GKFLAVKGDWRTHEKNCGKRWLC---V 222 (266)
Q Consensus 152 ~~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C------~k~f~~~~~L~~H~~~~~k~~~C---~ 222 (266)
.-.|..|. ..|.....|.+|++.++ |.|..| +-.|....+|..|-+. ..|.| .
T Consensus 182 hp~C~~C~------------~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~--~HflCE~~~ 243 (669)
T KOG2231|consen 182 HPLCKFCH------------ERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRK--GHFLCEEEF 243 (669)
T ss_pred Cccchhhh------------hhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhh--cCccccccc
Confidence 25688998 78999999999999765 556555 4568888999999884 33445 2
Q ss_pred cC-ccccCchHHHHHHHh---hCCCCCCccCC
Q 037179 223 CG-SDFKHKRSLKDHIKA---FGSGHGPFSRP 250 (266)
Q Consensus 223 C~-k~F~~~~~L~~H~~~---~H~~~~p~~C~ 250 (266)
|. +.|..--.+..|++. ++.-++.|.|.
T Consensus 244 C~~~~f~~~~~~ei~lk~~~~~~~~e~~~~~~ 275 (669)
T KOG2231|consen 244 CRTKKFYVAFELEIELKAHNRFIQHEKCYICR 275 (669)
T ss_pred cccceeeehhHHHHHHHhhccccchheeccCC
Confidence 32 223333234444442 23445556554
No 62
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.76 E-value=0.22 Score=41.72 Aligned_cols=25 Identities=20% Similarity=0.506 Sum_probs=15.4
Q ss_pred eeccc--ccccccChhhHHhhhhhcCC
Q 037179 109 FSCHV--CFKTFNRYNNLQMHMWGHGS 133 (266)
Q Consensus 109 ~~C~~--C~k~F~~~~~L~~H~~~h~~ 133 (266)
|.|+. |.........|+.|.++.++
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~ 178 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG 178 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC
Confidence 66765 55555555677778766543
No 63
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=88.90 E-value=0.54 Score=39.48 Aligned_cols=23 Identities=35% Similarity=0.600 Sum_probs=20.8
Q ss_pred eecccccccccChhhHHhhhhhc
Q 037179 109 FSCHVCFKTFNRYNNLQMHMWGH 131 (266)
Q Consensus 109 ~~C~~C~k~F~~~~~L~~H~~~h 131 (266)
+.|-.|.+.|..+..|..|||..
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhc
Confidence 78999999999999999999753
No 64
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.08 E-value=0.16 Score=39.35 Aligned_cols=77 Identities=21% Similarity=0.405 Sum_probs=59.4
Q ss_pred cCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHHH------------hCCCEE
Q 037179 153 IPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEKN------------CGKRWL 220 (266)
Q Consensus 153 ~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~------------~~k~~~ 220 (266)
+.|.+-+.. ..|........|..+-+|. .|..|.+.|.+...|..|+.. +..-|+
T Consensus 80 ~~cqvagc~----------~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ 146 (253)
T KOG4173|consen 80 FACQVAGCC----------QVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQ 146 (253)
T ss_pred ccccccchH----------HHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHH
Confidence 677776643 6677777777777654443 799999999999999999871 234599
Q ss_pred e---EcCccccCchHHHHHHHhhCC
Q 037179 221 C---VCGSDFKHKRSLKDHIKAFGS 242 (266)
Q Consensus 221 C---~C~k~F~~~~~L~~H~~~~H~ 242 (266)
| .|+-.|.+...-..|+-..|.
T Consensus 147 ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 147 CLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 9 599999999999999877664
No 65
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=85.92 E-value=0.37 Score=28.91 Aligned_cols=28 Identities=21% Similarity=0.554 Sum_probs=23.5
Q ss_pred hhcCCCCeecccccccccchhhHHHHHH
Q 037179 186 RKHGLKPFMCRKCGKFLAVKGDWRTHEK 213 (266)
Q Consensus 186 ~h~~~kp~~C~~C~k~f~~~~~L~~H~~ 213 (266)
...||.-+.|+-||..|....+..+|..
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 3457778899999999999999998887
No 66
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=85.64 E-value=0.82 Score=36.78 Aligned_cols=46 Identities=28% Similarity=0.602 Sum_probs=31.0
Q ss_pred cCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHH
Q 037179 153 IPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEK 213 (266)
Q Consensus 153 ~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~ 213 (266)
|.|..||+.++ +..+.+|+..-++ .-|.|-.||+.|.. .+...|..
T Consensus 4 FtCnvCgEsvK-------------Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVK-------------KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcc-------------ccchHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 77888885422 3466777776666 56788888888877 55566665
No 67
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.29 E-value=0.49 Score=37.79 Aligned_cols=44 Identities=7% Similarity=-0.041 Sum_probs=30.5
Q ss_pred CCCCCCCcccccccccCCCchhhhh---h-------cCCCc-----eecccccccccCh
Q 037179 78 NNPSAKGNANVAAAKQYWIPTPEQI---L-------IGFTH-----FSCHVCFKTFNRY 121 (266)
Q Consensus 78 ~~~~~C~~C~~~f~~~~~l~~H~~~---h-------~~~k~-----~~C~~C~k~F~~~ 121 (266)
++.+.|++|++.|....-.....++ . .+..| ..|+.||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 3568899999999987665555442 1 12233 5799999987654
No 68
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=83.07 E-value=2.5 Score=36.23 Aligned_cols=49 Identities=20% Similarity=0.415 Sum_probs=40.3
Q ss_pred CCeecccccccccchhhHHHHHHHh-------------------------CCCEEe-EcC---ccccCchHHHHHHHh
Q 037179 191 KPFMCRKCGKFLAVKGDWRTHEKNC-------------------------GKRWLC-VCG---SDFKHKRSLKDHIKA 239 (266)
Q Consensus 191 kp~~C~~C~k~f~~~~~L~~H~~~~-------------------------~k~~~C-~C~---k~F~~~~~L~~H~~~ 239 (266)
-|-.|-.|++.|..-..-..||..+ ...|.| .|. +.|.+....+.||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 3567888999999888888888731 245889 999 999999999999985
No 69
>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=80.13 E-value=2.2 Score=31.81 Aligned_cols=53 Identities=19% Similarity=0.299 Sum_probs=20.8
Q ss_pred cCCCceecccccccc------cChhhHHhhhhh-cCCCCCCCCCCcCCCCCCccCCcCCCCCCCC
Q 037179 104 IGFTHFSCHVCFKTF------NRYNNLQMHMWG-HGSQYRKGPESLKGTQPRAILGIPCYCCAEG 161 (266)
Q Consensus 104 ~~~k~~~C~~C~k~F------~~~~~L~~H~~~-h~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 161 (266)
...-..+|..|++.| +..+++..|+.. .+.+-...++.. .....++|+.||..
T Consensus 10 ~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~-----lgdt~leCy~Cg~~ 69 (152)
T PF09416_consen 10 DPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSP-----LGDTVLECYNCGSR 69 (152)
T ss_dssp -CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTST-----T-S-B---TTT---
T ss_pred CcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCC-----CCCcEEEEEecCCC
Confidence 334446777787777 344566667532 222211122222 23334899999943
No 70
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=79.92 E-value=1.2 Score=25.66 Aligned_cols=10 Identities=30% Similarity=1.172 Sum_probs=6.3
Q ss_pred EEe-EcCcccc
Q 037179 219 WLC-VCGSDFK 228 (266)
Q Consensus 219 ~~C-~C~k~F~ 228 (266)
|.| .||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 566 6666655
No 71
>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=79.79 E-value=1.4 Score=31.00 Aligned_cols=31 Identities=10% Similarity=0.101 Sum_probs=24.9
Q ss_pred CCCCCcccccccccCCCchhhhhhcCCCceecccccccccCh
Q 037179 80 PSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRY 121 (266)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~ 121 (266)
...|+.||+.|-. | +..|-.|+.||..|...
T Consensus 9 KR~Cp~CG~kFYD---L--------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYD---L--------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhcc---C--------CCCCccCCCCCCccCcc
Confidence 3679999999966 2 44688899999998776
No 72
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=78.96 E-value=0.85 Score=27.39 Aligned_cols=28 Identities=21% Similarity=0.288 Sum_probs=23.0
Q ss_pred hcCCCceecccccccccChhhHHhhhhh
Q 037179 103 LIGFTHFSCHVCFKTFNRYNNLQMHMWG 130 (266)
Q Consensus 103 h~~~k~~~C~~C~k~F~~~~~L~~H~~~ 130 (266)
--|+.-+.|+.||..|.......+|...
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3467778999999999999999998753
No 73
>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=78.55 E-value=1.3 Score=35.85 Aligned_cols=76 Identities=24% Similarity=0.472 Sum_probs=47.4
Q ss_pred hcCCCCeecccccccccchhhHHHHHHHh----CCCEEe-EcCccccCchHHH-------HHHHhh---CCCCCCccCCC
Q 037179 187 KHGLKPFMCRKCGKFLAVKGDWRTHEKNC----GKRWLC-VCGSDFKHKRSLK-------DHIKAF---GSGHGPFSRPF 251 (266)
Q Consensus 187 h~~~kp~~C~~C~k~f~~~~~L~~H~~~~----~k~~~C-~C~k~F~~~~~L~-------~H~~~~---H~~~~p~~C~~ 251 (266)
.+|.+.|+|..|.. |.-..+--.|+... ...|+| -|++. .+.+.|+ -|.|.. -...+|+.|+.
T Consensus 137 ~hGGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNrl-Gq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPK 214 (314)
T PF06524_consen 137 DHGGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNRL-GQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPK 214 (314)
T ss_pred cCCCeEEEeecCCC-eeeccchhhhhhhhhhhhcccccccccccc-cchhhhheeeeehhhhhhhcccccccCCCCCCCC
Confidence 45788999999974 55556666788753 345666 55542 3333332 354431 13458999999
Q ss_pred CCccccccccccc
Q 037179 252 DGVEVLDDASSSL 264 (266)
Q Consensus 252 C~k~f~~~~~~~~ 264 (266)
||..-..-..|++
T Consensus 215 Cg~et~eTkdLSm 227 (314)
T PF06524_consen 215 CGYETQETKDLSM 227 (314)
T ss_pred CCCccccccccee
Confidence 9977666555543
No 74
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=78.52 E-value=1.2 Score=26.23 Aligned_cols=10 Identities=30% Similarity=1.085 Sum_probs=6.5
Q ss_pred CEEe-EcCccc
Q 037179 218 RWLC-VCGSDF 227 (266)
Q Consensus 218 ~~~C-~C~k~F 227 (266)
.|.| .||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 3666 676666
No 75
>PF15269 zf-C2H2_7: Zinc-finger
Probab=77.75 E-value=1.8 Score=24.74 Aligned_cols=21 Identities=29% Similarity=0.551 Sum_probs=14.6
Q ss_pred EEe-EcCccccCchHHHHHHHh
Q 037179 219 WLC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 219 ~~C-~C~k~F~~~~~L~~H~~~ 239 (266)
|+| +|......++.|-.||+-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 566 777777777777777763
No 76
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=77.37 E-value=1.6 Score=25.29 Aligned_cols=30 Identities=10% Similarity=0.027 Sum_probs=21.9
Q ss_pred CCCCCcccccccccCCCchhhhhhcCCCceeccccccccc
Q 037179 80 PSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFN 119 (266)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~ 119 (266)
.|.|+.||..|...... ....|+.||..+.
T Consensus 3 ~y~C~~CG~~~~~~~~~----------~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYG----------TGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCC----------CceECCCCCCeEE
Confidence 58899999988764321 1578999997653
No 77
>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=77.15 E-value=2.3 Score=24.34 Aligned_cols=15 Identities=33% Similarity=0.702 Sum_probs=5.7
Q ss_pred CCCeecccccccccc
Q 037179 190 LKPFMCRKCGKFLAV 204 (266)
Q Consensus 190 ~kp~~C~~C~k~f~~ 204 (266)
.....|..|++.+..
T Consensus 14 ~~~a~C~~C~~~~~~ 28 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKY 28 (45)
T ss_dssp SS-EEETTTTEE---
T ss_pred cCeEEeCCCCeEEee
Confidence 334455555555544
No 78
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.06 E-value=3.5 Score=34.88 Aligned_cols=128 Identities=18% Similarity=0.273 Sum_probs=78.5
Q ss_pred CCCC--cccccccccCCCchhhhhhcC----------CCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCC
Q 037179 81 SAKG--NANVAAAKQYWIPTPEQILIG----------FTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPR 148 (266)
Q Consensus 81 ~~C~--~C~~~f~~~~~l~~H~~~h~~----------~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~ 148 (266)
|.|+ .|..+...-..|..|.+..++ .+.|.|. -...++..|..|......+ .
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E---~~lF~~~~Lr~H~~~G~~e-------------~ 215 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNE---IRLFRSSTLRDHKNGGLEE-------------E 215 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccc---eeeeecccccccccCCccc-------------c
Confidence 5666 344444444457777765443 3344443 3444556677776543211 1
Q ss_pred ccCC-cCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccc-------cccchhhHHHHHHHhCCCEE
Q 037179 149 AILG-IPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGK-------FLAVKGDWRTHEKNCGKRWL 220 (266)
Q Consensus 149 ~~~~-~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k-------~f~~~~~L~~H~~~~~k~~~ 220 (266)
.+.+ -.|..|. ..|.+...|..|+|..+ | .|-+|++ .|.....|-.|-+ ...|.
T Consensus 216 GFKGHP~C~FC~------------~~FYdDDEL~~HcR~~H-E---~ChICD~v~p~~~QYFK~Y~~Le~HF~--~~hy~ 277 (493)
T COG5236 216 GFKGHPLCIFCK------------IYFYDDDELRRHCRLRH-E---ACHICDMVGPIRYQYFKSYEDLEAHFR--NAHYC 277 (493)
T ss_pred CcCCCchhhhcc------------ceecChHHHHHHHHhhh-h---hhhhhhccCccchhhhhCHHHHHHHhh--cCceE
Confidence 1111 3589998 88999999999998654 2 4666655 3677777888776 45577
Q ss_pred e---EcC----ccccCchHHHHHHHhhCC
Q 037179 221 C---VCG----SDFKHKRSLKDHIKAFGS 242 (266)
Q Consensus 221 C---~C~----k~F~~~~~L~~H~~~~H~ 242 (266)
| .|- ..|.....|..|+-..|.
T Consensus 278 ct~qtc~~~k~~vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 278 CTFQTCRVGKCYVFPYHTELLEHLTRFHK 306 (493)
T ss_pred EEEEEEecCcEEEeccHHHHHHHHHHHhh
Confidence 7 353 358888889999876663
No 79
>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=76.58 E-value=1.2 Score=31.07 Aligned_cols=28 Identities=7% Similarity=0.040 Sum_probs=18.5
Q ss_pred CCCcccccccccCCCchhhhhhcCCCceecccccccccCh
Q 037179 82 AKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRY 121 (266)
Q Consensus 82 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~ 121 (266)
.|+.||..+... ...+.|+.|+..+...
T Consensus 2 fC~~Cg~~l~~~------------~~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 2 FCPKCGSLMTPK------------NGVYVCPSCGYEKEKK 29 (104)
T ss_pred CCcccCcccccC------------CCeEECcCCCCccccc
Confidence 488888766432 1258899999876543
No 80
>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=76.48 E-value=1.9 Score=21.77 Aligned_cols=10 Identities=30% Similarity=0.590 Sum_probs=6.5
Q ss_pred eccccccccc
Q 037179 110 SCHVCFKTFN 119 (266)
Q Consensus 110 ~C~~C~k~F~ 119 (266)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 3777777663
No 81
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=76.07 E-value=1.9 Score=39.21 Aligned_cols=27 Identities=19% Similarity=0.311 Sum_probs=21.8
Q ss_pred CCCCeecccccccccchhhHHHHHHHh
Q 037179 189 GLKPFMCRKCGKFLAVKGDWRTHEKNC 215 (266)
Q Consensus 189 ~~kp~~C~~C~k~f~~~~~L~~H~~~~ 215 (266)
...|..|..||..|........||..|
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhh
Confidence 356789999999999988888877644
No 82
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=75.93 E-value=2 Score=23.70 Aligned_cols=34 Identities=15% Similarity=0.118 Sum_probs=23.6
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceeccccccccc
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFN 119 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~ 119 (266)
..|+.|+..|.-... ++-.+....+|..|+..|.
T Consensus 3 i~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHH-----HcccCCcEEECCCCCcEee
Confidence 468999988876432 2334455688999998874
No 83
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=75.68 E-value=2.7 Score=24.88 Aligned_cols=11 Identities=45% Similarity=0.963 Sum_probs=5.9
Q ss_pred ecccccccccc
Q 037179 194 MCRKCGKFLAV 204 (266)
Q Consensus 194 ~C~~C~k~f~~ 204 (266)
.|..|++.+..
T Consensus 20 ~C~~C~~~l~~ 30 (50)
T smart00614 20 KCKYCGKKLSR 30 (50)
T ss_pred EecCCCCEeee
Confidence 45556555543
No 84
>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=75.04 E-value=2.6 Score=29.65 Aligned_cols=30 Identities=27% Similarity=0.696 Sum_probs=21.9
Q ss_pred cCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccch
Q 037179 153 IPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVK 205 (266)
Q Consensus 153 ~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~ 205 (266)
..|..|| +.|... +..|-.|+.||..|.-.
T Consensus 10 R~Cp~CG------------~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCG------------AKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCc------------chhccC-----------CCCCccCCCCCCccCcc
Confidence 5688888 666554 34678899998888765
No 85
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=74.57 E-value=1.3 Score=33.29 Aligned_cols=43 Identities=12% Similarity=0.110 Sum_probs=23.6
Q ss_pred CCCCccccccccc--CCCchhhhhhcCCCceecccccccccChhhHH
Q 037179 81 SAKGNANVAAAKQ--YWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQ 125 (266)
Q Consensus 81 ~~C~~C~~~f~~~--~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~ 125 (266)
+.|+.||..+... +.+..- .... .+.++|+.||++|.+...+.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~-~~~~-~~~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAED-GNAI-RRRRECLACGKRFTTFERVE 45 (154)
T ss_pred CcCCCCCCCCCEeEeccccCC-CCce-eeeeeccccCCcceEeEecc
Confidence 3699999655221 111111 0111 12388999999997765543
No 86
>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=74.08 E-value=2.5 Score=23.27 Aligned_cols=34 Identities=9% Similarity=-0.042 Sum_probs=22.2
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceeccccccccc
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFN 119 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~ 119 (266)
+.|+.|+..|.-.... +........|+.|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~-----~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ-----LGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHH-----cCCCCCEEECCCCCCEEE
Confidence 5699999888764321 112223578999998774
No 87
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=72.53 E-value=2.7 Score=22.99 Aligned_cols=34 Identities=15% Similarity=0.038 Sum_probs=22.7
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceeccccccccc
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFN 119 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~ 119 (266)
..|+.|+..|.-... ++-......+|..|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~-----~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDE-----KIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHH-----HCCCCCcEEECCCCCCEeC
Confidence 468899988876543 2223344578999988773
No 88
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.31 E-value=4.5 Score=28.52 Aligned_cols=16 Identities=6% Similarity=-0.213 Sum_probs=8.8
Q ss_pred CCCCChhhHHHHhhhh
Q 037179 172 KPLKDFRTLQTHYKRK 187 (266)
Q Consensus 172 k~f~~~~~l~~H~~~h 187 (266)
..|-..-++-.|...|
T Consensus 89 ~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 89 NVFCVDCDVFVHESLH 104 (112)
T ss_pred Cccccccchhhhhhcc
Confidence 5555555555555554
No 89
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.22 E-value=5.6 Score=28.05 Aligned_cols=45 Identities=20% Similarity=0.262 Sum_probs=26.5
Q ss_pred cccccccccchhhHHHHHHHhCCCEEe-EcCccccCchHHHHHHHh
Q 037179 195 CRKCGKFLAVKGDWRTHEKNCGKRWLC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 195 C~~C~k~f~~~~~L~~H~~~~~k~~~C-~C~k~F~~~~~L~~H~~~ 239 (266)
|--|.+.|........-.......|+| .|...|--.-..-.|...
T Consensus 58 C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~L 103 (112)
T TIGR00622 58 CFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESL 103 (112)
T ss_pred ccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhc
Confidence 777777776542111000112346778 788888777777777665
No 90
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=70.69 E-value=1.9 Score=40.80 Aligned_cols=13 Identities=31% Similarity=0.629 Sum_probs=10.0
Q ss_pred CCCCeeccccccc
Q 037179 189 GLKPFMCRKCGKF 201 (266)
Q Consensus 189 ~~kp~~C~~C~k~ 201 (266)
...|..|+.||-.
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 4568889999865
No 91
>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=70.67 E-value=13 Score=26.06 Aligned_cols=21 Identities=29% Similarity=0.620 Sum_probs=13.3
Q ss_pred eec----ccccccccchhhHHHHHH
Q 037179 193 FMC----RKCGKFLAVKGDWRTHEK 213 (266)
Q Consensus 193 ~~C----~~C~k~f~~~~~L~~H~~ 213 (266)
|.| ..|+..+.+...+.+|.+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~ 105 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWR 105 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHH
Confidence 556 666666666666666655
No 92
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=69.45 E-value=1.5 Score=28.27 Aligned_cols=16 Identities=13% Similarity=0.374 Sum_probs=8.4
Q ss_pred CCCeecc--cccccccch
Q 037179 190 LKPFMCR--KCGKFLAVK 205 (266)
Q Consensus 190 ~kp~~C~--~C~k~f~~~ 205 (266)
+.-+.|. .||..|...
T Consensus 25 ~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 25 ERYHQCQNVNCSATFITY 42 (72)
T ss_pred eeeeecCCCCCCCEEEEE
Confidence 3445565 566655543
No 93
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=69.38 E-value=6.4 Score=24.16 Aligned_cols=7 Identities=29% Similarity=0.809 Sum_probs=5.2
Q ss_pred cCCCCCC
Q 037179 153 IPCYCCA 159 (266)
Q Consensus 153 ~~C~~C~ 159 (266)
|.|+.||
T Consensus 49 Y~CP~CG 55 (59)
T PRK14890 49 YTCPKCG 55 (59)
T ss_pred eECCCCC
Confidence 7777777
No 94
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=69.11 E-value=2.8 Score=30.30 Aligned_cols=61 Identities=18% Similarity=0.149 Sum_probs=42.1
Q ss_pred hhcCCCCeecccccccccchhhHHHHHHHhCCCEEe----EcCccccCchHHHHHHHhhCCCCCCccCCCCCcccccccc
Q 037179 186 RKHGLKPFMCRKCGKFLAVKGDWRTHEKNCGKRWLC----VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEVLDDAS 261 (266)
Q Consensus 186 ~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~~k~~~C----~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f~~~~~ 261 (266)
.....+-|+|++|..+.....- -||-+| +|+..+. .|-+|-.+ | -+||+|.-+|...++
T Consensus 74 vF~d~~lYeCnIC~etS~ee~F--------LKPneCCgY~iCn~Cya---~LWK~~~~-y-----pvCPvCkTSFKss~~ 136 (140)
T PF05290_consen 74 VFLDPKLYECNICKETSAEERF--------LKPNECCGYSICNACYA---NLWKFCNL-Y-----PVCPVCKTSFKSSSS 136 (140)
T ss_pred eecCCCceeccCcccccchhhc--------CCcccccchHHHHHHHH---HHHHHccc-C-----CCCCccccccccccc
Confidence 3456688999999877655422 467777 4666654 55566554 2 369999999988776
Q ss_pred cc
Q 037179 262 SS 263 (266)
Q Consensus 262 ~~ 263 (266)
..
T Consensus 137 ~~ 138 (140)
T PF05290_consen 137 AS 138 (140)
T ss_pred cc
Confidence 54
No 95
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=69.08 E-value=2.3 Score=32.29 Aligned_cols=24 Identities=13% Similarity=0.015 Sum_probs=19.6
Q ss_pred CCCCCcccccccccCCCchhhhhhcCCCceecccccc
Q 037179 80 PSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFK 116 (266)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k 116 (266)
.|.|++||.. +.|+.|.+|+.||-
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 7999999953 45678999999994
No 96
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=67.62 E-value=2.4 Score=34.16 Aligned_cols=46 Identities=22% Similarity=0.188 Sum_probs=32.3
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHHhhhh
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQMHMW 129 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~ 129 (266)
|.|.+||.....+ .+.+|+-.-.+ .-|.|-.|++.|.. ..+..|..
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 6788888777654 46678765555 56888888888877 55566643
No 97
>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=67.25 E-value=2.5 Score=25.11 Aligned_cols=29 Identities=7% Similarity=-0.109 Sum_probs=19.3
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceecccccc
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFK 116 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k 116 (266)
|.|..|+..|.....+.. ..+-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-------~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-------DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCC-------CCCCCCCCCCC
Confidence 789999988875422211 34456999986
No 98
>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=66.08 E-value=4.9 Score=28.92 Aligned_cols=35 Identities=9% Similarity=-0.085 Sum_probs=26.1
Q ss_pred CCCCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHH
Q 037179 80 PSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQ 125 (266)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~ 125 (266)
...|+.||+.|-. | +..|-.|+.||..|.....+.
T Consensus 9 Kr~Cp~cg~kFYD---L--------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 9 KRICPNTGSKFYD---L--------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cccCCCcCccccc---c--------CCCCccCCCcCCccCcchhhc
Confidence 3679999999965 2 446888999999986654433
No 99
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.10 E-value=3.4 Score=31.98 Aligned_cols=30 Identities=20% Similarity=0.408 Sum_probs=16.7
Q ss_pred CCEEe-EcCccccCchHHHHHHHhhCCCCCCccCCCCCccc
Q 037179 217 KRWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEV 256 (266)
Q Consensus 217 k~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f 256 (266)
.-|.| .|++.|+.-..+. .-|.|+.||-..
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME----------YGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCC
Confidence 34666 6666666554432 236677776443
No 100
>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=64.78 E-value=3.9 Score=30.95 Aligned_cols=30 Identities=17% Similarity=0.322 Sum_probs=16.7
Q ss_pred CCEEe-EcCccccCchHHHHHHHhhCCCCCCccCCCCCccc
Q 037179 217 KRWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEV 256 (266)
Q Consensus 217 k~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f 256 (266)
.-|.| .|+..|+.-..+. .-|.|+.||...
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 34666 6666666555543 136666666543
No 101
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=64.58 E-value=3.6 Score=31.31 Aligned_cols=13 Identities=38% Similarity=0.930 Sum_probs=10.0
Q ss_pred hcCCCCeeccccc
Q 037179 187 KHGLKPFMCRKCG 199 (266)
Q Consensus 187 h~~~kp~~C~~C~ 199 (266)
+.|+-|-+|++||
T Consensus 144 ~~ge~P~~CPiCg 156 (166)
T COG1592 144 HEGEAPEVCPICG 156 (166)
T ss_pred ccCCCCCcCCCCC
Confidence 4567788888887
No 102
>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=63.72 E-value=4.1 Score=29.73 Aligned_cols=23 Identities=35% Similarity=0.779 Sum_probs=13.2
Q ss_pred CCCEEe-EcCccccCchHHHHHHHhhC
Q 037179 216 GKRWLC-VCGSDFKHKRSLKDHIKAFG 241 (266)
Q Consensus 216 ~k~~~C-~C~k~F~~~~~L~~H~~~~H 241 (266)
+.--.| +||+.|.. |.+|++.||
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~ 93 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHH 93 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT
T ss_pred cCeeEEccCCcccch---HHHHHHHcc
Confidence 344678 88888864 488888843
No 103
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=62.49 E-value=2 Score=36.36 Aligned_cols=50 Identities=16% Similarity=0.215 Sum_probs=34.5
Q ss_pred CCCEEe---EcCccccCchHHHHHHHhhCC------------------CCCCccCCCCCcccccccccccC
Q 037179 216 GKRWLC---VCGSDFKHKRSLKDHIKAFGS------------------GHGPFSRPFDGVEVLDDASSSLL 265 (266)
Q Consensus 216 ~k~~~C---~C~k~F~~~~~L~~H~~~~H~------------------~~~p~~C~~C~k~f~~~~~~~~~ 265 (266)
.++|.| .|.+.+.....|..|...-|. ..|||+|++|.+++..--.|+-|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 567777 477777777777777554331 35789999999988766555433
No 104
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=62.28 E-value=6.3 Score=26.26 Aligned_cols=32 Identities=13% Similarity=0.202 Sum_probs=22.4
Q ss_pred CCCCCCcccccccccCCCchhhhhhcCCCceecccccccccC
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNR 120 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~ 120 (266)
..|.|+.|++.-. .++ +..-|.|..|+..|.-
T Consensus 34 ~~~~Cp~C~~~~V--------kR~--a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRTTV--------KRI--ATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCcce--------eee--ccCeEEcCCCCCeecc
Confidence 4689999997622 222 2345999999998843
No 105
>PF14353 CpXC: CpXC protein
Probab=61.96 E-value=1.1 Score=32.60 Aligned_cols=48 Identities=21% Similarity=0.274 Sum_probs=30.5
Q ss_pred CCCCcccccccccCCCchhh--------hhhcCC-CceecccccccccChhhHHhhh
Q 037179 81 SAKGNANVAAAKQYWIPTPE--------QILIGF-THFSCHVCFKTFNRYNNLQMHM 128 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~--------~~h~~~-k~~~C~~C~k~F~~~~~L~~H~ 128 (266)
..|+.|+..|....+..... ++-.|. ..|.|+.||..|.-...+.-|-
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D 58 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHD 58 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEc
Confidence 46999999987665432221 122222 3489999999987666655554
No 106
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=61.93 E-value=5.2 Score=23.62 Aligned_cols=15 Identities=33% Similarity=0.804 Sum_probs=7.2
Q ss_pred CCEEe-EcCccccCch
Q 037179 217 KRWLC-VCGSDFKHKR 231 (266)
Q Consensus 217 k~~~C-~C~k~F~~~~ 231 (266)
+.+.| .||..|....
T Consensus 3 k~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTA 18 (49)
T ss_pred eeEEcccCCCeEEEeh
Confidence 34455 5555554443
No 107
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.17 E-value=4 Score=31.88 Aligned_cols=42 Identities=17% Similarity=0.326 Sum_probs=28.2
Q ss_pred CCCCChhhHHHHhhh-h---------cCCCCeecc--cccccccchhhHHHHHH
Q 037179 172 KPLKDFRTLQTHYKR-K---------HGLKPFMCR--KCGKFLAVKGDWRTHEK 213 (266)
Q Consensus 172 k~f~~~~~l~~H~~~-h---------~~~kp~~C~--~C~k~f~~~~~L~~H~~ 213 (266)
+.|.+.-.|..|+.- | .|.--|.|- .|+-.|.+......|+.
T Consensus 114 r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 114 RAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMI 167 (253)
T ss_pred HhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHH
Confidence 666666666666542 2 233447774 48888888888888876
No 108
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=60.57 E-value=4 Score=20.14 Aligned_cols=10 Identities=40% Similarity=0.584 Sum_probs=6.7
Q ss_pred CCccCCCCCc
Q 037179 245 GPFSRPFDGV 254 (266)
Q Consensus 245 ~p~~C~~C~k 254 (266)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 3577777773
No 109
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=60.05 E-value=5.2 Score=29.82 Aligned_cols=18 Identities=11% Similarity=0.388 Sum_probs=12.0
Q ss_pred CceecccccccccChhhH
Q 037179 107 THFSCHVCFKTFNRYNNL 124 (266)
Q Consensus 107 k~~~C~~C~k~F~~~~~L 124 (266)
.-|.|+.|+..|.....+
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~ 115 (147)
T smart00531 98 AYYKCPNCQSKYTFLEAN 115 (147)
T ss_pred cEEECcCCCCEeeHHHHH
Confidence 457788888777754443
No 110
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=59.41 E-value=7 Score=28.34 Aligned_cols=23 Identities=39% Similarity=0.634 Sum_probs=16.6
Q ss_pred EEe-EcCccccCchHHHHHHHhhCCCCC
Q 037179 219 WLC-VCGSDFKHKRSLKDHIKAFGSGHG 245 (266)
Q Consensus 219 ~~C-~C~k~F~~~~~L~~H~~~~H~~~~ 245 (266)
..| ++||.|. +|++|+.+ |-|..
T Consensus 77 IicLEDGkkfK---SLKRHL~t-~~gmT 100 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTT-HYGLT 100 (148)
T ss_pred EEEeccCcchH---HHHHHHhc-ccCCC
Confidence 468 8888885 67889888 44443
No 111
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=58.98 E-value=7.1 Score=23.95 Aligned_cols=14 Identities=21% Similarity=0.263 Sum_probs=8.0
Q ss_pred eecccccccccChh
Q 037179 109 FSCHVCFKTFNRYN 122 (266)
Q Consensus 109 ~~C~~C~k~F~~~~ 122 (266)
|.|+.||+.-..+.
T Consensus 28 F~CPnCGe~~I~Rc 41 (61)
T COG2888 28 FPCPNCGEVEIYRC 41 (61)
T ss_pred eeCCCCCceeeehh
Confidence 66777775544433
No 112
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=57.29 E-value=2.7 Score=24.57 Aligned_cols=34 Identities=21% Similarity=0.482 Sum_probs=14.0
Q ss_pred cccccccccchhhHHHHHHHhCCCEEe---EcCcccc
Q 037179 195 CRKCGKFLAVKGDWRTHEKNCGKRWLC---VCGSDFK 228 (266)
Q Consensus 195 C~~C~k~f~~~~~L~~H~~~~~k~~~C---~C~k~F~ 228 (266)
|+.||....-......+....+.-|+| .||..|.
T Consensus 2 CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred cCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEE
Confidence 444444333333333333333344455 3555554
No 113
>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=57.17 E-value=8.8 Score=27.63 Aligned_cols=17 Identities=12% Similarity=0.223 Sum_probs=12.0
Q ss_pred CCCCeecccccccccch
Q 037179 189 GLKPFMCRKCGKFLAVK 205 (266)
Q Consensus 189 ~~kp~~C~~C~k~f~~~ 205 (266)
+..|-.|+.||..|...
T Consensus 23 nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 23 NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred CCCCccCCCcCCccCcc
Confidence 34677888888877555
No 114
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=55.55 E-value=7.1 Score=30.19 Aligned_cols=20 Identities=20% Similarity=0.406 Sum_probs=14.9
Q ss_pred CCceecccccccccChhhHH
Q 037179 106 FTHFSCHVCFKTFNRYNNLQ 125 (266)
Q Consensus 106 ~k~~~C~~C~k~F~~~~~L~ 125 (266)
..-|.|+.|+..|+...++.
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~ 134 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME 134 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh
Confidence 34588988998888777653
No 115
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=54.44 E-value=9.4 Score=28.44 Aligned_cols=11 Identities=36% Similarity=0.449 Sum_probs=6.5
Q ss_pred ccCCCCCcccc
Q 037179 247 FSRPFDGVEVL 257 (266)
Q Consensus 247 ~~C~~C~k~f~ 257 (266)
|.|+.||....
T Consensus 124 f~Cp~Cg~~l~ 134 (147)
T smart00531 124 FTCPRCGEELE 134 (147)
T ss_pred EECCCCCCEEE
Confidence 66666665543
No 116
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=54.43 E-value=7.4 Score=28.96 Aligned_cols=33 Identities=15% Similarity=0.296 Sum_probs=15.1
Q ss_pred CCEEeEcCccccCchHHHHHHHhhCCCCCCccCCCCCc
Q 037179 217 KRWLCVCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGV 254 (266)
Q Consensus 217 k~~~C~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k 254 (266)
-+|.|.|+..|.+. ++|-.+ -.|+ .|.|..|+-
T Consensus 116 ~~Y~C~C~q~~l~~---RRhn~~-~~g~-~YrC~~C~g 148 (156)
T COG3091 116 YPYRCQCQQHYLRI---RRHNTV-RRGE-VYRCGKCGG 148 (156)
T ss_pred eeEEeecCCccchh---hhcccc-cccc-eEEeccCCc
Confidence 34555555554433 233322 2344 555655553
No 117
>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=53.30 E-value=4.6 Score=29.50 Aligned_cols=29 Identities=7% Similarity=-0.090 Sum_probs=18.3
Q ss_pred CCCCCCCCcccccccccCCCchhhhhhcCCCc
Q 037179 77 SNNPSAKGNANVAAAKQYWIPTPEQILIGFTH 108 (266)
Q Consensus 77 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~ 108 (266)
...-..|-+||+.|.. |.+|++.|+|-.|
T Consensus 69 ~~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 69 TPDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred ccCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 3445789999999987 6999999988655
No 118
>PHA00626 hypothetical protein
Probab=52.63 E-value=6.4 Score=23.81 Aligned_cols=12 Identities=8% Similarity=-0.225 Sum_probs=6.5
Q ss_pred CccCCCCCcccc
Q 037179 246 PFSRPFDGVEVL 257 (266)
Q Consensus 246 p~~C~~C~k~f~ 257 (266)
.|+|+.||..|+
T Consensus 23 rYkCkdCGY~ft 34 (59)
T PHA00626 23 DYVCCDCGYNDS 34 (59)
T ss_pred ceEcCCCCCeec
Confidence 455555555554
No 119
>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=52.45 E-value=8.6 Score=20.45 Aligned_cols=26 Identities=12% Similarity=0.119 Sum_probs=14.6
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceeccccccc
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKT 117 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~ 117 (266)
|.|..|+..+.... ..+-.|+.||..
T Consensus 1 Y~C~~Cg~~~~~~~-----------~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELKP-----------GDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BST-----------SSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcCC-----------CCcEECCcCCCe
Confidence 56777887766321 224568888754
No 120
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=51.36 E-value=7.1 Score=21.79 Aligned_cols=15 Identities=13% Similarity=0.031 Sum_probs=11.5
Q ss_pred CccCCCCCccccccc
Q 037179 246 PFSRPFDGVEVLDDA 260 (266)
Q Consensus 246 p~~C~~C~k~f~~~~ 260 (266)
||.|..|++.|=.+.
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 888999998885543
No 121
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=51.10 E-value=15 Score=31.71 Aligned_cols=25 Identities=20% Similarity=0.581 Sum_probs=18.4
Q ss_pred hCCCEEe-EcCccccCchHHHHHHHh
Q 037179 215 CGKRWLC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 215 ~~k~~~C-~C~k~F~~~~~L~~H~~~ 239 (266)
.+-++.| +|.|.|........|+..
T Consensus 65 ~~~~~~c~~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 65 AESVVYCEACNKSFASPKAHENHLKS 90 (390)
T ss_pred cccceehHHhhccccChhhHHHHHHH
Confidence 3566788 888888887777777664
No 122
>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=51.05 E-value=7.2 Score=21.62 Aligned_cols=13 Identities=8% Similarity=-0.268 Sum_probs=7.3
Q ss_pred ccCCCCCcccccc
Q 037179 247 FSRPFDGVEVLDD 259 (266)
Q Consensus 247 ~~C~~C~k~f~~~ 259 (266)
|+|..||..|..-
T Consensus 6 y~C~~Cg~~fe~~ 18 (41)
T smart00834 6 YRCEDCGHTFEVL 18 (41)
T ss_pred EEcCCCCCEEEEE
Confidence 5566666655433
No 123
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.41 E-value=8.8 Score=35.02 Aligned_cols=12 Identities=33% Similarity=0.714 Sum_probs=7.8
Q ss_pred CCCeeccccccc
Q 037179 190 LKPFMCRKCGKF 201 (266)
Q Consensus 190 ~kp~~C~~C~k~ 201 (266)
.-|..|+.||..
T Consensus 251 ~~~~~Cp~C~s~ 262 (505)
T TIGR00595 251 PIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCCCCCC
Confidence 346678888753
No 124
>PF12907 zf-met2: Zinc-binding
Probab=50.40 E-value=3.9 Score=23.02 Aligned_cols=31 Identities=19% Similarity=0.373 Sum_probs=19.1
Q ss_pred EEe-EcCccccC---chHHHHHHHhhCCCCCCccC
Q 037179 219 WLC-VCGSDFKH---KRSLKDHIKAFGSGHGPFSR 249 (266)
Q Consensus 219 ~~C-~C~k~F~~---~~~L~~H~~~~H~~~~p~~C 249 (266)
+.| +|-..|.. ...|..|....|.+..+-.|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~C 36 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEEC 36 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHc
Confidence 456 77755543 35588887766777554444
No 125
>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=50.35 E-value=15 Score=27.73 Aligned_cols=36 Identities=14% Similarity=0.312 Sum_probs=27.0
Q ss_pred hhcCCCCeecccccccccchhhHHHHHHHhCCCEEe-EcCcccc
Q 037179 186 RKHGLKPFMCRKCGKFLAVKGDWRTHEKNCGKRWLC-VCGSDFK 228 (266)
Q Consensus 186 ~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~~k~~~C-~C~k~F~ 228 (266)
...+..-|.|+.|+..|..-..+. ..|.| .||....
T Consensus 103 ~e~~~~~Y~Cp~c~~r~tf~eA~~-------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 103 FETNNMFFICPNMCVRFTFNEAME-------LNFTCPRCGAMLD 139 (158)
T ss_pred hccCCCeEECCCCCcEeeHHHHHH-------cCCcCCCCCCEee
Confidence 344556789999999888877764 37999 9997754
No 126
>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=50.04 E-value=11 Score=19.71 Aligned_cols=25 Identities=8% Similarity=-0.065 Sum_probs=12.3
Q ss_pred CCCcccccccccCCCchhhhhhcCCCceeccccccc
Q 037179 82 AKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKT 117 (266)
Q Consensus 82 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~ 117 (266)
.|+.|+..+.. .+...|.|+.|+..
T Consensus 4 ~Cp~C~se~~y-----------~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E-----------E-SSSEEETTTTEE
T ss_pred CCCCCCCccee-----------ccCCEEeCCccccc
Confidence 58888877665 34556889988764
No 127
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=49.86 E-value=8.6 Score=30.70 Aligned_cols=55 Identities=18% Similarity=0.154 Sum_probs=29.8
Q ss_pred CCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCCCCCCC
Q 037179 106 FTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCYCCAEG 161 (266)
Q Consensus 106 ~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 161 (266)
++.+.|++|++.|..+.-.....++-..... ....+.+..|.-.....|+.||..
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D-~~~~Y~~vnP~~Y~V~vCP~CgyA 57 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSD-FCPRYKGVNPLFYEVWVCPHCGYA 57 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCC-CccccCCCCCeeeeEEECCCCCCc
Confidence 3568899999999988665555543211000 000111223333334668888843
No 128
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=49.41 E-value=5.5 Score=37.23 Aligned_cols=24 Identities=33% Similarity=0.581 Sum_probs=21.8
Q ss_pred CeecccccccccchhhHHHHHHHh
Q 037179 192 PFMCRKCGKFLAVKGDWRTHEKNC 215 (266)
Q Consensus 192 p~~C~~C~k~f~~~~~L~~H~~~~ 215 (266)
-|.|.+|+|.|..-.++..||++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 389999999999999999999976
No 129
>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=49.20 E-value=7 Score=24.69 Aligned_cols=12 Identities=33% Similarity=1.112 Sum_probs=4.3
Q ss_pred CCeecccccccc
Q 037179 191 KPFMCRKCGKFL 202 (266)
Q Consensus 191 kp~~C~~C~k~f 202 (266)
+.+.|..||..|
T Consensus 24 rrhhCr~CG~~v 35 (69)
T PF01363_consen 24 RRHHCRNCGRVV 35 (69)
T ss_dssp -EEE-TTT--EE
T ss_pred eeEccCCCCCEE
Confidence 345566666544
No 130
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=48.96 E-value=3.4 Score=28.09 Aligned_cols=33 Identities=15% Similarity=0.112 Sum_probs=19.9
Q ss_pred CCCcccccccccCCCchhhhhhcCCCceecccccccccChh
Q 037179 82 AKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYN 122 (266)
Q Consensus 82 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~ 122 (266)
-|+.||........-. -..|.|+.|+..|....
T Consensus 3 FCP~Cgn~Live~g~~--------~~rf~C~tCpY~~~I~~ 35 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGES--------CNRFSCRTCPYVFPISR 35 (105)
T ss_pred ccCCCCCEEEEecCCe--------EeeEEcCCCCceeeEee
Confidence 4788875544332211 12488999998886653
No 131
>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=48.80 E-value=7.6 Score=22.01 Aligned_cols=16 Identities=19% Similarity=-0.124 Sum_probs=8.7
Q ss_pred ccCCCCCccccccccc
Q 037179 247 FSRPFDGVEVLDDASS 262 (266)
Q Consensus 247 ~~C~~C~k~f~~~~~~ 262 (266)
|+|..||..|..-.++
T Consensus 6 y~C~~Cg~~fe~~~~~ 21 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSI 21 (42)
T ss_pred EEeCCCCCEEEEEEEc
Confidence 5566666655544433
No 132
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=48.58 E-value=4.2 Score=37.95 Aligned_cols=25 Identities=32% Similarity=0.547 Sum_probs=22.8
Q ss_pred ceecccccccccChhhHHhhhhhcC
Q 037179 108 HFSCHVCFKTFNRYNNLQMHMWGHG 132 (266)
Q Consensus 108 ~~~C~~C~k~F~~~~~L~~H~~~h~ 132 (266)
-|.|.+|++.|....+++.||+.|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3899999999999999999999984
No 133
>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=48.41 E-value=15 Score=18.37 Aligned_cols=19 Identities=16% Similarity=0.253 Sum_probs=9.9
Q ss_pred ecccccccccchhhHHHHHH
Q 037179 194 MCRKCGKFLAVKGDWRTHEK 213 (266)
Q Consensus 194 ~C~~C~k~f~~~~~L~~H~~ 213 (266)
.|++|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 356666655 3345555543
No 134
>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=48.08 E-value=14 Score=29.42 Aligned_cols=27 Identities=30% Similarity=0.677 Sum_probs=17.4
Q ss_pred CCCEEe-EcCccccCchHHHHHHHhhCC
Q 037179 216 GKRWLC-VCGSDFKHKRSLKDHIKAFGS 242 (266)
Q Consensus 216 ~k~~~C-~C~k~F~~~~~L~~H~~~~H~ 242 (266)
+..|.| .|+|-|.-..-..+|+...|.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 345777 777777777777777776664
No 135
>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=47.45 E-value=6.5 Score=22.40 Aligned_cols=15 Identities=20% Similarity=0.100 Sum_probs=9.2
Q ss_pred CCccCCCCCcccccc
Q 037179 245 GPFSRPFDGVEVLDD 259 (266)
Q Consensus 245 ~p~~C~~C~k~f~~~ 259 (266)
-||.|+.|++.|=.+
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 578899999888543
No 136
>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=47.30 E-value=13 Score=21.42 Aligned_cols=27 Identities=22% Similarity=0.431 Sum_probs=17.6
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceecccccc
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFK 116 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k 116 (266)
+.|+.||.. ....|.. ...|.|..|++
T Consensus 19 ~~CP~Cg~~--~~~~~~~-------~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLKT-------RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeCC-------CCeEECCCCCC
Confidence 779999965 2222222 55699999875
No 137
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=47.23 E-value=7.2 Score=21.87 Aligned_cols=11 Identities=18% Similarity=0.733 Sum_probs=8.2
Q ss_pred eeccccccccc
Q 037179 109 FSCHVCFKTFN 119 (266)
Q Consensus 109 ~~C~~C~k~F~ 119 (266)
|.|..|+..|.
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 78888887654
No 138
>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=46.97 E-value=4.6 Score=20.74 Aligned_cols=18 Identities=39% Similarity=0.818 Sum_probs=8.5
Q ss_pred EEe-EcCccccCchHHHHHH
Q 037179 219 WLC-VCGSDFKHKRSLKDHI 237 (266)
Q Consensus 219 ~~C-~C~k~F~~~~~L~~H~ 237 (266)
|.| .|++.|. ....+.|.
T Consensus 1 ~sCiDC~~~F~-~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDFD-GDSYKSHT 19 (28)
T ss_dssp EEETTTTEEEE-GGGTTT--
T ss_pred CeeecCCCCcC-cCCcCCCC
Confidence 456 6777773 33344443
No 139
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=46.39 E-value=13 Score=17.98 Aligned_cols=8 Identities=13% Similarity=-0.014 Sum_probs=4.0
Q ss_pred CCcccccc
Q 037179 83 KGNANVAA 90 (266)
Q Consensus 83 C~~C~~~f 90 (266)
|+.||...
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 55555443
No 140
>PRK04023 DNA polymerase II large subunit; Validated
Probab=46.08 E-value=17 Score=35.65 Aligned_cols=10 Identities=0% Similarity=-0.190 Sum_probs=6.0
Q ss_pred CCCCCccccc
Q 037179 80 PSAKGNANVA 89 (266)
Q Consensus 80 ~~~C~~C~~~ 89 (266)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 3466777655
No 141
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=46.06 E-value=32 Score=29.10 Aligned_cols=35 Identities=11% Similarity=0.134 Sum_probs=25.8
Q ss_pred CCCCCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHHhh
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQMH 127 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~H 127 (266)
.-|.|+.|+...-+ -|-.|+.|+-+.-...+|.+-
T Consensus 275 ~Gy~CP~CkakvCs--------------LP~eCpiC~ltLVss~hLARS 309 (378)
T KOG2807|consen 275 GGYFCPQCKAKVCS--------------LPIECPICSLTLVSSPHLARS 309 (378)
T ss_pred CceeCCcccCeeec--------------CCccCCccceeEecchHHHHH
Confidence 44889988854432 367899999998888888753
No 142
>PRK14873 primosome assembly protein PriA; Provisional
Probab=45.70 E-value=13 Score=35.15 Aligned_cols=9 Identities=22% Similarity=0.147 Sum_probs=5.6
Q ss_pred CCCcccccc
Q 037179 82 AKGNANVAA 90 (266)
Q Consensus 82 ~C~~C~~~f 90 (266)
.|..||..+
T Consensus 385 ~C~~Cg~~~ 393 (665)
T PRK14873 385 ACARCRTPA 393 (665)
T ss_pred EhhhCcCee
Confidence 677777544
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=45.34 E-value=7.8 Score=26.13 Aligned_cols=31 Identities=16% Similarity=0.247 Sum_probs=20.3
Q ss_pred CCCCCCcccccccccCCCchhhhhhcCCCceeccccccccc
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFN 119 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~ 119 (266)
..|.|+.|++.-... .- .-.|.|..|++.|.
T Consensus 34 ~ky~Cp~Cgk~~vkR--------~a--~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKR--------VA--TGIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEEE--------EE--TTEEEETTTTEEEE
T ss_pred CCCcCCCCCCceeEE--------ee--eEEeecCCCCCEEe
Confidence 458899999754321 12 22499999998873
No 144
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=45.16 E-value=9.2 Score=29.72 Aligned_cols=16 Identities=31% Similarity=0.607 Sum_probs=12.6
Q ss_pred CCCeecccccccccch
Q 037179 190 LKPFMCRKCGKFLAVK 205 (266)
Q Consensus 190 ~kp~~C~~C~k~f~~~ 205 (266)
.-||.|.+|.+.|..+
T Consensus 194 ~IPF~C~iCKkdy~sp 209 (259)
T COG5152 194 KIPFLCGICKKDYESP 209 (259)
T ss_pred CCceeehhchhhccch
Confidence 3579999998888765
No 145
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=44.18 E-value=14 Score=32.37 Aligned_cols=42 Identities=10% Similarity=0.044 Sum_probs=28.4
Q ss_pred CCCCCCCCCCCcccccccccCCCchhhhhhcCCCceecccccccc
Q 037179 74 SHSSNNPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTF 118 (266)
Q Consensus 74 ~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F 118 (266)
..+...-|.|+.|.+.|.....+ ..+-...-.|.|..|+-..
T Consensus 122 d~t~~~~Y~Cp~C~kkyt~Lea~---~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 122 DDTNVAGYVCPNCQKKYTSLEAL---QLLDNETGEFHCENCGGEL 163 (436)
T ss_pred hccccccccCCccccchhhhHHH---HhhcccCceEEEecCCCch
Confidence 34555679999999999874332 3333334569999998543
No 146
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=44.15 E-value=11 Score=22.57 Aligned_cols=10 Identities=40% Similarity=1.311 Sum_probs=4.3
Q ss_pred eecccccccc
Q 037179 193 FMCRKCGKFL 202 (266)
Q Consensus 193 ~~C~~C~k~f 202 (266)
+.|..||+.|
T Consensus 19 ~~Cr~Cg~~~ 28 (57)
T cd00065 19 HHCRNCGRIF 28 (57)
T ss_pred cccCcCcCCc
Confidence 3444444443
No 147
>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=44.07 E-value=3.8 Score=22.85 Aligned_cols=10 Identities=20% Similarity=0.746 Sum_probs=7.6
Q ss_pred eecccccccc
Q 037179 109 FSCHVCFKTF 118 (266)
Q Consensus 109 ~~C~~C~k~F 118 (266)
|.|..|+..|
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 7788888765
No 148
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=44.06 E-value=8.9 Score=25.75 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=5.7
Q ss_pred CCEEe-EcCcccc
Q 037179 217 KRWLC-VCGSDFK 228 (266)
Q Consensus 217 k~~~C-~C~k~F~ 228 (266)
+|-+| .||..|.
T Consensus 57 ~Pa~CkkCGfef~ 69 (97)
T COG3357 57 RPARCKKCGFEFR 69 (97)
T ss_pred cChhhcccCcccc
Confidence 34445 5555554
No 149
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=43.32 E-value=14 Score=24.96 Aligned_cols=32 Identities=19% Similarity=0.141 Sum_probs=21.3
Q ss_pred CCCCCCcccccccccCCCchhhhhhcCCCceecccccccccC
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNR 120 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~ 120 (266)
..|.|+.|++.--.. .+.-.|.|..|++.|.-
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 458999998543221 12246999999998743
No 150
>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=42.88 E-value=15 Score=29.27 Aligned_cols=26 Identities=27% Similarity=0.377 Sum_probs=20.6
Q ss_pred CCCCeecccccccccchhhHHHHHHH
Q 037179 189 GLKPFMCRKCGKFLAVKGDWRTHEKN 214 (266)
Q Consensus 189 ~~kp~~C~~C~k~f~~~~~L~~H~~~ 214 (266)
.+..|.|..|+|.|.-..-+.+|+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhh
Confidence 34569999999999999999999883
No 151
>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=42.80 E-value=16 Score=33.33 Aligned_cols=35 Identities=9% Similarity=-0.017 Sum_probs=18.5
Q ss_pred CCCcccccccccCCCchhhhhhcCCCceeccccccc
Q 037179 82 AKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKT 117 (266)
Q Consensus 82 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~ 117 (266)
.|..||.......- ...+..|.......|..||..
T Consensus 215 ~C~~Cg~~~~C~~C-~~~l~~h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 215 LCRSCGYILCCPNC-DVSLTYHKKEGKLRCHYCGYQ 249 (505)
T ss_pred EhhhCcCccCCCCC-CCceEEecCCCeEEcCCCcCc
Confidence 56666665554321 122333444555677777754
No 152
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=42.64 E-value=15 Score=21.77 Aligned_cols=12 Identities=33% Similarity=0.739 Sum_probs=7.2
Q ss_pred CCeecccccccc
Q 037179 191 KPFMCRKCGKFL 202 (266)
Q Consensus 191 kp~~C~~C~k~f 202 (266)
..+.|..||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 356677676544
No 153
>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=41.02 E-value=14 Score=20.01 Aligned_cols=16 Identities=6% Similarity=0.113 Sum_probs=8.3
Q ss_pred CCCCcccccccccCCC
Q 037179 81 SAKGNANVAAAKQYWI 96 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l 96 (266)
-.|..|++.|.....+
T Consensus 4 ~~C~eC~~~f~dSyL~ 19 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLL 19 (34)
T ss_dssp EE-TTT--EES-SSCC
T ss_pred chHhHhCCHHHHHHHH
Confidence 3588899988876544
No 154
>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=40.76 E-value=14 Score=25.02 Aligned_cols=31 Identities=13% Similarity=0.138 Sum_probs=20.8
Q ss_pred CCCCCCcccccccccCCCchhhhhhcCCCceeccccccccc
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFN 119 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~ 119 (266)
..|.|+.|++.-... .+--.|.|..|++.|.
T Consensus 34 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPFCGKKTVKR----------GSTGIWTCRKCGAKFA 64 (91)
T ss_pred cCccCCCCCCCceEE----------EeeEEEEcCCCCCEEe
Confidence 458999998543221 1223599999999874
No 155
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.01 E-value=13 Score=27.25 Aligned_cols=39 Identities=13% Similarity=0.060 Sum_probs=22.7
Q ss_pred CCCCCCcccccccccC---CCch--hhhhhc----CCCceeccccccc
Q 037179 79 NPSAKGNANVAAAKQY---WIPT--PEQILI----GFTHFSCHVCFKT 117 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~---~l~~--H~~~h~----~~k~~~C~~C~k~ 117 (266)
..+.|..||..|.... .|.. +.-+|. ....+.|+.||..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 4589999998887641 1100 111221 1344679999964
No 156
>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 PRK04023 DNA polymerase II large subunit; Validated
Probab=38.90 E-value=35 Score=33.61 Aligned_cols=10 Identities=20% Similarity=-0.190 Sum_probs=6.4
Q ss_pred CccCCCCCcc
Q 037179 246 PFSRPFDGVE 255 (266)
Q Consensus 246 p~~C~~C~k~ 255 (266)
++.|+.||..
T Consensus 663 ~y~CPKCG~E 672 (1121)
T PRK04023 663 EDECEKCGRE 672 (1121)
T ss_pred CCcCCCCCCC
Confidence 3667777743
No 158
>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=38.46 E-value=17 Score=20.67 Aligned_cols=15 Identities=27% Similarity=0.616 Sum_probs=9.9
Q ss_pred cccccccccChhhHH
Q 037179 111 CHVCFKTFNRYNNLQ 125 (266)
Q Consensus 111 C~~C~k~F~~~~~L~ 125 (266)
|..|+..|+......
T Consensus 11 C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 11 CPVCGRPFTWRKKWA 25 (42)
T ss_pred CcccCCcchHHHHHH
Confidence 777777777665443
No 159
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=38.11 E-value=17 Score=21.98 Aligned_cols=28 Identities=21% Similarity=0.423 Sum_probs=11.4
Q ss_pred chHHHHHHHhhCCCCCCccCCC----CCccccc
Q 037179 230 KRSLKDHIKAFGSGHGPFSRPF----DGVEVLD 258 (266)
Q Consensus 230 ~~~L~~H~~~~H~~~~p~~C~~----C~k~f~~ 258 (266)
+..|..|+.. -=..++..|++ |+..+..
T Consensus 23 r~~l~~H~~~-~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 23 RKELDDHLEN-ECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp CCCHHHHHHT-TSTTSEEE-SS----S--EEEH
T ss_pred HHHHHHHHHc-cCCCCcEECCCCCCCCCCccch
Confidence 3345555553 12334455555 5554443
No 160
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=37.74 E-value=17 Score=25.95 Aligned_cols=22 Identities=32% Similarity=0.763 Sum_probs=13.5
Q ss_pred CEEe-EcCccccCchHHHHHHHh
Q 037179 218 RWLC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 218 ~~~C-~C~k~F~~~~~L~~H~~~ 239 (266)
.|.| .|.+-|.....|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 3556 666666666666666553
No 161
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=37.31 E-value=22 Score=21.65 Aligned_cols=11 Identities=0% Similarity=-0.384 Sum_probs=5.8
Q ss_pred CCCccCCCCCc
Q 037179 244 HGPFSRPFDGV 254 (266)
Q Consensus 244 ~~p~~C~~C~k 254 (266)
...|-|+.|.-
T Consensus 29 i~tYmC~eC~~ 39 (56)
T PF09963_consen 29 IHTYMCDECKE 39 (56)
T ss_pred CcceeChhHHH
Confidence 34456666653
No 162
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=36.04 E-value=14 Score=22.13 Aligned_cols=13 Identities=15% Similarity=0.278 Sum_probs=7.0
Q ss_pred cCCCCCccccccc
Q 037179 248 SRPFDGVEVLDDA 260 (266)
Q Consensus 248 ~C~~C~k~f~~~~ 260 (266)
.||+|++.|....
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 8999999987654
No 163
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=35.71 E-value=40 Score=34.12 Aligned_cols=27 Identities=30% Similarity=0.586 Sum_probs=15.2
Q ss_pred CCEEe-EcCccccCchHHHHHHHhhCCCCCCccCCCCCcc
Q 037179 217 KRWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVE 255 (266)
Q Consensus 217 k~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~ 255 (266)
.+|.| .||....... ++ ...|+.||..
T Consensus 691 ~vy~CPsCGaev~~de----------s~--a~~CP~CGtp 718 (1337)
T PRK14714 691 PVYVCPDCGAEVPPDE----------SG--RVECPRCDVE 718 (1337)
T ss_pred CceeCccCCCccCCCc----------cc--cccCCCCCCc
Confidence 45778 7887543210 11 3458888844
No 164
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=35.71 E-value=24 Score=25.02 Aligned_cols=10 Identities=20% Similarity=0.494 Sum_probs=5.2
Q ss_pred EEe-EcCcccc
Q 037179 219 WLC-VCGSDFK 228 (266)
Q Consensus 219 ~~C-~C~k~F~ 228 (266)
+.| .||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 455 5555544
No 165
>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=35.49 E-value=16 Score=20.39 Aligned_cols=32 Identities=16% Similarity=0.119 Sum_probs=15.5
Q ss_pred CCCCCcccccccccCCCchhhhhhcCCCceeccccccc
Q 037179 80 PSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKT 117 (266)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~ 117 (266)
|..|..|+--+. -...+..+.+.|.|..|+..
T Consensus 2 p~rC~~C~aylN------p~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLN------PFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-------TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEEC------CcceEcCCCCEEECcCCCCc
Confidence 456777764333 33344446677999999864
No 166
>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=35.30 E-value=25 Score=24.55 Aligned_cols=24 Identities=13% Similarity=0.254 Sum_probs=15.8
Q ss_pred eec----ccccccccChhhHHhhhhhcC
Q 037179 109 FSC----HVCFKTFNRYNNLQMHMWGHG 132 (266)
Q Consensus 109 ~~C----~~C~k~F~~~~~L~~H~~~h~ 132 (266)
|.| ..|+..+.....+.+|.+.++
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 566 667776777777777766543
No 167
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=35.20 E-value=26 Score=20.68 Aligned_cols=9 Identities=44% Similarity=1.173 Sum_probs=5.0
Q ss_pred Ceecccccc
Q 037179 192 PFMCRKCGK 200 (266)
Q Consensus 192 p~~C~~C~k 200 (266)
.+.|..||.
T Consensus 37 R~~CGkCgy 45 (51)
T COG1998 37 RWACGKCGY 45 (51)
T ss_pred eeEeccccc
Confidence 455666654
No 168
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=34.43 E-value=17 Score=26.37 Aligned_cols=15 Identities=33% Similarity=0.895 Sum_probs=12.4
Q ss_pred Ceecccccccccchh
Q 037179 192 PFMCRKCGKFLAVKG 206 (266)
Q Consensus 192 p~~C~~C~k~f~~~~ 206 (266)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999998765
No 169
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.33 E-value=14 Score=29.64 Aligned_cols=40 Identities=15% Similarity=0.199 Sum_probs=29.2
Q ss_pred CCCCCCCcccccccccCCCchhhhhhcCCC----------c-----eeccccccc
Q 037179 78 NNPSAKGNANVAAAKQYWIPTPEQILIGFT----------H-----FSCHVCFKT 117 (266)
Q Consensus 78 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k----------~-----~~C~~C~k~ 117 (266)
++...|++|+-.|.....+..-.|+-.|+. | +.|+.|..+
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yA 71 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYA 71 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHH
Confidence 456899999999998777666666555432 2 479999865
No 170
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=34.05 E-value=5.7 Score=33.32 Aligned_cols=35 Identities=11% Similarity=0.125 Sum_probs=14.2
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceecccccccc
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTF 118 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F 118 (266)
-.|++||..-.- +.|..-.. .|.+-..|..|+-..
T Consensus 173 g~CPvCGs~P~~-s~l~~~~~--~G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 173 GYCPVCGSPPVL-SVLRGGER--EGKRYLHCSLCGTEW 207 (290)
T ss_dssp SS-TTT---EEE-EEEE--------EEEEEETTT--EE
T ss_pred CcCCCCCCcCce-EEEecCCC--CccEEEEcCCCCCee
Confidence 579999954332 22222111 255667899998653
No 171
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=33.56 E-value=20 Score=24.19 Aligned_cols=31 Identities=16% Similarity=0.293 Sum_probs=20.5
Q ss_pred CCCCCCcccccccccCCCchhhhhhcCCCceeccccccccc
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFN 119 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~ 119 (266)
..|.|+.|++.--.. .+--.|.|..|++.|.
T Consensus 35 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPVCGRPKVKR----------VGTGIWECRKCGAKFA 65 (90)
T ss_pred cCccCCCCCCCceEE----------EEEEEEEcCCCCCEEe
Confidence 458999997543221 1223589999999874
No 172
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=33.30 E-value=26 Score=33.05 Aligned_cols=35 Identities=11% Similarity=0.114 Sum_probs=20.4
Q ss_pred cCccccCchHHHHHHHhhCCCCCCccCCCCCcccccccccc
Q 037179 223 CGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEVLDDASSS 263 (266)
Q Consensus 223 C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f~~~~~~~ 263 (266)
||-.|...- +..-. +.+.-+||.|+.+|...+-.+
T Consensus 661 C~H~FC~~C-vq~r~-----etRqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 661 CGHVFCEEC-VQTRY-----ETRQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred cchHHHHHH-HHHHH-----HHhcCCCCCCCCCCCcccccc
Confidence 666665432 22222 234456999999998765544
No 173
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=32.67 E-value=13 Score=27.37 Aligned_cols=23 Identities=30% Similarity=0.748 Sum_probs=17.5
Q ss_pred CCEEe-EcCccccCchHHHHHHHh
Q 037179 217 KRWLC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 217 k~~~C-~C~k~F~~~~~L~~H~~~ 239 (266)
-+|.| .||..+.....|..|..+
T Consensus 128 S~ysC~~CG~kyCsv~C~~~HneT 151 (156)
T KOG3362|consen 128 SKYSCVNCGTKYCSVRCLKTHNET 151 (156)
T ss_pred chhHHHhcCCceeechhhhhcccc
Confidence 35668 888888888888877654
No 174
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=32.31 E-value=27 Score=25.41 Aligned_cols=16 Identities=13% Similarity=0.098 Sum_probs=8.0
Q ss_pred CCCccCCCCCcccccc
Q 037179 244 HGPFSRPFDGVEVLDD 259 (266)
Q Consensus 244 ~~p~~C~~C~k~f~~~ 259 (266)
...|+|..|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 3345555555555443
No 175
>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=31.66 E-value=25 Score=19.45 Aligned_cols=16 Identities=6% Similarity=0.021 Sum_probs=6.2
Q ss_pred CCccCCCCCccccccc
Q 037179 245 GPFSRPFDGVEVLDDA 260 (266)
Q Consensus 245 ~p~~C~~C~k~f~~~~ 260 (266)
+.|-|++|++-|++.+
T Consensus 2 ~ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDS 17 (38)
T ss_dssp -S-B-TTT--B-S--S
T ss_pred cCeecccccceecCCC
Confidence 4588999999985544
No 176
>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=31.45 E-value=27 Score=24.80 Aligned_cols=11 Identities=18% Similarity=0.567 Sum_probs=5.6
Q ss_pred EEe-EcCccccC
Q 037179 219 WLC-VCGSDFKH 229 (266)
Q Consensus 219 ~~C-~C~k~F~~ 229 (266)
..| .||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 445 55555543
No 177
>PRK05580 primosome assembly protein PriA; Validated
Probab=31.40 E-value=25 Score=33.46 Aligned_cols=13 Identities=31% Similarity=0.672 Sum_probs=8.7
Q ss_pred CCCCeeccccccc
Q 037179 189 GLKPFMCRKCGKF 201 (266)
Q Consensus 189 ~~kp~~C~~C~k~ 201 (266)
...|..|+.||..
T Consensus 418 ~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 418 EPIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCCcCC
Confidence 3446778888764
No 178
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=31.17 E-value=96 Score=26.40 Aligned_cols=49 Identities=18% Similarity=0.291 Sum_probs=30.0
Q ss_pred CCeecccccccccchhhHHHHHH------------H-----------------hCCCEEe-EcCccccCchHHHHHHHh
Q 037179 191 KPFMCRKCGKFLAVKGDWRTHEK------------N-----------------CGKRWLC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 191 kp~~C~~C~k~f~~~~~L~~H~~------------~-----------------~~k~~~C-~C~k~F~~~~~L~~H~~~ 239 (266)
-|-.|+.|+-.......|.+-.+ . ..-.|+| .|...|----..-.|...
T Consensus 289 LP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesL 367 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESL 367 (378)
T ss_pred CCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhhh
Confidence 36677888777766666654332 0 1234777 777777766666666655
No 179
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.41 E-value=17 Score=30.27 Aligned_cols=16 Identities=38% Similarity=0.777 Sum_probs=12.6
Q ss_pred CCCeecccccccccch
Q 037179 190 LKPFMCRKCGKFLAVK 205 (266)
Q Consensus 190 ~kp~~C~~C~k~f~~~ 205 (266)
.-||.|.+|.+.|...
T Consensus 239 ~~Pf~c~icr~~f~~p 254 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRP 254 (313)
T ss_pred cCCccccccccccccc
Confidence 3578999999888765
No 180
>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=30.19 E-value=28 Score=19.02 Aligned_cols=32 Identities=6% Similarity=-0.056 Sum_probs=19.0
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceecccccccccC
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNR 120 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~ 120 (266)
..|+.||+.|...+. ....+-.|..||..+.+
T Consensus 2 r~C~~Cg~~Yh~~~~--------pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHIEFN--------PPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEETTTB----------SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCccccccC--------CCCCCCccCCCCCeeEe
Confidence 358888888865432 12334568888776543
No 181
>COG1773 Rubredoxin [Energy production and conversion]
Probab=29.74 E-value=25 Score=21.35 Aligned_cols=13 Identities=23% Similarity=0.631 Sum_probs=7.4
Q ss_pred Ceecccccccccc
Q 037179 192 PFMCRKCGKFLAV 204 (266)
Q Consensus 192 p~~C~~C~k~f~~ 204 (266)
.|+|..||..|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 3566666665544
No 182
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.62 E-value=17 Score=31.99 Aligned_cols=22 Identities=14% Similarity=0.001 Sum_probs=16.2
Q ss_pred CCCccCCCCCcccccccccccC
Q 037179 244 HGPFSRPFDGVEVLDDASSSLL 265 (266)
Q Consensus 244 ~~p~~C~~C~k~f~~~~~~~~~ 265 (266)
..-|.|+.|.+.|+.-.+++++
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~ 147 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLL 147 (436)
T ss_pred cccccCCccccchhhhHHHHhh
Confidence 3458888888888877766654
No 183
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=29.61 E-value=31 Score=18.86 Aligned_cols=18 Identities=17% Similarity=-0.047 Sum_probs=9.7
Q ss_pred CccCCCCCcccccccccc
Q 037179 246 PFSRPFDGVEVLDDASSS 263 (266)
Q Consensus 246 p~~C~~C~k~f~~~~~~~ 263 (266)
|-.|+-|+|.|-+.+..+
T Consensus 2 ~~~CprC~kg~Hwa~~C~ 19 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECR 19 (36)
T ss_dssp --C-TTTSSSCS-TTT--
T ss_pred CccCcccCCCcchhhhhh
Confidence 346888999888776544
No 184
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=29.48 E-value=24 Score=29.56 Aligned_cols=106 Identities=15% Similarity=0.161 Sum_probs=54.2
Q ss_pred CCCCCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHHhhhhhcCCCCCCCCCCcCCCCCCccCCcCCCCC
Q 037179 79 NPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQMHMWGHGSQYRKGPESLKGTQPRAILGIPCYCC 158 (266)
Q Consensus 79 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~C~~C 158 (266)
.-|.|+.|....-+ -|-.|+.|.-......+|.+-..---.-++.. +...+..+ ..--|..|
T Consensus 307 gGy~CP~CktkVCs--------------LPi~CP~Csl~LilsthLarSyhhL~PLk~f~-E~p~~~~~---ks~~Cf~C 368 (421)
T COG5151 307 GGYECPVCKTKVCS--------------LPISCPICSLQLILSTHLARSYHHLYPLKPFV-EKPEGTNP---KSTHCFVC 368 (421)
T ss_pred CceeCCcccceeec--------------CCccCcchhHHHHHHHHHHHHHHhhccCcccc-cccCCCCC---CCccceec
Confidence 44889988743322 36779999887766666654321110000000 00011111 12447777
Q ss_pred CCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHHHhC
Q 037179 159 AEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEKNCG 216 (266)
Q Consensus 159 ~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~~ 216 (266)
. -.|.....-..-. -+..-.|.|..|...|-..-+.-.|...|.
T Consensus 369 Q------------~~fp~~~~~~~~~--~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 369 Q------------GPFPKPPVSPFDE--STSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred c------------CCCCCCCCCcccc--cccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 7 3343221100000 112335899999998887777777766554
No 185
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=29.46 E-value=38 Score=16.80 Aligned_cols=8 Identities=13% Similarity=-0.134 Sum_probs=5.1
Q ss_pred CCCCcccc
Q 037179 81 SAKGNANV 88 (266)
Q Consensus 81 ~~C~~C~~ 88 (266)
..|+.||.
T Consensus 3 ~~Cp~Cg~ 10 (26)
T PF13248_consen 3 MFCPNCGA 10 (26)
T ss_pred CCCcccCC
Confidence 34777775
No 186
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.27 E-value=44 Score=23.37 Aligned_cols=15 Identities=20% Similarity=0.286 Sum_probs=11.9
Q ss_pred CCCCeeccccccccc
Q 037179 189 GLKPFMCRKCGKFLA 203 (266)
Q Consensus 189 ~~kp~~C~~C~k~f~ 203 (266)
...|..|++||++|.
T Consensus 23 NrdPiVsPytG~s~P 37 (129)
T COG4530 23 NRDPIVSPYTGKSYP 37 (129)
T ss_pred CCCccccCcccccch
Confidence 456888999999883
No 187
>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=28.94 E-value=21 Score=24.51 Aligned_cols=20 Identities=30% Similarity=0.705 Sum_probs=14.9
Q ss_pred hhhhcCCCCeecccccccccc
Q 037179 184 YKRKHGLKPFMCRKCGKFLAV 204 (266)
Q Consensus 184 ~~~h~~~kp~~C~~C~k~f~~ 204 (266)
+..+.| +|++|..||..|.-
T Consensus 72 ~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 72 MWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEEeCC-CceeCCCCCcEEEE
Confidence 345555 79999999988864
No 188
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=28.83 E-value=37 Score=18.92 Aligned_cols=37 Identities=8% Similarity=-0.001 Sum_probs=22.3
Q ss_pred CCCcccccccccCCCchhhhhhcCCCceecccccccccChhhHHh
Q 037179 82 AKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYNNLQM 126 (266)
Q Consensus 82 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~~L~~ 126 (266)
.|+.|+....... + .+-..+.|..|+-.+-....|.+
T Consensus 1 ~CP~C~~~l~~~~-~-------~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELEPVR-L-------GDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccceEE-E-------CCEEEEECCCCCeEEccHHHHHH
Confidence 3777775433211 1 23345779999988877776654
No 189
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=28.70 E-value=47 Score=20.13 Aligned_cols=30 Identities=13% Similarity=0.347 Sum_probs=16.2
Q ss_pred EcCccccCchHHHHHHHhhCCCCCCccCCCCCccccc
Q 037179 222 VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEVLD 258 (266)
Q Consensus 222 ~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f~~ 258 (266)
.||..|.. ..+..+++. + ..|++|++.+..
T Consensus 18 ~~G~v~~~-~~i~~~~~~-~-----~~cP~~~~~~~~ 47 (63)
T smart00504 18 PSGQTYER-RAIEKWLLS-H-----GTDPVTGQPLTH 47 (63)
T ss_pred CCCCEEeH-HHHHHHHHH-C-----CCCCCCcCCCCh
Confidence 46666643 344555543 1 357777776643
No 190
>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=28.63 E-value=27 Score=20.86 Aligned_cols=25 Identities=20% Similarity=0.383 Sum_probs=14.9
Q ss_pred CceecccccccccChhhHHhhhhhc
Q 037179 107 THFSCHVCFKTFNRYNNLQMHMWGH 131 (266)
Q Consensus 107 k~~~C~~C~k~F~~~~~L~~H~~~h 131 (266)
..|.|+.|...|-..-.+-.|...|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 4588888888888888888887776
No 191
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=27.80 E-value=28 Score=21.05 Aligned_cols=14 Identities=21% Similarity=0.245 Sum_probs=10.1
Q ss_pred ccCCCCCccccccc
Q 037179 247 FSRPFDGVEVLDDA 260 (266)
Q Consensus 247 ~~C~~C~k~f~~~~ 260 (266)
.+|++||+.|..+.
T Consensus 6 ~~C~~Cg~~~~~~d 19 (54)
T PF14446_consen 6 CKCPVCGKKFKDGD 19 (54)
T ss_pred ccChhhCCcccCCC
Confidence 46888888886543
No 192
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.27 E-value=26 Score=21.61 Aligned_cols=41 Identities=27% Similarity=0.608 Sum_probs=22.4
Q ss_pred cCCCCCCCCccCCCCCCCCCCCCChhhHHHHhhhhcCCCCeecccccccccc
Q 037179 153 IPCYCCAEGCKNSINHPKAKPLKDFRTLQTHYKRKHGLKPFMCRKCGKFLAV 204 (266)
Q Consensus 153 ~~C~~C~~~~~~~~~~~~~k~f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~ 204 (266)
-+|.+|+. ..|.+...+..-+..-..-+.|.|+.|.-....
T Consensus 3 vkCiiCd~-----------v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva~ 43 (68)
T COG4896 3 VKCIICDR-----------VDEIDNRTFKTKRLRNKPIRTYMCPECEHRVAI 43 (68)
T ss_pred ceEEEecc-----------eeeecchhHHHHHhhCCCceeEechhhHhhhch
Confidence 45777773 344444444444333334456888888654433
No 193
>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=27.20 E-value=16 Score=27.32 Aligned_cols=10 Identities=10% Similarity=-0.021 Sum_probs=4.5
Q ss_pred ccCCCCCccc
Q 037179 247 FSRPFDGVEV 256 (266)
Q Consensus 247 ~~C~~C~k~f 256 (266)
|.|..|+..|
T Consensus 144 ~~C~~C~~~l 153 (157)
T PF10263_consen 144 YRCGRCGGPL 153 (157)
T ss_pred EECCCCCCEE
Confidence 4444444433
No 194
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=27.13 E-value=43 Score=32.06 Aligned_cols=32 Identities=13% Similarity=0.068 Sum_probs=18.6
Q ss_pred CCCCcccccccccC---CCchhhhhhcCCCceecccccc
Q 037179 81 SAKGNANVAAAKQY---WIPTPEQILIGFTHFSCHVCFK 116 (266)
Q Consensus 81 ~~C~~C~~~f~~~~---~l~~H~~~h~~~k~~~C~~C~k 116 (266)
..|..||..+.... .|..| .......|.+||.
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H----~~~~~L~CH~Cg~ 470 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLH----KATGQLRCHYCGY 470 (730)
T ss_pred eecccCCCcccCCCCCcceEEe----cCCCeeEeCCCCC
Confidence 36777777766542 23333 3345567777775
No 195
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=27.09 E-value=24 Score=26.19 Aligned_cols=12 Identities=8% Similarity=0.014 Sum_probs=6.9
Q ss_pred CCccCCCCCccc
Q 037179 245 GPFSRPFDGVEV 256 (266)
Q Consensus 245 ~p~~C~~C~k~f 256 (266)
..|.|..|+-.|
T Consensus 132 ~~y~C~~C~g~l 143 (146)
T smart00731 132 SRYRCGKCGGKL 143 (146)
T ss_pred ceEEcCCCCCEE
Confidence 446666666544
No 196
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=26.67 E-value=28 Score=31.83 Aligned_cols=32 Identities=19% Similarity=0.119 Sum_probs=23.5
Q ss_pred hhhHHHHhhhhcCCCCeecccccccccchhhH
Q 037179 177 FRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDW 208 (266)
Q Consensus 177 ~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L 208 (266)
.+.+.+|-.+|....--+|..|||.|.++-.+
T Consensus 238 E~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~F 269 (1004)
T KOG0782|consen 238 ESGFVRHHWVHRRRQEGKCNTCGKGFQQKFFF 269 (1004)
T ss_pred cccchHHhHhhHhhhccccchhhhhhhhheee
Confidence 34777887777666667899999998776543
No 197
>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=26.11 E-value=24 Score=19.88 Aligned_cols=12 Identities=33% Similarity=0.736 Sum_probs=8.5
Q ss_pred CCccCCCCCccc
Q 037179 245 GPFSRPFDGVEV 256 (266)
Q Consensus 245 ~p~~C~~C~k~f 256 (266)
++-.|++||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 356788887776
No 198
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=25.95 E-value=35 Score=23.52 Aligned_cols=13 Identities=31% Similarity=0.991 Sum_probs=6.9
Q ss_pred Ceecccccccccc
Q 037179 192 PFMCRKCGKFLAV 204 (266)
Q Consensus 192 p~~C~~C~k~f~~ 204 (266)
|+.|..||..|..
T Consensus 2 pH~CtrCG~vf~~ 14 (112)
T COG3364 2 PHQCTRCGEVFDD 14 (112)
T ss_pred Cceeccccccccc
Confidence 3455555555554
No 199
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=25.56 E-value=49 Score=19.28 Aligned_cols=15 Identities=20% Similarity=0.266 Sum_probs=10.7
Q ss_pred ceecccccccccChh
Q 037179 108 HFSCHVCFKTFNRYN 122 (266)
Q Consensus 108 ~~~C~~C~k~F~~~~ 122 (266)
.|.|+.||..+....
T Consensus 20 ~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 20 RFVCRKCGYEEPIEQ 34 (52)
T ss_pred EEECCcCCCeEECCC
Confidence 588999987765443
No 200
>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=25.31 E-value=29 Score=25.78 Aligned_cols=16 Identities=19% Similarity=0.615 Sum_probs=10.3
Q ss_pred eecccccccccChhhH
Q 037179 109 FSCHVCFKTFNRYNNL 124 (266)
Q Consensus 109 ~~C~~C~k~F~~~~~L 124 (266)
=.|..|++.|++-..+
T Consensus 29 ReC~~C~~RFTTyErv 44 (147)
T TIGR00244 29 RECLECHERFTTFERA 44 (147)
T ss_pred ccCCccCCccceeeec
Confidence 3577777777765443
No 201
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=25.12 E-value=32 Score=25.68 Aligned_cols=15 Identities=20% Similarity=0.569 Sum_probs=9.7
Q ss_pred eecccccccccChhh
Q 037179 109 FSCHVCFKTFNRYNN 123 (266)
Q Consensus 109 ~~C~~C~k~F~~~~~ 123 (266)
=.|..|+..|++-..
T Consensus 29 ReC~~C~~RFTTfE~ 43 (156)
T COG1327 29 RECLECGERFTTFER 43 (156)
T ss_pred hcccccccccchhhe
Confidence 357777777766543
No 202
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=25.08 E-value=28 Score=26.10 Aligned_cols=42 Identities=17% Similarity=0.127 Sum_probs=24.9
Q ss_pred CCCcccccccccCCCchhhhh-hcCCCceecccccccccChhh
Q 037179 82 AKGNANVAAAKQYWIPTPEQI-LIGFTHFSCHVCFKTFNRYNN 123 (266)
Q Consensus 82 ~C~~C~~~f~~~~~l~~H~~~-h~~~k~~~C~~C~k~F~~~~~ 123 (266)
.|+.|+-...-.++...=.-. ..-+.|.-|..||+.|.|-..
T Consensus 41 ~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred HCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHHH
Confidence 577777555544332221111 223467779999999988754
No 203
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=25.06 E-value=58 Score=19.83 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=12.8
Q ss_pred CCCEEe-EcCccccCchHHHHHHHhhCCCCCCccCCC
Q 037179 216 GKRWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRPF 251 (266)
Q Consensus 216 ~k~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~ 251 (266)
+.|+.. .||..|-.. .+...+ ...+..+|++
T Consensus 22 ~~PV~s~~C~H~fek~-aI~~~i----~~~~~~~CPv 53 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKE-AILQYI----QRNGSKRCPV 53 (57)
T ss_dssp SSEEEESSS--EEEHH-HHHHHC----TTTS-EE-SC
T ss_pred hCCcCcCCCCCeecHH-HHHHHH----HhcCCCCCCC
Confidence 445555 666666443 233333 1344556666
No 204
>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=24.94 E-value=52 Score=20.61 Aligned_cols=29 Identities=17% Similarity=0.161 Sum_probs=19.5
Q ss_pred CCCcccccccccCCCchhhhhhcCCCceecccccccccC
Q 037179 82 AKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNR 120 (266)
Q Consensus 82 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~ 120 (266)
.|+.||..-.. -...+.|.|+.||..+..
T Consensus 30 ~C~~CG~~~~~----------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 30 TCPRCGHRNKK----------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccccccc----------ccccceEEcCCCCCEECc
Confidence 48888865544 123456889999987544
No 205
>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=24.89 E-value=21 Score=19.53 Aligned_cols=19 Identities=21% Similarity=0.662 Sum_probs=12.9
Q ss_pred HHHHhhhhcCCCCeecccc
Q 037179 180 LQTHYKRKHGLKPFMCRKC 198 (266)
Q Consensus 180 l~~H~~~h~~~kp~~C~~C 198 (266)
+.+|=+...|...|.|..|
T Consensus 17 v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 17 VKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred ceeCCCCCCCCEeEecCcC
Confidence 4455555567777888877
No 206
>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=24.34 E-value=46 Score=20.11 Aligned_cols=15 Identities=27% Similarity=0.319 Sum_probs=9.2
Q ss_pred ccCCCCCcccccccc
Q 037179 247 FSRPFDGVEVLDDAS 261 (266)
Q Consensus 247 ~~C~~C~k~f~~~~~ 261 (266)
|.|+.||..+.-...
T Consensus 3 ~~CP~CG~~iev~~~ 17 (54)
T TIGR01206 3 FECPDCGAEIELENP 17 (54)
T ss_pred cCCCCCCCEEecCCC
Confidence 567777776654443
No 207
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.25 E-value=47 Score=29.40 Aligned_cols=31 Identities=13% Similarity=0.127 Sum_probs=23.5
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceecccccccccChh
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRYN 122 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~~ 122 (266)
-.|+.||....++ |.+-|+|+.||..+....
T Consensus 351 p~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 351 PVCPRCGGRMKSA-----------GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCCccCCchhhc-----------CCCCcccccccccCCccc
Confidence 4799999877664 444799999999876544
No 208
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=24.16 E-value=48 Score=23.69 Aligned_cols=24 Identities=25% Similarity=0.589 Sum_probs=21.0
Q ss_pred CCeecccccccccchhhHHHHHHH
Q 037179 191 KPFMCRKCGKFLAVKGDWRTHEKN 214 (266)
Q Consensus 191 kp~~C~~C~k~f~~~~~L~~H~~~ 214 (266)
-.|-|-.|.+-|.....|..|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 348899999999999999999884
No 209
>PF04641 Rtf2: Rtf2 RING-finger
Probab=24.12 E-value=84 Score=25.90 Aligned_cols=52 Identities=25% Similarity=0.459 Sum_probs=35.6
Q ss_pred CCCCeecccccccccchhhHHHHHHHhCCCEEe--EcCccccCchHHHHHHHhhCCCCCCccCCCCCcccccc
Q 037179 189 GLKPFMCRKCGKFLAVKGDWRTHEKNCGKRWLC--VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDGVEVLDD 259 (266)
Q Consensus 189 ~~kp~~C~~C~k~f~~~~~L~~H~~~~~k~~~C--~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~k~f~~~ 259 (266)
..-+|.|++.++.|.. .-+|.+ .||-.|.... |.. ++ +--.|++||+.|...
T Consensus 110 ~~~~~~CPvt~~~~~~-----------~~~fv~l~~cG~V~s~~a-lke-~k------~~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNG-----------KHKFVYLRPCGCVFSEKA-LKE-LK------KSKKCPVCGKPFTEE 163 (260)
T ss_pred CCceeECCCCCcccCC-----------ceeEEEEcCCCCEeeHHH-HHh-hc------ccccccccCCccccC
Confidence 4557999999988843 346777 6999998663 221 11 123499999999854
No 210
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=23.82 E-value=38 Score=19.05 Aligned_cols=27 Identities=30% Similarity=0.415 Sum_probs=13.8
Q ss_pred cCccccCchHHHHHHHhhCCCCCCccCCCC
Q 037179 223 CGSDFKHKRSLKDHIKAFGSGHGPFSRPFD 252 (266)
Q Consensus 223 C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C 252 (266)
||-.|-.. -|.+-++. .+...+.|++|
T Consensus 16 CGH~FC~~-Cl~~~~~~--~~~~~~~CP~C 42 (42)
T PF15227_consen 16 CGHSFCRS-CLERLWKE--PSGSGFSCPEC 42 (42)
T ss_dssp SSSEEEHH-HHHHHHCC--SSSST---SSS
T ss_pred CcCHHHHH-HHHHHHHc--cCCcCCCCcCC
Confidence 77777654 46665554 23333888876
No 211
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=23.62 E-value=42 Score=20.33 Aligned_cols=12 Identities=33% Similarity=0.368 Sum_probs=7.8
Q ss_pred cCCCCCcccccc
Q 037179 248 SRPFDGVEVLDD 259 (266)
Q Consensus 248 ~C~~C~k~f~~~ 259 (266)
-|++|++.|...
T Consensus 41 gCPfC~~~~~~~ 52 (55)
T PF14447_consen 41 GCPFCGTPFEFD 52 (55)
T ss_pred CCCCCCCcccCC
Confidence 377777777543
No 212
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=23.55 E-value=1.7e+02 Score=25.85 Aligned_cols=80 Identities=9% Similarity=-0.264 Sum_probs=41.7
Q ss_pred CCChhhHHHHhhhhcCCCCeecccccccccchhhHHHHHHHh--CCCEEe-EcCccccCchHHHHHHHhhCCCCCCccCC
Q 037179 174 LKDFRTLQTHYKRKHGLKPFMCRKCGKFLAVKGDWRTHEKNC--GKRWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRP 250 (266)
Q Consensus 174 f~~~~~l~~H~~~h~~~kp~~C~~C~k~f~~~~~L~~H~~~~--~k~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~ 250 (266)
+.....+..+...+++..+.-+..+.+.+.....+..|...+ +.++.+ .+...+.....+..+..+ |.....+.+.
T Consensus 313 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 391 (396)
T KOG2461|consen 313 LPKQLVLDQSEVPATVSVWTGETIPVRTPAGQLIYTQSHSMEVAEPTDMAPNQIWKIYHTGVLGFLIIT-TDESECNNMS 391 (396)
T ss_pred cccccccccccccccccccCcCcccccccccccchhhhhhcccCCCCcccccccccceeccccceeeee-cccccccccc
Confidence 334445556666666666666666666666666666665533 344444 222222222333444444 4555566666
Q ss_pred CCCc
Q 037179 251 FDGV 254 (266)
Q Consensus 251 ~C~k 254 (266)
.|++
T Consensus 392 ~~~~ 395 (396)
T KOG2461|consen 392 FVCK 395 (396)
T ss_pred ccCC
Confidence 5543
No 213
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=23.42 E-value=17 Score=19.62 Aligned_cols=11 Identities=27% Similarity=0.905 Sum_probs=6.8
Q ss_pred CCeeccccccc
Q 037179 191 KPFMCRKCGKF 201 (266)
Q Consensus 191 kp~~C~~C~k~ 201 (266)
..+.|..||..
T Consensus 21 ~R~vC~~Cg~I 31 (34)
T PF14803_consen 21 ERLVCPACGFI 31 (34)
T ss_dssp -EEEETTTTEE
T ss_pred cceECCCCCCE
Confidence 34677777754
No 214
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=23.17 E-value=59 Score=29.07 Aligned_cols=21 Identities=38% Similarity=0.879 Sum_probs=18.6
Q ss_pred EEe-EcCccccCchHHHHHHHh
Q 037179 219 WLC-VCGSDFKHKRSLKDHIKA 239 (266)
Q Consensus 219 ~~C-~C~k~F~~~~~L~~H~~~ 239 (266)
+.| +|.|+|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 889 999999999999999654
No 215
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=23.13 E-value=23 Score=31.44 Aligned_cols=44 Identities=11% Similarity=0.082 Sum_probs=19.6
Q ss_pred HHHHHhC-CCEEe-EcCccccCchHHHHHHHhhCCCCCCccCCCCC
Q 037179 210 THEKNCG-KRWLC-VCGSDFKHKRSLKDHIKAFGSGHGPFSRPFDG 253 (266)
Q Consensus 210 ~H~~~~~-k~~~C-~C~k~F~~~~~L~~H~~~~H~~~~p~~C~~C~ 253 (266)
.|++-|+ -.|.| -=++.+..-..-.+|.-..|+=..|.-|+.||
T Consensus 83 vHkrChefVtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCG 128 (683)
T KOG0696|consen 83 VHKRCHEFVTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCG 128 (683)
T ss_pred hhhhhcceEEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHH
Confidence 3444443 23444 44444444444444444334444444444444
No 216
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=22.63 E-value=25 Score=24.14 Aligned_cols=39 Identities=8% Similarity=0.079 Sum_probs=23.9
Q ss_pred CCCCCCCcccccccccCCCchhhhhhcCCCceecccccccccC
Q 037179 78 NNPSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNR 120 (266)
Q Consensus 78 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~ 120 (266)
.+.|.|+.||..-.....+.. -.+.-...|..||..|..
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk----~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKK----TVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred CceEecCccCCeeeeEEEEEe----cCceeEEEcccCcceEEE
Confidence 466999999976555333221 122223579999988743
No 217
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=22.61 E-value=33 Score=18.78 Aligned_cols=12 Identities=17% Similarity=-0.006 Sum_probs=6.4
Q ss_pred CCccCCCCCccc
Q 037179 245 GPFSRPFDGVEV 256 (266)
Q Consensus 245 ~p~~C~~C~k~f 256 (266)
.-|+|.+||.-.
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 358899998644
No 218
>PRK04351 hypothetical protein; Provisional
Probab=22.22 E-value=44 Score=24.98 Aligned_cols=34 Identities=6% Similarity=0.169 Sum_probs=22.9
Q ss_pred CCCCCcccccccccCCCchhhhhhcCCCceecccccccccCh
Q 037179 80 PSAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNRY 121 (266)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~~ 121 (266)
.|.|..|+..+... .+ + +...|.|..|+-.+...
T Consensus 112 ~Y~C~~Cg~~~~r~------Rr-~-n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 112 LYECQSCGQQYLRK------RR-I-NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEECCCCCCEeeee------ee-c-CCCcEEeCCCCcEeeec
Confidence 38899999766542 11 2 34669999999776543
No 219
>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=22.08 E-value=33 Score=24.21 Aligned_cols=10 Identities=40% Similarity=1.052 Sum_probs=4.6
Q ss_pred EEe-EcCcccc
Q 037179 219 WLC-VCGSDFK 228 (266)
Q Consensus 219 ~~C-~C~k~F~ 228 (266)
+.| .||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PF01155_consen 71 ARCRDCGHEFE 81 (113)
T ss_dssp EEETTTS-EEE
T ss_pred EECCCCCCEEe
Confidence 445 5555554
No 220
>PRK05978 hypothetical protein; Provisional
Probab=21.76 E-value=48 Score=24.79 Aligned_cols=31 Identities=10% Similarity=0.161 Sum_probs=20.1
Q ss_pred CCCCcccccccccCCCchhhhhhcCCCceecccccccccC
Q 037179 81 SAKGNANVAAAKQYWIPTPEQILIGFTHFSCHVCFKTFNR 120 (266)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~k~F~~ 120 (266)
-.|+.||+.=-....|+.+ -.|+.||..|..
T Consensus 34 grCP~CG~G~LF~g~Lkv~---------~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPV---------DHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCcccccccccC---------CCccccCCcccc
Confidence 4799998654444444433 249999988744
No 221
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=21.30 E-value=41 Score=18.02 Aligned_cols=12 Identities=25% Similarity=0.074 Sum_probs=8.0
Q ss_pred CccCCCCCcccc
Q 037179 246 PFSRPFDGVEVL 257 (266)
Q Consensus 246 p~~C~~C~k~f~ 257 (266)
-|.|+.|++.+.
T Consensus 4 ~~~C~nC~R~v~ 15 (33)
T PF08209_consen 4 YVECPNCGRPVA 15 (33)
T ss_dssp EEE-TTTSSEEE
T ss_pred eEECCCCcCCcc
Confidence 367999988764
No 222
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.21 E-value=42 Score=20.79 Aligned_cols=15 Identities=33% Similarity=0.532 Sum_probs=9.0
Q ss_pred HhhhhcCCCCeeccc
Q 037179 183 HYKRKHGLKPFMCRK 197 (266)
Q Consensus 183 H~~~h~~~kp~~C~~ 197 (266)
|..++.+.+++.|.-
T Consensus 15 ~~~I~~~~~~l~C~g 29 (62)
T COG4391 15 HETIEIGDLPLMCPG 29 (62)
T ss_pred ceEEEeCCeeEEcCC
Confidence 455556666666654
No 223
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=21.00 E-value=54 Score=28.74 Aligned_cols=23 Identities=13% Similarity=0.426 Sum_probs=18.9
Q ss_pred CEEe---EcCccccCchHHHHHHHhh
Q 037179 218 RWLC---VCGSDFKHKRSLKDHIKAF 240 (266)
Q Consensus 218 ~~~C---~C~k~F~~~~~L~~H~~~~ 240 (266)
.|-| -|+..|...+.+..|.|.|
T Consensus 401 hfhc~r~Gc~~tl~s~sqm~shkrkh 426 (480)
T KOG4377|consen 401 HFHCDRLGCEATLYSVSQMASHKRKH 426 (480)
T ss_pred eeeecccCCceEEEehhhhhhhhhhh
Confidence 3567 5999999999999998873
No 224
>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=20.81 E-value=34 Score=25.51 Aligned_cols=10 Identities=20% Similarity=0.497 Sum_probs=7.6
Q ss_pred CCcCCCCCCC
Q 037179 151 LGIPCYCCAE 160 (266)
Q Consensus 151 ~~~~C~~C~~ 160 (266)
+.|.|..||.
T Consensus 111 G~l~C~~Cg~ 120 (146)
T PF07295_consen 111 GTLVCENCGH 120 (146)
T ss_pred ceEecccCCC
Confidence 3488999993
No 225
>PRK01343 zinc-binding protein; Provisional
Probab=20.03 E-value=64 Score=19.76 Aligned_cols=12 Identities=17% Similarity=-0.072 Sum_probs=7.5
Q ss_pred ccCCCCCccccc
Q 037179 247 FSRPFDGVEVLD 258 (266)
Q Consensus 247 ~~C~~C~k~f~~ 258 (266)
..|++|++.|..
T Consensus 10 ~~CP~C~k~~~~ 21 (57)
T PRK01343 10 RPCPECGKPSTR 21 (57)
T ss_pred CcCCCCCCcCcC
Confidence 457777776643
Done!