Query 044606
Match_columns 413
No_of_seqs 322 out of 3649
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 04:58:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044606.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044606hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1074 Transcriptional repres 99.9 1.2E-23 2.7E-28 212.9 10.6 92 273-366 602-700 (958)
2 KOG2462 C2H2-type Zn-finger pr 99.9 3.6E-24 7.9E-29 193.4 4.2 90 263-356 176-265 (279)
3 KOG2462 C2H2-type Zn-finger pr 99.8 1.8E-19 3.9E-24 163.1 3.6 109 249-361 131-242 (279)
4 KOG1074 Transcriptional repres 99.7 2.7E-18 5.8E-23 174.5 6.1 61 4-75 328-388 (958)
5 KOG3623 Homeobox transcription 99.5 4.5E-15 9.7E-20 148.9 0.3 83 271-355 889-971 (1007)
6 KOG3576 Ovo and related transc 99.5 6.9E-15 1.5E-19 126.9 0.8 87 271-359 112-198 (267)
7 KOG3623 Homeobox transcription 99.2 2E-12 4.3E-17 130.1 2.0 105 250-356 212-331 (1007)
8 KOG3576 Ovo and related transc 99.2 1.7E-12 3.6E-17 112.3 -0.8 112 248-361 117-239 (267)
9 KOG3608 Zn finger proteins [Ge 99.2 5.9E-12 1.3E-16 117.3 0.9 104 257-361 272-379 (467)
10 KOG3608 Zn finger proteins [Ge 99.1 1.8E-11 3.8E-16 114.2 2.7 111 249-364 238-351 (467)
11 PHA00733 hypothetical protein 98.9 4.5E-10 9.8E-15 93.6 2.3 95 261-359 25-124 (128)
12 PHA02768 hypothetical protein; 98.6 2E-08 4.4E-13 69.5 2.2 37 276-314 5-41 (55)
13 PHA00616 hypothetical protein 98.5 3.1E-08 6.6E-13 65.2 1.4 31 40-70 1-31 (44)
14 PHA02768 hypothetical protein; 98.5 5.5E-08 1.2E-12 67.3 1.3 45 304-352 5-49 (55)
15 PF00096 zf-C2H2: Zinc finger, 98.4 1.3E-07 2.8E-12 54.2 1.3 23 41-63 1-23 (23)
16 PF13465 zf-H2C2_2: Zinc-finge 98.4 5.6E-08 1.2E-12 57.4 -0.4 23 292-314 2-24 (26)
17 PLN03086 PRLI-interacting fact 98.3 4.6E-07 9.9E-12 92.5 4.5 62 276-344 453-514 (567)
18 PLN03086 PRLI-interacting fact 98.2 8.3E-07 1.8E-11 90.6 3.8 99 251-356 456-562 (567)
19 PF13465 zf-H2C2_2: Zinc-finge 98.2 5.8E-07 1.2E-11 53.0 1.2 25 322-346 2-26 (26)
20 KOG3993 Transcription factor ( 98.1 1.5E-06 3.3E-11 83.5 1.8 39 27-65 282-320 (500)
21 PHA00616 hypothetical protein 98.0 1.4E-06 3.1E-11 57.4 0.8 34 276-309 1-34 (44)
22 PHA00732 hypothetical protein 98.0 3.8E-06 8.2E-11 63.7 2.9 36 276-314 1-37 (79)
23 PF13894 zf-C2H2_4: C2H2-type 98.0 3.3E-06 7.2E-11 48.5 1.6 24 41-64 1-24 (24)
24 KOG3993 Transcription factor ( 98.0 1.1E-06 2.3E-11 84.6 -0.9 116 248-364 267-386 (500)
25 PHA00733 hypothetical protein 97.9 1.1E-05 2.3E-10 67.4 3.2 59 264-327 62-120 (128)
26 PF13912 zf-C2H2_6: C2H2-type 97.8 9.4E-06 2E-10 48.3 1.0 26 40-65 1-26 (27)
27 COG5189 SFP1 Putative transcri 97.7 2.2E-05 4.8E-10 73.0 3.2 71 273-355 346-419 (423)
28 PF09237 GAGA: GAGA factor; I 97.7 2.3E-05 4.9E-10 52.8 2.1 36 33-68 17-52 (54)
29 smart00355 ZnF_C2H2 zinc finge 97.6 3E-05 6.6E-10 45.1 2.0 25 41-65 1-25 (26)
30 PF00096 zf-C2H2: Zinc finger, 97.6 8.9E-06 1.9E-10 46.4 -0.7 23 335-357 1-23 (23)
31 PF12874 zf-met: Zinc-finger o 97.4 6.5E-05 1.4E-09 43.7 0.9 24 41-64 1-24 (25)
32 PF13912 zf-C2H2_6: C2H2-type 97.3 6.5E-05 1.4E-09 44.6 0.2 26 334-359 1-26 (27)
33 PF12171 zf-C2H2_jaz: Zinc-fin 97.2 0.00011 2.3E-09 43.7 0.7 24 40-63 1-24 (27)
34 PF05605 zf-Di19: Drought indu 97.2 0.00017 3.8E-09 50.6 1.7 51 276-358 2-53 (54)
35 PF13894 zf-C2H2_4: C2H2-type 97.2 7.3E-05 1.6E-09 42.7 -0.3 24 335-358 1-24 (24)
36 PHA00732 hypothetical protein 96.8 0.0006 1.3E-08 51.7 1.8 26 40-65 1-27 (79)
37 PF12756 zf-C2H2_2: C2H2 type 96.7 0.0004 8.7E-09 54.9 0.2 74 278-358 1-74 (100)
38 PF13913 zf-C2HC_2: zinc-finge 96.7 0.00089 1.9E-08 38.9 1.5 21 41-62 3-23 (25)
39 smart00355 ZnF_C2H2 zinc finge 96.4 0.00083 1.8E-08 38.8 0.2 24 335-358 1-24 (26)
40 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0024 5.3E-08 36.6 1.4 24 41-65 1-24 (24)
41 PF09237 GAGA: GAGA factor; I 95.8 0.0053 1.1E-07 41.6 1.6 34 271-304 19-52 (54)
42 PF12874 zf-met: Zinc-finger o 95.5 0.0032 7E-08 36.4 -0.2 23 335-357 1-23 (25)
43 PF12171 zf-C2H2_jaz: Zinc-fin 95.5 0.0074 1.6E-07 35.6 1.3 23 335-357 2-24 (27)
44 PRK04860 hypothetical protein; 95.4 0.0077 1.7E-07 52.2 1.6 35 276-314 119-153 (160)
45 PF12756 zf-C2H2_2: C2H2 type 95.1 0.011 2.5E-07 46.4 1.7 25 40-64 50-74 (100)
46 PRK04860 hypothetical protein; 95.1 0.0075 1.6E-07 52.2 0.6 40 303-348 118-157 (160)
47 smart00451 ZnF_U1 U1-like zinc 95.1 0.013 2.9E-07 36.7 1.6 25 39-63 2-26 (35)
48 PF13909 zf-H2C2_5: C2H2-type 94.1 0.0099 2.1E-07 34.0 -0.6 24 335-359 1-24 (24)
49 KOG2893 Zn finger protein [Gen 92.2 0.053 1.1E-06 48.9 0.7 47 278-358 12-59 (341)
50 PF13913 zf-C2HC_2: zinc-finge 91.8 0.053 1.1E-06 31.4 0.1 21 335-356 3-23 (25)
51 COG5048 FOG: Zn-finger [Genera 91.1 0.28 6.1E-06 48.9 4.7 71 275-347 288-366 (467)
52 COG5048 FOG: Zn-finger [Genera 90.7 0.2 4.3E-06 50.0 3.1 61 251-311 292-358 (467)
53 PF05605 zf-Di19: Drought indu 90.0 0.29 6.3E-06 34.1 2.6 25 40-65 2-27 (54)
54 PF02892 zf-BED: BED zinc fing 89.9 0.14 3.1E-06 34.0 0.9 28 36-63 12-44 (45)
55 KOG1146 Homeobox protein [Gene 88.7 0.15 3.3E-06 56.6 0.6 78 273-356 462-540 (1406)
56 smart00614 ZnF_BED BED zinc fi 88.0 0.26 5.6E-06 33.7 1.2 26 39-64 17-48 (50)
57 smart00451 ZnF_U1 U1-like zinc 87.8 0.32 7E-06 30.2 1.4 24 275-298 2-25 (35)
58 KOG2231 Predicted E3 ubiquitin 87.5 0.58 1.3E-05 49.2 3.8 98 253-358 187-301 (669)
59 KOG2893 Zn finger protein [Gen 86.1 0.22 4.7E-06 45.1 -0.1 46 20-65 11-60 (341)
60 smart00734 ZnF_Rad18 Rad18-lik 85.3 0.58 1.3E-05 27.3 1.4 20 42-62 3-22 (26)
61 PF09538 FYDLN_acid: Protein o 83.2 0.79 1.7E-05 36.9 1.9 30 305-347 10-39 (108)
62 PF05443 ROS_MUCR: ROS/MUCR tr 80.6 0.67 1.5E-05 38.7 0.7 25 41-68 73-97 (132)
63 COG5189 SFP1 Putative transcri 77.0 0.88 1.9E-05 43.1 0.3 25 273-297 395-419 (423)
64 cd00350 rubredoxin_like Rubred 76.7 1.6 3.6E-05 26.9 1.4 10 277-286 2-11 (33)
65 KOG2231 Predicted E3 ubiquitin 76.6 1.5 3.1E-05 46.4 1.8 16 343-358 221-236 (669)
66 COG4957 Predicted transcriptio 75.8 1.3 2.8E-05 36.6 1.0 25 42-69 78-102 (148)
67 KOG4167 Predicted DNA-binding 75.6 0.62 1.3E-05 48.8 -1.1 28 38-65 790-817 (907)
68 COG1198 PriA Primosomal protei 75.3 1.7 3.6E-05 46.8 1.9 49 277-343 436-484 (730)
69 PRK00464 nrdR transcriptional 75.2 1.4 3E-05 37.9 1.1 20 334-353 28-47 (154)
70 TIGR02300 FYDLN_acid conserved 74.4 2.4 5.3E-05 34.8 2.2 34 305-351 10-43 (129)
71 PF04959 ARS2: Arsenite-resist 73.9 1.6 3.4E-05 39.7 1.1 38 28-65 65-102 (214)
72 PF09986 DUF2225: Uncharacteri 73.7 1.5 3.2E-05 40.0 1.0 24 274-297 3-26 (214)
73 KOG1146 Homeobox protein [Gene 73.3 0.9 1.9E-05 50.9 -0.7 82 276-362 1260-1356(1406)
74 TIGR00622 ssl1 transcription f 71.3 6.2 0.00013 31.9 3.8 81 274-358 13-105 (112)
75 COG4049 Uncharacterized protei 70.4 0.91 2E-05 31.4 -0.9 31 328-358 11-41 (65)
76 COG3677 Transposase and inacti 68.7 2.4 5.2E-05 35.4 1.0 26 28-53 41-66 (129)
77 COG1592 Rubrerythrin [Energy p 68.4 3 6.5E-05 36.3 1.6 10 332-341 147-156 (166)
78 cd00729 rubredoxin_SM Rubredox 68.4 3.5 7.6E-05 25.7 1.5 10 333-342 17-26 (34)
79 PF12013 DUF3505: Protein of u 68.0 3.2 6.9E-05 33.4 1.6 25 41-65 81-109 (109)
80 TIGR00595 priA primosomal prot 65.3 3.4 7.5E-05 42.9 1.6 48 278-343 215-262 (505)
81 KOG2593 Transcription initiati 65.1 3.4 7.4E-05 41.0 1.5 50 5-58 76-146 (436)
82 KOG2482 Predicted C2H2-type Zn 64.8 3.2 7E-05 39.8 1.2 74 277-358 280-358 (423)
83 PRK00398 rpoP DNA-directed RNA 61.8 5.4 0.00012 26.6 1.6 11 334-344 21-31 (46)
84 PRK00464 nrdR transcriptional 61.6 3.5 7.6E-05 35.5 0.7 42 277-318 1-42 (154)
85 PRK14873 primosome assembly pr 60.7 4.2 9.1E-05 43.6 1.3 47 278-343 385-431 (665)
86 PRK14890 putative Zn-ribbon RN 60.6 4.4 9.6E-05 28.6 1.0 11 332-342 46-56 (59)
87 PF14353 CpXC: CpXC protein 59.8 4 8.6E-05 33.8 0.8 25 334-358 38-62 (128)
88 PF10571 UPF0547: Uncharacteri 59.8 6.7 0.00015 22.9 1.5 12 334-345 14-25 (26)
89 COG1997 RPL43A Ribosomal prote 58.5 6.3 0.00014 30.1 1.5 14 334-347 53-66 (89)
90 TIGR00373 conserved hypothetic 58.3 5.5 0.00012 34.5 1.4 18 275-292 108-125 (158)
91 KOG2071 mRNA cleavage and poly 56.9 5.8 0.00012 41.1 1.5 31 35-65 413-443 (579)
92 PRK06266 transcription initiat 56.2 6.3 0.00014 34.8 1.5 16 276-291 117-132 (178)
93 KOG4124 Putative transcription 55.5 6.1 0.00013 38.1 1.3 70 274-355 347-419 (442)
94 COG5236 Uncharacterized conser 54.6 5.6 0.00012 38.2 0.9 87 262-356 167-273 (493)
95 PRK09678 DNA-binding transcrip 54.0 5.5 0.00012 29.5 0.6 19 332-350 25-45 (72)
96 KOG2186 Cell growth-regulating 53.6 4.7 0.0001 37.2 0.2 37 277-315 4-40 (276)
97 PF09723 Zn-ribbon_8: Zinc rib 53.6 7.2 0.00016 25.5 1.1 9 334-342 26-34 (42)
98 TIGR02605 CxxC_CxxC_SSSS putat 53.3 6.1 0.00013 27.0 0.7 11 277-287 6-16 (52)
99 smart00834 CxxC_CXXC_SSSS Puta 52.4 6.6 0.00014 25.1 0.7 9 334-342 26-34 (41)
100 COG4049 Uncharacterized protei 52.4 5.6 0.00012 27.6 0.4 29 272-300 13-41 (65)
101 PF09538 FYDLN_acid: Protein o 52.2 6.2 0.00013 31.8 0.7 15 38-52 7-21 (108)
102 PF09986 DUF2225: Uncharacteri 52.2 3.2 7E-05 37.8 -1.1 27 39-65 4-31 (214)
103 smart00531 TFIIE Transcription 52.0 13 0.00029 31.6 2.7 19 273-291 96-114 (147)
104 PF05443 ROS_MUCR: ROS/MUCR tr 50.9 4.2 9E-05 34.0 -0.5 26 332-360 70-95 (132)
105 PRK05580 primosome assembly pr 49.2 8.8 0.00019 41.4 1.5 49 277-343 382-430 (679)
106 COG1592 Rubrerythrin [Energy p 49.2 11 0.00023 32.9 1.7 25 275-312 133-157 (166)
107 KOG0978 E3 ubiquitin ligase in 48.1 9.1 0.0002 40.8 1.3 22 333-354 677-698 (698)
108 PF10013 DUF2256: Uncharacteri 47.7 9.6 0.00021 24.9 0.9 17 41-57 9-25 (42)
109 TIGR00373 conserved hypothetic 47.5 17 0.00037 31.4 2.7 44 291-345 96-139 (158)
110 KOG3214 Uncharacterized Zn rib 47.2 8.6 0.00019 30.1 0.7 41 15-55 22-62 (109)
111 COG2888 Predicted Zn-ribbon RN 47.1 7.3 0.00016 27.5 0.3 11 332-342 48-58 (61)
112 TIGR02098 MJ0042_CXXC MJ0042 f 46.5 13 0.00029 23.4 1.5 12 334-345 25-36 (38)
113 PF05290 Baculo_IE-1: Baculovi 46.3 12 0.00026 31.1 1.5 61 272-349 76-136 (140)
114 COG4530 Uncharacterized protei 46.2 12 0.00026 29.8 1.4 14 332-345 24-37 (129)
115 KOG2186 Cell growth-regulating 46.0 9.7 0.00021 35.2 1.0 20 333-353 28-47 (276)
116 smart00531 TFIIE Transcription 45.8 12 0.00027 31.8 1.6 41 299-345 94-134 (147)
117 PHA00626 hypothetical protein 45.3 9.7 0.00021 26.5 0.7 18 37-54 20-37 (59)
118 PF13719 zinc_ribbon_5: zinc-r 44.6 11 0.00024 23.8 0.9 14 332-345 23-36 (37)
119 PF04216 FdhE: Protein involve 44.2 5.7 0.00012 38.0 -0.8 36 277-315 173-208 (290)
120 TIGR02300 FYDLN_acid conserved 44.0 10 0.00022 31.3 0.7 15 38-52 7-21 (129)
121 PRK03564 formate dehydrogenase 43.7 18 0.0004 34.8 2.6 39 274-315 185-223 (309)
122 COG1773 Rubredoxin [Energy pro 43.6 8.9 0.00019 26.7 0.3 13 38-50 1-13 (55)
123 PRK06266 transcription initiat 42.5 21 0.00045 31.5 2.6 45 291-346 104-148 (178)
124 PF04780 DUF629: Protein of un 42.0 14 0.00031 37.5 1.6 25 42-66 59-84 (466)
125 PF04423 Rad50_zn_hook: Rad50 41.8 8.6 0.00019 26.6 0.0 14 42-55 22-35 (54)
126 PF01363 FYVE: FYVE zinc finge 41.8 15 0.00032 26.6 1.3 13 333-345 24-36 (69)
127 PF06524 NOA36: NOA36 protein; 41.6 22 0.00048 33.0 2.6 88 272-360 138-235 (314)
128 PF14447 Prok-RING_4: Prokaryo 40.7 12 0.00026 26.1 0.6 17 37-53 35-52 (55)
129 smart00659 RPOLCX RNA polymera 40.7 19 0.00042 23.8 1.6 11 277-287 3-13 (44)
130 PF01780 Ribosomal_L37ae: Ribo 40.0 13 0.00028 28.8 0.7 12 38-49 33-44 (90)
131 PF09845 DUF2072: Zn-ribbon co 39.2 14 0.00031 30.6 0.9 15 40-54 1-15 (131)
132 PRK01343 zinc-binding protein; 38.9 16 0.00034 25.8 0.9 14 39-52 8-21 (57)
133 PF13717 zinc_ribbon_4: zinc-r 37.9 18 0.0004 22.7 1.1 12 333-344 24-35 (36)
134 KOG0320 Predicted E3 ubiquitin 37.7 16 0.00035 32.0 1.0 55 272-348 127-181 (187)
135 PF03604 DNA_RNApol_7kD: DNA d 37.4 27 0.00058 21.5 1.7 9 334-342 17-25 (32)
136 PF08790 zf-LYAR: LYAR-type C2 37.1 12 0.00025 22.3 0.1 19 41-60 1-19 (28)
137 PF12013 DUF3505: Protein of u 37.1 11 0.00025 30.1 0.0 25 335-359 81-109 (109)
138 PF10276 zf-CHCC: Zinc-finger 36.4 11 0.00025 24.4 -0.1 11 40-50 29-39 (40)
139 KOG0717 Molecular chaperone (D 36.2 17 0.00037 36.6 1.1 22 41-62 293-314 (508)
140 PF15135 UPF0515: Uncharacteri 35.9 29 0.00063 32.0 2.4 13 274-286 110-122 (278)
141 PF12230 PRP21_like_P: Pre-mRN 35.9 12 0.00026 34.4 0.0 33 37-70 165-197 (229)
142 smart00154 ZnF_AN1 AN1-like Zi 35.7 17 0.00036 23.4 0.6 14 40-53 12-25 (39)
143 COG3357 Predicted transcriptio 35.5 23 0.0005 27.3 1.4 13 275-287 57-69 (97)
144 KOG3408 U1-like Zn-finger-cont 35.5 17 0.00036 29.7 0.7 29 37-65 54-84 (129)
145 PF06220 zf-U1: U1 zinc finger 35.5 21 0.00046 22.8 1.1 24 38-61 1-26 (38)
146 PF07754 DUF1610: Domain of un 34.3 18 0.00038 20.7 0.5 11 38-48 14-24 (24)
147 COG1996 RPC10 DNA-directed RNA 34.3 20 0.00042 24.4 0.8 11 276-286 6-16 (49)
148 TIGR00280 L37a ribosomal prote 34.3 18 0.0004 28.0 0.8 12 38-49 33-44 (91)
149 cd00065 FYVE FYVE domain; Zinc 33.9 27 0.0006 24.0 1.6 14 333-346 17-30 (57)
150 PTZ00255 60S ribosomal protein 33.5 19 0.00041 27.9 0.7 11 38-48 34-44 (90)
151 PF14787 zf-CCHC_5: GAG-polypr 33.5 22 0.00048 22.4 0.9 16 41-56 3-18 (36)
152 COG4391 Uncharacterized protei 33.5 15 0.00032 26.1 0.1 11 42-52 50-60 (62)
153 KOG2785 C2H2-type Zn-finger pr 33.4 14 0.00031 36.2 0.0 79 276-356 3-90 (390)
154 COG3364 Zn-ribbon containing p 33.2 21 0.00045 28.2 0.9 17 40-56 2-18 (112)
155 COG4338 Uncharacterized protei 32.7 15 0.00033 24.6 0.1 17 41-57 13-29 (54)
156 PF09845 DUF2072: Zn-ribbon co 32.0 22 0.00048 29.5 0.9 11 304-314 1-11 (131)
157 PRK03976 rpl37ae 50S ribosomal 31.8 21 0.00045 27.7 0.7 12 38-49 34-45 (90)
158 PRK12496 hypothetical protein; 31.0 27 0.00058 30.4 1.4 11 304-314 127-137 (164)
159 smart00064 FYVE Protein presen 30.8 31 0.00068 24.8 1.5 10 278-287 12-21 (68)
160 COG3677 Transposase and inacti 30.5 29 0.00064 28.9 1.5 13 303-315 52-64 (129)
161 KOG4377 Zn-finger protein [Gen 30.5 31 0.00068 34.2 1.8 85 277-364 314-433 (480)
162 PRK04023 DNA polymerase II lar 30.0 36 0.00078 37.9 2.3 11 275-285 625-635 (1121)
163 COG4957 Predicted transcriptio 29.4 24 0.00051 29.4 0.7 25 277-304 77-101 (148)
164 PRK03824 hypA hydrogenase nick 29.4 28 0.00061 29.2 1.2 16 274-289 68-83 (135)
165 PF07295 DUF1451: Protein of u 29.1 39 0.00085 28.8 2.0 9 334-342 130-138 (146)
166 KOG1842 FYVE finger-containing 28.8 23 0.0005 35.5 0.6 32 34-65 9-41 (505)
167 KOG2071 mRNA cleavage and poly 28.1 24 0.00053 36.7 0.7 29 331-359 415-443 (579)
168 PHA02446 hypothetical protein 27.6 35 0.00075 27.6 1.3 45 4-49 27-71 (166)
169 PF04959 ARS2: Arsenite-resist 27.1 13 0.00027 33.9 -1.4 28 332-359 75-102 (214)
170 KOG0402 60S ribosomal protein 27.0 21 0.00045 27.0 -0.0 12 38-49 34-45 (92)
171 COG5236 Uncharacterized conser 26.6 25 0.00054 34.0 0.4 75 277-359 221-306 (493)
172 KOG4173 Alpha-SNAP protein [In 26.3 12 0.00025 33.5 -1.7 21 277-297 107-127 (253)
173 TIGR01562 FdhE formate dehydro 26.3 51 0.0011 31.8 2.4 37 276-314 184-220 (305)
174 PTZ00448 hypothetical protein; 26.2 49 0.0011 32.5 2.3 24 39-62 313-336 (373)
175 PF01927 Mut7-C: Mut7-C RNAse 26.1 37 0.00081 28.8 1.4 21 332-352 122-142 (147)
176 PF12760 Zn_Tnp_IS1595: Transp 26.1 66 0.0014 21.3 2.3 10 333-342 36-45 (46)
177 PF05741 zf-nanos: Nanos RNA b 25.9 29 0.00063 24.3 0.5 13 37-49 30-42 (55)
178 PF03884 DUF329: Domain of unk 25.8 20 0.00042 25.3 -0.3 12 41-52 3-14 (57)
179 PF09332 Mcm10: Mcm10 replicat 25.8 27 0.00059 34.2 0.5 56 275-343 251-312 (344)
180 PF01428 zf-AN1: AN1-like Zinc 25.7 22 0.00047 23.3 -0.1 14 39-52 12-25 (43)
181 cd00924 Cyt_c_Oxidase_Vb Cytoc 25.1 29 0.00062 27.4 0.5 20 326-346 72-91 (97)
182 COG2331 Uncharacterized protei 25.1 29 0.00063 25.8 0.4 10 277-286 13-22 (82)
183 KOG0978 E3 ubiquitin ligase in 24.2 28 0.00062 37.2 0.3 24 37-60 675-698 (698)
184 PF05191 ADK_lid: Adenylate ki 23.9 49 0.0011 20.9 1.3 11 335-345 22-32 (36)
185 KOG2785 C2H2-type Zn-finger pr 23.4 24 0.00052 34.6 -0.3 71 274-355 164-241 (390)
186 COG3091 SprT Zn-dependent meta 23.3 38 0.00083 28.9 0.9 17 325-342 132-148 (156)
187 PF01844 HNH: HNH endonuclease 22.9 21 0.00046 23.3 -0.6 17 43-59 1-17 (47)
188 PF12907 zf-met2: Zinc-binding 22.9 19 0.00041 23.4 -0.8 25 41-65 2-30 (40)
189 KOG3408 U1-like Zn-finger-cont 22.4 39 0.00084 27.6 0.7 27 272-298 53-79 (129)
190 KOG2593 Transcription initiati 22.4 53 0.0012 32.9 1.8 36 273-311 125-160 (436)
191 smart00661 RPOL9 RNA polymeras 21.9 70 0.0015 21.4 1.9 16 334-349 20-35 (52)
192 PRK12380 hydrogenase nickel in 21.9 47 0.001 26.9 1.1 8 276-283 70-77 (113)
193 smart00440 ZnF_C2C2 C2C2 Zinc 21.8 32 0.0007 22.2 0.1 12 334-345 28-39 (40)
194 PF00301 Rubredoxin: Rubredoxi 21.8 31 0.00067 23.3 0.0 7 277-283 35-41 (47)
195 PF14369 zf-RING_3: zinc-finge 21.6 51 0.0011 20.6 1.0 30 20-51 3-32 (35)
196 PRK04023 DNA polymerase II lar 21.3 71 0.0015 35.7 2.6 37 276-345 638-674 (1121)
197 KOG2482 Predicted C2H2-type Zn 21.2 48 0.001 32.1 1.2 82 276-358 195-303 (423)
198 PF15269 zf-C2H2_7: Zinc-finge 21.0 61 0.0013 21.5 1.3 25 38-62 18-42 (54)
199 PF09889 DUF2116: Uncharacteri 21.0 46 0.00099 23.7 0.8 7 43-49 6-12 (59)
200 COG1571 Predicted DNA-binding 20.5 64 0.0014 32.5 1.9 32 306-350 352-383 (421)
201 COG4640 Predicted membrane pro 20.4 56 0.0012 32.3 1.5 33 19-58 1-33 (465)
202 PRK00432 30S ribosomal protein 20.2 75 0.0016 21.7 1.7 12 333-344 36-47 (50)
203 cd02335 ZZ_ADA2 Zinc finger, Z 20.2 64 0.0014 21.7 1.3 20 339-358 26-45 (49)
204 PF07975 C1_4: TFIIH C1-like d 20.1 50 0.0011 22.7 0.8 27 274-300 19-45 (51)
No 1
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.89 E-value=1.2e-23 Score=212.86 Aligned_cols=92 Identities=18% Similarity=0.307 Sum_probs=81.5
Q ss_pred CCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCC----CccccC---CcCcccC
Q 044606 273 SRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVK----KVHECP---VCFRVFS 345 (413)
Q Consensus 273 ~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~----kp~~C~---~C~k~F~ 345 (413)
...|..|-+|.|+....+.|+.|.|+|+||+||+|++|+.+|+ .+.+|+.|+.+|... -+|.|+ +|.+.|.
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFt--TkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kft 679 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFT--TKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFT 679 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhc--cccchhhcccccccCccccccccCCchhhhccccc
Confidence 4467999999999999999999999999999999999999996 667888999888654 358999 9999999
Q ss_pred CchhhcccccccccCCCCCCC
Q 044606 346 SGQALGGHKRTHVTGLVASTS 366 (413)
Q Consensus 346 ~~~~L~~H~r~H~~~~~~~~~ 366 (413)
..-.|..|+|+|.++..+...
T Consensus 680 n~V~lpQhIriH~~~~~s~g~ 700 (958)
T KOG1074|consen 680 NAVTLPQHIRIHLGGQISNGG 700 (958)
T ss_pred ccccccceEEeecCCCCCCCc
Confidence 999999999999977666543
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.89 E-value=3.6e-24 Score=193.44 Aligned_cols=90 Identities=21% Similarity=0.283 Sum_probs=83.8
Q ss_pred HHHHhhhhcCCCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCc
Q 044606 263 EFKSFNNKNRSRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFR 342 (413)
Q Consensus 263 ~~~~~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k 342 (413)
.++-|++.|+ -+++|.+|||.|.+.+.|+.|+|+|||||||.|..|+++| ....+|+.|+.+|.+.|+|+|..|+|
T Consensus 176 ALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAF--ADRSNLRAHmQTHS~~K~~qC~~C~K 251 (279)
T KOG2462|consen 176 ALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAF--ADRSNLRAHMQTHSDVKKHQCPRCGK 251 (279)
T ss_pred HHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchh--cchHHHHHHHHhhcCCccccCcchhh
Confidence 4566888886 7899999999999999999999999999999999999999 57789999999999999999999999
Q ss_pred ccCCchhhcccccc
Q 044606 343 VFSSGQALGGHKRT 356 (413)
Q Consensus 343 ~F~~~~~L~~H~r~ 356 (413)
+|+..+.|.+|...
T Consensus 252 sFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 252 SFALKSYLNKHSES 265 (279)
T ss_pred HHHHHHHHHHhhhh
Confidence 99999999999764
No 3
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.76 E-value=1.8e-19 Score=163.08 Aligned_cols=109 Identities=19% Similarity=0.221 Sum_probs=97.6
Q ss_pred hhhhcccCcCcchHHHHHhhhhcC---CCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhh
Q 044606 249 EEAEKSMDETDESEEFKSFNNKNR---SRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLA 325 (413)
Q Consensus 249 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h 325 (413)
..|.++...+....+|-.|++.|. ..+-+.|.+|+|.|.+-..|+.|+|+|+ -+++|.+||+.| .+..-|+.|
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaF--SRPWLLQGH 206 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAF--SRPWLLQGH 206 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccc--cchHHhhcc
Confidence 345556677788888889988886 4788999999999999999999999998 689999999999 477789999
Q ss_pred cCCCCCCCccccCCcCcccCCchhhcccccccccCC
Q 044606 326 SPPLSVKKVHECPVCFRVFSSGQALGGHKRTHVTGL 361 (413)
Q Consensus 326 ~~~h~g~kp~~C~~C~k~F~~~~~L~~H~r~H~~~~ 361 (413)
+|+|||||||.|+.|+|+|+.+++|+.||+||.+--
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K 242 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVK 242 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCc
Confidence 999999999999999999999999999999998643
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.73 E-value=2.7e-18 Score=174.50 Aligned_cols=61 Identities=31% Similarity=0.336 Sum_probs=55.5
Q ss_pred cCCCCCCCCccchhhheeeeeeEEeeccccccccccccccCcccccCCChhhhhhHHHhhcCCCCCCCchhh
Q 044606 4 LSHRKEKPPELTTFKLLFIIYVYVFFKKRKSLFVMEKHKCRLCFKNFSNGRALGGHMRSHMLNLPIPQKIQE 75 (413)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~iC~K~F~~~~~L~~HmR~Htg~~p~~~~~~~ 75 (413)
+..++.||++.+.|. ....+.....+|+|.||+|+|...++|+.|+|+||||+||.|+.|-
T Consensus 328 a~p~~~k~~~~~~~~-----------v~~~~~~~~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG 388 (958)
T KOG1074|consen 328 ASPGLLKEKNGSYFS-----------VEGPSEKPFFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCG 388 (958)
T ss_pred cCcccCCcccccccc-----------cccCCccccccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccc
Confidence 567888999999888 9999999999999999999999999999999999999999975443
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.48 E-value=4.5e-15 Score=148.85 Aligned_cols=83 Identities=20% Similarity=0.383 Sum_probs=78.3
Q ss_pred cCCCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchhh
Q 044606 271 NRSRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQAL 350 (413)
Q Consensus 271 ~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L 350 (413)
.+..+.|.|++|.|+|...+.|.+|.--|+|.+||+|.+|.++|+ .+-.|..|+|.|.|+|||.|..|+|+|+...+.
T Consensus 889 kte~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFK--HKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSY 966 (1007)
T KOG3623|consen 889 KTEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFK--HKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSY 966 (1007)
T ss_pred cCccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhh--hhhhhhhhhhhccCCCcchhhhhhhhcccccch
Confidence 446688999999999999999999999999999999999999994 677899999999999999999999999999999
Q ss_pred ccccc
Q 044606 351 GGHKR 355 (413)
Q Consensus 351 ~~H~r 355 (413)
..||.
T Consensus 967 SQHMN 971 (1007)
T KOG3623|consen 967 SQHMN 971 (1007)
T ss_pred Hhhhc
Confidence 99985
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.48 E-value=6.9e-15 Score=126.92 Aligned_cols=87 Identities=16% Similarity=0.241 Sum_probs=77.6
Q ss_pred cCCCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchhh
Q 044606 271 NRSRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQAL 350 (413)
Q Consensus 271 ~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L 350 (413)
..+...|.|.+|+|.|.....|.+|++-|...|.|-|..||+.| .....|.+|+++|+|.+||+|..|+|+|+++-+|
T Consensus 112 ssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgf--ndtfdlkrh~rthtgvrpykc~~c~kaftqrcsl 189 (267)
T KOG3576|consen 112 SSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGF--NDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSL 189 (267)
T ss_pred CCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcc--cchhhhhhhhccccCccccchhhhhHHHHhhccH
Confidence 34556799999999999999999999999999999999999999 4667799999999999999999999999999999
Q ss_pred ccccccccc
Q 044606 351 GGHKRTHVT 359 (413)
Q Consensus 351 ~~H~r~H~~ 359 (413)
..|++.-+|
T Consensus 190 eshl~kvhg 198 (267)
T KOG3576|consen 190 ESHLKKVHG 198 (267)
T ss_pred HHHHHHHcC
Confidence 999775544
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.24 E-value=2e-12 Score=130.11 Aligned_cols=105 Identities=16% Similarity=0.217 Sum_probs=88.4
Q ss_pred hhhcccCcCcchHHHHHhhhhc--CCCCccccCCccccccChhhhhhhhhhcCC-------------CcccCCCCCCccc
Q 044606 250 EAEKSMDETDESEEFKSFNNKN--RSRGKYKCETCKKVFKSYQALGGHRASHKK-------------IKFYTPVQETELD 314 (413)
Q Consensus 250 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~-------------~kp~~C~~C~~~f 314 (413)
.|..+...+.....++.|+... ..+..|.|.+|..+|.+...|.+|+.+|.. .+-|+|..|+++|
T Consensus 212 tcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAF 291 (1007)
T KOG3623|consen 212 TCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAF 291 (1007)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhh
Confidence 3445556666777788887553 345569999999999999999999998864 3569999999999
Q ss_pred ccccchhhhhhcCCCCCCCccccCCcCcccCCchhhcccccc
Q 044606 315 QENAGASINLASPPLSVKKVHECPVCFRVFSSGQALGGHKRT 356 (413)
Q Consensus 315 ~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L~~H~r~ 356 (413)
+ .+-.|..|+|+|.|+|||.|+-|+|+|+...++..||-.
T Consensus 292 K--fKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 292 K--FKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred h--hHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 6 566899999999999999999999999999999999854
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.20 E-value=1.7e-12 Score=112.34 Aligned_cols=112 Identities=12% Similarity=0.045 Sum_probs=94.4
Q ss_pred hhhhhcccCcCcchHHHHHhhhhcCCCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcC
Q 044606 248 DEEAEKSMDETDESEEFKSFNNKNRSRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASP 327 (413)
Q Consensus 248 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~ 327 (413)
...|..+...+.-..-+..|++-|..-+.|.|..|||.|.....|++|+|+|+|.+||+|..|+++|++... |..|.+
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcs--leshl~ 194 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCS--LESHLK 194 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhcc--HHHHHH
Confidence 344666777888888899999999999999999999999999999999999999999999999999986554 444432
Q ss_pred -CC----------CCCCccccCCcCcccCCchhhcccccccccCC
Q 044606 328 -PL----------SVKKVHECPVCFRVFSSGQALGGHKRTHVTGL 361 (413)
Q Consensus 328 -~h----------~g~kp~~C~~C~k~F~~~~~L~~H~r~H~~~~ 361 (413)
+| ..+|.|.|..||.+-.....+..|++.|+...
T Consensus 195 kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 195 KVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred HHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 22 23678999999999999999999999998654
No 9
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.16 E-value=5.9e-12 Score=117.29 Aligned_cols=104 Identities=14% Similarity=0.196 Sum_probs=81.9
Q ss_pred cCcchHHHHHhhh-hcCCCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCC-CCCC--
Q 044606 257 ETDESEEFKSFNN-KNRSRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPP-LSVK-- 332 (413)
Q Consensus 257 ~~~~~~~~~~~~~-~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~-h~g~-- 332 (413)
+....+.+..|++ .|...|||+|+.|.+.|.+.+.|.+|..+|+ +-.|.|..-.+.|.....-.+.+|++- |.|.
T Consensus 272 tc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np 350 (467)
T KOG3608|consen 272 TCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNP 350 (467)
T ss_pred CCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCC
Confidence 3455667777765 4778999999999999999999999999999 678999984444444566667788764 4354
Q ss_pred CccccCCcCcccCCchhhcccccccccCC
Q 044606 333 KVHECPVCFRVFSSGQALGGHKRTHVTGL 361 (413)
Q Consensus 333 kp~~C~~C~k~F~~~~~L~~H~r~H~~~~ 361 (413)
-+|.|..|.|.|++..+|.+|++..++-.
T Consensus 351 ~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~ 379 (467)
T KOG3608|consen 351 ILYACHCCDRFFTSGKSLSAHLMKKHGFR 379 (467)
T ss_pred CceeeecchhhhccchhHHHHHHHhhccc
Confidence 46999999999999999999977655433
No 10
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.14 E-value=1.8e-11 Score=114.16 Aligned_cols=111 Identities=17% Similarity=0.140 Sum_probs=93.9
Q ss_pred hhhhcccCcCcchHHHHHhhhhcCCCCccccCCccccccChhhhhhhhhh-cCCCcccCCCCCCcccccccchhhhhhcC
Q 044606 249 EEAEKSMDETDESEEFKSFNNKNRSRGKYKCETCKKVFKSYQALGGHRAS-HKKIKFYTPVQETELDQENAGASINLASP 327 (413)
Q Consensus 249 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~-H~~~kp~~C~~C~~~f~~~~~~~l~~h~~ 327 (413)
.+|..+...+.....++.|+..|. .-|+|+.|..+....+.|..|++. |+..|||+|+.|.+.| .....|.+|..
T Consensus 238 fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c--~~esdL~kH~~ 313 (467)
T KOG3608|consen 238 FQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRC--VRESDLAKHVQ 313 (467)
T ss_pred hHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhh--ccHHHHHHHHH
Confidence 344555556666777888888875 569999999999999999999986 9999999999999988 57778999999
Q ss_pred CCCCCCccccCC--cCcccCCchhhcccccccccCCCCC
Q 044606 328 PLSVKKVHECPV--CFRVFSSGQALGGHKRTHVTGLVAS 364 (413)
Q Consensus 328 ~h~g~kp~~C~~--C~k~F~~~~~L~~H~r~H~~~~~~~ 364 (413)
.|+ +-.|.|.. |..+|.+...|.+|++.|+.+..+.
T Consensus 314 ~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~ 351 (467)
T KOG3608|consen 314 VHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPI 351 (467)
T ss_pred hcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCC
Confidence 898 77899988 9999999999999999888555443
No 11
>PHA00733 hypothetical protein
Probab=98.92 E-value=4.5e-10 Score=93.65 Aligned_cols=95 Identities=16% Similarity=0.142 Sum_probs=74.4
Q ss_pred hHHHHHhhhhcCCCCccccCCccccccChhhhhhh--h---hhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCcc
Q 044606 261 SEEFKSFNNKNRSRGKYKCETCKKVFKSYQALGGH--R---ASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVH 335 (413)
Q Consensus 261 ~~~~~~~~~~~~~~~~~~C~~C~k~F~~~~~L~~H--~---~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~ 335 (413)
.+++..+-......+++.|.+|.+.|.....|..| + ..+.+.+||.|..|++.|. ....|..|++.| +.+|
T Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fs--s~s~L~~H~r~h--~~~~ 100 (128)
T PHA00733 25 LEELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFS--SSVSLKQHIRYT--EHSK 100 (128)
T ss_pred HHHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCC--CHHHHHHHHhcC--CcCc
Confidence 34455544444567889999999999888777665 2 1334588999999999994 666777888876 4689
Q ss_pred ccCCcCcccCCchhhccccccccc
Q 044606 336 ECPVCFRVFSSGQALGGHKRTHVT 359 (413)
Q Consensus 336 ~C~~C~k~F~~~~~L~~H~r~H~~ 359 (413)
.|.+|++.|.....|..|++..++
T Consensus 101 ~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 101 VCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred cCCCCCCccCCHHHHHHHHHHhcC
Confidence 999999999999999999987765
No 12
>PHA02768 hypothetical protein; Provisional
Probab=98.61 E-value=2e-08 Score=69.47 Aligned_cols=37 Identities=14% Similarity=0.357 Sum_probs=28.9
Q ss_pred ccccCCccccccChhhhhhhhhhcCCCcccCCCCCCccc
Q 044606 276 KYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELD 314 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f 314 (413)
.|.|+.||+.|...++|..|+++|+ ++|+|..|++.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f 41 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRIS 41 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCccccee
Confidence 3899999999999999999999997 455555544444
No 13
>PHA00616 hypothetical protein
Probab=98.53 E-value=3.1e-08 Score=65.21 Aligned_cols=31 Identities=16% Similarity=0.179 Sum_probs=29.6
Q ss_pred ccccCcccccCCChhhhhhHHHhhcCCCCCC
Q 044606 40 KHKCRLCFKNFSNGRALGGHMRSHMLNLPIP 70 (413)
Q Consensus 40 ~~~C~iC~K~F~~~~~L~~HmR~Htg~~p~~ 70 (413)
+|+|+.||+.|.+.+.|..|||.|+|++|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 6899999999999999999999999999984
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.46 E-value=5.5e-08 Score=67.33 Aligned_cols=45 Identities=11% Similarity=-0.115 Sum_probs=38.9
Q ss_pred ccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchhhcc
Q 044606 304 FYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQALGG 352 (413)
Q Consensus 304 p~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L~~ 352 (413)
-|.|+.|++.|. ...+|..|+++|+ ++|+|..|+|.|++.+.|..
T Consensus 5 ~y~C~~CGK~Fs--~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 5 GYECPICGEIYI--KRKSMITHLRKHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred ccCcchhCCeec--cHHHHHHHHHhcC--CcccCCcccceecccceeEE
Confidence 389999999994 6778899999998 79999999999998888753
No 15
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.38 E-value=1.3e-07 Score=54.19 Aligned_cols=23 Identities=48% Similarity=0.811 Sum_probs=22.2
Q ss_pred cccCcccccCCChhhhhhHHHhh
Q 044606 41 HKCRLCFKNFSNGRALGGHMRSH 63 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~~HmR~H 63 (413)
|+|++|+|.|.+...|..||++|
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 78999999999999999999987
No 16
>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=98.37 E-value=5.6e-08 Score=57.39 Aligned_cols=23 Identities=22% Similarity=0.013 Sum_probs=11.5
Q ss_pred hhhhhhhcCCCcccCCCCCCccc
Q 044606 292 LGGHRASHKKIKFYTPVQETELD 314 (413)
Q Consensus 292 L~~H~~~H~~~kp~~C~~C~~~f 314 (413)
|.+|+++|+|++||.|+.|++.|
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEE
T ss_pred HHHHhhhcCCCCCCCCCCCcCee
Confidence 55555555554444444444433
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.32 E-value=4.6e-07 Score=92.46 Aligned_cols=62 Identities=11% Similarity=0.191 Sum_probs=28.2
Q ss_pred ccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCccc
Q 044606 276 KYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVF 344 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F 344 (413)
.+.|..|++.|. ...|..|+++|+ ++|.|+ |+..+ ....|..|..+|...+++.|..|++.|
T Consensus 453 H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~---~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 453 HVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL---EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred CccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc---chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 344555555443 344455544442 444554 44322 223444444444445555555555544
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.22 E-value=8.3e-07 Score=90.62 Aligned_cols=99 Identities=15% Similarity=0.161 Sum_probs=77.6
Q ss_pred hhcccCcCcchHHHHHhhhhcCCCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccc--------cchhh
Q 044606 251 AEKSMDETDESEEFKSFNNKNRSRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQEN--------AGASI 322 (413)
Q Consensus 251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~--------~~~~l 322 (413)
|..+...+. ...++.|...+. +++.|. ||+.| ....|..|+++|.+.+++.|.+|+..+... ....|
T Consensus 456 C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~L 530 (567)
T PLN03086 456 CEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGM 530 (567)
T ss_pred CCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhH
Confidence 444545553 567889998874 899999 99765 678999999999999999999999988411 13357
Q ss_pred hhhcCCCCCCCccccCCcCcccCCchhhcccccc
Q 044606 323 NLASPPLSVKKVHECPVCFRVFSSGQALGGHKRT 356 (413)
Q Consensus 323 ~~h~~~h~g~kp~~C~~C~k~F~~~~~L~~H~r~ 356 (413)
..|.... |.+++.|..||+.|..+ .|..|+..
T Consensus 531 t~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 531 SEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIA 562 (567)
T ss_pred HHHHHhc-CCcceEccccCCeeeeh-hHHHHHHH
Confidence 8888875 89999999999998876 56666543
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.19 E-value=5.8e-07 Score=53.04 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=19.1
Q ss_pred hhhhcCCCCCCCccccCCcCcccCC
Q 044606 322 INLASPPLSVKKVHECPVCFRVFSS 346 (413)
Q Consensus 322 l~~h~~~h~g~kp~~C~~C~k~F~~ 346 (413)
|.+|+++|+|+|||.|++|++.|.+
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 5677777888888888888887763
No 20
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.06 E-value=1.5e-06 Score=83.52 Aligned_cols=39 Identities=28% Similarity=0.330 Sum_probs=32.9
Q ss_pred EeeccccccccccccccCcccccCCChhhhhhHHHhhcC
Q 044606 27 VFFKKRKSLFVMEKHKCRLCFKNFSNGRALGGHMRSHML 65 (413)
Q Consensus 27 ~~~~~~~~~~~~~~~~C~iC~K~F~~~~~L~~HmR~Htg 65 (413)
++-.|+=+.+.---|+|+-|+|+|.+...|.-|.|.|--
T Consensus 282 ~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKP 320 (500)
T KOG3993|consen 282 ALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKP 320 (500)
T ss_pred HHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCC
Confidence 344566666677779999999999999999999999976
No 21
>PHA00616 hypothetical protein
Probab=98.04 E-value=1.4e-06 Score=57.37 Aligned_cols=34 Identities=24% Similarity=0.328 Sum_probs=31.9
Q ss_pred ccccCCccccccChhhhhhhhhhcCCCcccCCCC
Q 044606 276 KYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQ 309 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~ 309 (413)
||+|..||+.|..++.|..|++.|+|++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899999999999999999999999999998864
No 22
>PHA00732 hypothetical protein
Probab=98.02 E-value=3.8e-06 Score=63.69 Aligned_cols=36 Identities=19% Similarity=0.168 Sum_probs=27.1
Q ss_pred ccccCCccccccChhhhhhhhhh-cCCCcccCCCCCCccc
Q 044606 276 KYKCETCKKVFKSYQALGGHRAS-HKKIKFYTPVQETELD 314 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~-H~~~kp~~C~~C~~~f 314 (413)
||.|..|++.|.+...|..|++. |.+ +.|..|++.|
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF 37 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSY 37 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEe
Confidence 58899999999999999999874 653 3555555555
No 23
>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=97.98 E-value=3.3e-06 Score=48.51 Aligned_cols=24 Identities=38% Similarity=0.761 Sum_probs=20.7
Q ss_pred cccCcccccCCChhhhhhHHHhhc
Q 044606 41 HKCRLCFKNFSNGRALGGHMRSHM 64 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~~HmR~Ht 64 (413)
|.|++|++.|.+...|..||++|.
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 689999999999999999999984
No 24
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.98 E-value=1.1e-06 Score=84.60 Aligned_cols=116 Identities=20% Similarity=0.260 Sum_probs=73.9
Q ss_pred hhhhhcccCcCcchHHHHHhhhhcCCCCccccCCccccccChhhhhhhhhhcCCCcccCC-CC-CCcccccccchhhhhh
Q 044606 248 DEEAEKSMDETDESEEFKSFNNKNRSRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTP-VQ-ETELDQENAGASINLA 325 (413)
Q Consensus 248 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C-~~-C~~~f~~~~~~~l~~h 325 (413)
+.-|.-+...+++...|-.|.....-.--|+|..|+|+|+...||..|.|.|.-..--.- .. -.+.-. ......+.-
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~-~~rae~~ea 345 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAV-ETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhh-hhhhhhhhc
Confidence 344556667777777888887666556679999999999999999999999975321100 00 000000 000000011
Q ss_pred cCC--CCCCCccccCCcCcccCCchhhcccccccccCCCCC
Q 044606 326 SPP--LSVKKVHECPVCFRVFSSGQALGGHKRTHVTGLVAS 364 (413)
Q Consensus 326 ~~~--h~g~kp~~C~~C~k~F~~~~~L~~H~r~H~~~~~~~ 364 (413)
.+. ...+-.|.|.+|+|.|.+...|++|+-+|+......
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 111 112347999999999999999999999998654443
No 25
>PHA00733 hypothetical protein
Probab=97.86 E-value=1.1e-05 Score=67.42 Aligned_cols=59 Identities=14% Similarity=-0.004 Sum_probs=47.2
Q ss_pred HHHhhhhcCCCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcC
Q 044606 264 FKSFNNKNRSRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASP 327 (413)
Q Consensus 264 ~~~~~~~~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~ 327 (413)
+..+... .+.++|.|..|++.|.+...|..|++.| ..+|.|..|++.|. ....|..|+.
T Consensus 62 l~~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~--~~~sL~~H~~ 120 (128)
T PHA00733 62 LYKLLTS-KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFR--NTDSTLDHVC 120 (128)
T ss_pred HHhhccc-CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccC--CHHHHHHHHH
Confidence 4444433 4588999999999999999999999987 45799999999995 5556666664
No 26
>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=97.77 E-value=9.4e-06 Score=48.28 Aligned_cols=26 Identities=42% Similarity=0.558 Sum_probs=24.3
Q ss_pred ccccCcccccCCChhhhhhHHHhhcC
Q 044606 40 KHKCRLCFKNFSNGRALGGHMRSHML 65 (413)
Q Consensus 40 ~~~C~iC~K~F~~~~~L~~HmR~Htg 65 (413)
+|+|.+|++.|.+...|..|||.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 58999999999999999999999964
No 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.72 E-value=2.2e-05 Score=72.97 Aligned_cols=71 Identities=23% Similarity=0.367 Sum_probs=52.0
Q ss_pred CCCccccCC--ccccccChhhhhhhhhh-cCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchh
Q 044606 273 SRGKYKCET--CKKVFKSYQALGGHRAS-HKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQA 349 (413)
Q Consensus 273 ~~~~~~C~~--C~k~F~~~~~L~~H~~~-H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~ 349 (413)
++|||+|++ |.|+|.....|+.|+.- |...+...-+.-.+ +.......|||.|++|+|+|.....
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~------------~~~F~~~~KPYrCevC~KRYKNlNG 413 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEK------------MNIFSAKDKPYRCEVCDKRYKNLNG 413 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccc------------cccccccCCceeccccchhhccCcc
Confidence 469999998 99999999999999764 54444332221111 1111334799999999999999999
Q ss_pred hccccc
Q 044606 350 LGGHKR 355 (413)
Q Consensus 350 L~~H~r 355 (413)
|+.|..
T Consensus 414 LKYHr~ 419 (423)
T COG5189 414 LKYHRK 419 (423)
T ss_pred ceeccc
Confidence 999965
No 28
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.70 E-value=2.3e-05 Score=52.77 Aligned_cols=36 Identities=17% Similarity=0.310 Sum_probs=26.4
Q ss_pred cccccccccccCcccccCCChhhhhhHHHhhcCCCC
Q 044606 33 KSLFVMEKHKCRLCFKNFSNGRALGGHMRSHMLNLP 68 (413)
Q Consensus 33 ~~~~~~~~~~C~iC~K~F~~~~~L~~HmR~Htg~~p 68 (413)
....+.++.+||+|+..+.....|.+||.++++.+|
T Consensus 17 ~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 17 SKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred HhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 345578999999999999999999999999988776
No 29
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.65 E-value=3e-05 Score=45.12 Aligned_cols=25 Identities=40% Similarity=0.622 Sum_probs=23.3
Q ss_pred cccCcccccCCChhhhhhHHHhhcC
Q 044606 41 HKCRLCFKNFSNGRALGGHMRSHML 65 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~~HmR~Htg 65 (413)
|+|..|++.|.....|..||+.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999999864
No 30
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.61 E-value=8.9e-06 Score=46.40 Aligned_cols=23 Identities=43% Similarity=0.817 Sum_probs=21.5
Q ss_pred cccCCcCcccCCchhhccccccc
Q 044606 335 HECPVCFRVFSSGQALGGHKRTH 357 (413)
Q Consensus 335 ~~C~~C~k~F~~~~~L~~H~r~H 357 (413)
|.|++|++.|.+...|..|+++|
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 78999999999999999999875
No 31
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.37 E-value=6.5e-05 Score=43.70 Aligned_cols=24 Identities=38% Similarity=0.721 Sum_probs=22.3
Q ss_pred cccCcccccCCChhhhhhHHHhhc
Q 044606 41 HKCRLCFKNFSNGRALGGHMRSHM 64 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~~HmR~Ht 64 (413)
|.|.+|.+.|.+...|+.||+.|.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~ 24 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKK 24 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCC
Confidence 679999999999999999999873
No 32
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.29 E-value=6.5e-05 Score=44.59 Aligned_cols=26 Identities=46% Similarity=0.696 Sum_probs=24.1
Q ss_pred ccccCCcCcccCCchhhccccccccc
Q 044606 334 VHECPVCFRVFSSGQALGGHKRTHVT 359 (413)
Q Consensus 334 p~~C~~C~k~F~~~~~L~~H~r~H~~ 359 (413)
||.|..|++.|.+...|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 68999999999999999999999864
No 33
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.23 E-value=0.00011 Score=43.72 Aligned_cols=24 Identities=38% Similarity=0.628 Sum_probs=21.8
Q ss_pred ccccCcccccCCChhhhhhHHHhh
Q 044606 40 KHKCRLCFKNFSNGRALGGHMRSH 63 (413)
Q Consensus 40 ~~~C~iC~K~F~~~~~L~~HmR~H 63 (413)
+|-|.+|+|.|.+...|.+||+++
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCCcccCCCCcCCHHHHHHHHccC
Confidence 588999999999999999999974
No 34
>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=97.21 E-value=0.00017 Score=50.57 Aligned_cols=51 Identities=25% Similarity=0.417 Sum_probs=33.9
Q ss_pred ccccCCccccccChhhhhhhhhh-cCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchhhcccc
Q 044606 276 KYKCETCKKVFKSYQALGGHRAS-HKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQALGGHK 354 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~-H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L~~H~ 354 (413)
.|.|++|++. .....|..|... |..+ .+.+.|++|...+.. +|..|+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~-----------------------------~~~v~CPiC~~~~~~--~l~~Hl 49 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSE-----------------------------SKNVVCPICSSRVTD--NLIRHL 49 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCC-----------------------------CCCccCCCchhhhhh--HHHHHH
Confidence 3788888884 456778888654 5432 235677777776553 777787
Q ss_pred cccc
Q 044606 355 RTHV 358 (413)
Q Consensus 355 r~H~ 358 (413)
.+++
T Consensus 50 ~~~H 53 (54)
T PF05605_consen 50 NSQH 53 (54)
T ss_pred HHhc
Confidence 7665
No 35
>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=97.19 E-value=7.3e-05 Score=42.72 Aligned_cols=24 Identities=42% Similarity=0.801 Sum_probs=20.3
Q ss_pred cccCCcCcccCCchhhcccccccc
Q 044606 335 HECPVCFRVFSSGQALGGHKRTHV 358 (413)
Q Consensus 335 ~~C~~C~k~F~~~~~L~~H~r~H~ 358 (413)
|.|++|++.|.+...|..|+++|+
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 689999999999999999999874
No 36
>PHA00732 hypothetical protein
Probab=96.83 E-value=0.0006 Score=51.71 Aligned_cols=26 Identities=35% Similarity=0.409 Sum_probs=23.6
Q ss_pred ccccCcccccCCChhhhhhHHHh-hcC
Q 044606 40 KHKCRLCFKNFSNGRALGGHMRS-HML 65 (413)
Q Consensus 40 ~~~C~iC~K~F~~~~~L~~HmR~-Htg 65 (413)
+|.|.+|++.|.....|++|||. |++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~ 27 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL 27 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC
Confidence 58999999999999999999995 764
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.73 E-value=0.0004 Score=54.92 Aligned_cols=74 Identities=23% Similarity=0.312 Sum_probs=22.5
Q ss_pred ccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchhhccccccc
Q 044606 278 KCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQALGGHKRTH 357 (413)
Q Consensus 278 ~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L~~H~r~H 357 (413)
+|.+|+..|.....|..|+....+...-..... .....+..+.+.. -...+.|.+|++.|.+...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l------~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYL------VDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Ccccccccccccccccccccccccccccccccc------ccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 599999999999999999976444221111000 0111111122111 123699999999999999999999975
Q ss_pred c
Q 044606 358 V 358 (413)
Q Consensus 358 ~ 358 (413)
.
T Consensus 74 ~ 74 (100)
T PF12756_consen 74 H 74 (100)
T ss_dssp T
T ss_pred c
Confidence 4
No 38
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.72 E-value=0.00089 Score=38.89 Aligned_cols=21 Identities=29% Similarity=0.570 Sum_probs=18.9
Q ss_pred cccCcccccCCChhhhhhHHHh
Q 044606 41 HKCRLCFKNFSNGRALGGHMRS 62 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~~HmR~ 62 (413)
..|++||++| +..+|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 99999999874
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.44 E-value=0.00083 Score=38.79 Aligned_cols=24 Identities=50% Similarity=0.815 Sum_probs=22.0
Q ss_pred cccCCcCcccCCchhhcccccccc
Q 044606 335 HECPVCFRVFSSGQALGGHKRTHV 358 (413)
Q Consensus 335 ~~C~~C~k~F~~~~~L~~H~r~H~ 358 (413)
|.|..|++.|.....|..|+++|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999999775
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.25 E-value=0.0024 Score=36.56 Aligned_cols=24 Identities=29% Similarity=0.434 Sum_probs=19.7
Q ss_pred cccCcccccCCChhhhhhHHHhhcC
Q 044606 41 HKCRLCFKNFSNGRALGGHMRSHML 65 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~~HmR~Htg 65 (413)
|+|++|.-... ...|.+||+.|.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 78999999888 9999999999764
No 41
>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=0.0053 Score=41.55 Aligned_cols=34 Identities=21% Similarity=0.271 Sum_probs=24.5
Q ss_pred cCCCCccccCCccccccChhhhhhhhhhcCCCcc
Q 044606 271 NRSRGKYKCETCKKVFKSYQALGGHRASHKKIKF 304 (413)
Q Consensus 271 ~~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp 304 (413)
+....|..|++|+..+.+..+|.+|+.++.+.||
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 4567899999999999999999999988877664
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.50 E-value=0.0032 Score=36.36 Aligned_cols=23 Identities=35% Similarity=0.671 Sum_probs=21.2
Q ss_pred cccCCcCcccCCchhhccccccc
Q 044606 335 HECPVCFRVFSSGQALGGHKRTH 357 (413)
Q Consensus 335 ~~C~~C~k~F~~~~~L~~H~r~H 357 (413)
|.|.+|++.|.+...|..|++.+
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 67999999999999999999875
No 43
>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=95.48 E-value=0.0074 Score=35.65 Aligned_cols=23 Identities=30% Similarity=0.567 Sum_probs=21.3
Q ss_pred cccCCcCcccCCchhhccccccc
Q 044606 335 HECPVCFRVFSSGQALGGHKRTH 357 (413)
Q Consensus 335 ~~C~~C~k~F~~~~~L~~H~r~H 357 (413)
|.|.+|++.|.+...|..|++++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 78999999999999999999864
No 44
>PRK04860 hypothetical protein; Provisional
Probab=95.38 E-value=0.0077 Score=52.17 Aligned_cols=35 Identities=17% Similarity=0.318 Sum_probs=17.8
Q ss_pred ccccCCccccccChhhhhhhhhhcCCCcccCCCCCCccc
Q 044606 276 KYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELD 314 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f 314 (413)
+|.|. |++ ....+.+|.++|+++++|.|..|+..+
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 35554 554 444455555555555555544444443
No 45
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.12 E-value=0.011 Score=46.45 Aligned_cols=25 Identities=40% Similarity=0.715 Sum_probs=22.5
Q ss_pred ccccCcccccCCChhhhhhHHHhhc
Q 044606 40 KHKCRLCFKNFSNGRALGGHMRSHM 64 (413)
Q Consensus 40 ~~~C~iC~K~F~~~~~L~~HmR~Ht 64 (413)
.+.|.+|++.|.+...|+.||+.|.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 6999999999999999999999864
No 46
>PRK04860 hypothetical protein; Provisional
Probab=95.06 E-value=0.0075 Score=52.23 Aligned_cols=40 Identities=13% Similarity=0.048 Sum_probs=33.5
Q ss_pred cccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCch
Q 044606 303 KFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQ 348 (413)
Q Consensus 303 kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~ 348 (413)
-+|.|. |+. ....+.+|.++|+|+++|.|..|++.|....
T Consensus 118 ~~Y~C~-C~~-----~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE-----HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC-----eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 369997 876 4456889999999999999999999987654
No 47
>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=95.05 E-value=0.013 Score=36.73 Aligned_cols=25 Identities=20% Similarity=0.586 Sum_probs=22.5
Q ss_pred cccccCcccccCCChhhhhhHHHhh
Q 044606 39 EKHKCRLCFKNFSNGRALGGHMRSH 63 (413)
Q Consensus 39 ~~~~C~iC~K~F~~~~~L~~HmR~H 63 (413)
.+|.|.+|++.|.....|..|++..
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHChH
Confidence 4689999999999999999999863
No 48
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.13 E-value=0.0099 Score=33.97 Aligned_cols=24 Identities=29% Similarity=0.462 Sum_probs=18.7
Q ss_pred cccCCcCcccCCchhhccccccccc
Q 044606 335 HECPVCFRVFSSGQALGGHKRTHVT 359 (413)
Q Consensus 335 ~~C~~C~k~F~~~~~L~~H~r~H~~ 359 (413)
|+|+.|..... ...|.+|+++|++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 68999998887 8899999998763
No 49
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=92.23 E-value=0.053 Score=48.92 Aligned_cols=47 Identities=28% Similarity=0.518 Sum_probs=34.2
Q ss_pred ccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchhhccc-ccc
Q 044606 278 KCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQALGGH-KRT 356 (413)
Q Consensus 278 ~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L~~H-~r~ 356 (413)
-|.+|++-|.....|..|++ .|.|+|.+|.|..-+.-.|..| |++
T Consensus 12 wcwycnrefddekiliqhqk----------------------------------akhfkchichkkl~sgpglsihcmqv 57 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK----------------------------------AKHFKCHICHKKLFSGPGLSIHCMQV 57 (341)
T ss_pred eeeecccccchhhhhhhhhh----------------------------------hccceeeeehhhhccCCCceeehhhh
Confidence 47788888877777766642 4567888888887778788887 556
Q ss_pred cc
Q 044606 357 HV 358 (413)
Q Consensus 357 H~ 358 (413)
|.
T Consensus 58 hk 59 (341)
T KOG2893|consen 58 HK 59 (341)
T ss_pred hh
Confidence 64
No 50
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.75 E-value=0.053 Score=31.42 Aligned_cols=21 Identities=33% Similarity=0.746 Sum_probs=16.7
Q ss_pred cccCCcCcccCCchhhcccccc
Q 044606 335 HECPVCFRVFSSGQALGGHKRT 356 (413)
Q Consensus 335 ~~C~~C~k~F~~~~~L~~H~r~ 356 (413)
..|+.||+.| ....|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 66788888754
No 51
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.09 E-value=0.28 Score=48.91 Aligned_cols=71 Identities=14% Similarity=0.038 Sum_probs=48.6
Q ss_pred CccccCCccccccChhhhhhhhh--hcCCC--cccCCC--CCCcccccccchhhhhhcCCCCCCCccccCC--cCcccCC
Q 044606 275 GKYKCETCKKVFKSYQALGGHRA--SHKKI--KFYTPV--QETELDQENAGASINLASPPLSVKKVHECPV--CFRVFSS 346 (413)
Q Consensus 275 ~~~~C~~C~k~F~~~~~L~~H~~--~H~~~--kp~~C~--~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~--C~k~F~~ 346 (413)
.++.|..|...|.....|..|.+ .|+++ +++.|. .|++.| .....+..|..+|++.+++.|.. |.+.+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLF--SRNDALKRHILLHTSISPAKEKLLNSSSKFSP 365 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccc--cccccccCCcccccCCCccccccccCcccccc
Confidence 46888888888888888888888 78887 777777 566666 35555666666777666666654 4444433
Q ss_pred c
Q 044606 347 G 347 (413)
Q Consensus 347 ~ 347 (413)
.
T Consensus 366 ~ 366 (467)
T COG5048 366 L 366 (467)
T ss_pred c
Confidence 3
No 52
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.68 E-value=0.2 Score=50.04 Aligned_cols=61 Identities=16% Similarity=0.211 Sum_probs=50.3
Q ss_pred hhcccCcCcchHHHHHhhh--hcCCC--CccccC--CccccccChhhhhhhhhhcCCCcccCCCCCC
Q 044606 251 AEKSMDETDESEEFKSFNN--KNRSR--GKYKCE--TCKKVFKSYQALGGHRASHKKIKFYTPVQET 311 (413)
Q Consensus 251 ~~~~~~~~~~~~~~~~~~~--~~~~~--~~~~C~--~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~ 311 (413)
+..+...+.....+..|.+ .|.++ +++.|. .|++.|.....+..|...|++.+++.|....
T Consensus 292 ~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 358 (467)
T COG5048 292 SKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLN 358 (467)
T ss_pred CccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccccccc
Confidence 3444555666677788888 79999 999999 7999999999999999999999988775533
No 53
>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=90.00 E-value=0.29 Score=34.09 Aligned_cols=25 Identities=32% Similarity=0.507 Sum_probs=19.1
Q ss_pred ccccCcccccCCChhhhhhHHHh-hcC
Q 044606 40 KHKCRLCFKNFSNGRALGGHMRS-HML 65 (413)
Q Consensus 40 ~~~C~iC~K~F~~~~~L~~HmR~-Htg 65 (413)
.|.||+|++.|. ...|..|+.. |..
T Consensus 2 ~f~CP~C~~~~~-~~~L~~H~~~~H~~ 27 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ESSLVEHCEDEHRS 27 (54)
T ss_pred CcCCCCCCCccC-HHHHHHHHHhHCcC
Confidence 588999999655 5689999776 444
No 54
>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=89.90 E-value=0.14 Score=34.02 Aligned_cols=28 Identities=29% Similarity=0.452 Sum_probs=18.8
Q ss_pred ccccccccCcccccCCCh----hhhhhHH-Hhh
Q 044606 36 FVMEKHKCRLCFKNFSNG----RALGGHM-RSH 63 (413)
Q Consensus 36 ~~~~~~~C~iC~K~F~~~----~~L~~Hm-R~H 63 (413)
.....-+|.+|++.|... +.|..|+ +.|
T Consensus 12 ~~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 12 GDKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp GCSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CCcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 556778899999999885 8899999 444
No 55
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=88.72 E-value=0.15 Score=56.64 Aligned_cols=78 Identities=19% Similarity=0.178 Sum_probs=48.1
Q ss_pred CCCccccCCccccccChhhhhhhhhh-cCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchhhc
Q 044606 273 SRGKYKCETCKKVFKSYQALGGHRAS-HKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQALG 351 (413)
Q Consensus 273 ~~~~~~C~~C~k~F~~~~~L~~H~~~-H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L~ 351 (413)
-.+.|+|+.|+-.|.....|..|+|+ |..-+. .+|.... ....+-+....-.+-++|.|..|...|+.+.+|.
T Consensus 462 ~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~~gq---~~~~~arg~~~~~~~~p~~C~~C~~stttng~Ls 535 (1406)
T KOG1146|consen 462 FFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCKAGQ---NHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLS 535 (1406)
T ss_pred ccccccCCccchhhhhHHHhhhcccccccccch---hHhHhcc---ccccccccccccCCCCcccceeeeeeeecchHHH
Confidence 34678888888888888888888876 333222 1111110 0000001111123457999999999999999999
Q ss_pred ccccc
Q 044606 352 GHKRT 356 (413)
Q Consensus 352 ~H~r~ 356 (413)
.|+..
T Consensus 536 ihlqS 540 (1406)
T KOG1146|consen 536 IHLQS 540 (1406)
T ss_pred HHHHH
Confidence 99873
No 56
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=88.03 E-value=0.26 Score=33.73 Aligned_cols=26 Identities=35% Similarity=0.704 Sum_probs=21.7
Q ss_pred cccccCcccccCCCh-----hhhhhHHH-hhc
Q 044606 39 EKHKCRLCFKNFSNG-----RALGGHMR-SHM 64 (413)
Q Consensus 39 ~~~~C~iC~K~F~~~-----~~L~~HmR-~Ht 64 (413)
..=.|.+|++.++.. +.|.+||+ +|.
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 456799999999877 69999999 674
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=87.79 E-value=0.32 Score=30.23 Aligned_cols=24 Identities=21% Similarity=0.555 Sum_probs=20.8
Q ss_pred CccccCCccccccChhhhhhhhhh
Q 044606 275 GKYKCETCKKVFKSYQALGGHRAS 298 (413)
Q Consensus 275 ~~~~C~~C~k~F~~~~~L~~H~~~ 298 (413)
.+|.|.+|++.|.....+..|++.
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHCh
Confidence 358899999999999999999764
No 58
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.47 E-value=0.58 Score=49.22 Aligned_cols=98 Identities=12% Similarity=0.071 Sum_probs=49.2
Q ss_pred cccCcCcchHHHHHhhhhcCCCCccccCCcc------ccccChhhhhhhhhhcCCCcccCCC--CCCc-ccc-c-ccchh
Q 044606 253 KSMDETDESEEFKSFNNKNRSRGKYKCETCK------KVFKSYQALGGHRASHKKIKFYTPV--QETE-LDQ-E-NAGAS 321 (413)
Q Consensus 253 ~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~------k~F~~~~~L~~H~~~H~~~kp~~C~--~C~~-~f~-~-~~~~~ 321 (413)
-+...+.+..++..|.+.+. |.|..|. --|.....|..|-+.+. |.|. .|.. .|. + .....
T Consensus 187 ~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~~~~f~~~~~~ei~ 258 (669)
T KOG2231|consen 187 FCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCRTKKFYVAFELEIE 258 (669)
T ss_pred hhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC----ccccccccccceeeehhHHHHH
Confidence 33445556666666654433 7777774 44566667777766543 5665 4542 221 1 11223
Q ss_pred hhhhcCCCCCCCccccC--CcCc----ccCCchhhcccccccc
Q 044606 322 INLASPPLSVKKVHECP--VCFR----VFSSGQALGGHKRTHV 358 (413)
Q Consensus 322 l~~h~~~h~g~kp~~C~--~C~k----~F~~~~~L~~H~r~H~ 358 (413)
|+.|.+.+.-++-|.|. .=|+ .|.....+..|.++-.
T Consensus 259 lk~~~~~~~~e~~~~~~~~r~Gr~s~~~r~~~~~~~~~~~~~~ 301 (669)
T KOG2231|consen 259 LKAHNRFIQHEKCYICRPSRPGRPSSRYRGPYRRLESHFRVSD 301 (669)
T ss_pred HHhhccccchheeccCCcccCCCCcccccCCcccccccccccc
Confidence 44444444446666664 2222 3333334455555443
No 59
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=86.13 E-value=0.22 Score=45.06 Aligned_cols=46 Identities=28% Similarity=0.474 Sum_probs=38.5
Q ss_pred eeeeeeEEeeccccccc---cccccccCcccccCCChhhhhhH-HHhhcC
Q 044606 20 LFIIYVYVFFKKRKSLF---VMEKHKCRLCFKNFSNGRALGGH-MRSHML 65 (413)
Q Consensus 20 ~~~~~~~~~~~~~~~~~---~~~~~~C~iC~K~F~~~~~L~~H-mR~Htg 65 (413)
-.|.|+++-|..-+..+ ..+-|+|.||.|+.-..--|.+| |.+|..
T Consensus 11 pwcwycnrefddekiliqhqkakhfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred ceeeecccccchhhhhhhhhhhccceeeeehhhhccCCCceeehhhhhhh
Confidence 67999999998888777 34558999999999999999999 677754
No 60
>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=85.25 E-value=0.58 Score=27.33 Aligned_cols=20 Identities=25% Similarity=0.796 Sum_probs=16.7
Q ss_pred ccCcccccCCChhhhhhHHHh
Q 044606 42 KCRLCFKNFSNGRALGGHMRS 62 (413)
Q Consensus 42 ~C~iC~K~F~~~~~L~~HmR~ 62 (413)
.||||++.+ ....+..|+..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 3 QCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHHH
Confidence 699999999 66788888763
No 61
>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=83.20 E-value=0.79 Score=36.93 Aligned_cols=30 Identities=20% Similarity=0.106 Sum_probs=22.2
Q ss_pred cCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCc
Q 044606 305 YTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSG 347 (413)
Q Consensus 305 ~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~ 347 (413)
..|..||+.|...+ ..|-.|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDLn-------------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN-------------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCC-------------CCCccCCCCCCccCcc
Confidence 46788887775332 4588899999988777
No 62
>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=80.58 E-value=0.67 Score=38.71 Aligned_cols=25 Identities=36% Similarity=0.542 Sum_probs=16.4
Q ss_pred cccCcccccCCChhhhhhHHHhhcCCCC
Q 044606 41 HKCRLCFKNFSNGRALGGHMRSHMLNLP 68 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~~HmR~Htg~~p 68 (413)
-.|-+|||.|.. |++|+++|.|..|
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eEEccCCcccch---HHHHHHHccCCCH
Confidence 449999999975 6999999999554
No 63
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=76.98 E-value=0.88 Score=43.08 Aligned_cols=25 Identities=36% Similarity=0.753 Sum_probs=22.0
Q ss_pred CCCccccCCccccccChhhhhhhhh
Q 044606 273 SRGKYKCETCKKVFKSYQALGGHRA 297 (413)
Q Consensus 273 ~~~~~~C~~C~k~F~~~~~L~~H~~ 297 (413)
..|||+|.+|+|.|.....|+.|+.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCCceeccccchhhccCccceeccc
Confidence 4599999999999999999999854
No 64
>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=76.72 E-value=1.6 Score=26.94 Aligned_cols=10 Identities=30% Similarity=1.119 Sum_probs=5.7
Q ss_pred cccCCccccc
Q 044606 277 YKCETCKKVF 286 (413)
Q Consensus 277 ~~C~~C~k~F 286 (413)
|.|.+||..+
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 5566666544
No 65
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.59 E-value=1.5 Score=46.36 Aligned_cols=16 Identities=19% Similarity=0.179 Sum_probs=8.8
Q ss_pred ccCCchhhcccccccc
Q 044606 343 VFSSGQALGGHKRTHV 358 (413)
Q Consensus 343 ~F~~~~~L~~H~r~H~ 358 (413)
-|.....|..|.|.+|
T Consensus 221 yy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 221 YYNDYDDLEEHFRKGH 236 (669)
T ss_pred hcccchHHHHHhhhcC
Confidence 3455555666665554
No 66
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=75.79 E-value=1.3 Score=36.58 Aligned_cols=25 Identities=28% Similarity=0.283 Sum_probs=21.5
Q ss_pred ccCcccccCCChhhhhhHHHhhcCCCCC
Q 044606 42 KCRLCFKNFSNGRALGGHMRSHMLNLPI 69 (413)
Q Consensus 42 ~C~iC~K~F~~~~~L~~HmR~Htg~~p~ 69 (413)
.|--|||+|. +|++|+++|.|..|-
T Consensus 78 icLEDGkkfK---SLKRHL~t~~gmTPd 102 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHYGLTPD 102 (148)
T ss_pred EEeccCcchH---HHHHHHhcccCCCHH
Confidence 3999999996 799999999996653
No 67
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=75.56 E-value=0.62 Score=48.83 Aligned_cols=28 Identities=29% Similarity=0.438 Sum_probs=25.4
Q ss_pred ccccccCcccccCCChhhhhhHHHhhcC
Q 044606 38 MEKHKCRLCFKNFSNGRALGGHMRSHML 65 (413)
Q Consensus 38 ~~~~~C~iC~K~F~~~~~L~~HmR~Htg 65 (413)
---|-|..|+|+|-.-.+|..||++|.-
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 3447899999999999999999999987
No 68
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=75.28 E-value=1.7 Score=46.83 Aligned_cols=49 Identities=14% Similarity=0.152 Sum_probs=32.9
Q ss_pred cccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcc
Q 044606 277 YKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRV 343 (413)
Q Consensus 277 ~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~ 343 (413)
..|..||..+.... ...-+..|...+-..|.+|+... ..|+.|+.||-.
T Consensus 436 l~C~~Cg~v~~Cp~-Cd~~lt~H~~~~~L~CH~Cg~~~-----------------~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYIAECPN-CDSPLTLHKATGQLRCHYCGYQE-----------------PIPQSCPECGSE 484 (730)
T ss_pred eecccCCCcccCCC-CCcceEEecCCCeeEeCCCCCCC-----------------CCCCCCCCCCCC
Confidence 35888888775432 22334445555677888887643 679999999864
No 69
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=75.22 E-value=1.4 Score=37.91 Aligned_cols=20 Identities=20% Similarity=0.318 Sum_probs=12.7
Q ss_pred ccccCCcCcccCCchhhccc
Q 044606 334 VHECPVCFRVFSSGQALGGH 353 (413)
Q Consensus 334 p~~C~~C~k~F~~~~~L~~H 353 (413)
-++|+.||++|...-.+..-
T Consensus 28 ~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 28 RRECLACGKRFTTFERVELV 47 (154)
T ss_pred eeeccccCCcceEeEeccCc
Confidence 37777777777766554433
No 70
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=74.36 E-value=2.4 Score=34.81 Aligned_cols=34 Identities=12% Similarity=-0.015 Sum_probs=22.4
Q ss_pred cCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchhhc
Q 044606 305 YTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQALG 351 (413)
Q Consensus 305 ~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L~ 351 (413)
..|+.|++.|...+ ..|-.|+.||..|.-...++
T Consensus 10 r~Cp~cg~kFYDLn-------------k~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 10 RICPNTGSKFYDLN-------------RRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred ccCCCcCccccccC-------------CCCccCCCcCCccCcchhhc
Confidence 45777777774322 45788888888876664444
No 71
>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=73.85 E-value=1.6 Score=39.72 Aligned_cols=38 Identities=24% Similarity=0.322 Sum_probs=28.2
Q ss_pred eeccccccccccccccCcccccCCChhhhhhHHHhhcC
Q 044606 28 FFKKRKSLFVMEKHKCRLCFKNFSNGRALGGHMRSHML 65 (413)
Q Consensus 28 ~~~~~~~~~~~~~~~C~iC~K~F~~~~~L~~HmR~Htg 65 (413)
|+.+......-.+|.|++|+|.|.-......||..=+.
T Consensus 65 ~v~~~~~e~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 65 FVQKNTKEEDEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp GEEEEE-SSSSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred HHHHHHHHHcCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 44555556677789999999999999999999998544
No 72
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=73.74 E-value=1.5 Score=40.05 Aligned_cols=24 Identities=29% Similarity=0.522 Sum_probs=18.0
Q ss_pred CCccccCCccccccChhhhhhhhh
Q 044606 274 RGKYKCETCKKVFKSYQALGGHRA 297 (413)
Q Consensus 274 ~~~~~C~~C~k~F~~~~~L~~H~~ 297 (413)
++...|++|++.|.+..-.....+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCce
Confidence 456899999999988766655554
No 73
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=73.33 E-value=0.9 Score=50.91 Aligned_cols=82 Identities=15% Similarity=0.099 Sum_probs=47.6
Q ss_pred ccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchh---------------hhhhcCCCCCCCccccCCc
Q 044606 276 KYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGAS---------------INLASPPLSVKKVHECPVC 340 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~---------------l~~h~~~h~g~kp~~C~~C 340 (413)
-+.|..|.+.|.....+. |+- -..+|.|..|...|....... ..-+...+..-++| |..|
T Consensus 1260 e~~c~~~~~~~~~~~~~~-~l~---~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c 1334 (1406)
T KOG1146|consen 1260 EGECGAVDELLTPSFGIS-TLD---VTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLAC 1334 (1406)
T ss_pred cchhhhccccccCcccee-ecc---cchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHH
Confidence 355666666655554444 321 123455555555553222111 12222334445677 9999
Q ss_pred CcccCCchhhcccccccccCCC
Q 044606 341 FRVFSSGQALGGHKRTHVTGLV 362 (413)
Q Consensus 341 ~k~F~~~~~L~~H~r~H~~~~~ 362 (413)
...|+....|..|||+-.+...
T Consensus 1335 ~~~~~~~~alqihm~~~~~~~k 1356 (1406)
T KOG1146|consen 1335 EVLLSGREALQIHMRSSAHRRK 1356 (1406)
T ss_pred HhhcchhHHHHHHHHHhhhccc
Confidence 9999999999999997555443
No 74
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=71.33 E-value=6.2 Score=31.90 Aligned_cols=81 Identities=15% Similarity=0.108 Sum_probs=52.0
Q ss_pred CCccccCCccccccChhhhhhhhhhcCCCccc------------CCCCCCcccccccchhhhhhcCCCCCCCccccCCcC
Q 044606 274 RGKYKCETCKKVFKSYQALGGHRASHKKIKFY------------TPVQETELDQENAGASINLASPPLSVKKVHECPVCF 341 (413)
Q Consensus 274 ~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~------------~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~ 341 (413)
+-|..|.+||-+......|.+...---..++| .|-.|...|........ ..-.....|.|+.|.
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~----~~~~~~~~y~C~~C~ 88 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF----DELKDSHRYVCAVCK 88 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc----cccccccceeCCCCC
Confidence 45789999999888888887642211111222 37778777743211100 001224479999999
Q ss_pred cccCCchhhcccccccc
Q 044606 342 RVFSSGQALGGHKRTHV 358 (413)
Q Consensus 342 k~F~~~~~L~~H~r~H~ 358 (413)
..|--.-.+-.|...|.
T Consensus 89 ~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 89 NVFCVDCDVFVHESLHC 105 (112)
T ss_pred CccccccchhhhhhccC
Confidence 99999888888888886
No 75
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=70.42 E-value=0.91 Score=31.39 Aligned_cols=31 Identities=19% Similarity=0.255 Sum_probs=24.8
Q ss_pred CCCCCCccccCCcCcccCCchhhcccccccc
Q 044606 328 PLSVKKVHECPVCFRVFSSGQALGGHKRTHV 358 (413)
Q Consensus 328 ~h~g~kp~~C~~C~k~F~~~~~L~~H~r~H~ 358 (413)
...|+--+.|+-||+.|.......+|...-+
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 3456778999999999999999999976433
No 76
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=68.65 E-value=2.4 Score=35.39 Aligned_cols=26 Identities=19% Similarity=0.223 Sum_probs=21.1
Q ss_pred eeccccccccccccccCcccccCCCh
Q 044606 28 FFKKRKSLFVMEKHKCRLCFKNFSNG 53 (413)
Q Consensus 28 ~~~~~~~~~~~~~~~C~iC~K~F~~~ 53 (413)
.++......+.++|+|+-|++.|...
T Consensus 41 ~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 41 VVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred eeeECCccccccccccCCcCcceeee
Confidence 55666666679999999999999754
No 77
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=68.43 E-value=3 Score=36.25 Aligned_cols=10 Identities=30% Similarity=0.866 Sum_probs=6.1
Q ss_pred CCccccCCcC
Q 044606 332 KKVHECPVCF 341 (413)
Q Consensus 332 ~kp~~C~~C~ 341 (413)
+-|-.||+||
T Consensus 147 e~P~~CPiCg 156 (166)
T COG1592 147 EAPEVCPICG 156 (166)
T ss_pred CCCCcCCCCC
Confidence 5566666665
No 78
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=68.39 E-value=3.5 Score=25.70 Aligned_cols=10 Identities=30% Similarity=0.909 Sum_probs=6.4
Q ss_pred CccccCCcCc
Q 044606 333 KVHECPVCFR 342 (413)
Q Consensus 333 kp~~C~~C~k 342 (413)
.|..|++||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 4567777764
No 79
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=68.05 E-value=3.2 Score=33.40 Aligned_cols=25 Identities=16% Similarity=0.222 Sum_probs=23.5
Q ss_pred ccc----CcccccCCChhhhhhHHHhhcC
Q 044606 41 HKC----RLCFKNFSNGRALGGHMRSHML 65 (413)
Q Consensus 41 ~~C----~iC~K~F~~~~~L~~HmR~Htg 65 (413)
|.| +.|+..+.+..+++.|+|.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 779 9999999999999999999876
No 80
>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=65.30 E-value=3.4 Score=42.86 Aligned_cols=48 Identities=17% Similarity=0.145 Sum_probs=33.5
Q ss_pred ccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcc
Q 044606 278 KCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRV 343 (413)
Q Consensus 278 ~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~ 343 (413)
.|..||...... +....+..|.......|..|+... .-|..|+.||-.
T Consensus 215 ~C~~Cg~~~~C~-~C~~~l~~h~~~~~l~Ch~Cg~~~-----------------~~~~~Cp~C~s~ 262 (505)
T TIGR00595 215 LCRSCGYILCCP-NCDVSLTYHKKEGKLRCHYCGYQE-----------------PIPKTCPQCGSE 262 (505)
T ss_pred EhhhCcCccCCC-CCCCceEEecCCCeEEcCCCcCcC-----------------CCCCCCCCCCCC
Confidence 677777665432 234455666677788999998655 558899999863
No 81
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=65.05 E-value=3.4 Score=41.03 Aligned_cols=50 Identities=16% Similarity=0.202 Sum_probs=32.9
Q ss_pred CCCCCCCCccchhhheeeeeeEEeeccccccc---------------------cccccccCcccccCCChhhhhh
Q 044606 5 SHRKEKPPELTTFKLLFIIYVYVFFKKRKSLF---------------------VMEKHKCRLCFKNFSNGRALGG 58 (413)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~C~iC~K~F~~~~~L~~ 58 (413)
.+|+.++||-.+..+ ++|+|+.=+.... .++-|.||+|+|+|+.--+|+.
T Consensus 76 ~~r~E~~~nGr~~~~----~~YyyInY~~~idvVKyKlh~m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L 146 (436)
T KOG2593|consen 76 RTRTETAENGRAVDK----HTYYYINYAQVIDVVKYKLHQMRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQL 146 (436)
T ss_pred hhhhhcCCCCcceee----eEEEEeehHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCccccchhhhHHHHh
Confidence 578889996555542 4444443322211 4566899999999998888753
No 82
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=64.78 E-value=3.2 Score=39.81 Aligned_cols=74 Identities=16% Similarity=0.142 Sum_probs=43.7
Q ss_pred cccCCccccccChhhhhhhhhh-cCCCcccCCCCCCcccccccchhhhhhcCC----CCCCCccccCCcCcccCCchhhc
Q 044606 277 YKCETCKKVFKSYQALGGHRAS-HKKIKFYTPVQETELDQENAGASINLASPP----LSVKKVHECPVCFRVFSSGQALG 351 (413)
Q Consensus 277 ~~C~~C~k~F~~~~~L~~H~~~-H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~----h~g~kp~~C~~C~k~F~~~~~L~ 351 (413)
-.|-.|....-+...|..||.+ |.=. .-+ ... ..+++.....+. ....+.-.|-.|.-.|.....|.
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~D-l~K------i~s-d~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~ 351 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFD-LLK------IQS-DYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLL 351 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhh-HHh------hcc-ccccchhhhhhHHHHHHHHhhccccccccccccCcchhh
Confidence 5899999988889999999985 4310 000 000 001111111110 01123446778889999999999
Q ss_pred ccccccc
Q 044606 352 GHKRTHV 358 (413)
Q Consensus 352 ~H~r~H~ 358 (413)
.||.-+.
T Consensus 352 ~hm~e~k 358 (423)
T KOG2482|consen 352 IHMVEDK 358 (423)
T ss_pred hhccccc
Confidence 9987544
No 83
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=61.78 E-value=5.4 Score=26.59 Aligned_cols=11 Identities=27% Similarity=0.504 Sum_probs=7.0
Q ss_pred ccccCCcCccc
Q 044606 334 VHECPVCFRVF 344 (413)
Q Consensus 334 p~~C~~C~k~F 344 (413)
.+.|+.||-.+
T Consensus 21 ~~~Cp~CG~~~ 31 (46)
T PRK00398 21 GVRCPYCGYRI 31 (46)
T ss_pred ceECCCCCCeE
Confidence 56777777544
No 84
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=61.58 E-value=3.5 Score=35.49 Aligned_cols=42 Identities=5% Similarity=-0.099 Sum_probs=21.4
Q ss_pred cccCCccccccChhhhhhhhhhcCCCcccCCCCCCccccccc
Q 044606 277 YKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENA 318 (413)
Q Consensus 277 ~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~ 318 (413)
++|++||..++..-.-..-..-..-.+.++|+.||+.|....
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e 42 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFE 42 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeE
Confidence 479999965522111110000111123488999999886443
No 85
>PRK14873 primosome assembly protein PriA; Provisional
Probab=60.65 E-value=4.2 Score=43.62 Aligned_cols=47 Identities=13% Similarity=0.082 Sum_probs=32.0
Q ss_pred ccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcc
Q 044606 278 KCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRV 343 (413)
Q Consensus 278 ~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~ 343 (413)
.|..||..+... +....+..|...+...|..||.. ..|+.|+.||-.
T Consensus 385 ~C~~Cg~~~~C~-~C~~~L~~h~~~~~l~Ch~CG~~------------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCR-HCTGPLGLPSAGGTPRCRWCGRA------------------APDWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECC-CCCCceeEecCCCeeECCCCcCC------------------CcCccCCCCcCC
Confidence 688888776543 23344455666677889999853 248899999864
No 86
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=60.64 E-value=4.4 Score=28.60 Aligned_cols=11 Identities=27% Similarity=0.525 Sum_probs=8.7
Q ss_pred CCccccCCcCc
Q 044606 332 KKVHECPVCFR 342 (413)
Q Consensus 332 ~kp~~C~~C~k 342 (413)
..+|.|+.||.
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 45899999984
No 87
>PF14353 CpXC: CpXC protein
Probab=59.82 E-value=4 Score=33.84 Aligned_cols=25 Identities=24% Similarity=0.329 Sum_probs=20.3
Q ss_pred ccccCCcCcccCCchhhcccccccc
Q 044606 334 VHECPVCFRVFSSGQALGGHKRTHV 358 (413)
Q Consensus 334 p~~C~~C~k~F~~~~~L~~H~r~H~ 358 (413)
.|.|+.||+.|.-...+..|-..|.
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~~~ 62 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPEKK 62 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCCCC
Confidence 5899999999998888888865543
No 88
>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=59.82 E-value=6.7 Score=22.86 Aligned_cols=12 Identities=33% Similarity=0.631 Sum_probs=8.9
Q ss_pred ccccCCcCcccC
Q 044606 334 VHECPVCFRVFS 345 (413)
Q Consensus 334 p~~C~~C~k~F~ 345 (413)
.-.|+.||..|.
T Consensus 14 ~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 14 AKFCPHCGYDFE 25 (26)
T ss_pred cCcCCCCCCCCc
Confidence 346888888885
No 89
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=58.46 E-value=6.3 Score=30.13 Aligned_cols=14 Identities=29% Similarity=0.750 Sum_probs=8.6
Q ss_pred ccccCCcCcccCCc
Q 044606 334 VHECPVCFRVFSSG 347 (413)
Q Consensus 334 p~~C~~C~k~F~~~ 347 (413)
.+.|..||..|.-.
T Consensus 53 IW~C~kCg~~fAGg 66 (89)
T COG1997 53 IWKCRKCGAKFAGG 66 (89)
T ss_pred eEEcCCCCCeeccc
Confidence 56666677666543
No 90
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=58.27 E-value=5.5 Score=34.49 Aligned_cols=18 Identities=17% Similarity=0.189 Sum_probs=8.9
Q ss_pred CccccCCccccccChhhh
Q 044606 275 GKYKCETCKKVFKSYQAL 292 (413)
Q Consensus 275 ~~~~C~~C~k~F~~~~~L 292 (413)
.-|.|+.|+..|+.-..+
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CeEECCCCCcEeeHHHHH
Confidence 345555555555544444
No 91
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=56.91 E-value=5.8 Score=41.10 Aligned_cols=31 Identities=23% Similarity=0.411 Sum_probs=27.0
Q ss_pred cccccccccCcccccCCChhhhhhHHHhhcC
Q 044606 35 LFVMEKHKCRLCFKNFSNGRALGGHMRSHML 65 (413)
Q Consensus 35 ~~~~~~~~C~iC~K~F~~~~~L~~HmR~Htg 65 (413)
...-.+++|..||++|.+......||-.|..
T Consensus 413 Ly~~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 413 LYKDSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred hccCCcchhcccccccccchhhhhHhhhhhh
Confidence 3456678999999999999999999999887
No 92
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=56.15 E-value=6.3 Score=34.82 Aligned_cols=16 Identities=25% Similarity=0.492 Sum_probs=7.4
Q ss_pred ccccCCccccccChhh
Q 044606 276 KYKCETCKKVFKSYQA 291 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~ 291 (413)
-|.|+.|++.|+.-..
T Consensus 117 ~Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA 132 (178)
T ss_pred EEECCCCCcEEeHHHH
Confidence 3445555544444433
No 93
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=55.53 E-value=6.1 Score=38.09 Aligned_cols=70 Identities=23% Similarity=0.349 Sum_probs=43.9
Q ss_pred CCccccCC--ccccccChhhhhhhhhh-cCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchhh
Q 044606 274 RGKYKCET--CKKVFKSYQALGGHRAS-HKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQAL 350 (413)
Q Consensus 274 ~~~~~C~~--C~k~F~~~~~L~~H~~~-H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L 350 (413)
.++|+|.+ |.+.+.....|+.|... |... ..- ....-.-|.-.....|+|.|++|.+++.....|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~--i~~----------~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l 414 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSP--ITT----------PTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGL 414 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCC--CCC----------CCCCCCCcceeeeccCcccChhhhhhhccCCCC
Confidence 57899987 99999888888887543 2210 000 000011122223347899999999999888777
Q ss_pred ccccc
Q 044606 351 GGHKR 355 (413)
Q Consensus 351 ~~H~r 355 (413)
+-|..
T Consensus 415 ~~~~~ 419 (442)
T KOG4124|consen 415 KYHRT 419 (442)
T ss_pred Cceee
Confidence 76643
No 94
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=54.65 E-value=5.6 Score=38.23 Aligned_cols=87 Identities=18% Similarity=0.232 Sum_probs=48.1
Q ss_pred HHHHHhhhhcCCCCccccCCcc---cccc------ChhhhhhhhhhcCCCccc----CCCCCCcccccccchhhhhhcCC
Q 044606 262 EEFKSFNNKNRSRGKYKCETCK---KVFK------SYQALGGHRASHKKIKFY----TPVQETELDQENAGASINLASPP 328 (413)
Q Consensus 262 ~~~~~~~~~~~~~~~~~C~~C~---k~F~------~~~~L~~H~~~H~~~kp~----~C~~C~~~f~~~~~~~l~~h~~~ 328 (413)
..++.|..... ..+.|.+|- +.|. ++..|..|...-..+.-| .|..|.+.|. ....|..|++
T Consensus 167 k~lk~H~K~~H--~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FY--dDDEL~~HcR- 241 (493)
T COG5236 167 KELKKHYKAQH--GFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFY--DDDELRRHCR- 241 (493)
T ss_pred HHHHHHHHhhc--CcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccceec--ChHHHHHHHH-
Confidence 34455544322 246676663 3443 344555565433222223 4778877763 4555777776
Q ss_pred CCCCCccccCCcCc-------ccCCchhhcccccc
Q 044606 329 LSVKKVHECPVCFR-------VFSSGQALGGHKRT 356 (413)
Q Consensus 329 h~g~kp~~C~~C~k-------~F~~~~~L~~H~r~ 356 (413)
++.-.|.+|++ -|.....|-.|.+.
T Consensus 242 ---~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~ 273 (493)
T COG5236 242 ---LRHEACHICDMVGPIRYQYFKSYEDLEAHFRN 273 (493)
T ss_pred ---hhhhhhhhhhccCccchhhhhCHHHHHHHhhc
Confidence 44456666654 36677777777663
No 95
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=54.04 E-value=5.5 Score=29.54 Aligned_cols=19 Identities=21% Similarity=0.614 Sum_probs=14.7
Q ss_pred CCccccC--CcCcccCCchhh
Q 044606 332 KKVHECP--VCFRVFSSGQAL 350 (413)
Q Consensus 332 ~kp~~C~--~C~k~F~~~~~L 350 (413)
++.+.|. .||.+|.....+
T Consensus 25 ~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 25 ERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred eeeeecCCCCCCCEEEEEEEE
Confidence 6678898 899999876554
No 96
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=53.61 E-value=4.7 Score=37.16 Aligned_cols=37 Identities=11% Similarity=0.375 Sum_probs=27.9
Q ss_pred cccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccc
Q 044606 277 YKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQ 315 (413)
Q Consensus 277 ~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~ 315 (413)
|.|.+||-+.. +..+.+|+-..++ .-|.|..|++.|.
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~ 40 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFE 40 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccC-CeeEEeecccccc
Confidence 78999997654 4557778877777 6688888888884
No 97
>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=53.56 E-value=7.2 Score=25.50 Aligned_cols=9 Identities=33% Similarity=0.704 Sum_probs=4.9
Q ss_pred ccccCCcCc
Q 044606 334 VHECPVCFR 342 (413)
Q Consensus 334 p~~C~~C~k 342 (413)
+-.|+.||.
T Consensus 26 ~~~CP~Cg~ 34 (42)
T PF09723_consen 26 PVPCPECGS 34 (42)
T ss_pred CCcCCCCCC
Confidence 445666654
No 98
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=53.33 E-value=6.1 Score=26.95 Aligned_cols=11 Identities=36% Similarity=1.201 Sum_probs=6.1
Q ss_pred cccCCcccccc
Q 044606 277 YKCETCKKVFK 287 (413)
Q Consensus 277 ~~C~~C~k~F~ 287 (413)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 55555555554
No 99
>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=52.44 E-value=6.6 Score=25.14 Aligned_cols=9 Identities=33% Similarity=0.866 Sum_probs=4.8
Q ss_pred ccccCCcCc
Q 044606 334 VHECPVCFR 342 (413)
Q Consensus 334 p~~C~~C~k 342 (413)
.-.|+.||.
T Consensus 26 ~~~CP~Cg~ 34 (41)
T smart00834 26 LATCPECGG 34 (41)
T ss_pred CCCCCCCCC
Confidence 345666654
No 100
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=52.36 E-value=5.6 Score=27.61 Aligned_cols=29 Identities=17% Similarity=0.338 Sum_probs=23.4
Q ss_pred CCCCccccCCccccccChhhhhhhhhhcC
Q 044606 272 RSRGKYKCETCKKVFKSYQALGGHRASHK 300 (413)
Q Consensus 272 ~~~~~~~C~~C~k~F~~~~~L~~H~~~H~ 300 (413)
-++--++|+-|+..|.......+|...-.
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 35667899999999999999999976433
No 101
>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=52.22 E-value=6.2 Score=31.81 Aligned_cols=15 Identities=27% Similarity=0.507 Sum_probs=12.5
Q ss_pred ccccccCcccccCCC
Q 044606 38 MEKHKCRLCFKNFSN 52 (413)
Q Consensus 38 ~~~~~C~iC~K~F~~ 52 (413)
..|+.|+-||++|--
T Consensus 7 GtKR~Cp~CG~kFYD 21 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYD 21 (108)
T ss_pred CCcccCCCCcchhcc
Confidence 568899999999953
No 102
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=52.19 E-value=3.2 Score=37.84 Aligned_cols=27 Identities=26% Similarity=0.506 Sum_probs=22.5
Q ss_pred cccccCcccccCCChhhhhhHHHh-hcC
Q 044606 39 EKHKCRLCFKNFSNGRALGGHMRS-HML 65 (413)
Q Consensus 39 ~~~~C~iC~K~F~~~~~L~~HmR~-Htg 65 (413)
+..+||+|++.|.....+....|. +..
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d 31 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRD 31 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeec
Confidence 467899999999999999888876 443
No 103
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=52.00 E-value=13 Score=31.63 Aligned_cols=19 Identities=26% Similarity=0.702 Sum_probs=11.7
Q ss_pred CCCccccCCccccccChhh
Q 044606 273 SRGKYKCETCKKVFKSYQA 291 (413)
Q Consensus 273 ~~~~~~C~~C~k~F~~~~~ 291 (413)
...-|.|+.|+..|.....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea 114 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEA 114 (147)
T ss_pred CCcEEECcCCCCEeeHHHH
Confidence 3445777777777765433
No 104
>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=50.88 E-value=4.2 Score=34.01 Aligned_cols=26 Identities=31% Similarity=0.368 Sum_probs=16.3
Q ss_pred CCccccCCcCcccCCchhhcccccccccC
Q 044606 332 KKVHECPVCFRVFSSGQALGGHKRTHVTG 360 (413)
Q Consensus 332 ~kp~~C~~C~k~F~~~~~L~~H~r~H~~~ 360 (413)
..--.|-+|||.|.. |++|++.|+|-
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S
T ss_pred cCeeEEccCCcccch---HHHHHHHccCC
Confidence 344679999998876 49999999764
No 105
>PRK05580 primosome assembly protein PriA; Validated
Probab=49.24 E-value=8.8 Score=41.45 Aligned_cols=49 Identities=14% Similarity=0.172 Sum_probs=30.6
Q ss_pred cccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcc
Q 044606 277 YKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRV 343 (413)
Q Consensus 277 ~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~ 343 (413)
..|..||..+.... ....+..|...+...|..|+... ..|..|+.||..
T Consensus 382 ~~C~~Cg~~~~C~~-C~~~l~~h~~~~~l~Ch~Cg~~~-----------------~~~~~Cp~Cg~~ 430 (679)
T PRK05580 382 LLCRDCGWVAECPH-CDASLTLHRFQRRLRCHHCGYQE-----------------PIPKACPECGST 430 (679)
T ss_pred eEhhhCcCccCCCC-CCCceeEECCCCeEECCCCcCCC-----------------CCCCCCCCCcCC
Confidence 45777776653221 22233445556677888888654 557899999764
No 106
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=49.15 E-value=11 Score=32.93 Aligned_cols=25 Identities=12% Similarity=0.062 Sum_probs=21.0
Q ss_pred CccccCCccccccChhhhhhhhhhcCCCcccCCCCCCc
Q 044606 275 GKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETE 312 (413)
Q Consensus 275 ~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~ 312 (413)
+.|.|.+||.+ |.|+-|-+|++|+-
T Consensus 133 ~~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 37999999964 66788999999984
No 107
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=48.13 E-value=9.1 Score=40.79 Aligned_cols=22 Identities=23% Similarity=0.527 Sum_probs=17.5
Q ss_pred CccccCCcCcccCCchhhcccc
Q 044606 333 KVHECPVCFRVFSSGQALGGHK 354 (413)
Q Consensus 333 kp~~C~~C~k~F~~~~~L~~H~ 354 (413)
|.-+||.|+..|+...-+..|+
T Consensus 677 RqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred hcCCCCCCCCCCCcccccccCC
Confidence 4558999999999887776664
No 108
>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=47.73 E-value=9.6 Score=24.92 Aligned_cols=17 Identities=18% Similarity=0.491 Sum_probs=13.7
Q ss_pred cccCcccccCCChhhhh
Q 044606 41 HKCRLCFKNFSNGRALG 57 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~ 57 (413)
-.|++||+-|++....+
T Consensus 9 K~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWA 25 (42)
T ss_pred CcCcccCCcchHHHHHH
Confidence 46999999999876543
No 109
>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=47.47 E-value=17 Score=31.44 Aligned_cols=44 Identities=14% Similarity=0.101 Sum_probs=32.0
Q ss_pred hhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccC
Q 044606 291 ALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFS 345 (413)
Q Consensus 291 ~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~ 345 (413)
.|..-+...++..-|.|+.|+..|++..... .-|.|+.||....
T Consensus 96 ~lk~~l~~e~~~~~Y~Cp~c~~r~tf~eA~~-----------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 96 KLREKLEFETNNMFFICPNMCVRFTFNEAME-----------LNFTCPRCGAMLD 139 (158)
T ss_pred HHHHHHhhccCCCeEECCCCCcEeeHHHHHH-----------cCCcCCCCCCEee
Confidence 4455555667778899999999887555442 3699999997643
No 110
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=47.16 E-value=8.6 Score=30.11 Aligned_cols=41 Identities=22% Similarity=0.286 Sum_probs=22.5
Q ss_pred chhhheeeeeeEEeeccccccccccccccCcccccCCChhh
Q 044606 15 TTFKLLFIIYVYVFFKKRKSLFVMEKHKCRLCFKNFSNGRA 55 (413)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~iC~K~F~~~~~ 55 (413)
+-|.-|||..--+.--+......+-.-.|.||+..|.+...
T Consensus 22 t~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it 62 (109)
T KOG3214|consen 22 TQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTIT 62 (109)
T ss_pred eeeccCccccccceeeeehhhcCcceeeeeehhhhhccchH
Confidence 44554555544333222222223444569999999987654
No 111
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=47.09 E-value=7.3 Score=27.50 Aligned_cols=11 Identities=27% Similarity=0.504 Sum_probs=8.8
Q ss_pred CCccccCCcCc
Q 044606 332 KKVHECPVCFR 342 (413)
Q Consensus 332 ~kp~~C~~C~k 342 (413)
..+|.|+.||-
T Consensus 48 g~~Y~Cp~CGF 58 (61)
T COG2888 48 GNPYRCPKCGF 58 (61)
T ss_pred CCceECCCcCc
Confidence 46899999984
No 112
>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=46.49 E-value=13 Score=23.40 Aligned_cols=12 Identities=25% Similarity=0.470 Sum_probs=7.8
Q ss_pred ccccCCcCcccC
Q 044606 334 VHECPVCFRVFS 345 (413)
Q Consensus 334 p~~C~~C~k~F~ 345 (413)
...|+.|+..|.
T Consensus 25 ~v~C~~C~~~~~ 36 (38)
T TIGR02098 25 KVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEE
Confidence 456777776663
No 113
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=46.31 E-value=12 Score=31.05 Aligned_cols=61 Identities=20% Similarity=0.193 Sum_probs=36.1
Q ss_pred CCCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchh
Q 044606 272 RSRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQA 349 (413)
Q Consensus 272 ~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~ 349 (413)
...+.|+|++|..+......|+ |-.| ||..--..--.+|+.|..+|. .|++|.-+|.+...
T Consensus 76 ~d~~lYeCnIC~etS~ee~FLK----------PneC--CgY~iCn~Cya~LWK~~~~yp-----vCPvCkTSFKss~~ 136 (140)
T PF05290_consen 76 LDPKLYECNICKETSAEERFLK----------PNEC--CGYSICNACYANLWKFCNLYP-----VCPVCKTSFKSSSS 136 (140)
T ss_pred cCCCceeccCcccccchhhcCC----------cccc--cchHHHHHHHHHHHHHcccCC-----CCCccccccccccc
Confidence 3557899999998766554443 3333 221111111234666665443 79999999987643
No 114
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.20 E-value=12 Score=29.82 Aligned_cols=14 Identities=7% Similarity=0.131 Sum_probs=11.1
Q ss_pred CCccccCCcCcccC
Q 044606 332 KKVHECPVCFRVFS 345 (413)
Q Consensus 332 ~kp~~C~~C~k~F~ 345 (413)
..|-.|++||++|.
T Consensus 24 rdPiVsPytG~s~P 37 (129)
T COG4530 24 RDPIVSPYTGKSYP 37 (129)
T ss_pred CCccccCcccccch
Confidence 46888888988884
No 115
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=46.02 E-value=9.7 Score=35.16 Aligned_cols=20 Identities=20% Similarity=0.426 Sum_probs=9.1
Q ss_pred CccccCCcCcccCCchhhccc
Q 044606 333 KVHECPVCFRVFSSGQALGGH 353 (413)
Q Consensus 333 kp~~C~~C~k~F~~~~~L~~H 353 (413)
.-|.|--|++.|.+ .....|
T Consensus 28 ~~fSCIDC~k~F~~-~sYknH 47 (276)
T KOG2186|consen 28 AYFSCIDCGKTFER-VSYKNH 47 (276)
T ss_pred CeeEEeeccccccc-chhhhh
Confidence 34455555555544 333444
No 116
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=45.78 E-value=12 Score=31.82 Aligned_cols=41 Identities=10% Similarity=0.117 Sum_probs=26.0
Q ss_pred cCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccC
Q 044606 299 HKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFS 345 (413)
Q Consensus 299 H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~ 345 (413)
-.+..-|.|+.|+..|.+.....+. . . ..-|.|+.||....
T Consensus 94 e~~~~~Y~Cp~C~~~y~~~ea~~~~-d----~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 94 ETNNAYYKCPNCQSKYTFLEANQLL-D----M-DGTFTCPRCGEELE 134 (147)
T ss_pred ccCCcEEECcCCCCEeeHHHHHHhc-C----C-CCcEECCCCCCEEE
Confidence 3445679999999988643322211 1 1 23499999998653
No 117
>PHA00626 hypothetical protein
Probab=45.32 E-value=9.7 Score=26.52 Aligned_cols=18 Identities=22% Similarity=0.124 Sum_probs=15.4
Q ss_pred cccccccCcccccCCChh
Q 044606 37 VMEKHKCRLCFKNFSNGR 54 (413)
Q Consensus 37 ~~~~~~C~iC~K~F~~~~ 54 (413)
..+.|+|+.||-.|+...
T Consensus 20 ~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 20 WSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred cCcceEcCCCCCeechhh
Confidence 468999999999998754
No 118
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=44.63 E-value=11 Score=23.84 Aligned_cols=14 Identities=36% Similarity=0.781 Sum_probs=9.6
Q ss_pred CCccccCCcCcccC
Q 044606 332 KKVHECPVCFRVFS 345 (413)
Q Consensus 332 ~kp~~C~~C~k~F~ 345 (413)
.+..+|+.|+-.|.
T Consensus 23 ~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 23 GRKVRCPKCGHVFR 36 (37)
T ss_pred CcEEECCCCCcEee
Confidence 44677888877764
No 119
>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=44.20 E-value=5.7 Score=38.04 Aligned_cols=36 Identities=11% Similarity=0.089 Sum_probs=14.7
Q ss_pred cccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccc
Q 044606 277 YKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQ 315 (413)
Q Consensus 277 ~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~ 315 (413)
-.|++||.. ...+.|..-.. .|.|-..|..|+..+.
T Consensus 173 g~CPvCGs~-P~~s~l~~~~~--~G~R~L~Cs~C~t~W~ 208 (290)
T PF04216_consen 173 GYCPVCGSP-PVLSVLRGGER--EGKRYLHCSLCGTEWR 208 (290)
T ss_dssp SS-TTT----EEEEEEE--------EEEEEETTT--EEE
T ss_pred CcCCCCCCc-CceEEEecCCC--CccEEEEcCCCCCeee
Confidence 589999953 22222222211 3667777888876663
No 120
>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=43.99 E-value=10 Score=31.26 Aligned_cols=15 Identities=20% Similarity=0.184 Sum_probs=12.4
Q ss_pred ccccccCcccccCCC
Q 044606 38 MEKHKCRLCFKNFSN 52 (413)
Q Consensus 38 ~~~~~C~iC~K~F~~ 52 (413)
..|+.|+-||++|--
T Consensus 7 GtKr~Cp~cg~kFYD 21 (129)
T TIGR02300 7 GTKRICPNTGSKFYD 21 (129)
T ss_pred CccccCCCcCccccc
Confidence 468899999999954
No 121
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=43.73 E-value=18 Score=34.82 Aligned_cols=39 Identities=5% Similarity=0.054 Sum_probs=24.3
Q ss_pred CCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccc
Q 044606 274 RGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQ 315 (413)
Q Consensus 274 ~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~ 315 (413)
.....|++||..=. .+ + .+.....|.+-..|..|+..+.
T Consensus 185 ~~~~~CPvCGs~P~-~s-~-v~~~~~~G~RyL~CslC~teW~ 223 (309)
T PRK03564 185 EQRQFCPVCGSMPV-SS-V-VQIGTTQGLRYLHCNLCESEWH 223 (309)
T ss_pred cCCCCCCCCCCcch-hh-e-eeccCCCCceEEEcCCCCCccc
Confidence 34578999996422 12 1 2334456777788888876653
No 122
>COG1773 Rubredoxin [Energy production and conversion]
Probab=43.56 E-value=8.9 Score=26.74 Aligned_cols=13 Identities=23% Similarity=0.777 Sum_probs=8.8
Q ss_pred ccccccCcccccC
Q 044606 38 MEKHKCRLCFKNF 50 (413)
Q Consensus 38 ~~~~~C~iC~K~F 50 (413)
|.+|+|.+||-.|
T Consensus 1 m~~~~C~~CG~vY 13 (55)
T COG1773 1 MKRWRCSVCGYVY 13 (55)
T ss_pred CCceEecCCceEe
Confidence 4567777777665
No 123
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=42.55 E-value=21 Score=31.54 Aligned_cols=45 Identities=11% Similarity=0.110 Sum_probs=31.4
Q ss_pred hhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCC
Q 044606 291 ALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSS 346 (413)
Q Consensus 291 ~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~ 346 (413)
.|+.-+..-....-|.|+.|+..|++.... +.-|.|+.||-....
T Consensus 104 klk~~l~~e~~~~~Y~Cp~C~~rytf~eA~-----------~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 104 KLKEQLEEEENNMFFFCPNCHIRFTFDEAM-----------EYGFRCPQCGEMLEE 148 (178)
T ss_pred HHHHHhhhccCCCEEECCCCCcEEeHHHHh-----------hcCCcCCCCCCCCee
Confidence 444444455566789999999988755433 347999999976543
No 124
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=41.96 E-value=14 Score=37.51 Aligned_cols=25 Identities=32% Similarity=0.542 Sum_probs=22.5
Q ss_pred ccCcccccCCChhhhhhHHHh-hcCC
Q 044606 42 KCRLCFKNFSNGRALGGHMRS-HMLN 66 (413)
Q Consensus 42 ~C~iC~K~F~~~~~L~~HmR~-Htg~ 66 (413)
.|++|.++|.....+..||.. |.+.
T Consensus 59 iCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 59 ICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eCCcccceeCCHHHHHHHHHHhhhhh
Confidence 399999999999999999995 8873
No 125
>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=41.84 E-value=8.6 Score=26.59 Aligned_cols=14 Identities=21% Similarity=0.536 Sum_probs=8.0
Q ss_pred ccCcccccCCChhh
Q 044606 42 KCRLCFKNFSNGRA 55 (413)
Q Consensus 42 ~C~iC~K~F~~~~~ 55 (413)
.||+|++.|.....
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 89999999986554
No 126
>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=41.78 E-value=15 Score=26.61 Aligned_cols=13 Identities=38% Similarity=0.772 Sum_probs=4.5
Q ss_pred CccccCCcCcccC
Q 044606 333 KVHECPVCFRVFS 345 (413)
Q Consensus 333 kp~~C~~C~k~F~ 345 (413)
+.|.|..||+.|=
T Consensus 24 rrhhCr~CG~~vC 36 (69)
T PF01363_consen 24 RRHHCRNCGRVVC 36 (69)
T ss_dssp -EEE-TTT--EEE
T ss_pred eeEccCCCCCEEC
Confidence 3445555555543
No 127
>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=41.62 E-value=22 Score=33.01 Aligned_cols=88 Identities=19% Similarity=0.217 Sum_probs=52.3
Q ss_pred CCCCccccCCccccccChhhhhhhhhhc--CCCcccCCCCCCccccc--------ccchhhhhhcCCCCCCCccccCCcC
Q 044606 272 RSRGKYKCETCKKVFKSYQALGGHRASH--KKIKFYTPVQETELDQE--------NAGASINLASPPLSVKKVHECPVCF 341 (413)
Q Consensus 272 ~~~~~~~C~~C~k~F~~~~~L~~H~~~H--~~~kp~~C~~C~~~f~~--------~~~~~l~~h~~~h~g~kp~~C~~C~ 341 (413)
.+-+.|+|.+|.. |.-...-..|+.+- .....|+|..|.+.-.. .-.....+..-.....+++.|+.||
T Consensus 138 hGGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg 216 (314)
T PF06524_consen 138 HGGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCG 216 (314)
T ss_pred CCCeEEEeecCCC-eeeccchhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCCC
Confidence 3567899999986 44444445676543 22345777666543210 0111111111112335799999999
Q ss_pred cccCCchhhcccccccccC
Q 044606 342 RVFSSGQALGGHKRTHVTG 360 (413)
Q Consensus 342 k~F~~~~~L~~H~r~H~~~ 360 (413)
.-......|..-.|+|.=+
T Consensus 217 ~et~eTkdLSmStR~hkyG 235 (314)
T PF06524_consen 217 YETQETKDLSMSTRSHKYG 235 (314)
T ss_pred Ccccccccceeeeecchhc
Confidence 9988888888888887633
No 128
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=40.73 E-value=12 Score=26.06 Aligned_cols=17 Identities=24% Similarity=0.430 Sum_probs=12.3
Q ss_pred cccccc-cCcccccCCCh
Q 044606 37 VMEKHK-CRLCFKNFSNG 53 (413)
Q Consensus 37 ~~~~~~-C~iC~K~F~~~ 53 (413)
+..+|. ||+|++.|-..
T Consensus 35 ~~~rYngCPfC~~~~~~~ 52 (55)
T PF14447_consen 35 PGERYNGCPFCGTPFEFD 52 (55)
T ss_pred ChhhccCCCCCCCcccCC
Confidence 344454 99999999654
No 129
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.69 E-value=19 Score=23.84 Aligned_cols=11 Identities=27% Similarity=0.776 Sum_probs=5.6
Q ss_pred cccCCcccccc
Q 044606 277 YKCETCKKVFK 287 (413)
Q Consensus 277 ~~C~~C~k~F~ 287 (413)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 45555555443
No 130
>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=39.95 E-value=13 Score=28.82 Aligned_cols=12 Identities=33% Similarity=0.622 Sum_probs=8.1
Q ss_pred ccccccCccccc
Q 044606 38 MEKHKCRLCFKN 49 (413)
Q Consensus 38 ~~~~~C~iC~K~ 49 (413)
-++|.|++|||.
T Consensus 33 ~~ky~Cp~Cgk~ 44 (90)
T PF01780_consen 33 HAKYTCPFCGKT 44 (90)
T ss_dssp HS-BEESSSSSS
T ss_pred hCCCcCCCCCCc
Confidence 456778888874
No 131
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=39.23 E-value=14 Score=30.63 Aligned_cols=15 Identities=33% Similarity=0.859 Sum_probs=13.7
Q ss_pred ccccCcccccCCChh
Q 044606 40 KHKCRLCFKNFSNGR 54 (413)
Q Consensus 40 ~~~C~iC~K~F~~~~ 54 (413)
+|+|.-||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 699999999999876
No 132
>PRK01343 zinc-binding protein; Provisional
Probab=38.85 E-value=16 Score=25.77 Aligned_cols=14 Identities=21% Similarity=0.358 Sum_probs=11.2
Q ss_pred cccccCcccccCCC
Q 044606 39 EKHKCRLCFKNFSN 52 (413)
Q Consensus 39 ~~~~C~iC~K~F~~ 52 (413)
....|++|+|.|.+
T Consensus 8 p~~~CP~C~k~~~~ 21 (57)
T PRK01343 8 PTRPCPECGKPSTR 21 (57)
T ss_pred CCCcCCCCCCcCcC
Confidence 34679999999864
No 133
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=37.88 E-value=18 Score=22.74 Aligned_cols=12 Identities=33% Similarity=0.747 Sum_probs=8.6
Q ss_pred CccccCCcCccc
Q 044606 333 KVHECPVCFRVF 344 (413)
Q Consensus 333 kp~~C~~C~k~F 344 (413)
+..+|+.|+..|
T Consensus 24 ~~v~C~~C~~~f 35 (36)
T PF13717_consen 24 RKVRCSKCGHVF 35 (36)
T ss_pred cEEECCCCCCEe
Confidence 456788887776
No 134
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.65 E-value=16 Score=31.99 Aligned_cols=55 Identities=20% Similarity=0.396 Sum_probs=31.0
Q ss_pred CCCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCch
Q 044606 272 RSRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQ 348 (413)
Q Consensus 272 ~~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~ 348 (413)
..+..|+|++|--.|..+.- .-..||..|-......+ . .+..+|++|+|....+.
T Consensus 127 ~~~~~~~CPiCl~~~sek~~--------------vsTkCGHvFC~~Cik~a---l-----k~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVP--------------VSTKCGHVFCSQCIKDA---L-----KNTNKCPTCRKKITHKQ 181 (187)
T ss_pred ccccccCCCceecchhhccc--------------cccccchhHHHHHHHHH---H-----HhCCCCCCcccccchhh
Confidence 34556999999877654432 22346655531111111 1 34679999998554443
No 135
>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=37.45 E-value=27 Score=21.46 Aligned_cols=9 Identities=33% Similarity=0.759 Sum_probs=4.4
Q ss_pred ccccCCcCc
Q 044606 334 VHECPVCFR 342 (413)
Q Consensus 334 p~~C~~C~k 342 (413)
+-.|+.||.
T Consensus 17 ~irC~~CG~ 25 (32)
T PF03604_consen 17 PIRCPECGH 25 (32)
T ss_dssp TSSBSSSS-
T ss_pred cEECCcCCC
Confidence 345666653
No 136
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=37.13 E-value=12 Score=22.29 Aligned_cols=19 Identities=32% Similarity=0.711 Sum_probs=12.9
Q ss_pred cccCcccccCCChhhhhhHH
Q 044606 41 HKCRLCFKNFSNGRALGGHM 60 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~~Hm 60 (413)
|.|--|++.| ....-+.|.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 5799999999 555555554
No 137
>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=37.08 E-value=11 Score=30.14 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=23.1
Q ss_pred ccc----CCcCcccCCchhhccccccccc
Q 044606 335 HEC----PVCFRVFSSGQALGGHKRTHVT 359 (413)
Q Consensus 335 ~~C----~~C~k~F~~~~~L~~H~r~H~~ 359 (413)
|.| ..|+..+.+...+.+|++.+++
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999998775
No 138
>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=36.35 E-value=11 Score=24.41 Aligned_cols=11 Identities=18% Similarity=0.549 Sum_probs=9.6
Q ss_pred ccccCcccccC
Q 044606 40 KHKCRLCFKNF 50 (413)
Q Consensus 40 ~~~C~iC~K~F 50 (413)
.-.|++|+.+|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 56899999988
No 139
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=36.17 E-value=17 Score=36.61 Aligned_cols=22 Identities=32% Similarity=0.596 Sum_probs=20.7
Q ss_pred cccCcccccCCChhhhhhHHHh
Q 044606 41 HKCRLCFKNFSNGRALGGHMRS 62 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~~HmR~ 62 (413)
+-|.+|.|+|.+.-.|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7799999999999999999877
No 140
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=35.94 E-value=29 Score=32.02 Aligned_cols=13 Identities=15% Similarity=0.920 Sum_probs=9.4
Q ss_pred CCccccCCccccc
Q 044606 274 RGKYKCETCKKVF 286 (413)
Q Consensus 274 ~~~~~C~~C~k~F 286 (413)
.+.|.|..|...+
T Consensus 110 drqFaC~~Cd~~W 122 (278)
T PF15135_consen 110 DRQFACSSCDHMW 122 (278)
T ss_pred ceeeeccccchHH
Confidence 4778888887554
No 141
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=35.93 E-value=12 Score=34.42 Aligned_cols=33 Identities=15% Similarity=0.196 Sum_probs=0.0
Q ss_pred cccccccCcccccCCChhhhhhHHHhhcCCCCCC
Q 044606 37 VMEKHKCRLCFKNFSNGRALGGHMRSHMLNLPIP 70 (413)
Q Consensus 37 ~~~~~~C~iC~K~F~~~~~L~~HmR~Htg~~p~~ 70 (413)
...-..|||||+..+ ..-|..|||+.....-|+
T Consensus 165 ~~~~~~cPitGe~IP-~~e~~eHmRi~LlDP~wk 197 (229)
T PF12230_consen 165 KEKMIICPITGEMIP-ADEMDEHMRIELLDPRWK 197 (229)
T ss_dssp ----------------------------------
T ss_pred ccccccccccccccc-cccccccccccccccccc
Confidence 455578999999887 467999999999966563
No 142
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=35.68 E-value=17 Score=23.41 Aligned_cols=14 Identities=36% Similarity=0.645 Sum_probs=12.1
Q ss_pred ccccCcccccCCCh
Q 044606 40 KHKCRLCFKNFSNG 53 (413)
Q Consensus 40 ~~~C~iC~K~F~~~ 53 (413)
+++|..|++.|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999999654
No 143
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=35.53 E-value=23 Score=27.32 Aligned_cols=13 Identities=23% Similarity=0.682 Sum_probs=7.4
Q ss_pred CccccCCcccccc
Q 044606 275 GKYKCETCKKVFK 287 (413)
Q Consensus 275 ~~~~C~~C~k~F~ 287 (413)
+|-.|..||..|.
T Consensus 57 ~Pa~CkkCGfef~ 69 (97)
T COG3357 57 RPARCKKCGFEFR 69 (97)
T ss_pred cChhhcccCcccc
Confidence 4555666665554
No 144
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=35.52 E-value=17 Score=29.69 Aligned_cols=29 Identities=24% Similarity=0.432 Sum_probs=26.0
Q ss_pred cccccccCcccccCCChhhhhhHHHh--hcC
Q 044606 37 VMEKHKCRLCFKNFSNGRALGGHMRS--HML 65 (413)
Q Consensus 37 ~~~~~~C~iC~K~F~~~~~L~~HmR~--Htg 65 (413)
++-+|-|-.|.|-|.+..+|+.|.|+ |-.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK~HKr 84 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTKVHKR 84 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhccHHHH
Confidence 67889999999999999999999997 544
No 145
>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=35.50 E-value=21 Score=22.80 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=9.8
Q ss_pred ccccccCcccccCCChhh-h-hhHHH
Q 044606 38 MEKHKCRLCFKNFSNGRA-L-GGHMR 61 (413)
Q Consensus 38 ~~~~~C~iC~K~F~~~~~-L-~~HmR 61 (413)
|.+|=|.+|.+-|++.+. - +.|.+
T Consensus 1 m~ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp --S-B-TTT--B-S--SHHHHHHHT-
T ss_pred CcCeecccccceecCCChHHHHHhhc
Confidence 678999999999966653 3 45544
No 146
>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=34.34 E-value=18 Score=20.73 Aligned_cols=11 Identities=18% Similarity=0.205 Sum_probs=9.0
Q ss_pred ccccccCcccc
Q 044606 38 MEKHKCRLCFK 48 (413)
Q Consensus 38 ~~~~~C~iC~K 48 (413)
.-.|.||-||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45799999985
No 147
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=34.27 E-value=20 Score=24.44 Aligned_cols=11 Identities=36% Similarity=1.053 Sum_probs=7.2
Q ss_pred ccccCCccccc
Q 044606 276 KYKCETCKKVF 286 (413)
Q Consensus 276 ~~~C~~C~k~F 286 (413)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 46676777666
No 148
>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=34.26 E-value=18 Score=28.01 Aligned_cols=12 Identities=33% Similarity=0.578 Sum_probs=8.9
Q ss_pred ccccccCccccc
Q 044606 38 MEKHKCRLCFKN 49 (413)
Q Consensus 38 ~~~~~C~iC~K~ 49 (413)
-++|.|++|+|.
T Consensus 33 ~a~y~CpfCgk~ 44 (91)
T TIGR00280 33 KAKYVCPFCGKK 44 (91)
T ss_pred hcCccCCCCCCC
Confidence 456889999763
No 149
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=33.87 E-value=27 Score=23.98 Aligned_cols=14 Identities=43% Similarity=0.925 Sum_probs=8.1
Q ss_pred CccccCCcCcccCC
Q 044606 333 KVHECPVCFRVFSS 346 (413)
Q Consensus 333 kp~~C~~C~k~F~~ 346 (413)
+.+.|..||+.|-.
T Consensus 17 rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 17 RRHHCRNCGRIFCS 30 (57)
T ss_pred cccccCcCcCCcCh
Confidence 44566666666554
No 150
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=33.53 E-value=19 Score=27.91 Aligned_cols=11 Identities=36% Similarity=0.561 Sum_probs=8.5
Q ss_pred ccccccCcccc
Q 044606 38 MEKHKCRLCFK 48 (413)
Q Consensus 38 ~~~~~C~iC~K 48 (413)
-.+|.|++|+|
T Consensus 34 ~a~y~CpfCgk 44 (90)
T PTZ00255 34 HAKYFCPFCGK 44 (90)
T ss_pred hCCccCCCCCC
Confidence 45688999976
No 151
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=33.52 E-value=22 Score=22.40 Aligned_cols=16 Identities=25% Similarity=0.351 Sum_probs=10.5
Q ss_pred cccCcccccCCChhhh
Q 044606 41 HKCRLCFKNFSNGRAL 56 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L 56 (413)
-.|+-|+|.|-+++.-
T Consensus 3 ~~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 3 GLCPRCGKGFHWASEC 18 (36)
T ss_dssp -C-TTTSSSCS-TTT-
T ss_pred ccCcccCCCcchhhhh
Confidence 3599999999998765
No 152
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.48 E-value=15 Score=26.15 Aligned_cols=11 Identities=18% Similarity=0.603 Sum_probs=9.4
Q ss_pred ccCcccccCCC
Q 044606 42 KCRLCFKNFSN 52 (413)
Q Consensus 42 ~C~iC~K~F~~ 52 (413)
.|++|+++|.-
T Consensus 50 ~CPYC~t~y~l 60 (62)
T COG4391 50 VCPYCSTRYRL 60 (62)
T ss_pred ecCccccEEEe
Confidence 49999999964
No 153
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=33.42 E-value=14 Score=36.18 Aligned_cols=79 Identities=20% Similarity=0.302 Sum_probs=45.7
Q ss_pred ccccCCccccccChhhhhhhhhh--cCC---CcccCCCCCCcccccccchhhhhh----cCCCCCCCccccCCcCcccCC
Q 044606 276 KYKCETCKKVFKSYQALGGHRAS--HKK---IKFYTPVQETELDQENAGASINLA----SPPLSVKKVHECPVCFRVFSS 346 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~--H~~---~kp~~C~~C~~~f~~~~~~~l~~h----~~~h~g~kp~~C~~C~k~F~~ 346 (413)
-|.|.-|...|.....-+.|+++ |.- .+.+.- -+..+..+....+-.. ...-.+.-++.|.+|.|.|..
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~l--PPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s 80 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASL--PPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFAS 80 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcC--CCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccC
Confidence 48999999999999888888874 431 111111 1111110010000000 001223557999999999999
Q ss_pred chhhcccccc
Q 044606 347 GQALGGHKRT 356 (413)
Q Consensus 347 ~~~L~~H~r~ 356 (413)
..+-..|+..
T Consensus 81 ~~a~~~hl~S 90 (390)
T KOG2785|consen 81 PKAHENHLKS 90 (390)
T ss_pred hhhHHHHHHH
Confidence 8888888653
No 154
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=33.23 E-value=21 Score=28.19 Aligned_cols=17 Identities=29% Similarity=0.679 Sum_probs=14.5
Q ss_pred ccccCcccccCCChhhh
Q 044606 40 KHKCRLCFKNFSNGRAL 56 (413)
Q Consensus 40 ~~~C~iC~K~F~~~~~L 56 (413)
+|.|.-||..|...+.+
T Consensus 2 pH~CtrCG~vf~~g~~~ 18 (112)
T COG3364 2 PHQCTRCGEVFDDGSEE 18 (112)
T ss_pred CceecccccccccccHH
Confidence 69999999999997543
No 155
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.67 E-value=15 Score=24.63 Aligned_cols=17 Identities=24% Similarity=0.556 Sum_probs=13.5
Q ss_pred cccCcccccCCChhhhh
Q 044606 41 HKCRLCFKNFSNGRALG 57 (413)
Q Consensus 41 ~~C~iC~K~F~~~~~L~ 57 (413)
--|++|++-|++..--+
T Consensus 13 KICpvCqRPFsWRkKW~ 29 (54)
T COG4338 13 KICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhhcCchHHHHHHH
Confidence 35999999999876544
No 156
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=32.03 E-value=22 Score=29.51 Aligned_cols=11 Identities=0% Similarity=-0.421 Sum_probs=7.6
Q ss_pred ccCCCCCCccc
Q 044606 304 FYTPVQETELD 314 (413)
Q Consensus 304 p~~C~~C~~~f 314 (413)
|++|..|++.|
T Consensus 1 PH~Ct~Cg~~f 11 (131)
T PF09845_consen 1 PHQCTKCGRVF 11 (131)
T ss_pred CcccCcCCCCc
Confidence 56677777766
No 157
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=31.84 E-value=21 Score=27.68 Aligned_cols=12 Identities=33% Similarity=0.731 Sum_probs=8.6
Q ss_pred ccccccCccccc
Q 044606 38 MEKHKCRLCFKN 49 (413)
Q Consensus 38 ~~~~~C~iC~K~ 49 (413)
-++|.|++|+|.
T Consensus 34 ~a~y~CpfCgk~ 45 (90)
T PRK03976 34 RAKHVCPVCGRP 45 (90)
T ss_pred hcCccCCCCCCC
Confidence 456889998763
No 158
>PRK12496 hypothetical protein; Provisional
Probab=30.97 E-value=27 Score=30.40 Aligned_cols=11 Identities=0% Similarity=-0.532 Sum_probs=8.8
Q ss_pred ccCCCCCCccc
Q 044606 304 FYTPVQETELD 314 (413)
Q Consensus 304 p~~C~~C~~~f 314 (413)
-|.|..|++.|
T Consensus 127 ~~~C~gC~~~~ 137 (164)
T PRK12496 127 RKVCKGCKKKY 137 (164)
T ss_pred eEECCCCCccc
Confidence 47788888877
No 159
>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 COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.54 E-value=29 Score=28.86 Aligned_cols=13 Identities=8% Similarity=-0.205 Sum_probs=6.3
Q ss_pred cccCCCCCCcccc
Q 044606 303 KFYTPVQETELDQ 315 (413)
Q Consensus 303 kp~~C~~C~~~f~ 315 (413)
.-|+|..|++.|.
T Consensus 52 qRyrC~~C~~tf~ 64 (129)
T COG3677 52 QRYKCKSCGSTFT 64 (129)
T ss_pred cccccCCcCccee
Confidence 3455555555543
No 161
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=30.49 E-value=31 Score=34.17 Aligned_cols=85 Identities=18% Similarity=0.188 Sum_probs=53.6
Q ss_pred cccC--CccccccChhhhhhhhhhcCCCc-------ccCCCCCCcccccccchhhhhhcCCCCCCC--------------
Q 044606 277 YKCE--TCKKVFKSYQALGGHRASHKKIK-------FYTPVQETELDQENAGASINLASPPLSVKK-------------- 333 (413)
Q Consensus 277 ~~C~--~C~k~F~~~~~L~~H~~~H~~~k-------p~~C~~C~~~f~~~~~~~l~~h~~~h~g~k-------------- 333 (413)
|.|. .|.| +.+++..|...|+... -|.|.-|++.+++.-...-..|.+-+.++.
T Consensus 314 yhC~~~~C~k---sTsdV~~h~nFht~~~n~GfrrthfhC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay 390 (480)
T KOG4377|consen 314 YHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRTHFHCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAY 390 (480)
T ss_pred chhhhcccCc---ccccccccCccccccccCceecceeEEeccCCccccccccccccccCcchhhhhhhhhhhccccCCc
Confidence 6776 4888 5677888888886532 367888887776553332233333333221
Q ss_pred ----------ccccC--CcCcccCCchhhcccccccccCCCCC
Q 044606 334 ----------VHECP--VCFRVFSSGQALGGHKRTHVTGLVAS 364 (413)
Q Consensus 334 ----------p~~C~--~C~k~F~~~~~L~~H~r~H~~~~~~~ 364 (413)
.|.|. -|+.+|...+.+..|.|.|....++.
T Consensus 391 ~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~shkrkheRqeqge 433 (480)
T KOG4377|consen 391 TGCKYSGICNHFHCDRLGCEATLYSVSQMASHKRKHERQEQGE 433 (480)
T ss_pred cCcccccceeeeeecccCCceEEEehhhhhhhhhhhhhhhhcc
Confidence 12232 27889999999999999987654443
No 162
>PRK04023 DNA polymerase II large subunit; Validated
Probab=30.04 E-value=36 Score=37.87 Aligned_cols=11 Identities=45% Similarity=1.056 Sum_probs=8.0
Q ss_pred CccccCCcccc
Q 044606 275 GKYKCETCKKV 285 (413)
Q Consensus 275 ~~~~C~~C~k~ 285 (413)
....|..||..
T Consensus 625 g~RfCpsCG~~ 635 (1121)
T PRK04023 625 GRRKCPSCGKE 635 (1121)
T ss_pred cCccCCCCCCc
Confidence 45678888876
No 163
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=29.43 E-value=24 Score=29.40 Aligned_cols=25 Identities=32% Similarity=0.336 Sum_probs=21.0
Q ss_pred cccCCccccccChhhhhhhhhhcCCCcc
Q 044606 277 YKCETCKKVFKSYQALGGHRASHKKIKF 304 (413)
Q Consensus 277 ~~C~~C~k~F~~~~~L~~H~~~H~~~kp 304 (413)
..|-.|||.|.+ |++|+.+|-|--|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 579999999964 9999999988544
No 164
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.40 E-value=28 Score=29.21 Aligned_cols=16 Identities=19% Similarity=0.493 Sum_probs=12.2
Q ss_pred CCccccCCccccccCh
Q 044606 274 RGKYKCETCKKVFKSY 289 (413)
Q Consensus 274 ~~~~~C~~C~k~F~~~ 289 (413)
...+.|..||..|...
T Consensus 68 p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK 83 (135)
T ss_pred ceEEECCCCCCEEecc
Confidence 3568999999888654
No 165
>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=29.13 E-value=39 Score=28.80 Aligned_cols=9 Identities=33% Similarity=0.907 Sum_probs=5.6
Q ss_pred ccccCCcCc
Q 044606 334 VHECPVCFR 342 (413)
Q Consensus 334 p~~C~~C~k 342 (413)
.-.|+.||.
T Consensus 130 l~~Cp~C~~ 138 (146)
T PF07295_consen 130 LPPCPKCGH 138 (146)
T ss_pred CCCCCCCCC
Confidence 346777764
No 166
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=28.79 E-value=23 Score=35.47 Aligned_cols=32 Identities=28% Similarity=0.500 Sum_probs=26.5
Q ss_pred ccccccccccCcccccCCChhhhhhHHHh-hcC
Q 044606 34 SLFVMEKHKCRLCFKNFSNGRALGGHMRS-HML 65 (413)
Q Consensus 34 ~~~~~~~~~C~iC~K~F~~~~~L~~HmR~-Htg 65 (413)
+....+=|.||||.+.|.+-..|.-|.-. |.+
T Consensus 9 s~~i~egflCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 9 SGEILEGFLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred cchhhhcccCchHhhhhhhHHHHHHHHhhhccc
Confidence 34456778999999999999999999966 554
No 167
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=28.06 E-value=24 Score=36.68 Aligned_cols=29 Identities=17% Similarity=0.300 Sum_probs=24.9
Q ss_pred CCCccccCCcCcccCCchhhccccccccc
Q 044606 331 VKKVHECPVCFRVFSSGQALGGHKRTHVT 359 (413)
Q Consensus 331 g~kp~~C~~C~k~F~~~~~L~~H~r~H~~ 359 (413)
..+|..|..||++|.......+||-+|..
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhh
Confidence 35689999999999999999998888763
No 168
>PHA02446 hypothetical protein
Probab=27.58 E-value=35 Score=27.57 Aligned_cols=45 Identities=27% Similarity=0.428 Sum_probs=30.8
Q ss_pred cCCCCCCCCccchhhheeeeeeEEeeccccccccccccccCccccc
Q 044606 4 LSHRKEKPPELTTFKLLFIIYVYVFFKKRKSLFVMEKHKCRLCFKN 49 (413)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~iC~K~ 49 (413)
|-.|.-|-|++.+-++-||+ +.-+-..+.-....+.-+|++||..
T Consensus 27 lvrrrp~lpevelarr~~ct-vrtierdra~lp~a~~q~cp~cg~d 71 (166)
T PHA02446 27 LVRRRPNLPEVELARRSFCT-VRTIERDRADLPDAEQQQCPLCGQD 71 (166)
T ss_pred HHhcCCCCchhHHhhhccce-eEeeecccccCchhhhhcCCCcccc
Confidence 44577788999988877765 3333344444556777889999973
No 169
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=27.05 E-value=13 Score=33.92 Aligned_cols=28 Identities=18% Similarity=0.432 Sum_probs=19.0
Q ss_pred CCccccCCcCcccCCchhhccccccccc
Q 044606 332 KKVHECPVCFRVFSSGQALGGHKRTHVT 359 (413)
Q Consensus 332 ~kp~~C~~C~k~F~~~~~L~~H~r~H~~ 359 (413)
+..|.|++|+|.|.-..-..+|+..-|.
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 4458888888888888888888775543
No 170
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=27.03 E-value=21 Score=27.01 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=9.3
Q ss_pred ccccccCccccc
Q 044606 38 MEKHKCRLCFKN 49 (413)
Q Consensus 38 ~~~~~C~iC~K~ 49 (413)
-.+|.|.+|||.
T Consensus 34 haky~CsfCGK~ 45 (92)
T KOG0402|consen 34 HAKYTCSFCGKK 45 (92)
T ss_pred hhhhhhhhcchh
Confidence 346889999984
No 171
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=26.62 E-value=25 Score=34.02 Aligned_cols=75 Identities=16% Similarity=0.071 Sum_probs=48.9
Q ss_pred cccCCccccccChhhhhhhhhhcCCCcccCCCCCCccc-----ccccchhhhhhcCCCCCCCccccCC--c--C--cccC
Q 044606 277 YKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELD-----QENAGASINLASPPLSVKKVHECPV--C--F--RVFS 345 (413)
Q Consensus 277 ~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f-----~~~~~~~l~~h~~~h~g~kp~~C~~--C--~--k~F~ 345 (413)
-.|..|.+.|.....|.+|+|... ++ |-+|.+.- .+..-..|..|-+ .-.|.|.+ | | ..|.
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~H-E~---ChICD~v~p~~~QYFK~Y~~Le~HF~----~~hy~ct~qtc~~~k~~vf~ 292 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRH-EA---CHICDMVGPIRYQYFKSYEDLEAHFR----NAHYCCTFQTCRVGKCYVFP 292 (493)
T ss_pred chhhhccceecChHHHHHHHHhhh-hh---hhhhhccCccchhhhhCHHHHHHHhh----cCceEEEEEEEecCcEEEec
Confidence 469999999999999999988644 34 44554332 1233344666654 33567754 4 3 3788
Q ss_pred Cchhhccccccccc
Q 044606 346 SGQALGGHKRTHVT 359 (413)
Q Consensus 346 ~~~~L~~H~r~H~~ 359 (413)
....|..|+-.-++
T Consensus 293 ~~~el~~h~~~~h~ 306 (493)
T COG5236 293 YHTELLEHLTRFHK 306 (493)
T ss_pred cHHHHHHHHHHHhh
Confidence 88889999754443
No 172
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.35 E-value=12 Score=33.54 Aligned_cols=21 Identities=29% Similarity=0.581 Sum_probs=16.8
Q ss_pred cccCCccccccChhhhhhhhh
Q 044606 277 YKCETCKKVFKSYQALGGHRA 297 (413)
Q Consensus 277 ~~C~~C~k~F~~~~~L~~H~~ 297 (413)
..|.+|.+.|.+...|..|+.
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~ 127 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHIL 127 (253)
T ss_pred chhHHHHHhCCchhhhhHHHH
Confidence 478888888888888888864
No 173
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=26.26 E-value=51 Score=31.80 Aligned_cols=37 Identities=5% Similarity=0.064 Sum_probs=21.2
Q ss_pred ccccCCccccccChhhhhhhhhhcCCCcccCCCCCCccc
Q 044606 276 KYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELD 314 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f 314 (413)
...|++||..= ..+ +.+.-....|.|-..|..|+..+
T Consensus 184 ~~~CPvCGs~P-~~s-~~~~~~~~~G~RyL~CslC~teW 220 (305)
T TIGR01562 184 RTLCPACGSPP-VAS-MVRQGGKETGLRYLSCSLCATEW 220 (305)
T ss_pred CCcCCCCCChh-hhh-hhcccCCCCCceEEEcCCCCCcc
Confidence 45899999642 111 11111125667777888887665
No 174
>PTZ00448 hypothetical protein; Provisional
Probab=26.20 E-value=49 Score=32.51 Aligned_cols=24 Identities=29% Similarity=0.463 Sum_probs=22.0
Q ss_pred cccccCcccccCCChhhhhhHHHh
Q 044606 39 EKHKCRLCFKNFSNGRALGGHMRS 62 (413)
Q Consensus 39 ~~~~C~iC~K~F~~~~~L~~HmR~ 62 (413)
-.|+|..|+-.|.+...-+.|||+
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CCccccccccccCCHHHHHHHhhh
Confidence 368999999999999999999998
No 175
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=26.14 E-value=37 Score=28.82 Aligned_cols=21 Identities=19% Similarity=0.550 Sum_probs=16.2
Q ss_pred CCccccCCcCcccCCchhhcc
Q 044606 332 KKVHECPVCFRVFSSGQALGG 352 (413)
Q Consensus 332 ~kp~~C~~C~k~F~~~~~L~~ 352 (413)
+.-+.|+.|||.|-..++..+
T Consensus 122 ~~f~~C~~C~kiyW~GsH~~~ 142 (147)
T PF01927_consen 122 DEFWRCPGCGKIYWEGSHWRR 142 (147)
T ss_pred CeEEECCCCCCEecccccHHH
Confidence 346789999999988876654
No 176
>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=26.05 E-value=66 Score=21.26 Aligned_cols=10 Identities=20% Similarity=0.570 Sum_probs=5.3
Q ss_pred CccccCCcCc
Q 044606 333 KVHECPVCFR 342 (413)
Q Consensus 333 kp~~C~~C~k 342 (413)
..|+|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 3455555554
No 177
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=25.94 E-value=29 Score=24.26 Aligned_cols=13 Identities=31% Similarity=0.659 Sum_probs=6.0
Q ss_pred cccccccCccccc
Q 044606 37 VMEKHKCRLCFKN 49 (413)
Q Consensus 37 ~~~~~~C~iC~K~ 49 (413)
..++|.|++||-+
T Consensus 30 vLr~y~Cp~CgAt 42 (55)
T PF05741_consen 30 VLRKYVCPICGAT 42 (55)
T ss_dssp TGGG---TTT---
T ss_pred HHhcCcCCCCcCc
Confidence 5788999999975
No 178
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=25.76 E-value=20 Score=25.31 Aligned_cols=12 Identities=33% Similarity=0.553 Sum_probs=6.7
Q ss_pred cccCcccccCCC
Q 044606 41 HKCRLCFKNFSN 52 (413)
Q Consensus 41 ~~C~iC~K~F~~ 52 (413)
..||+|+|.+.+
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 579999998877
No 179
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=25.75 E-value=27 Score=34.20 Aligned_cols=56 Identities=16% Similarity=0.262 Sum_probs=25.4
Q ss_pred CccccCCccccccChhhh---hhhh-hhcCCC-cccCCCCCCcccccccchhhhhhcCCCCCCCc-cccCCcCcc
Q 044606 275 GKYKCETCKKVFKSYQAL---GGHR-ASHKKI-KFYTPVQETELDQENAGASINLASPPLSVKKV-HECPVCFRV 343 (413)
Q Consensus 275 ~~~~C~~C~k~F~~~~~L---~~H~-~~H~~~-kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp-~~C~~C~k~ 343 (413)
+-+.|.+|.+++...... ..|. ..|... +.|+|..|+....... .-| ..|..||-.
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~sl~-------------r~P~~~C~~Cg~~ 312 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTISLE-------------RLPKKHCSNCGSS 312 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEESS-------------SS--S--TTT-S-
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeeecc-------------cCCCCCCCcCCcC
Confidence 458899998776655543 3342 334444 5689999997654221 112 479889864
No 180
>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=25.67 E-value=22 Score=23.32 Aligned_cols=14 Identities=36% Similarity=0.631 Sum_probs=9.1
Q ss_pred cccccCcccccCCC
Q 044606 39 EKHKCRLCFKNFSN 52 (413)
Q Consensus 39 ~~~~C~iC~K~F~~ 52 (413)
-+++|+.|++.|=.
T Consensus 12 ~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 12 LPFKCKHCGKSFCL 25 (43)
T ss_dssp SHEE-TTTS-EE-T
T ss_pred CCeECCCCCcccCc
Confidence 47899999999854
No 181
>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=25.15 E-value=29 Score=27.38 Aligned_cols=20 Identities=30% Similarity=0.338 Sum_probs=13.9
Q ss_pred cCCCCCCCccccCCcCcccCC
Q 044606 326 SPPLSVKKVHECPVCFRVFSS 346 (413)
Q Consensus 326 ~~~h~g~kp~~C~~C~k~F~~ 346 (413)
+..+.| +|+.|..||..|.-
T Consensus 72 ~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 72 MWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEEeCC-CceeCCCCCcEEEE
Confidence 334455 68888889888753
No 182
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.13 E-value=29 Score=25.84 Aligned_cols=10 Identities=40% Similarity=1.215 Sum_probs=5.8
Q ss_pred cccCCccccc
Q 044606 277 YKCETCKKVF 286 (413)
Q Consensus 277 ~~C~~C~k~F 286 (413)
|+|..|+..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 5666666544
No 183
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=24.19 E-value=28 Score=37.21 Aligned_cols=24 Identities=21% Similarity=0.392 Sum_probs=20.4
Q ss_pred cccccccCcccccCCChhhhhhHH
Q 044606 37 VMEKHKCRLCFKNFSNGRALGGHM 60 (413)
Q Consensus 37 ~~~~~~C~iC~K~F~~~~~L~~Hm 60 (413)
..+.-+||.|+..|+-...+..||
T Consensus 675 etRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 675 ETRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred HHhcCCCCCCCCCCCcccccccCC
Confidence 566778999999999998887775
No 184
>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=23.90 E-value=49 Score=20.85 Aligned_cols=11 Identities=18% Similarity=0.295 Sum_probs=5.6
Q ss_pred cccCCcCcccC
Q 044606 335 HECPVCFRVFS 345 (413)
Q Consensus 335 ~~C~~C~k~F~ 345 (413)
-.|..||-.+.
T Consensus 22 ~~Cd~cg~~L~ 32 (36)
T PF05191_consen 22 GVCDNCGGELV 32 (36)
T ss_dssp TBCTTTTEBEB
T ss_pred CccCCCCCeeE
Confidence 45666654443
No 185
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=23.41 E-value=24 Score=34.63 Aligned_cols=71 Identities=24% Similarity=0.175 Sum_probs=46.8
Q ss_pred CCccccCCccccccChhhhhhhhhhcCCCc----ccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcC---cccCC
Q 044606 274 RGKYKCETCKKVFKSYQALGGHRASHKKIK----FYTPVQETELDQENAGASINLASPPLSVKKVHECPVCF---RVFSS 346 (413)
Q Consensus 274 ~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k----p~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~---k~F~~ 346 (413)
..|-.|-.|++.|.+-.....||..+.|-- -|--+.-| +--....++ ..-|.|-.|+ +.|.+
T Consensus 164 ~~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~G--------Ll~YLgeKV---~~~~~CL~CN~~~~~f~s 232 (390)
T KOG2785|consen 164 LIPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKG--------LLKYLGEKV---GIGFICLFCNELGRPFSS 232 (390)
T ss_pred cCCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhH--------HHHHHHHHh---ccCceEEEeccccCcccc
Confidence 345789999999999999999999888721 11111000 000011111 2357888888 99999
Q ss_pred chhhccccc
Q 044606 347 GQALGGHKR 355 (413)
Q Consensus 347 ~~~L~~H~r 355 (413)
..+.+.||+
T Consensus 233 leavr~HM~ 241 (390)
T KOG2785|consen 233 LEAVRAHMR 241 (390)
T ss_pred cHHHHHHHh
Confidence 999999986
No 186
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=23.34 E-value=38 Score=28.88 Aligned_cols=17 Identities=18% Similarity=0.178 Sum_probs=8.7
Q ss_pred hcCCCCCCCccccCCcCc
Q 044606 325 ASPPLSVKKVHECPVCFR 342 (413)
Q Consensus 325 h~~~h~g~kp~~C~~C~k 342 (413)
|-..-.|+ .|.|..|+-
T Consensus 132 hn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 132 HNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred cccccccc-eEEeccCCc
Confidence 33333444 666666653
No 187
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=22.93 E-value=21 Score=23.30 Aligned_cols=17 Identities=35% Similarity=0.550 Sum_probs=7.2
Q ss_pred cCcccccCCChhhhhhH
Q 044606 43 CRLCFKNFSNGRALGGH 59 (413)
Q Consensus 43 C~iC~K~F~~~~~L~~H 59 (413)
|.+|++.|.....|..|
T Consensus 1 C~~C~~~~~~~~~~~v~ 17 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVH 17 (47)
T ss_dssp -TTT--B--GG-GEEEE
T ss_pred CCCCCCcCccCcceEeE
Confidence 78899888877444433
No 188
>PF12907 zf-met2: Zinc-binding
Probab=22.91 E-value=19 Score=23.38 Aligned_cols=25 Identities=24% Similarity=0.498 Sum_probs=18.4
Q ss_pred cccCcccccCCCh---hhhhhHHHh-hcC
Q 044606 41 HKCRLCFKNFSNG---RALGGHMRS-HML 65 (413)
Q Consensus 41 ~~C~iC~K~F~~~---~~L~~HmR~-Htg 65 (413)
+.|.||--.|..- ..|.+|--. |..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK 30 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPK 30 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCC
Confidence 6899999777554 569988874 554
No 189
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=22.42 E-value=39 Score=27.63 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=23.9
Q ss_pred CCCCccccCCccccccChhhhhhhhhh
Q 044606 272 RSRGKYKCETCKKVFKSYQALGGHRAS 298 (413)
Q Consensus 272 ~~~~~~~C~~C~k~F~~~~~L~~H~~~ 298 (413)
.|-+.|-|-.|.+-|.....|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 366779999999999999999999775
No 190
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.36 E-value=53 Score=32.91 Aligned_cols=36 Identities=19% Similarity=0.324 Sum_probs=17.0
Q ss_pred CCCccccCCccccccChhhhhhhhhhcCCCcccCCCCCC
Q 044606 273 SRGKYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQET 311 (413)
Q Consensus 273 ~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~ 311 (413)
...-|.|+.|.+.|+....+. ..-...--|.|..|+
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCG 160 (436)
T ss_pred ccccccCCccccchhhhHHHH---hhcccCceEEEecCC
Confidence 344566666666655433332 222222345555554
No 191
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.90 E-value=70 Score=21.42 Aligned_cols=16 Identities=19% Similarity=0.079 Sum_probs=11.1
Q ss_pred ccccCCcCcccCCchh
Q 044606 334 VHECPVCFRVFSSGQA 349 (413)
Q Consensus 334 p~~C~~C~k~F~~~~~ 349 (413)
.|.|+.||..+.-...
T Consensus 20 ~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 20 RFVCRKCGYEEPIEQK 35 (52)
T ss_pred EEECCcCCCeEECCCc
Confidence 6778888877665444
No 192
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=21.86 E-value=47 Score=26.89 Aligned_cols=8 Identities=25% Similarity=0.609 Sum_probs=4.3
Q ss_pred ccccCCcc
Q 044606 276 KYKCETCK 283 (413)
Q Consensus 276 ~~~C~~C~ 283 (413)
.+.|..||
T Consensus 70 ~~~C~~Cg 77 (113)
T PRK12380 70 QAWCWDCS 77 (113)
T ss_pred EEEcccCC
Confidence 35555555
No 193
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.78 E-value=32 Score=22.19 Aligned_cols=12 Identities=17% Similarity=0.395 Sum_probs=7.9
Q ss_pred ccccCCcCcccC
Q 044606 334 VHECPVCFRVFS 345 (413)
Q Consensus 334 p~~C~~C~k~F~ 345 (413)
-|.|..|+..|.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 367777776654
No 194
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=21.78 E-value=31 Score=23.26 Aligned_cols=7 Identities=29% Similarity=1.132 Sum_probs=2.1
Q ss_pred cccCCcc
Q 044606 277 YKCETCK 283 (413)
Q Consensus 277 ~~C~~C~ 283 (413)
|.|++|+
T Consensus 35 w~CP~C~ 41 (47)
T PF00301_consen 35 WVCPVCG 41 (47)
T ss_dssp -B-TTTS
T ss_pred CcCcCCC
Confidence 3444443
No 195
>PF14369 zf-RING_3: zinc-finger
Probab=21.62 E-value=51 Score=20.64 Aligned_cols=30 Identities=17% Similarity=0.177 Sum_probs=16.5
Q ss_pred eeeeeeEEeeccccccccccccccCcccccCC
Q 044606 20 LFIIYVYVFFKKRKSLFVMEKHKCRLCFKNFS 51 (413)
Q Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~C~iC~K~F~ 51 (413)
++|.-..++|.-....... -.||.|+-.|-
T Consensus 3 ywCh~C~~~V~~~~~~~~~--~~CP~C~~gFv 32 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSD--VACPRCHGGFV 32 (35)
T ss_pred EeCccCCCEeEeCcCCCCC--cCCcCCCCcEe
Confidence 4444455555443322222 16999998884
No 196
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.33 E-value=71 Score=35.69 Aligned_cols=37 Identities=19% Similarity=0.219 Sum_probs=23.2
Q ss_pred ccccCCccccccChhhhhhhhhhcCCCcccCCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccC
Q 044606 276 KYKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFS 345 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~H~~~kp~~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~ 345 (413)
.+.|+.||.. ....|.|+.|+... .++.|+.||..-.
T Consensus 638 ~frCP~CG~~---------------Te~i~fCP~CG~~~------------------~~y~CPKCG~El~ 674 (1121)
T PRK04023 638 YRRCPFCGTH---------------TEPVYRCPRCGIEV------------------EEDECEKCGREPT 674 (1121)
T ss_pred cccCCCCCCC---------------CCcceeCccccCcC------------------CCCcCCCCCCCCC
Confidence 3677777764 23456777775442 2577888886443
No 197
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=21.24 E-value=48 Score=32.10 Aligned_cols=82 Identities=15% Similarity=0.216 Sum_probs=48.3
Q ss_pred ccccCCccccccChhhhhhhhhh--cCCCcccCCC----------CCCcccccccchhhhhhcCC----C---------C
Q 044606 276 KYKCETCKKVFKSYQALGGHRAS--HKKIKFYTPV----------QETELDQENAGASINLASPP----L---------S 330 (413)
Q Consensus 276 ~~~C~~C~k~F~~~~~L~~H~~~--H~~~kp~~C~----------~C~~~f~~~~~~~l~~h~~~----h---------~ 330 (413)
.+.|-.|.|.|..+..|+.|||. |....|-.-. .-+++.+-.. ..+.+-... + .
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~-~e~dret~~d~~E~D~~wsDw~ed 273 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVH-SEDDRETNEDINETDDTWSDWNED 273 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhh-hhhhhhhhccccccccchhhhhcC
Confidence 48999999999999999999974 6554442110 1122221000 000000000 0 0
Q ss_pred CCCc--cccCCcCcccCCchhhcccccccc
Q 044606 331 VKKV--HECPVCFRVFSSGQALGGHKRTHV 358 (413)
Q Consensus 331 g~kp--~~C~~C~k~F~~~~~L~~H~r~H~ 358 (413)
+.-+ -.|-.|....-....|..||++-|
T Consensus 274 ~a~a~~v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 274 DAEALSVVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred CCCccceEEEeeccchhhHHHHHHHHHHHH
Confidence 1122 489999998888999999998644
No 198
>PF15269 zf-C2H2_7: Zinc-finger
Probab=21.03 E-value=61 Score=21.48 Aligned_cols=25 Identities=28% Similarity=0.251 Sum_probs=20.4
Q ss_pred ccccccCcccccCCChhhhhhHHHh
Q 044606 38 MEKHKCRLCFKNFSNGRALGGHMRS 62 (413)
Q Consensus 38 ~~~~~C~iC~K~F~~~~~L~~HmR~ 62 (413)
-.+|+|=.|.-+-.-.+.|-.||+-
T Consensus 18 p~~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 18 PFKYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred CccceeecCCcccchHHHHHHHHHH
Confidence 4567898898888888999999974
No 199
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=20.96 E-value=46 Score=23.65 Aligned_cols=7 Identities=43% Similarity=0.999 Sum_probs=4.7
Q ss_pred cCccccc
Q 044606 43 CRLCFKN 49 (413)
Q Consensus 43 C~iC~K~ 49 (413)
|++||+.
T Consensus 6 C~~CG~~ 12 (59)
T PF09889_consen 6 CPVCGKP 12 (59)
T ss_pred CCcCCCc
Confidence 7777763
No 200
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.52 E-value=64 Score=32.46 Aligned_cols=32 Identities=6% Similarity=-0.082 Sum_probs=22.6
Q ss_pred CCCCCCcccccccchhhhhhcCCCCCCCccccCCcCcccCCchhh
Q 044606 306 TPVQETELDQENAGASINLASPPLSVKKVHECPVCFRVFSSGQAL 350 (413)
Q Consensus 306 ~C~~C~~~f~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L 350 (413)
.|+.||..... .|.+-|+|+.||+.+......
T Consensus 352 ~Cp~Cg~~m~S-------------~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGRMKS-------------AGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCchhh-------------cCCCCcccccccccCCccccc
Confidence 68888876532 234489999999998876543
No 201
>COG4640 Predicted membrane protein [Function unknown]
Probab=20.38 E-value=56 Score=32.33 Aligned_cols=33 Identities=18% Similarity=0.322 Sum_probs=0.0
Q ss_pred heeeeeeEEeeccccccccccccccCcccccCCChhhhhh
Q 044606 19 LLFIIYVYVFFKKRKSLFVMEKHKCRLCFKNFSNGRALGG 58 (413)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~C~iC~K~F~~~~~L~~ 58 (413)
|+|| +++.+....--++|+-||..|+.+.++..
T Consensus 1 M~fC-------~kcG~qk~Ed~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 1 MKFC-------PKCGSQKAEDDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred CCcc-------cccccccccccccccccCCcCCchhhhhh
No 202
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.21 E-value=75 Score=21.66 Aligned_cols=12 Identities=17% Similarity=0.193 Sum_probs=7.8
Q ss_pred CccccCCcCccc
Q 044606 333 KVHECPVCFRVF 344 (413)
Q Consensus 333 kp~~C~~C~k~F 344 (413)
..+.|..||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 456777777654
No 203
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=20.15 E-value=64 Score=21.71 Aligned_cols=20 Identities=35% Similarity=0.891 Sum_probs=13.8
Q ss_pred CcCcccCCchhhcccccccc
Q 044606 339 VCFRVFSSGQALGGHKRTHV 358 (413)
Q Consensus 339 ~C~k~F~~~~~L~~H~r~H~ 358 (413)
+|..-|.....-..|...|.
T Consensus 26 LC~~Cf~~g~~~~~H~~~H~ 45 (49)
T cd02335 26 LCLECFSAGAEIGKHRNDHN 45 (49)
T ss_pred hhHHhhhCcCCCCCCCCCCC
Confidence 35567777777777877774
No 204
>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=20.13 E-value=50 Score=22.69 Aligned_cols=27 Identities=26% Similarity=0.479 Sum_probs=16.8
Q ss_pred CCccccCCccccccChhhhhhhhhhcC
Q 044606 274 RGKYKCETCKKVFKSYQALGGHRASHK 300 (413)
Q Consensus 274 ~~~~~C~~C~k~F~~~~~L~~H~~~H~ 300 (413)
...|+|+.|...|-..-.+-.|...|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CCeEECCCCCCccccCcChhhhccccC
Confidence 356999999999999988888876664
Done!