Query psy3231
Match_columns 420
No_of_seqs 394 out of 2934
Neff 10.5
Searched_HMMs 46136
Date Fri Aug 16 19:43:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3231hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3608|consensus 100.0 1.8E-28 3.9E-33 209.3 12.3 221 152-400 135-377 (467)
2 KOG1074|consensus 99.9 1.7E-28 3.7E-33 231.3 4.0 106 205-312 605-732 (958)
3 KOG1074|consensus 99.9 6.3E-28 1.4E-32 227.5 3.6 101 260-361 605-731 (958)
4 KOG3608|consensus 99.9 1.7E-26 3.6E-31 197.3 11.0 233 93-327 133-398 (467)
5 KOG2462|consensus 99.9 7E-27 1.5E-31 195.0 4.2 133 203-337 128-265 (279)
6 KOG2462|consensus 99.9 6.5E-27 1.4E-31 195.2 2.4 128 259-419 129-259 (279)
7 KOG3623|consensus 99.9 3.7E-22 8.1E-27 185.6 7.5 102 124-225 211-329 (1007)
8 KOG3623|consensus 99.8 1.9E-21 4.2E-26 181.0 7.6 107 6-172 211-330 (1007)
9 KOG3576|consensus 99.6 2.4E-16 5.3E-21 125.1 3.5 85 90-175 113-197 (267)
10 KOG3576|consensus 99.6 3.2E-16 7E-21 124.4 1.8 51 261-312 118-168 (267)
11 PLN03086 PRLI-interacting fact 99.2 3.9E-11 8.5E-16 113.8 7.4 60 236-299 455-514 (567)
12 PLN03086 PRLI-interacting fact 99.1 8.7E-11 1.9E-15 111.5 5.8 132 262-416 409-554 (567)
13 PHA02768 hypothetical protein; 99.0 1.3E-10 2.8E-15 73.2 2.3 42 376-419 6-47 (55)
14 PHA00733 hypothetical protein 99.0 4.8E-10 1E-14 86.7 5.1 83 203-285 38-124 (128)
15 PHA00733 hypothetical protein 99.0 5.8E-10 1.3E-14 86.2 4.0 48 287-334 71-118 (128)
16 PHA02768 hypothetical protein; 98.8 3.2E-09 7E-14 66.9 2.2 42 290-331 6-47 (55)
17 PF13465 zf-H2C2_2: Zinc-finge 98.8 4.1E-09 8.8E-14 56.7 2.2 25 390-414 1-25 (26)
18 KOG3993|consensus 98.7 3.5E-09 7.5E-14 94.2 2.1 25 260-284 356-380 (500)
19 PHA00616 hypothetical protein 98.7 1.1E-08 2.5E-13 61.1 2.7 42 375-416 1-42 (44)
20 KOG3993|consensus 98.7 3.2E-09 6.9E-14 94.4 0.5 108 94-202 267-380 (500)
21 PF13465 zf-H2C2_2: Zinc-finge 98.3 2.5E-07 5.4E-12 49.7 1.7 26 275-301 1-26 (26)
22 KOG1146|consensus 98.3 6.1E-07 1.3E-11 91.4 4.6 81 316-398 1261-1351(1406)
23 PHA00732 hypothetical protein 98.2 1.3E-06 2.7E-11 61.1 2.9 47 260-312 1-47 (79)
24 PHA00616 hypothetical protein 98.2 1.1E-06 2.3E-11 52.7 1.9 34 260-294 1-34 (44)
25 PHA00732 hypothetical protein 98.2 1.3E-06 2.9E-11 61.0 2.6 46 289-337 1-46 (79)
26 PF05605 zf-Di19: Drought indu 98.1 5.9E-06 1.3E-10 53.6 4.0 50 260-312 2-52 (54)
27 PF05605 zf-Di19: Drought indu 98.0 9.4E-06 2E-10 52.6 4.4 51 94-147 2-53 (54)
28 PF00096 zf-C2H2: Zinc finger, 97.9 4.3E-06 9.4E-11 43.6 1.5 23 376-398 1-23 (23)
29 PF13894 zf-C2H2_4: C2H2-type 97.6 3E-05 6.4E-10 40.8 1.7 24 376-399 1-24 (24)
30 PF00096 zf-C2H2: Zinc finger, 97.6 2.3E-05 5E-10 40.8 1.2 22 261-282 1-22 (23)
31 PF13912 zf-C2H2_6: C2H2-type 97.6 3.5E-05 7.5E-10 41.9 1.4 26 375-400 1-26 (27)
32 PF12756 zf-C2H2_2: C2H2 type 97.5 6.8E-05 1.5E-09 56.0 2.5 73 96-174 1-73 (100)
33 PF12756 zf-C2H2_2: C2H2 type 97.4 6.7E-05 1.4E-09 56.0 1.9 71 207-282 1-72 (100)
34 PF13894 zf-C2H2_4: C2H2-type 97.4 0.0001 2.2E-09 38.7 1.7 23 261-283 1-23 (24)
35 COG5189 SFP1 Putative transcri 97.3 6.6E-05 1.4E-09 64.9 0.4 51 259-309 348-418 (423)
36 COG5189 SFP1 Putative transcri 97.3 6.2E-05 1.3E-09 65.1 -0.1 72 2-115 346-419 (423)
37 PF13912 zf-C2H2_6: C2H2-type 97.2 0.00021 4.6E-09 38.8 1.4 24 289-312 1-24 (27)
38 PF13909 zf-H2C2_5: C2H2-type 97.1 0.00025 5.5E-09 37.2 1.4 24 376-400 1-24 (24)
39 smart00355 ZnF_C2H2 zinc finge 97.0 0.00055 1.2E-08 36.5 2.2 24 376-399 1-24 (26)
40 PRK04860 hypothetical protein; 96.9 0.00078 1.7E-08 54.2 2.7 41 374-418 118-158 (160)
41 PF12874 zf-met: Zinc-finger o 96.7 0.00078 1.7E-08 35.7 1.3 23 376-398 1-23 (25)
42 PF09237 GAGA: GAGA factor; I 96.7 0.0016 3.5E-08 40.0 2.6 32 372-403 21-52 (54)
43 KOG2482|consensus 96.6 0.0033 7.2E-08 55.3 5.1 156 247-402 128-363 (423)
44 KOG2231|consensus 96.5 0.005 1.1E-07 60.3 5.9 69 95-172 183-260 (669)
45 KOG2231|consensus 96.4 0.0055 1.2E-07 60.0 5.7 113 235-361 100-234 (669)
46 smart00355 ZnF_C2H2 zinc finge 96.3 0.0026 5.5E-08 33.8 1.7 23 290-312 1-23 (26)
47 COG5236 Uncharacterized conser 96.3 0.0066 1.4E-07 53.5 5.0 125 179-312 152-305 (493)
48 PF12171 zf-C2H2_jaz: Zinc-fin 96.3 0.0015 3.2E-08 35.4 0.5 22 376-397 2-23 (27)
49 PF09237 GAGA: GAGA factor; I 96.2 0.0022 4.8E-08 39.4 1.1 23 123-145 24-46 (54)
50 PF12874 zf-met: Zinc-finger o 96.1 0.0028 6.1E-08 33.5 1.0 21 290-310 1-21 (25)
51 KOG1146|consensus 96.0 0.0027 5.8E-08 65.9 1.2 146 263-416 439-631 (1406)
52 PF13909 zf-H2C2_5: C2H2-type 95.8 0.008 1.7E-07 31.4 2.0 23 95-118 1-23 (24)
53 KOG2482|consensus 95.3 0.044 9.5E-07 48.5 6.0 23 151-173 195-217 (423)
54 COG5236 Uncharacterized conser 95.2 0.046 1E-06 48.4 5.8 135 5-173 151-303 (493)
55 PF13913 zf-C2HC_2: zinc-finge 95.2 0.016 3.5E-07 30.5 1.9 20 341-361 4-23 (25)
56 PF12171 zf-C2H2_jaz: Zinc-fin 95.1 0.0089 1.9E-07 32.3 0.7 17 318-334 4-20 (27)
57 PF13913 zf-C2HC_2: zinc-finge 94.5 0.03 6.5E-07 29.5 1.8 21 376-397 3-23 (25)
58 PRK04860 hypothetical protein; 94.2 0.022 4.8E-07 45.9 1.3 37 123-163 119-155 (160)
59 smart00451 ZnF_U1 U1-like zinc 93.7 0.046 1E-06 31.5 1.7 22 375-396 3-24 (35)
60 KOG2893|consensus 93.4 0.025 5.5E-07 47.2 0.3 46 262-312 12-58 (341)
61 KOG2785|consensus 92.1 0.3 6.6E-06 44.3 5.2 23 94-116 3-25 (390)
62 KOG4173|consensus 92.0 0.12 2.7E-06 42.3 2.5 52 262-313 108-171 (253)
63 smart00451 ZnF_U1 U1-like zinc 91.7 0.12 2.5E-06 29.8 1.6 23 339-361 3-25 (35)
64 KOG2785|consensus 91.5 0.41 8.9E-06 43.5 5.4 53 259-311 165-242 (390)
65 COG5048 FOG: Zn-finger [Genera 90.5 0.058 1.3E-06 52.0 -0.9 148 259-412 288-455 (467)
66 COG4049 Uncharacterized protei 89.5 0.18 3.9E-06 31.7 1.0 31 89-119 12-42 (65)
67 KOG4173|consensus 89.3 0.26 5.7E-06 40.4 2.1 77 92-172 77-167 (253)
68 cd00350 rubredoxin_like Rubred 88.7 0.2 4.3E-06 28.4 0.8 10 402-411 16-25 (33)
69 TIGR00622 ssl1 transcription f 87.7 1 2.2E-05 33.7 4.1 88 290-399 2-105 (112)
70 PF12013 DUF3505: Protein of u 87.2 0.95 2.1E-05 34.1 3.9 73 92-175 9-108 (109)
71 PF10571 UPF0547: Uncharacteri 85.2 0.53 1.2E-05 25.0 1.1 9 341-349 16-24 (26)
72 KOG2893|consensus 84.7 0.24 5.2E-06 41.6 -0.5 41 318-358 13-53 (341)
73 COG4049 Uncharacterized protei 83.9 0.51 1.1E-05 29.7 0.8 31 370-400 12-42 (65)
74 PF12013 DUF3505: Protein of u 82.8 1.3 2.9E-05 33.3 2.9 25 376-400 81-109 (109)
75 COG5048 FOG: Zn-finger [Genera 82.5 0.68 1.5E-05 44.6 1.6 54 205-258 289-347 (467)
76 COG2888 Predicted Zn-ribbon RN 82.5 1 2.2E-05 29.0 1.8 12 312-323 47-58 (61)
77 TIGR00622 ssl1 transcription f 80.9 1.1 2.5E-05 33.4 1.9 24 289-312 81-104 (112)
78 cd00729 rubredoxin_SM Rubredox 80.0 0.82 1.8E-05 26.1 0.7 11 376-386 3-13 (34)
79 PF09986 DUF2225: Uncharacteri 78.8 0.26 5.6E-06 42.2 -2.4 11 290-300 49-59 (214)
80 KOG2186|consensus 77.3 1.5 3.3E-05 37.5 1.8 45 124-171 4-48 (276)
81 PF09538 FYDLN_acid: Protein o 76.8 1.4 2.9E-05 33.0 1.2 30 290-328 10-39 (108)
82 PF12907 zf-met2: Zinc-binding 76.3 2.8 6E-05 24.9 2.2 32 261-292 2-36 (40)
83 PRK14890 putative Zn-ribbon RN 76.1 1.8 3.8E-05 28.0 1.4 11 313-323 46-56 (59)
84 TIGR02098 MJ0042_CXXC MJ0042 f 74.7 1.7 3.7E-05 25.4 1.1 7 292-298 5-11 (38)
85 PF09538 FYDLN_acid: Protein o 74.4 1.8 4E-05 32.3 1.4 15 374-388 25-39 (108)
86 PF09986 DUF2225: Uncharacteri 74.4 1.1 2.4E-05 38.4 0.3 12 340-351 49-60 (214)
87 smart00834 CxxC_CXXC_SSSS Puta 72.3 1.3 2.8E-05 26.3 0.2 9 317-325 7-15 (41)
88 COG1592 Rubrerythrin [Energy p 72.2 1.8 4E-05 35.0 1.0 12 285-296 145-156 (166)
89 smart00734 ZnF_Rad18 Rad18-lik 72.0 4.2 9.1E-05 21.5 2.0 20 341-361 3-22 (26)
90 PF09723 Zn-ribbon_8: Zinc rib 71.5 1.2 2.6E-05 26.8 -0.1 10 316-325 6-15 (42)
91 PF13717 zinc_ribbon_4: zinc-r 69.9 3.6 7.7E-05 23.8 1.6 7 378-384 28-34 (36)
92 smart00659 RPOLCX RNA polymera 69.7 2.2 4.7E-05 26.0 0.7 26 376-412 3-28 (44)
93 PF13719 zinc_ribbon_5: zinc-r 69.1 3.6 7.7E-05 24.0 1.5 12 207-218 4-15 (37)
94 TIGR02605 CxxC_CxxC_SSSS putat 68.1 1.9 4.2E-05 27.3 0.3 9 317-325 7-15 (52)
95 PF03604 DNA_RNApol_7kD: DNA d 67.0 2.7 5.8E-05 23.6 0.7 7 341-347 19-25 (32)
96 PRK00398 rpoP DNA-directed RNA 66.4 2.1 4.5E-05 26.4 0.2 7 341-347 23-29 (46)
97 PRK00464 nrdR transcriptional 65.8 2.6 5.7E-05 33.8 0.7 11 340-350 29-39 (154)
98 smart00531 TFIIE Transcription 64.9 2.5 5.4E-05 33.8 0.4 35 374-413 98-133 (147)
99 TIGR02300 FYDLN_acid conserved 62.7 4.6 9.9E-05 30.8 1.4 30 290-328 10-39 (129)
100 smart00531 TFIIE Transcription 62.6 4.3 9.3E-05 32.5 1.4 35 288-325 98-133 (147)
101 TIGR00373 conserved hypothetic 61.2 3.4 7.5E-05 33.5 0.6 30 374-412 108-137 (158)
102 PF02892 zf-BED: BED zinc fing 60.0 9.4 0.0002 23.1 2.3 26 92-117 14-43 (45)
103 cd00730 rubredoxin Rubredoxin; 59.2 6 0.00013 24.9 1.3 8 318-325 4-11 (50)
104 TIGR02300 FYDLN_acid conserved 59.0 6.4 0.00014 30.1 1.6 15 374-388 25-39 (129)
105 PRK06266 transcription initiat 58.4 3.8 8.3E-05 33.9 0.4 29 375-412 117-145 (178)
106 smart00614 ZnF_BED BED zinc fi 57.7 7.3 0.00016 24.4 1.5 22 377-398 20-47 (50)
107 PHA00626 hypothetical protein 57.6 5.1 0.00011 25.5 0.8 16 373-388 21-36 (59)
108 KOG2272|consensus 57.5 6.7 0.00015 33.6 1.7 114 233-350 98-232 (332)
109 PF04959 ARS2: Arsenite-resist 57.3 5.8 0.00012 33.8 1.3 26 260-285 77-102 (214)
110 COG5151 SSL1 RNA polymerase II 57.2 9.2 0.0002 33.9 2.5 26 374-399 387-412 (421)
111 PRK09678 DNA-binding transcrip 55.8 4.2 9E-05 27.8 0.2 12 376-387 28-41 (72)
112 COG1997 RPL43A Ribosomal prote 55.6 7.2 0.00016 27.5 1.3 31 314-350 34-64 (89)
113 KOG2186|consensus 55.6 7.5 0.00016 33.5 1.7 45 261-309 4-48 (276)
114 COG1198 PriA Primosomal protei 54.3 8.7 0.00019 39.3 2.2 10 316-325 436-445 (730)
115 KOG2807|consensus 53.3 17 0.00037 32.6 3.5 27 373-399 343-369 (378)
116 PF09845 DUF2072: Zn-ribbon co 53.1 9.3 0.0002 29.4 1.7 10 291-300 3-12 (131)
117 PF06524 NOA36: NOA36 protein; 52.8 4.7 0.0001 34.7 0.1 39 120-159 139-179 (314)
118 PF14353 CpXC: CpXC protein 52.3 1.9 4E-05 33.6 -2.3 21 315-335 38-58 (128)
119 TIGR00373 conserved hypothetic 52.2 14 0.00031 29.9 2.8 12 124-135 110-121 (158)
120 COG1592 Rubrerythrin [Energy p 50.9 8.8 0.00019 31.2 1.3 24 205-242 134-157 (166)
121 PF15269 zf-C2H2_7: Zinc-finge 50.0 10 0.00023 22.7 1.2 23 375-397 20-42 (54)
122 PF05443 ROS_MUCR: ROS/MUCR tr 48.4 9.3 0.0002 29.7 1.1 25 376-403 73-97 (132)
123 COG1198 PriA Primosomal protei 47.4 12 0.00025 38.4 1.9 40 261-324 445-484 (730)
124 COG1996 RPC10 DNA-directed RNA 47.1 7.8 0.00017 24.2 0.4 11 375-385 6-16 (49)
125 PRK06266 transcription initiat 45.8 18 0.00039 30.0 2.5 13 151-163 117-129 (178)
126 PF13240 zinc_ribbon_2: zinc-r 45.7 12 0.00026 19.1 0.9 6 318-323 2-7 (23)
127 PF06524 NOA36: NOA36 protein; 44.2 6.4 0.00014 34.0 -0.4 25 288-312 208-232 (314)
128 KOG2593|consensus 43.4 19 0.00042 33.8 2.4 35 374-411 127-161 (436)
129 KOG3408|consensus 43.1 14 0.00029 27.9 1.2 24 374-397 56-79 (129)
130 KOG2071|consensus 42.6 15 0.00032 36.1 1.6 25 3-27 416-440 (579)
131 COG3364 Zn-ribbon containing p 41.9 17 0.00036 26.5 1.4 11 317-327 4-14 (112)
132 PF02176 zf-TRAF: TRAF-type zi 41.7 17 0.00038 23.5 1.5 38 123-161 9-52 (60)
133 PF13878 zf-C2H2_3: zinc-finge 41.6 23 0.0005 21.1 1.8 24 376-399 14-39 (41)
134 KOG2272|consensus 41.1 16 0.00035 31.4 1.5 17 336-352 277-293 (332)
135 PF05290 Baculo_IE-1: Baculovi 40.3 24 0.00053 27.2 2.2 12 291-302 123-134 (140)
136 PF06220 zf-U1: U1 zinc finger 39.2 20 0.00043 21.0 1.3 22 375-396 3-26 (38)
137 PF07754 DUF1610: Domain of un 38.6 17 0.00037 18.9 0.8 9 314-322 15-23 (24)
138 PF08209 Sgf11: Sgf11 (transcr 38.4 24 0.00052 20.0 1.4 24 340-364 5-28 (33)
139 TIGR00595 priA primosomal prot 38.0 21 0.00047 35.2 2.1 28 284-324 235-262 (505)
140 PF04959 ARS2: Arsenite-resist 37.6 27 0.00057 29.9 2.3 30 90-119 73-102 (214)
141 PRK04023 DNA polymerase II lar 37.1 30 0.00065 36.5 2.9 9 340-348 664-672 (1121)
142 PRK04023 DNA polymerase II lar 36.2 29 0.00062 36.6 2.6 14 314-327 662-675 (1121)
143 COG4530 Uncharacterized protei 35.1 14 0.00029 27.3 0.2 13 373-385 24-36 (129)
144 COG1773 Rubredoxin [Energy pro 34.2 21 0.00046 22.9 0.9 11 290-300 4-14 (55)
145 PF08790 zf-LYAR: LYAR-type C2 33.8 8.9 0.00019 20.7 -0.7 20 376-396 1-20 (28)
146 PF08274 PhnA_Zn_Ribbon: PhnA 33.5 15 0.00033 20.3 0.1 24 377-411 4-27 (30)
147 PRK14873 primosome assembly pr 32.6 26 0.00057 35.8 1.8 27 284-324 405-431 (665)
148 PF13248 zf-ribbon_3: zinc-rib 32.1 28 0.0006 18.3 1.0 6 318-323 5-10 (26)
149 PF14446 Prok-RING_1: Prokaryo 31.1 23 0.00051 22.6 0.7 11 377-387 7-17 (54)
150 PF07975 C1_4: TFIIH C1-like d 31.0 10 0.00022 23.9 -0.9 26 374-399 20-45 (51)
151 KOG2593|consensus 30.9 30 0.00066 32.6 1.7 38 203-244 126-163 (436)
152 PF13451 zf-trcl: Probable zin 30.7 33 0.00071 21.5 1.3 21 93-113 3-23 (49)
153 PF12760 Zn_Tnp_IS1595: Transp 29.9 63 0.0014 19.7 2.5 7 317-323 20-26 (46)
154 PF04780 DUF629: Protein of un 29.3 35 0.00075 32.9 1.8 29 259-287 56-84 (466)
155 KOG1842|consensus 29.3 37 0.0008 32.1 1.9 29 259-287 14-42 (505)
156 TIGR01206 lysW lysine biosynth 29.0 25 0.00055 22.5 0.6 7 291-297 4-10 (54)
157 COG3357 Predicted transcriptio 28.8 30 0.00066 24.6 1.0 13 315-327 58-70 (97)
158 COG4888 Uncharacterized Zn rib 28.7 17 0.00037 26.4 -0.2 9 341-349 48-56 (104)
159 KOG0717|consensus 28.7 28 0.00061 33.1 1.1 21 376-396 293-313 (508)
160 PF10083 DUF2321: Uncharacteri 28.6 11 0.00024 29.9 -1.2 16 400-415 65-80 (158)
161 COG5188 PRP9 Splicing factor 3 28.3 34 0.00074 31.1 1.5 55 340-394 239-394 (470)
162 KOG4377|consensus 27.9 40 0.00087 31.4 1.9 24 152-175 272-297 (480)
163 COG0068 HypF Hydrogenase matur 27.9 21 0.00045 36.0 0.1 56 207-268 125-181 (750)
164 PF05191 ADK_lid: Adenylate ki 27.7 26 0.00057 20.3 0.5 30 377-414 3-32 (36)
165 PF01780 Ribosomal_L37ae: Ribo 27.4 23 0.0005 25.4 0.3 13 338-350 52-64 (90)
166 PTZ00255 60S ribosomal protein 27.3 28 0.0006 25.0 0.6 13 338-350 53-65 (90)
167 KOG4124|consensus 26.9 12 0.00025 33.9 -1.6 50 259-308 348-417 (442)
168 PRK14714 DNA polymerase II lar 26.8 51 0.0011 35.9 2.7 7 235-241 668-674 (1337)
169 KOG0717|consensus 26.7 35 0.00075 32.5 1.3 21 376-396 461-481 (508)
170 KOG1280|consensus 26.2 62 0.0013 29.6 2.7 28 260-287 79-106 (381)
171 KOG2807|consensus 26.1 75 0.0016 28.8 3.2 20 259-278 289-308 (378)
172 PRK00432 30S ribosomal protein 25.8 37 0.00079 21.4 0.9 9 340-348 38-46 (50)
173 KOG4167|consensus 25.4 18 0.00038 36.4 -0.8 27 374-400 791-817 (907)
174 TIGR00280 L37a ribosomal prote 25.2 28 0.0006 25.0 0.3 13 338-350 52-64 (91)
175 KOG1842|consensus 24.1 31 0.00067 32.6 0.5 28 205-232 15-42 (505)
176 COG5151 SSL1 RNA polymerase II 23.8 33 0.00073 30.6 0.6 47 263-312 365-411 (421)
177 TIGR00595 priA primosomal prot 23.8 49 0.0011 32.7 1.8 18 331-348 232-249 (505)
178 COG1998 RPS31 Ribosomal protei 23.7 51 0.0011 20.6 1.2 8 340-347 38-45 (51)
179 PF07503 zf-HYPF: HypF finger; 23.6 34 0.00074 19.6 0.5 12 314-325 20-31 (35)
180 PF04606 Ogr_Delta: Ogr/Delta- 23.5 19 0.00042 22.2 -0.6 6 409-414 33-38 (47)
181 KOG4167|consensus 23.5 36 0.00078 34.3 0.9 25 4-28 791-815 (907)
182 KOG4124|consensus 23.5 20 0.00043 32.6 -0.8 19 11-29 19-37 (442)
183 PF14205 Cys_rich_KTR: Cystein 23.4 47 0.001 21.2 1.1 9 339-347 28-36 (55)
184 PRK05580 primosome assembly pr 23.4 48 0.001 34.2 1.8 34 316-349 382-418 (679)
185 PRK14873 primosome assembly pr 23.3 42 0.0009 34.4 1.3 31 317-347 385-418 (665)
186 PF04780 DUF629: Protein of un 22.6 59 0.0013 31.4 2.1 29 93-121 56-84 (466)
187 PF13453 zf-TFIIB: Transcripti 22.3 51 0.0011 19.5 1.1 19 150-168 18-36 (41)
188 smart00661 RPOL9 RNA polymeras 22.3 49 0.0011 20.6 1.0 11 340-350 21-31 (52)
189 COG4957 Predicted transcriptio 22.2 48 0.001 25.6 1.1 25 376-403 77-101 (148)
190 COG3677 Transposase and inacti 22.1 77 0.0017 24.7 2.3 12 339-350 53-64 (129)
191 PF07649 C1_3: C1-like domain; 21.9 39 0.00085 18.4 0.5 12 374-385 14-25 (30)
192 COG3091 SprT Zn-dependent meta 21.8 36 0.00078 27.0 0.4 33 375-412 117-149 (156)
193 smart00440 ZnF_C2C2 C2C2 Zinc 21.6 33 0.00072 20.3 0.1 8 376-383 29-36 (40)
194 smart00154 ZnF_AN1 AN1-like Zi 21.1 40 0.00088 19.8 0.4 14 375-388 12-25 (39)
195 COG0068 HypF Hydrogenase matur 20.5 19 0.00041 36.3 -1.7 37 290-331 102-139 (750)
196 PF05495 zf-CHY: CHY zinc fing 20.3 23 0.0005 24.2 -0.8 11 234-244 41-51 (71)
197 KOG3408|consensus 20.3 57 0.0012 24.7 1.2 25 4-28 56-80 (129)
198 PRK03976 rpl37ae 50S ribosomal 20.1 38 0.00083 24.3 0.2 13 338-350 53-65 (90)
199 PF05129 Elf1: Transcription e 20.0 20 0.00043 25.3 -1.2 11 340-350 47-57 (81)
No 1
>KOG3608|consensus
Probab=99.96 E-value=1.8e-28 Score=209.27 Aligned_cols=221 Identities=24% Similarity=0.594 Sum_probs=185.1
Q ss_pred ccc--ccccccccChHHHHHHHHHhcC------------C--CCCc--chhhhccCCHHHHHHHHHhhC-CCccccCCCc
Q psy3231 152 FTC--AQCDKAFSLKSNLSKHVRHHME------------N--VKQC--KICLEIFEDDEVLEEHVKSHQ-NRRFKCPCCE 212 (420)
Q Consensus 152 ~~C--~~C~~~f~~~~~l~~H~~~h~~------------~--~~~C--~~C~~~f~~~~~l~~H~~~h~-~~~~~C~~C~ 212 (420)
|.| ..|+..|.+...|..|+..|.. + .+.| ..|.+.+.++..|.+|++.|+ ++...|+.||
T Consensus 135 f~C~WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg 214 (467)
T KOG3608|consen 135 FRCGWEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCG 214 (467)
T ss_pred hccChhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHH
Confidence 556 5799999999999999987752 1 2345 458999999999999999998 7889999999
Q ss_pred cccCCHHHHHcccccc-CCCCCceecccccccccChHHHHHHhhccCCCccCcchhhcCCCHHHHHHHHHhhcCCCCccc
Q psy3231 213 RIFTSETRMRNHIDMK-HADENLFKCKKCLKVFSDEIKFHLHGRAHAKFYRCSECEKRFATEDIMRQHFRNYHNKEDAYV 291 (420)
Q Consensus 213 ~~f~~~~~l~~H~~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~ 291 (420)
..|.+...|.+|++.. -....+|.|..|.+.|.++..|..|+..|..-|+|++|+.+....+.|..|++..|..++||+
T Consensus 215 ~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfK 294 (467)
T KOG3608|consen 215 ELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFK 294 (467)
T ss_pred HHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCcc
Confidence 9999999999998543 234568999999999999999999999999999999999999999999999999999999999
Q ss_pred cccchhccCChhHHHHHHhhCCCcccCCccCCcCCCchhhhcccCCCcccccc--cccccCChhHHHHHHHHhhccCCcc
Q psy3231 292 CNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLMFPDEKNLRNHECTSCFTCPF--CQRKYKIEKHLEKHIESCIQLNPTT 369 (420)
Q Consensus 292 C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~ 369 (420)
|+.|++.|.+.++|++|+..|..+ .|.|.. |..++.+...|+.|++.++..+..
T Consensus 295 Cd~Cd~~c~~esdL~kH~~~HS~~-----------------------~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np- 350 (467)
T KOG3608|consen 295 CDECDTRCVRESDLAKHVQVHSKT-----------------------VYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNP- 350 (467)
T ss_pred ccchhhhhccHHHHHHHHHhcccc-----------------------ceecCCCCCcHHHHHHHHHHHHHHHhccCCCC-
Confidence 999999999999999999988643 245555 777777777888888775543332
Q ss_pred ccccccccccccccccCChhHHHHHHhhhcC
Q psy3231 370 TVLKTLQKCRYCQRMFRNEDKLTAHELSHTM 400 (420)
Q Consensus 370 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~ 400 (420)
.+|.|..|++.|++..+|.+|++.-++
T Consensus 351 ----~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 351 ----ILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred ----CceeeecchhhhccchhHHHHHHHhhc
Confidence 368899999999999999999865444
No 2
>KOG1074|consensus
Probab=99.94 E-value=1.7e-28 Score=231.30 Aligned_cols=106 Identities=25% Similarity=0.523 Sum_probs=83.5
Q ss_pred ccccCCCccccCCHHHHHccccccCCCCCceecccccccccChHHHHHHhhccC------CCccCc---chhhcCCCHHH
Q psy3231 205 RFKCPCCERIFTSETRMRNHIDMKHADENLFKCKKCLKVFSDEIKFHLHGRAHA------KFYRCS---ECEKRFATEDI 275 (420)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~------~~~~C~---~C~~~f~~~~~ 275 (420)
|-+|-+|.++..-.+.|+.|. ..|++++||+|.+||+.|.++.+|+.|+.+|. -++.|+ +|-+.|...-.
T Consensus 605 PNqCiiC~rVlSC~saLqmHy-rtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~ 683 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHY-RTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVT 683 (958)
T ss_pred ccceeeeeecccchhhhhhhh-hcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccc
Confidence 356888888888888888888 45888888888888888888888888888885 358888 88888888888
Q ss_pred HHHHHHhhcCC-CC------------ccccccchhccCChhHHHHHHhhC
Q psy3231 276 MRQHFRNYHNK-ED------------AYVCNYCYDSFETKSTLVDHFFHH 312 (420)
Q Consensus 276 l~~H~~~~H~~-~~------------~~~C~~C~~~f~~~~~l~~H~~~h 312 (420)
|..|++. |.+ .. .-+|..|.+.|.+...+..++..|
T Consensus 684 lpQhIri-H~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se~ 732 (958)
T KOG1074|consen 684 LPQHIRI-HLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISEQ 732 (958)
T ss_pred ccceEEe-ecCCCCCCCcccccccchhcccchhhhcccccccchhhhhcc
Confidence 8888887 652 21 246888888888777777776544
No 3
>KOG1074|consensus
Probab=99.94 E-value=6.3e-28 Score=227.52 Aligned_cols=101 Identities=23% Similarity=0.507 Sum_probs=85.8
Q ss_pred CccCcchhhcCCCHHHHHHHHHhhcCCCCccccccchhccCChhHHHHHHhhCC------CcccCC---ccCCcCCCchh
Q psy3231 260 FYRCSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCYDSFETKSTLVDHFFHHG------NPYMCN---HCFLMFPDEKN 330 (420)
Q Consensus 260 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~h~------~~~~C~---~C~~~f~~~~~ 330 (420)
|-+|-+|.+...=++.|+.|+++ |+||+||+|.+||+.|.++.+|+.|+-+|. .++.|+ +|-+.|.....
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrt-HtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~ 683 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRT-HTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVT 683 (958)
T ss_pred ccceeeeeecccchhhhhhhhhc-ccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccc
Confidence 37899999999999999999998 999999999999999999999999999983 368999 99999999888
Q ss_pred hhcccCC-----------------CcccccccccccCChhHHHHHHHH
Q psy3231 331 LRNHECT-----------------SCFTCPFCQRKYKIEKHLEKHIES 361 (420)
Q Consensus 331 l~~H~~~-----------------~~~~C~~C~~~f~~~~~l~~H~~~ 361 (420)
|..|.+. ..-+|..|.+.|.....+..++..
T Consensus 684 lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~a~~f~~~~se 731 (958)
T KOG1074|consen 684 LPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSDARSFSQQISE 731 (958)
T ss_pred ccceEEeecCCCCCCCcccccccchhcccchhhhcccccccchhhhhc
Confidence 8777543 124688888888777777777654
No 4
>KOG3608|consensus
Probab=99.94 E-value=1.7e-26 Score=197.31 Aligned_cols=233 Identities=27% Similarity=0.610 Sum_probs=202.6
Q ss_pred Cccccc--cCccccCCHHHHHHHHHHhcCC------------C-Cccccc--cccccccCchHHHHHHhhccCCCccccc
Q psy3231 93 RKFKCE--MCPKSFDHKSNIRRHMAATHDL------------Q-KKYKCK--LCARMYRYKWNLKAHLKMHKGPKIFTCA 155 (420)
Q Consensus 93 ~~~~C~--~C~~~f~~~~~l~~H~~~~h~~------------~-~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~C~ 155 (420)
..|.|. .|+..|.+...+..|+. .|.. + ..+.|. -|.+.+.+++.|++|++.|++++...|+
T Consensus 133 ~~f~C~WedCe~~F~s~~ef~dHV~-~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp 211 (467)
T KOG3608|consen 133 QNFRCGWEDCEREFVSIVEFQDHVV-KHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACP 211 (467)
T ss_pred hhhccChhhcCCcccCHHHHHHHHH-HhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecc
Confidence 347885 69999999999999987 4521 1 235564 4899999999999999999999999999
Q ss_pred cccccccChHHHHHHHHHhc---CCCCCcchhhhccCCHHHHHHHHHhhCCCccccCCCccccCCHHHHHccccccCCCC
Q psy3231 156 QCDKAFSLKSNLSKHVRHHM---ENVKQCKICLEIFEDDEVLEEHVKSHQNRRFKCPCCERIFTSETRMRNHIDMKHADE 232 (420)
Q Consensus 156 ~C~~~f~~~~~l~~H~~~h~---~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 232 (420)
.||.-|.++..|..|++... .++|.|..|.+.|.+...|..|+..|-+ -|+|+.|+.+....++|.+|++..|..+
T Consensus 212 ~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn-~ykCplCdmtc~~~ssL~~H~r~rHs~d 290 (467)
T KOG3608|consen 212 HCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN-CYKCPLCDMTCSSASSLTTHIRYRHSKD 290 (467)
T ss_pred hHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh-cccccccccCCCChHHHHHHHHhhhccC
Confidence 99999999999999998665 4599999999999999999999988754 5999999999999999999999999999
Q ss_pred CceecccccccccChHHHHHHhhccC-CCccCcc--hhhcCCCHHHHHHHHHhhcCCC--CccccccchhccCChhHHHH
Q psy3231 233 NLFKCKKCLKVFSDEIKFHLHGRAHA-KFYRCSE--CEKRFATEDIMRQHFRNYHNKE--DAYVCNYCYDSFETKSTLVD 307 (420)
Q Consensus 233 ~~~~C~~C~~~f~~~~~l~~H~~~h~-~~~~C~~--C~~~f~~~~~l~~H~~~~H~~~--~~~~C~~C~~~f~~~~~l~~ 307 (420)
+||+|+.|++.+.+.+.|..|..+|. ..|+|.. |...|.+...|++|++.+|.|. .+|.|-.|++.|++-.+|..
T Consensus 291 kpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~ 370 (467)
T KOG3608|consen 291 KPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSA 370 (467)
T ss_pred CCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHH
Confidence 99999999999999999999999998 5699987 9999999999999999989655 56999999999999999999
Q ss_pred HH-hhCC-------CcccCCccCCcCCC
Q psy3231 308 HF-FHHG-------NPYMCNHCFLMFPD 327 (420)
Q Consensus 308 H~-~~h~-------~~~~C~~C~~~f~~ 327 (420)
|+ +.|+ ..|.=.+|...|..
T Consensus 371 HL~kkH~f~~PsGh~RFtYk~~edG~mR 398 (467)
T KOG3608|consen 371 HLMKKHGFRLPSGHKRFTYKVDEDGFMR 398 (467)
T ss_pred HHHHhhcccCCCCCCceeeeeccCceee
Confidence 96 4553 23444555555533
No 5
>KOG2462|consensus
Probab=99.93 E-value=7e-27 Score=194.98 Aligned_cols=133 Identities=27% Similarity=0.588 Sum_probs=115.4
Q ss_pred CCccccCCCccccCCHHHHHccccccCC---CCCceecccccccccChHHHHHHhhccCCCccCcchhhcCCCHHHHHHH
Q psy3231 203 NRRFKCPCCERIFTSETRMRNHIDMKHA---DENLFKCKKCLKVFSDEIKFHLHGRAHAKFYRCSECEKRFATEDIMRQH 279 (420)
Q Consensus 203 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~---~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H 279 (420)
...|+|+.||+.+.+...|.+|.+. |. ..+.+.|++|++.|.+...|..|+++|.-+.+|.+||+.|.....|+-|
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~-H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQT-HRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred CCceeccccccccccccccchhhcc-cccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcc
Confidence 4568899999999999999999854 43 3567899999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCccccccchhccCChhHHHHHHhhCC--CcccCCccCCcCCCchhhhcccCC
Q psy3231 280 FRNYHNKEDAYVCNYCYDSFETKSTLVDHFFHHG--NPYMCNHCFLMFPDEKNLRNHECT 337 (420)
Q Consensus 280 ~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~h~--~~~~C~~C~~~f~~~~~l~~H~~~ 337 (420)
+++ |+||+||.|+.|++.|.++++|+.||++|. ++|+|..|+++|...+.|..|...
T Consensus 207 iRT-HTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 207 IRT-HTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ccc-ccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 998 999999999999999999999999999995 677766666666666666666533
No 6
>KOG2462|consensus
Probab=99.93 E-value=6.5e-27 Score=195.17 Aligned_cols=128 Identities=25% Similarity=0.437 Sum_probs=90.7
Q ss_pred CCccCcchhhcCCCHHHHHHHHHhhcC---CCCccccccchhccCChhHHHHHHhhCCCcccCCccCCcCCCchhhhccc
Q psy3231 259 KFYRCSECEKRFATEDIMRQHFRNYHN---KEDAYVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLMFPDEKNLRNHE 335 (420)
Q Consensus 259 ~~~~C~~C~~~f~~~~~l~~H~~~~H~---~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H~ 335 (420)
..|+|+.||+.+.+...|.+|.++ |- ..+.+.|++|++.|.+...|..|+++|+-|..|.+||+.|..+-.|
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~-H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLL---- 203 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQT-HRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLL---- 203 (279)
T ss_pred Cceeccccccccccccccchhhcc-cccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHh----
Confidence 457788888888888888888776 53 2456778888888888888888877777666666666655555444
Q ss_pred CCCcccccccccccCChhHHHHHHHHhhccCCccccccccccccccccccCChhHHHHHHhhhcCCcccccccceeeEEe
Q psy3231 336 CTSCFTCPFCQRKYKIEKHLEKHIESCIQLNPTTTVLKTLQKCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATVSVCL 415 (420)
Q Consensus 336 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~~~~~ 415 (420)
.-|+|+ ++|++||.|+.|++.|.++++|+.||++|++.|+|.|..|+|+|++
T Consensus 204 --------------------QGHiRT--------HTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 204 --------------------QGHIRT--------HTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred --------------------hccccc--------ccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHH
Confidence 444554 7777777777777777777777777777777777777777777776
Q ss_pred eccc
Q psy3231 416 GMKT 419 (420)
Q Consensus 416 ~~~~ 419 (420)
.++|
T Consensus 256 ~SyL 259 (279)
T KOG2462|consen 256 KSYL 259 (279)
T ss_pred HHHH
Confidence 6665
No 7
>KOG3623|consensus
Probab=99.86 E-value=3.7e-22 Score=185.64 Aligned_cols=102 Identities=28% Similarity=0.664 Sum_probs=88.4
Q ss_pred cccccccccccCchHHHHHHhhc--cCCCccccccccccccChHHHHHHHHHhcC--------------CCCCcchhhhc
Q psy3231 124 YKCKLCARMYRYKWNLKAHLKMH--KGPKIFTCAQCDKAFSLKSNLSKHVRHHME--------------NVKQCKICLEI 187 (420)
Q Consensus 124 ~~C~~C~~~f~~~~~l~~H~~~h--~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~--------------~~~~C~~C~~~ 187 (420)
..|++|+..+.....|+.|++.- ..+..|.|..|..+|..+..|.+|+..|.. +.|+|.+|++.
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 67999999999999999998653 345679999999999999999999988742 25899999999
Q ss_pred cCCHHHHHHHHHhhC-CCccccCCCccccCCHHHHHccc
Q psy3231 188 FEDDEVLEEHVKSHQ-NRRFKCPCCERIFTSETRMRNHI 225 (420)
Q Consensus 188 f~~~~~l~~H~~~h~-~~~~~C~~C~~~f~~~~~l~~H~ 225 (420)
|.-+-.|++|+++|. ++||.|+.|++.|+....+..||
T Consensus 291 FKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHm 329 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHM 329 (1007)
T ss_pred hhhHHHHHhhheeecCCCCcCCcccccccccCCcccccc
Confidence 999999999999998 89999999999999998888887
No 8
>KOG3623|consensus
Probab=99.84 E-value=1.9e-21 Score=180.97 Aligned_cols=107 Identities=35% Similarity=0.805 Sum_probs=91.3
Q ss_pred eecchhhHHHHhhhhhhhhhcccCCCCCCCCCCCCCcccccCcceeeeeccCCCccccceeehhhhhhhhhhhhhhhccC
Q psy3231 6 YTCDFCSAAFALKHSIADHIQTEHMGNPKHQDTKQYPAFRNGSFYIRADIEQPKVKVEHETIMSYARRQVEYEQEQQIPA 85 (420)
Q Consensus 6 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (420)
..|+.|+..+..-..|+.|++.+|...
T Consensus 211 ltcpycdrgykrltslkeHikyrhekn----------------------------------------------------- 237 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKN----------------------------------------------------- 237 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhC-----------------------------------------------------
Confidence 468888888888888888888766443
Q ss_pred CCCCccCCccccccCccccCCHHHHHHHHHHhcCC-------------CCccccccccccccCchHHHHHHhhccCCCcc
Q psy3231 86 QGKSIQERKFKCEMCPKSFDHKSNIRRHMAATHDL-------------QKKYKCKLCARMYRYKWNLKAHLKMHKGPKIF 152 (420)
Q Consensus 86 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~-------------~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 152 (420)
+..|.|..|.++|..+..|.+||. .|.. .+.|+|+.|++.|+.+-.|++|+|+|.|++||
T Consensus 238 ------e~nfsC~lCsytFAyRtQLErhm~-~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPf 310 (1007)
T KOG3623|consen 238 ------EPNFSCMLCSYTFAYRTQLERHMQ-LHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPF 310 (1007)
T ss_pred ------CCCCcchhhhhhhhhHHHHHHHHH-hhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCc
Confidence 123779999999999999999998 5532 25699999999999999999999999999999
Q ss_pred ccccccccccChHHHHHHHH
Q psy3231 153 TCAQCDKAFSLKSNLSKHVR 172 (420)
Q Consensus 153 ~C~~C~~~f~~~~~l~~H~~ 172 (420)
.|+.|+++|...+.+..||-
T Consensus 311 eCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 311 ECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred CCcccccccccCCccccccc
Confidence 99999999999999999974
No 9
>KOG3576|consensus
Probab=99.61 E-value=2.4e-16 Score=125.08 Aligned_cols=85 Identities=27% Similarity=0.680 Sum_probs=79.4
Q ss_pred ccCCccccccCccccCCHHHHHHHHHHhcCCCCccccccccccccCchHHHHHHhhccCCCccccccccccccChHHHHH
Q psy3231 90 IQERKFKCEMCPKSFDHKSNIRRHMAATHDLQKKYKCKLCARMYRYKWNLKAHLKMHKGPKIFTCAQCDKAFSLKSNLSK 169 (420)
Q Consensus 90 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 169 (420)
.+...|.|.+|++.|.-...|.+|++ .|...+.+.|..||+.|....+|++|+++|+|.+||+|..|++.|..+-.|..
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~k-ch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLK-CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhh-hccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHH
Confidence 34567999999999999999999998 89999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhc
Q psy3231 170 HVRHHM 175 (420)
Q Consensus 170 H~~~h~ 175 (420)
|++.-+
T Consensus 192 hl~kvh 197 (267)
T KOG3576|consen 192 HLKKVH 197 (267)
T ss_pred HHHHHc
Confidence 987544
No 10
>KOG3576|consensus
Probab=99.59 E-value=3.2e-16 Score=124.40 Aligned_cols=51 Identities=24% Similarity=0.644 Sum_probs=26.3
Q ss_pred ccCcchhhcCCCHHHHHHHHHhhcCCCCccccccchhccCChhHHHHHHhhC
Q psy3231 261 YRCSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCYDSFETKSTLVDHFFHH 312 (420)
Q Consensus 261 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~h 312 (420)
|.|.+|++.|.....|.+|++- |++.+.+.|..||+.|.+..+|++|+++|
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kc-h~~vkr~lct~cgkgfndtfdlkrh~rth 168 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKC-HSDVKRHLCTFCGKGFNDTFDLKRHTRTH 168 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhh-ccHHHHHHHhhccCcccchhhhhhhhccc
Confidence 4455555555555555555543 55555555555555555555555555544
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.18 E-value=3.9e-11 Score=113.84 Aligned_cols=60 Identities=22% Similarity=0.476 Sum_probs=30.4
Q ss_pred ecccccccccChHHHHHHhhccCCCccCcchhhcCCCHHHHHHHHHhhcCCCCccccccchhcc
Q psy3231 236 KCKKCLKVFSDEIKFHLHGRAHAKFYRCSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCYDSF 299 (420)
Q Consensus 236 ~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f 299 (420)
.|+.|++.|. ...|..|+..++.++.|+ ||+.+ .+..|..|+.+ |...+++.|+.|++.|
T Consensus 455 ~C~~Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~t-hCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 455 HCEKCGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQAS-TCPLRLITCRFCGDMV 514 (567)
T ss_pred cCCCCCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhc-cCCCCceeCCCCCCcc
Confidence 4555555553 344555555544555555 55433 33455555443 4555555555555555
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.11 E-value=8.7e-11 Score=111.54 Aligned_cols=132 Identities=21% Similarity=0.376 Sum_probs=73.2
Q ss_pred cCcchhhcCCCHHHHHHHHHhhcCCCCcccccc--chhccCChhHHHHHHhhCCCcccCCccCCcCCCchhhhcccCC--
Q psy3231 262 RCSECEKRFATEDIMRQHFRNYHNKEDAYVCNY--CYDSFETKSTLVDHFFHHGNPYMCNHCFLMFPDEKNLRNHECT-- 337 (420)
Q Consensus 262 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H~~~-- 337 (420)
.|+.|.+.... ..|..|... -.-....|+. |+..|. +..|..| +.|+.|++.|. ...|..|+..
T Consensus 409 ~C~NC~~~i~l-~~l~lHe~~--C~r~~V~Cp~~~Cg~v~~-r~el~~H-------~~C~~Cgk~f~-~s~LekH~~~~H 476 (567)
T PLN03086 409 ECRNCKHYIPS-RSIALHEAY--CSRHNVVCPHDGCGIVLR-VEEAKNH-------VHCEKCGQAFQ-QGEMEKHMKVFH 476 (567)
T ss_pred ECCCCCCccch-hHHHHHHhh--CCCcceeCCcccccceee-ccccccC-------ccCCCCCCccc-hHHHHHHHHhcC
Confidence 45555544433 233355432 1122344553 555552 2233333 34666666654 3455555443
Q ss_pred CcccccccccccCChhHHHHHHHHhhccCCccccccccccccccccccCC----------hhHHHHHHhhhcCCcccccc
Q psy3231 338 SCFTCPFCQRKYKIEKHLEKHIESCIQLNPTTTVLKTLQKCRYCQRMFRN----------EDKLTAHELSHTMEKTFYRN 407 (420)
Q Consensus 338 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~C~~C~~~f~~----------~~~l~~H~~~H~~~~~~~c~ 407 (420)
.++.|+ ||+.+ .+..|..|++. +-+.+++.|++|++.|.. .+.|..|+..+ |.+++.|.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~t--------hCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~ 545 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQAS--------TCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCD 545 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhc--------cCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEcc
Confidence 566666 66543 45667777664 555566777777777741 34677777775 67777777
Q ss_pred cceeeEEee
Q psy3231 408 VATVSVCLG 416 (420)
Q Consensus 408 ~c~~~~~~~ 416 (420)
.||+.|+..
T Consensus 546 ~Cgk~Vrlr 554 (567)
T PLN03086 546 SCGRSVMLK 554 (567)
T ss_pred ccCCeeeeh
Confidence 777777654
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.03 E-value=1.3e-10 Score=73.17 Aligned_cols=42 Identities=10% Similarity=0.173 Sum_probs=37.8
Q ss_pred ccccccccccCChhHHHHHHhhhcCCcccccccceeeEEeeccc
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATVSVCLGMKT 419 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~~~~~~~~~ 419 (420)
|.|+.||+.|+..++|..||++|+ +||.|..|+++|.+.+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 789999999999999999999998 799999999999987765
No 14
>PHA00733 hypothetical protein
Probab=99.00 E-value=4.8e-10 Score=86.69 Aligned_cols=83 Identities=19% Similarity=0.356 Sum_probs=46.0
Q ss_pred CCccccCCCccccCCHHHHHcc--c--cccCCCCCceecccccccccChHHHHHHhhccCCCccCcchhhcCCCHHHHHH
Q psy3231 203 NRRFKCPCCERIFTSETRMRNH--I--DMKHADENLFKCKKCLKVFSDEIKFHLHGRAHAKFYRCSECEKRFATEDIMRQ 278 (420)
Q Consensus 203 ~~~~~C~~C~~~f~~~~~l~~H--~--~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~ 278 (420)
.+++.|.+|...|.+...|..+ + -..+.++.+|.|+.|++.|.+...|..|++.+..+|.|+.|++.|.....|..
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~ 117 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLD 117 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHH
Confidence 3445555555555444444333 0 01223355666666666666666666666655555666666666666666666
Q ss_pred HHHhhcC
Q psy3231 279 HFRNYHN 285 (420)
Q Consensus 279 H~~~~H~ 285 (420)
|+...|+
T Consensus 118 H~~~~h~ 124 (128)
T PHA00733 118 HVCKKHN 124 (128)
T ss_pred HHHHhcC
Confidence 6665554
No 15
>PHA00733 hypothetical protein
Probab=98.96 E-value=5.8e-10 Score=86.25 Aligned_cols=48 Identities=23% Similarity=0.479 Sum_probs=23.0
Q ss_pred CCccccccchhccCChhHHHHHHhhCCCcccCCccCCcCCCchhhhcc
Q psy3231 287 EDAYVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLMFPDEKNLRNH 334 (420)
Q Consensus 287 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H 334 (420)
++||.|+.|++.|.+...|..|++.|..+|.|++|++.|.....|..|
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H 118 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDH 118 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHH
Confidence 445555555555555555555555443334444444444444444333
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.78 E-value=3.2e-09 Score=66.92 Aligned_cols=42 Identities=14% Similarity=0.400 Sum_probs=22.9
Q ss_pred cccccchhccCChhHHHHHHhhCCCcccCCccCCcCCCchhh
Q psy3231 290 YVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLMFPDEKNL 331 (420)
Q Consensus 290 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l 331 (420)
|.|+.||+.|...+.|..|+++|.+||+|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcCCcccCCcccceeccccee
Confidence 455555555555555555555555555555555555544443
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.77 E-value=4.1e-09 Score=56.75 Aligned_cols=25 Identities=28% Similarity=0.243 Sum_probs=23.6
Q ss_pred HHHHHHhhhcCCcccccccceeeEE
Q psy3231 390 KLTAHELSHTMEKTFYRNVATVSVC 414 (420)
Q Consensus 390 ~l~~H~~~H~~~~~~~c~~c~~~~~ 414 (420)
+|.+||++|+|++||.|++|+++|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 5899999999999999999999996
No 18
>KOG3993|consensus
Probab=98.75 E-value=3.5e-09 Score=94.21 Aligned_cols=25 Identities=24% Similarity=0.671 Sum_probs=15.3
Q ss_pred CccCcchhhcCCCHHHHHHHHHhhc
Q psy3231 260 FYRCSECEKRFATEDIMRQHFRNYH 284 (420)
Q Consensus 260 ~~~C~~C~~~f~~~~~l~~H~~~~H 284 (420)
.|.|..|++.|.....|+.|+.++|
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhhh
Confidence 4666666666666666666665544
No 19
>PHA00616 hypothetical protein
Probab=98.70 E-value=1.1e-08 Score=61.12 Aligned_cols=42 Identities=17% Similarity=0.322 Sum_probs=38.9
Q ss_pred cccccccccccCChhHHHHHHhhhcCCcccccccceeeEEee
Q psy3231 375 LQKCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATVSVCLG 416 (420)
Q Consensus 375 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~~~~~~ 416 (420)
||+|+.||+.|.++++|..|+++|+|++|+.|+.=-..|+++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~y~~f~v~ 42 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYFYIYFRVR 42 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeEEEEEEEee
Confidence 689999999999999999999999999999998888888765
No 20
>KOG3993|consensus
Probab=98.70 E-value=3.2e-09 Score=94.44 Aligned_cols=108 Identities=19% Similarity=0.447 Sum_probs=63.6
Q ss_pred ccccccCccccCCHHHHHHHHHHhcCCCCccccccccccccCchHHHHHHhhccCCCcccc-cc-ccc-cccChHHHHHH
Q psy3231 94 KFKCEMCPKSFDHKSNIRRHMAATHDLQKKYKCKLCARMYRYKWNLKAHLKMHKGPKIFTC-AQ-CDK-AFSLKSNLSKH 170 (420)
Q Consensus 94 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C-~~-C~~-~f~~~~~l~~H 170 (420)
.|.|..|...|.+.-.|.+|.- .-.....|+|+.|+++|.-..+|..|.+.|.....-.= .. =.+ ...+....+.-
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC-~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRC-PRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccC-CeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 4889999999999999988853 12222468899999999999999999888854211000 00 000 00111111111
Q ss_pred HHH---hcCCCCCcchhhhccCCHHHHHHHHHhhC
Q psy3231 171 VRH---HMENVKQCKICLEIFEDDEVLEEHVKSHQ 202 (420)
Q Consensus 171 ~~~---h~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 202 (420)
.+. -.+..|.|..|++.|.....|+.|+.+|+
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 110 01225777777777777777777766665
No 21
>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=98.34 E-value=2.5e-07 Score=49.74 Aligned_cols=26 Identities=42% Similarity=0.912 Sum_probs=22.8
Q ss_pred HHHHHHHhhcCCCCccccccchhccCC
Q psy3231 275 IMRQHFRNYHNKEDAYVCNYCYDSFET 301 (420)
Q Consensus 275 ~l~~H~~~~H~~~~~~~C~~C~~~f~~ 301 (420)
+|.+|+++ |++++||.|++|+++|.+
T Consensus 1 ~l~~H~~~-H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRT-HTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHH-HSSSSSEEESSSSEEESS
T ss_pred CHHHHhhh-cCCCCCCCCCCCcCeeCc
Confidence 48899997 999999999999999864
No 22
>KOG1146|consensus
Probab=98.29 E-value=6.1e-07 Score=91.40 Aligned_cols=81 Identities=15% Similarity=0.208 Sum_probs=56.1
Q ss_pred ccCCccCCcCCCchhhhcccCC-CcccccccccccCChhHHHHHHHHhhccCCcccccc---------cccccccccccc
Q psy3231 316 YMCNHCFLMFPDEKNLRNHECT-SCFTCPFCQRKYKIEKHLEKHIESCIQLNPTTTVLK---------TLQKCRYCQRMF 385 (420)
Q Consensus 316 ~~C~~C~~~f~~~~~l~~H~~~-~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~---------~~~~C~~C~~~f 385 (420)
+.|..|.+.|...-.+. |+.+ .+|.|..|.-.|.....|..|.+.+.........+. ..| |.+|...|
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~ 1338 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLDVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLL 1338 (1406)
T ss_pred chhhhccccccCcccee-ecccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhc
Confidence 44555555555444444 4433 669999999999999999999876433322211111 345 99999999
Q ss_pred CChhHHHHHHhhh
Q psy3231 386 RNEDKLTAHELSH 398 (420)
Q Consensus 386 ~~~~~l~~H~~~H 398 (420)
....+|+.||++-
T Consensus 1339 ~~~~alqihm~~~ 1351 (1406)
T KOG1146|consen 1339 SGREALQIHMRSS 1351 (1406)
T ss_pred chhHHHHHHHHHh
Confidence 9999999999953
No 23
>PHA00732 hypothetical protein
Probab=98.18 E-value=1.3e-06 Score=61.08 Aligned_cols=47 Identities=28% Similarity=0.595 Sum_probs=27.6
Q ss_pred CccCcchhhcCCCHHHHHHHHHhhcCCCCccccccchhccCChhHHHHHHhhC
Q psy3231 260 FYRCSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCYDSFETKSTLVDHFFHH 312 (420)
Q Consensus 260 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~h 312 (420)
||.|+.|++.|.+...|..|++..|.+ +.|+.|++.|. .|..|++..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---Chhhhhccc
Confidence 456666666666666666666533432 45666666665 355565544
No 24
>PHA00616 hypothetical protein
Probab=98.16 E-value=1.1e-06 Score=52.73 Aligned_cols=34 Identities=21% Similarity=0.531 Sum_probs=28.6
Q ss_pred CccCcchhhcCCCHHHHHHHHHhhcCCCCcccccc
Q psy3231 260 FYRCSECEKRFATEDIMRQHFRNYHNKEDAYVCNY 294 (420)
Q Consensus 260 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~ 294 (420)
||+|+.||+.|...+.|.+|++. |.+++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~-~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS-VHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH-hcCCCccceeE
Confidence 58899999999999999999987 66778888765
No 25
>PHA00732 hypothetical protein
Probab=98.16 E-value=1.3e-06 Score=60.98 Aligned_cols=46 Identities=20% Similarity=0.265 Sum_probs=32.4
Q ss_pred ccccccchhccCChhHHHHHHhhCCCcccCCccCCcCCCchhhhcccCC
Q psy3231 289 AYVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLMFPDEKNLRNHECT 337 (420)
Q Consensus 289 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H~~~ 337 (420)
||.|+.|++.|.+...|..|++.+..++.|++||+.|. .|..|..+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---Chhhhhcc
Confidence 57788888888888888888874323467777777776 46666544
No 26
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.06 E-value=5.9e-06 Score=53.55 Aligned_cols=50 Identities=24% Similarity=0.501 Sum_probs=39.6
Q ss_pred CccCcchhhcCCCHHHHHHHHHhhcCCC-CccccccchhccCChhHHHHHHhhC
Q psy3231 260 FYRCSECEKRFATEDIMRQHFRNYHNKE-DAYVCNYCYDSFETKSTLVDHFFHH 312 (420)
Q Consensus 260 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~-~~~~C~~C~~~f~~~~~l~~H~~~h 312 (420)
.|.||+|++ ..+...|..|+...|..+ +.+.|++|...+. .+|..|+..+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 488999999 566788999998888875 5699999998655 4888887653
No 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.02 E-value=9.4e-06 Score=52.59 Aligned_cols=51 Identities=27% Similarity=0.472 Sum_probs=39.8
Q ss_pred ccccccCccccCCHHHHHHHHHHhcCCC-CccccccccccccCchHHHHHHhhcc
Q psy3231 94 KFKCEMCPKSFDHKSNIRRHMAATHDLQ-KKYKCKLCARMYRYKWNLKAHLKMHK 147 (420)
Q Consensus 94 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~h~ 147 (420)
.|.|+.|++ ..+...|..|....|..+ +.+.|++|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 488999999 566788999988888764 5688999987654 48888887665
No 28
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.95 E-value=4.3e-06 Score=43.63 Aligned_cols=23 Identities=30% Similarity=0.645 Sum_probs=15.9
Q ss_pred ccccccccccCChhHHHHHHhhh
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELSH 398 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~H 398 (420)
|.|+.|++.|.+..+|+.|++.|
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 45777777777777777777654
No 29
>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=97.64 E-value=3e-05 Score=40.83 Aligned_cols=24 Identities=29% Similarity=0.677 Sum_probs=15.9
Q ss_pred ccccccccccCChhHHHHHHhhhc
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELSHT 399 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~H~ 399 (420)
|.|++|++.|.+..+|..|++.|+
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 467777777777777777777653
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=97.63 E-value=2.3e-05 Score=40.81 Aligned_cols=22 Identities=32% Similarity=0.931 Sum_probs=11.0
Q ss_pred ccCcchhhcCCCHHHHHHHHHh
Q psy3231 261 YRCSECEKRFATEDIMRQHFRN 282 (420)
Q Consensus 261 ~~C~~C~~~f~~~~~l~~H~~~ 282 (420)
|+|++|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 3455555555555555555443
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.58 E-value=3.5e-05 Score=41.94 Aligned_cols=26 Identities=27% Similarity=0.482 Sum_probs=21.0
Q ss_pred cccccccccccCChhHHHHHHhhhcC
Q psy3231 375 LQKCRYCQRMFRNEDKLTAHELSHTM 400 (420)
Q Consensus 375 ~~~C~~C~~~f~~~~~l~~H~~~H~~ 400 (420)
||.|..|++.|.+..+|..|++.|.+
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 57788888888888888888887753
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.49 E-value=6.8e-05 Score=55.99 Aligned_cols=73 Identities=23% Similarity=0.480 Sum_probs=19.2
Q ss_pred ccccCccccCCHHHHHHHHHHhcCCCCccccccccccccCchHHHHHHhhccCCCccccccccccccChHHHHHHHHHh
Q psy3231 96 KCEMCPKSFDHKSNIRRHMAATHDLQKKYKCKLCARMYRYKWNLKAHLKMHKGPKIFTCAQCDKAFSLKSNLSKHVRHH 174 (420)
Q Consensus 96 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 174 (420)
+|..|+..|.+...|..||...|....+ ....+.....+..+++... ...+.|..|++.|.+...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccccccccccccccccccccccccccc-----ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 4888999999999999998877754322 1111223333444443322 22588888888888888888888754
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.44 E-value=6.7e-05 Score=56.02 Aligned_cols=71 Identities=24% Similarity=0.484 Sum_probs=12.9
Q ss_pred ccCCCccccCCHHHHHccccccCCCCCceecccccccccChHHHHHHhhccC-CCccCcchhhcCCCHHHHHHHHHh
Q psy3231 207 KCPCCERIFTSETRMRNHIDMKHADENLFKCKKCLKVFSDEIKFHLHGRAHA-KFYRCSECEKRFATEDIMRQHFRN 282 (420)
Q Consensus 207 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~-~~~~C~~C~~~f~~~~~l~~H~~~ 282 (420)
+|..|+..|.+...|..|+...|.-..+ ....+.....+..+.+... ..+.|.+|++.|.+...|..|++.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred Cccccccccccccccccccccccccccc-----cccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcC
Confidence 3667777777777777777555543322 0111112222222222111 235555555555555555555554
No 34
>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=97.39 E-value=0.0001 Score=38.68 Aligned_cols=23 Identities=35% Similarity=0.829 Sum_probs=11.7
Q ss_pred ccCcchhhcCCCHHHHHHHHHhh
Q psy3231 261 YRCSECEKRFATEDIMRQHFRNY 283 (420)
Q Consensus 261 ~~C~~C~~~f~~~~~l~~H~~~~ 283 (420)
|.|++|++.|.+...|..|+.+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 34555555555555555555543
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.29 E-value=6.6e-05 Score=64.91 Aligned_cols=51 Identities=25% Similarity=0.625 Sum_probs=38.7
Q ss_pred CCccCcc--hhhcCCCHHHHHHHHHhhcC------------------CCCccccccchhccCChhHHHHHH
Q psy3231 259 KFYRCSE--CEKRFATEDIMRQHFRNYHN------------------KEDAYVCNYCYDSFETKSTLVDHF 309 (420)
Q Consensus 259 ~~~~C~~--C~~~f~~~~~l~~H~~~~H~------------------~~~~~~C~~C~~~f~~~~~l~~H~ 309 (420)
+||+|++ |.+.+.....|+.|+.--|. .++||+|++|++++++...|+.|.
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 8999987 99999999999999875552 235677777777777666666664
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.26 E-value=6.2e-05 Score=65.08 Aligned_cols=72 Identities=18% Similarity=0.468 Sum_probs=49.0
Q ss_pred cccceecch--hhHHHHhhhhhhhhhcccCCCCCCCCCCCCCcccccCcceeeeeccCCCccccceeehhhhhhhhhhhh
Q psy3231 2 TLKTYTCDF--CSAAFALKHSIADHIQTEHMGNPKHQDTKQYPAFRNGSFYIRADIEQPKVKVEHETIMSYARRQVEYEQ 79 (420)
Q Consensus 2 ~~k~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (420)
+.|||+|++ |+|++.+...|..|+..=|....- .+.+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~----~~~p~------------------------------------ 385 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKL----HENPS------------------------------------ 385 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCccc----CCCCC------------------------------------
Confidence 359999998 999999999999997643322200 00000
Q ss_pred hhhccCCCCCccCCccccccCccccCCHHHHHHHHH
Q psy3231 80 EQQIPAQGKSIQERKFKCEMCPKSFDHKSNIRRHMA 115 (420)
Q Consensus 80 ~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 115 (420)
..+.+.-....|||+|++|++.+.....|+-|..
T Consensus 386 --p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 386 --PEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred --ccccccccccCCceeccccchhhccCccceeccc
Confidence 0001111446789999999999999999988864
No 37
>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=97.16 E-value=0.00021 Score=38.76 Aligned_cols=24 Identities=29% Similarity=0.603 Sum_probs=16.2
Q ss_pred ccccccchhccCChhHHHHHHhhC
Q psy3231 289 AYVCNYCYDSFETKSTLVDHFFHH 312 (420)
Q Consensus 289 ~~~C~~C~~~f~~~~~l~~H~~~h 312 (420)
||.|..|++.|.+...|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 466777777777777777776655
No 38
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.12 E-value=0.00025 Score=37.21 Aligned_cols=24 Identities=25% Similarity=0.365 Sum_probs=17.5
Q ss_pred ccccccccccCChhHHHHHHhhhcC
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELSHTM 400 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~H~~ 400 (420)
|+|+.|+++.. ...|..|++.|++
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 67888888887 8888888887653
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.02 E-value=0.00055 Score=36.51 Aligned_cols=24 Identities=25% Similarity=0.631 Sum_probs=18.2
Q ss_pred ccccccccccCChhHHHHHHhhhc
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELSHT 399 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~H~ 399 (420)
|.|..|+++|.+...|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 467788888888888888877664
No 40
>PRK04860 hypothetical protein; Provisional
Probab=96.85 E-value=0.00078 Score=54.23 Aligned_cols=41 Identities=12% Similarity=0.207 Sum_probs=36.2
Q ss_pred ccccccccccccCChhHHHHHHhhhcCCcccccccceeeEEeecc
Q psy3231 374 TLQKCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATVSVCLGMK 418 (420)
Q Consensus 374 ~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~~~~~~~~ 418 (420)
-+|.|. |+. ....+++|.++|+|+++|.|..|+..|.....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEecc
Confidence 479998 998 88889999999999999999999999987654
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.74 E-value=0.00078 Score=35.70 Aligned_cols=23 Identities=30% Similarity=0.585 Sum_probs=17.2
Q ss_pred ccccccccccCChhHHHHHHhhh
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELSH 398 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~H 398 (420)
|.|..|++.|.+..+|+.|++.+
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 46778888888888888887654
No 42
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.72 E-value=0.0016 Score=40.03 Aligned_cols=32 Identities=19% Similarity=0.349 Sum_probs=21.0
Q ss_pred ccccccccccccccCChhHHHHHHhhhcCCcc
Q psy3231 372 LKTLQKCRYCQRMFRNEDKLTAHELSHTMEKT 403 (420)
Q Consensus 372 ~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~ 403 (420)
.+.|-.|+.|+..+.+..+|++|+.++++.||
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 34566788888888888888888888777776
No 43
>KOG2482|consensus
Probab=96.63 E-value=0.0033 Score=55.31 Aligned_cols=156 Identities=19% Similarity=0.305 Sum_probs=98.2
Q ss_pred hHHHHHHhhccC---CCccCcchhhcC-CCHHHHHHHHHhhcCC---------------------CCccccccchhccCC
Q psy3231 247 EIKFHLHGRAHA---KFYRCSECEKRF-ATEDIMRQHFRNYHNK---------------------EDAYVCNYCYDSFET 301 (420)
Q Consensus 247 ~~~l~~H~~~h~---~~~~C~~C~~~f-~~~~~l~~H~~~~H~~---------------------~~~~~C~~C~~~f~~ 301 (420)
...|..+++.-. ...+|-.|...+ ..++....|+...|.- -..+.|-.|.+.|.+
T Consensus 128 ~eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrd 207 (423)
T KOG2482|consen 128 KEALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRD 207 (423)
T ss_pred HHHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCC
Confidence 345666655443 457899998765 5677888898877741 123899999999999
Q ss_pred hhHHHHHHhhCC----Cc--------cc--CCccCCcCCC-chhh-----hcccCC------------Cc--cccccccc
Q psy3231 302 KSTLVDHFFHHG----NP--------YM--CNHCFLMFPD-EKNL-----RNHECT------------SC--FTCPFCQR 347 (420)
Q Consensus 302 ~~~l~~H~~~h~----~~--------~~--C~~C~~~f~~-~~~l-----~~H~~~------------~~--~~C~~C~~ 347 (420)
+..|+.||+.-+ +| |. =..=|++... .+.+ ..+..+ .+ ..|-+|..
T Consensus 208 kntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~ 287 (423)
T KOG2482|consen 208 KNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTN 287 (423)
T ss_pred cHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeecc
Confidence 999999996531 22 00 0011221110 0111 111100 22 58999999
Q ss_pred ccCChhHHHHHHHHhhccCCcccccc-------------------ccccccccccccCChhHHHHHHh--hhcCCc
Q psy3231 348 KYKIEKHLEKHIESCIQLNPTTTVLK-------------------TLQKCRYCQRMFRNEDKLTAHEL--SHTMEK 402 (420)
Q Consensus 348 ~f~~~~~l~~H~~~~~~~~~~~~~~~-------------------~~~~C~~C~~~f~~~~~l~~H~~--~H~~~~ 402 (420)
.......|..||+..+.-+-.-.+.. ..-.|..|+-+|-....|..||. .|++.-
T Consensus 288 ~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~k~l~i~ 363 (423)
T KOG2482|consen 288 FYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVEDKHLSIL 363 (423)
T ss_pred chhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccccccccc
Confidence 99999999999998443211100110 23369999999999999999996 555533
No 44
>KOG2231|consensus
Probab=96.50 E-value=0.005 Score=60.29 Aligned_cols=69 Identities=25% Similarity=0.562 Sum_probs=47.6
Q ss_pred cccccCccccCCHHHHHHHHHHhcCCCCcccccccc------ccccCchHHHHHHhhccCCCccccc--ccc-ccccChH
Q psy3231 95 FKCEMCPKSFDHKSNIRRHMAATHDLQKKYKCKLCA------RMYRYKWNLKAHLKMHKGPKIFTCA--QCD-KAFSLKS 165 (420)
Q Consensus 95 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~------~~f~~~~~l~~H~~~h~~~~~~~C~--~C~-~~f~~~~ 165 (420)
-.|..|...|-....|..|++..| |.|.+|+ ..|....+|..|.+..+ |.|. .|. +.|....
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h-----~~chfC~~~~~~neyy~~~~dLe~HfR~~H----flCE~~~C~~~~f~~~~ 253 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH-----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH----FLCEEEFCRTKKFYVAF 253 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce-----eheeecCcccccchhcccchHHHHHhhhcC----ccccccccccceeeehh
Confidence 468899999999999999988655 5666663 45667778888888765 6776 563 3343333
Q ss_pred HHHHHHH
Q psy3231 166 NLSKHVR 172 (420)
Q Consensus 166 ~l~~H~~ 172 (420)
.+..+++
T Consensus 254 ~~ei~lk 260 (669)
T KOG2231|consen 254 ELEIELK 260 (669)
T ss_pred HHHHHHH
Confidence 4555554
No 45
>KOG2231|consensus
Probab=96.42 E-value=0.0055 Score=60.02 Aligned_cols=113 Identities=24% Similarity=0.519 Sum_probs=79.3
Q ss_pred eecccccccccChHHHHHHhhccCCCccCcchhhcCCCHHHHHHHHHhhcCCCCccccccch---------hccCChhHH
Q psy3231 235 FKCKKCLKVFSDEIKFHLHGRAHAKFYRCSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCY---------DSFETKSTL 305 (420)
Q Consensus 235 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~---------~~f~~~~~l 305 (420)
+.|.+|+..|.... ..-.|..| -.|.+...|+.|+...|.. +.|.+|- ....+..+|
T Consensus 100 ~~C~~C~~~~~~~~----------~~~~~~~c-~~~~s~~~Lk~H~~~~H~~---~~c~lC~~~~kif~~e~k~Yt~~el 165 (669)
T KOG2231|consen 100 HSCHICDRRFRALY----------NKKECLHC-TEFKSVENLKNHMRDQHKL---HLCSLCLQNLKIFINERKLYTRAEL 165 (669)
T ss_pred hhcCccccchhhhc----------ccCCCccc-cchhHHHHHHHHHHHhhhh---hccccccccceeeeeeeehehHHHH
Confidence 56777777663211 11357777 6777888899998777753 4454442 233456778
Q ss_pred HHHHhhC-------CCcccCCccCCcCCCchhhhcccCCCcccccccc------cccCChhHHHHHHHH
Q psy3231 306 VDHFFHH-------GNPYMCNHCFLMFPDEKNLRNHECTSCFTCPFCQ------RKYKIEKHLEKHIES 361 (420)
Q Consensus 306 ~~H~~~h-------~~~~~C~~C~~~f~~~~~l~~H~~~~~~~C~~C~------~~f~~~~~l~~H~~~ 361 (420)
..|+..- .+--.|..|...|.....|..|++...|.|.+|. ..|.....|+.|.+.
T Consensus 166 ~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~ 234 (669)
T KOG2231|consen 166 NLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRK 234 (669)
T ss_pred HHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhh
Confidence 8887543 1235699999999999999999988888888884 456778889999886
No 46
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.31 E-value=0.0026 Score=33.80 Aligned_cols=23 Identities=39% Similarity=0.746 Sum_probs=13.3
Q ss_pred cccccchhccCChhHHHHHHhhC
Q psy3231 290 YVCNYCYDSFETKSTLVDHFFHH 312 (420)
Q Consensus 290 ~~C~~C~~~f~~~~~l~~H~~~h 312 (420)
|.|+.|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 34556666666666666665544
No 47
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.31 E-value=0.0066 Score=53.53 Aligned_cols=125 Identities=25% Similarity=0.481 Sum_probs=81.0
Q ss_pred CCcch--hhhccCCHHHHHHHHHhhCCCccccCCCc---------cccCCHHHHHccccccCCCC----Cceeccccccc
Q psy3231 179 KQCKI--CLEIFEDDEVLEEHVKSHQNRRFKCPCCE---------RIFTSETRMRNHIDMKHADE----NLFKCKKCLKV 243 (420)
Q Consensus 179 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~C~~C~---------~~f~~~~~l~~H~~~~h~~~----~~~~C~~C~~~ 243 (420)
|.|+. |.........|..|.+..+.+ +-|.+|- -..-+...|+.|... -..+ .--.|..|...
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~-~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~-G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGF-VLCSECIGNKKDFWNEIRLFRSSTLRDHKNG-GLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCc-EEhHhhhcCcccCccceeeeecccccccccC-CccccCcCCCchhhhccce
Confidence 45543 455555556666666655433 3355442 123345677888632 2222 12369999999
Q ss_pred ccChHHHHHHhhccCCCccCcchhh-------cCCCHHHHHHHHHhhcCCCCcccccc--ch----hccCChhHHHHHH-
Q psy3231 244 FSDEIKFHLHGRAHAKFYRCSECEK-------RFATEDIMRQHFRNYHNKEDAYVCNY--CY----DSFETKSTLVDHF- 309 (420)
Q Consensus 244 f~~~~~l~~H~~~h~~~~~C~~C~~-------~f~~~~~l~~H~~~~H~~~~~~~C~~--C~----~~f~~~~~l~~H~- 309 (420)
|.+...|..|++..+ -.|-+|++ -|.+...|..|.+..| |.|.+ |- ..|.....|+.|+
T Consensus 230 FYdDDEL~~HcR~~H--E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h-----y~ct~qtc~~~k~~vf~~~~el~~h~~ 302 (493)
T COG5236 230 FYDDDELRRHCRLRH--EACHICDMVGPIRYQYFKSYEDLEAHFRNAH-----YCCTFQTCRVGKCYVFPYHTELLEHLT 302 (493)
T ss_pred ecChHHHHHHHHhhh--hhhhhhhccCccchhhhhCHHHHHHHhhcCc-----eEEEEEEEecCcEEEeccHHHHHHHHH
Confidence 999999999998654 24555554 4788999999988766 67755 43 5789999999996
Q ss_pred hhC
Q psy3231 310 FHH 312 (420)
Q Consensus 310 ~~h 312 (420)
+-|
T Consensus 303 ~~h 305 (493)
T COG5236 303 RFH 305 (493)
T ss_pred HHh
Confidence 455
No 48
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.27 E-value=0.0015 Score=35.38 Aligned_cols=22 Identities=32% Similarity=0.640 Sum_probs=18.1
Q ss_pred ccccccccccCChhHHHHHHhh
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELS 397 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~ 397 (420)
|.|..|++.|.+..+|..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6788888888888888888864
No 49
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.22 E-value=0.0022 Score=39.44 Aligned_cols=23 Identities=30% Similarity=0.702 Sum_probs=7.5
Q ss_pred ccccccccccccCchHHHHHHhh
Q psy3231 123 KYKCKLCARMYRYKWNLKAHLKM 145 (420)
Q Consensus 123 ~~~C~~C~~~f~~~~~l~~H~~~ 145 (420)
|-.|++|+..+....+|++|+..
T Consensus 24 PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHH
T ss_pred CCCCCcchhhccchhhHHHHHHH
Confidence 33344444444444444444433
No 50
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.08 E-value=0.0028 Score=33.51 Aligned_cols=21 Identities=29% Similarity=0.790 Sum_probs=11.6
Q ss_pred cccccchhccCChhHHHHHHh
Q psy3231 290 YVCNYCYDSFETKSTLVDHFF 310 (420)
Q Consensus 290 ~~C~~C~~~f~~~~~l~~H~~ 310 (420)
|.|.+|+..|.+...|..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 345555555555555555554
No 51
>KOG1146|consensus
Probab=95.99 E-value=0.0027 Score=65.92 Aligned_cols=146 Identities=16% Similarity=0.210 Sum_probs=98.8
Q ss_pred CcchhhcCCCHHHHHHHHHhhcCCCCccccccchhccCChhHHHHHHhh-CCCcccCCccCCcCCCchhhhcccC-----
Q psy3231 263 CSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCYDSFETKSTLVDHFFH-HGNPYMCNHCFLMFPDEKNLRNHEC----- 336 (420)
Q Consensus 263 C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~C~~C~~~f~~~~~l~~H~~----- 336 (420)
|.-++..+.+...+..|+...|.-.+.++|+.|+..|+....|..|+|. |-..-. .+|. ..+.|.+
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~-~~c~-------~gq~~~~~arg~ 510 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS-AYCK-------AGQNHPRLARGE 510 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch-hHhH-------hccccccccccc
Confidence 4455666667777777777777778889999999999999999999876 311100 2221 1122221
Q ss_pred -----CCcccccccccccCChhHHHHHHHHhhccCC------------------------c----------c-ccccccc
Q psy3231 337 -----TSCFTCPFCQRKYKIEKHLEKHIESCIQLNP------------------------T----------T-TVLKTLQ 376 (420)
Q Consensus 337 -----~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~------------------------~----------~-~~~~~~~ 376 (420)
.++|.|..|..+++...+|.+|+........ . + ...+..+
T Consensus 511 ~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~~ag~~~~ags~~pktkP~~ 590 (1406)
T KOG1146|consen 511 VYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPEEAGLGPSAGSSGPKTKPSW 590 (1406)
T ss_pred cccCCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcccccCCCCCCCCCCCCCCCc
Confidence 1789999999999999999999976111000 0 0 1111457
Q ss_pred cccccccccCChhHHHHHHh-hhcCCcccccccceeeEEee
Q psy3231 377 KCRYCQRMFRNEDKLTAHEL-SHTMEKTFYRNVATVSVCLG 416 (420)
Q Consensus 377 ~C~~C~~~f~~~~~l~~H~~-~H~~~~~~~c~~c~~~~~~~ 416 (420)
.|..|++.-+-.-+|+.||. .++..-|--+-.++..+..-
T Consensus 591 ~C~vc~yetniarnlrihmtss~~s~~p~~~Lq~~it~~l~ 631 (1406)
T KOG1146|consen 591 RCEVCSYETNIARNLRIHMTASPSSSPPSLVLQQNITSSLA 631 (1406)
T ss_pred chhhhcchhhhhhccccccccCCCCCChHHHhhhcchhhcc
Confidence 99999999999999999997 45544446666666655443
No 52
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.80 E-value=0.008 Score=31.37 Aligned_cols=23 Identities=43% Similarity=0.886 Sum_probs=12.4
Q ss_pred cccccCccccCCHHHHHHHHHHhc
Q psy3231 95 FKCEMCPKSFDHKSNIRRHMAATH 118 (420)
Q Consensus 95 ~~C~~C~~~f~~~~~l~~H~~~~h 118 (420)
|+|+.|++... ...|.+|++..|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 45666666665 666666665443
No 53
>KOG2482|consensus
Probab=95.33 E-value=0.044 Score=48.52 Aligned_cols=23 Identities=35% Similarity=0.727 Sum_probs=16.6
Q ss_pred ccccccccccccChHHHHHHHHH
Q psy3231 151 IFTCAQCDKAFSLKSNLSKHVRH 173 (420)
Q Consensus 151 ~~~C~~C~~~f~~~~~l~~H~~~ 173 (420)
.+.|-.|.+.|.++..|+.||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 36777777777777777777753
No 54
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.23 E-value=0.046 Score=48.42 Aligned_cols=135 Identities=17% Similarity=0.365 Sum_probs=74.3
Q ss_pred ceecch--hhHHHHhhhhhhhhhcccCCCCCCCCCCCCCcccccC---cceeeeeccCCCccccceeehhhhhhhhhhhh
Q psy3231 5 TYTCDF--CSAAFALKHSIADHIQTEHMGNPKHQDTKQYPAFRNG---SFYIRADIEQPKVKVEHETIMSYARRQVEYEQ 79 (420)
Q Consensus 5 ~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (420)
.|.|+. |..+......|..|.+..|.. +.|..|- +.|.. ++ ..|.+.....
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~---------~~C~~C~~nKk~F~~-------------E~--~lF~~~~Lr~ 206 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF---------VLCSECIGNKKDFWN-------------EI--RLFRSSTLRD 206 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc---------EEhHhhhcCcccCcc-------------ce--eeeecccccc
Confidence 477775 777777788899999887743 3444442 11111 10 0111111112
Q ss_pred hhhccCCCCCccCCccccccCccccCCHHHHHHHHHHhcCCCCcccccccccc-------ccCchHHHHHHhhccCCCcc
Q psy3231 80 EQQIPAQGKSIQERKFKCEMCPKSFDHKSNIRRHMAATHDLQKKYKCKLCARM-------YRYKWNLKAHLKMHKGPKIF 152 (420)
Q Consensus 80 ~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~-------f~~~~~l~~H~~~h~~~~~~ 152 (420)
|.....++... ..--.|..|...|.+-..|..|++..|. .|.+|+++ |++..+|..|.+.- -|
T Consensus 207 H~~~G~~e~GF-KGHP~C~FC~~~FYdDDEL~~HcR~~HE-----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~----hy 276 (493)
T COG5236 207 HKNGGLEEEGF-KGHPLCIFCKIYFYDDDELRRHCRLRHE-----ACHICDMVGPIRYQYFKSYEDLEAHFRNA----HY 276 (493)
T ss_pred cccCCccccCc-CCCchhhhccceecChHHHHHHHHhhhh-----hhhhhhccCccchhhhhCHHHHHHHhhcC----ce
Confidence 22211111111 1123699999999999999999986664 57777654 45555666666532 24
Q ss_pred cccc--cc----ccccChHHHHHHHHH
Q psy3231 153 TCAQ--CD----KAFSLKSNLSKHVRH 173 (420)
Q Consensus 153 ~C~~--C~----~~f~~~~~l~~H~~~ 173 (420)
.|.+ |. ..|.....|..|+..
T Consensus 277 ~ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 277 CCTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred EEEEEEEecCcEEEeccHHHHHHHHHH
Confidence 4532 32 356666677777543
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.23 E-value=0.016 Score=30.55 Aligned_cols=20 Identities=45% Similarity=0.916 Sum_probs=14.3
Q ss_pred cccccccccCChhHHHHHHHH
Q psy3231 341 TCPFCQRKYKIEKHLEKHIES 361 (420)
Q Consensus 341 ~C~~C~~~f~~~~~l~~H~~~ 361 (420)
.|++||++| ..+.|..|+..
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 577777777 56777777765
No 56
>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=95.08 E-value=0.0089 Score=32.25 Aligned_cols=17 Identities=35% Similarity=0.862 Sum_probs=6.2
Q ss_pred CCccCCcCCCchhhhcc
Q psy3231 318 CNHCFLMFPDEKNLRNH 334 (420)
Q Consensus 318 C~~C~~~f~~~~~l~~H 334 (420)
|..|++.|.+...|..|
T Consensus 4 C~~C~k~f~~~~~~~~H 20 (27)
T PF12171_consen 4 CDACDKYFSSENQLKQH 20 (27)
T ss_dssp BTTTTBBBSSHHHHHCC
T ss_pred cccCCCCcCCHHHHHHH
Confidence 33333333333333333
No 57
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.51 E-value=0.03 Score=29.51 Aligned_cols=21 Identities=43% Similarity=0.770 Sum_probs=18.4
Q ss_pred ccccccccccCChhHHHHHHhh
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELS 397 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~ 397 (420)
..|+.||++| ..++|..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4699999999 88999999864
No 58
>PRK04860 hypothetical protein; Provisional
Probab=94.21 E-value=0.022 Score=45.94 Aligned_cols=37 Identities=22% Similarity=0.809 Sum_probs=25.7
Q ss_pred ccccccccccccCchHHHHHHhhccCCCccccccccccccC
Q psy3231 123 KYKCKLCARMYRYKWNLKAHLKMHKGPKIFTCAQCDKAFSL 163 (420)
Q Consensus 123 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 163 (420)
+|.|. |+. ....+.+|.++|.++++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 46776 766 55667777777777777777777766653
No 59
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.66 E-value=0.046 Score=31.47 Aligned_cols=22 Identities=27% Similarity=0.437 Sum_probs=18.6
Q ss_pred cccccccccccCChhHHHHHHh
Q psy3231 375 LQKCRYCQRMFRNEDKLTAHEL 396 (420)
Q Consensus 375 ~~~C~~C~~~f~~~~~l~~H~~ 396 (420)
+|.|.+|+..|.+..++..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4778999999998888888886
No 60
>KOG2893|consensus
Probab=93.39 E-value=0.025 Score=47.22 Aligned_cols=46 Identities=28% Similarity=0.568 Sum_probs=35.9
Q ss_pred cCcchhhcCCCHHHHHHHHHhhcCCCCccccccchhccCChhHHHHH-HhhC
Q psy3231 262 RCSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCYDSFETKSTLVDH-FFHH 312 (420)
Q Consensus 262 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H-~~~h 312 (420)
.|.+|++.|.....|.+|++..| |+|.+|.+..-+--.|..| +.+|
T Consensus 12 wcwycnrefddekiliqhqkakh-----fkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH-----FKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc-----ceeeeehhhhccCCCceeehhhhh
Confidence 58888888988888888877655 8899998887777777777 4444
No 61
>KOG2785|consensus
Probab=92.07 E-value=0.3 Score=44.33 Aligned_cols=23 Identities=30% Similarity=0.706 Sum_probs=20.1
Q ss_pred ccccccCccccCCHHHHHHHHHH
Q psy3231 94 KFKCEMCPKSFDHKSNIRRHMAA 116 (420)
Q Consensus 94 ~~~C~~C~~~f~~~~~l~~H~~~ 116 (420)
.|.|..|...|.+....+.|++.
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKS 25 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKS 25 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhh
Confidence 48999999999999999999863
No 62
>KOG4173|consensus
Probab=92.00 E-value=0.12 Score=42.29 Aligned_cols=52 Identities=31% Similarity=0.686 Sum_probs=37.8
Q ss_pred cCcchhhcCCCHHHHHHHHHhhcC---------CCCcccccc--chhccCChhHHHHHH-hhCC
Q psy3231 262 RCSECEKRFATEDIMRQHFRNYHN---------KEDAYVCNY--CYDSFETKSTLVDHF-FHHG 313 (420)
Q Consensus 262 ~C~~C~~~f~~~~~l~~H~~~~H~---------~~~~~~C~~--C~~~f~~~~~l~~H~-~~h~ 313 (420)
.|..|.+.|++...|..|+...|. |...|.|-+ |+..|.+...-..|+ +.|.
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 577777777777777777766663 456788855 888888888888885 5563
No 63
>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=91.72 E-value=0.12 Score=29.76 Aligned_cols=23 Identities=26% Similarity=0.644 Sum_probs=17.3
Q ss_pred cccccccccccCChhHHHHHHHH
Q psy3231 339 CFTCPFCQRKYKIEKHLEKHIES 361 (420)
Q Consensus 339 ~~~C~~C~~~f~~~~~l~~H~~~ 361 (420)
+|.|++|+..|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 46788888888877788887754
No 64
>KOG2785|consensus
Probab=91.45 E-value=0.41 Score=43.52 Aligned_cols=53 Identities=17% Similarity=0.349 Sum_probs=39.4
Q ss_pred CCccCcchhhcCCCHHHHHHHHHhhcCC----------------------CCccccccch---hccCChhHHHHHHhh
Q psy3231 259 KFYRCSECEKRFATEDIMRQHFRNYHNK----------------------EDAYVCNYCY---DSFETKSTLVDHFFH 311 (420)
Q Consensus 259 ~~~~C~~C~~~f~~~~~l~~H~~~~H~~----------------------~~~~~C~~C~---~~f~~~~~l~~H~~~ 311 (420)
.|-.|-.|++.+.+-..-..||...|+- ..-|.|-.|+ +.|.+....+.||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 3567888888888888888888876642 1237788888 888888888888753
No 65
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.48 E-value=0.058 Score=52.05 Aligned_cols=148 Identities=19% Similarity=0.282 Sum_probs=101.2
Q ss_pred CCccCcchhhcCCCHHHHHHHHHh-hcCCC--Cccccc--cchhccCChhHHHHHHhhCC--CcccCCc--cCCcCCCch
Q psy3231 259 KFYRCSECEKRFATEDIMRQHFRN-YHNKE--DAYVCN--YCYDSFETKSTLVDHFFHHG--NPYMCNH--CFLMFPDEK 329 (420)
Q Consensus 259 ~~~~C~~C~~~f~~~~~l~~H~~~-~H~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~--~~~~C~~--C~~~f~~~~ 329 (420)
.++.|..|...|.....|..|.+. .|.++ +++.|+ .|++.|.....+..|...|. .++.+.. +...+....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 368999999999999999999994 59999 999999 79999999999999998884 3444433 333333322
Q ss_pred hhhccc------C---CCcccccc--cccccCChhHHHHHHHHhhccCCccccccccccccccccccCChhHHHHHHhhh
Q psy3231 330 NLRNHE------C---TSCFTCPF--CQRKYKIEKHLEKHIESCIQLNPTTTVLKTLQKCRYCQRMFRNEDKLTAHELSH 398 (420)
Q Consensus 330 ~l~~H~------~---~~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H 398 (420)
.-..+. . ...+.+.. |-..+.....+..|...+. ......+.+..|.+.|.....+..|++.|
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 441 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHL------SFRPYNCKNPPCSKSFNRHYNLIPHKKIH 441 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhcccccccccccccc------ccCCcCCCCCcchhhccCccccccccccc
Confidence 211111 0 02333332 5555555555555544311 11123567899999999999999999999
Q ss_pred cCCcccccccceee
Q psy3231 399 TMEKTFYRNVATVS 412 (420)
Q Consensus 399 ~~~~~~~c~~c~~~ 412 (420)
....++.+...+..
T Consensus 442 ~~~~~~~~~~~~~~ 455 (467)
T COG5048 442 TNHAPLLCSILKSF 455 (467)
T ss_pred ccCCceeecccccc
Confidence 98887776655543
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.53 E-value=0.18 Score=31.67 Aligned_cols=31 Identities=23% Similarity=0.481 Sum_probs=25.8
Q ss_pred CccCCccccccCccccCCHHHHHHHHHHhcC
Q psy3231 89 SIQERKFKCEMCPKSFDHKSNIRRHMAATHD 119 (420)
Q Consensus 89 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 119 (420)
..++..+.|+.|+..|....+..+|+...|.
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3466778999999999999999999887764
No 67
>KOG4173|consensus
Probab=89.30 E-value=0.26 Score=40.44 Aligned_cols=77 Identities=23% Similarity=0.591 Sum_probs=59.0
Q ss_pred CCcccccc--CccccCCHHHHHHHHHHhcCCCCccccccccccccCchHHHHHHhhc----------cCCCcccc--ccc
Q psy3231 92 ERKFKCEM--CPKSFDHKSNIRRHMAATHDLQKKYKCKLCARMYRYKWNLKAHLKMH----------KGPKIFTC--AQC 157 (420)
Q Consensus 92 ~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h----------~~~~~~~C--~~C 157 (420)
...|.|++ |...|.+......|....|+ ..|.+|.+.|.+..-|..|+... .|...|+| ..|
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY~~~h~----~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgC 152 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHYHTLHG----NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGC 152 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhhhhccc----chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhh
Confidence 45578876 88899988888888765564 47999999999988888887543 24567888 458
Q ss_pred cccccChHHHHHHHH
Q psy3231 158 DKAFSLKSNLSKHVR 172 (420)
Q Consensus 158 ~~~f~~~~~l~~H~~ 172 (420)
+..|.+...-..|+-
T Consensus 153 t~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 153 TEKFKTSRDRKDHMI 167 (253)
T ss_pred hhhhhhhhhhhhHHH
Confidence 888888888777764
No 68
>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=88.74 E-value=0.2 Score=28.45 Aligned_cols=10 Identities=10% Similarity=0.069 Sum_probs=5.9
Q ss_pred ccccccccee
Q psy3231 402 KTFYRNVATV 411 (420)
Q Consensus 402 ~~~~c~~c~~ 411 (420)
.|+.|++||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 5556666654
No 69
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.72 E-value=1 Score=33.70 Aligned_cols=88 Identities=22% Similarity=0.318 Sum_probs=55.9
Q ss_pred cccccchhccCChhHHHHHHhhCCCcccCCccCCcCCCchhhhc---ccCC-Ccc------------cccccccccCChh
Q psy3231 290 YVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLMFPDEKNLRN---HECT-SCF------------TCPFCQRKYKIEK 353 (420)
Q Consensus 290 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~~~l~~---H~~~-~~~------------~C~~C~~~f~~~~ 353 (420)
|.|+.|+-..- .-|..|++||-+.....+|.+ |+-. ++| .|--|+..|....
T Consensus 2 Y~CPrC~skvC------------~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~ 69 (112)
T TIGR00622 2 YFCPQCRAKVC------------ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPP 69 (112)
T ss_pred ccCCCCCCCcc------------CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcc
Confidence 67777764432 247789999998888777754 3221 111 3777777776433
Q ss_pred HHHHHHHHhhccCCccccccccccccccccccCChhHHHHHHhhhc
Q psy3231 354 HLEKHIESCIQLNPTTTVLKTLQKCRYCQRMFRNEDKLTAHELSHT 399 (420)
Q Consensus 354 ~l~~H~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~ 399 (420)
... +........|.|+.|..-|-..-++-.|...|.
T Consensus 70 ~~~----------~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 70 VSP----------FDELKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ccc----------ccccccccceeCCCCCCccccccchhhhhhccC
Confidence 110 000122346889999999998888888887775
No 70
>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=87.17 E-value=0.95 Score=34.12 Aligned_cols=73 Identities=18% Similarity=0.337 Sum_probs=46.0
Q ss_pred CCccccccCccccCCHHHHHHHHHHhcCCCCccccccccccccCchHHHHHHhhcc-----------------------C
Q psy3231 92 ERKFKCEMCPKSFDHKSNIRRHMAATHDLQKKYKCKLCARMYRYKWNLKAHLKMHK-----------------------G 148 (420)
Q Consensus 92 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~-----------------------~ 148 (420)
-+...|..|+..... +++..|++..|.......- ..+..-.+... .
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~----------~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~ 77 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKRHHILKSQER----------QRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPV 77 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHH----------HHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCC
Confidence 355789999988766 8899999866643211100 01111111100 0
Q ss_pred CCcccc----ccccccccChHHHHHHHHHhc
Q psy3231 149 PKIFTC----AQCDKAFSLKSNLSKHVRHHM 175 (420)
Q Consensus 149 ~~~~~C----~~C~~~f~~~~~l~~H~~~h~ 175 (420)
...|.| ..|++.+.+...+..|++.++
T Consensus 78 ~~G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 78 YDGYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CCCeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 123899 999999999999999988654
No 71
>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=85.16 E-value=0.53 Score=24.98 Aligned_cols=9 Identities=33% Similarity=1.150 Sum_probs=4.9
Q ss_pred ccccccccc
Q psy3231 341 TCPFCQRKY 349 (420)
Q Consensus 341 ~C~~C~~~f 349 (420)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 355555555
No 72
>KOG2893|consensus
Probab=84.72 E-value=0.24 Score=41.61 Aligned_cols=41 Identities=34% Similarity=0.560 Sum_probs=23.8
Q ss_pred CCccCCcCCCchhhhcccCCCcccccccccccCChhHHHHH
Q psy3231 318 CNHCFLMFPDEKNLRNHECTSCFTCPFCQRKYKIEKHLEKH 358 (420)
Q Consensus 318 C~~C~~~f~~~~~l~~H~~~~~~~C~~C~~~f~~~~~l~~H 358 (420)
|=.|..-|.+..-|.+|...+.|+|.+|.+..-+--.|..|
T Consensus 13 cwycnrefddekiliqhqkakhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhhccceeeeehhhhccCCCceee
Confidence 44555555555566666655666666666665555555554
No 73
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=83.92 E-value=0.51 Score=29.71 Aligned_cols=31 Identities=16% Similarity=0.267 Sum_probs=25.3
Q ss_pred ccccccccccccccccCChhHHHHHHhhhcC
Q psy3231 370 TVLKTLQKCRYCQRMFRNEDKLTAHELSHTM 400 (420)
Q Consensus 370 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~ 400 (420)
..|+-.++|+-||+.|....++.+|...-++
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 4556678999999999999999999975444
No 74
>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=82.77 E-value=1.3 Score=33.30 Aligned_cols=25 Identities=16% Similarity=0.324 Sum_probs=23.3
Q ss_pred ccc----cccccccCChhHHHHHHhhhcC
Q psy3231 376 QKC----RYCQRMFRNEDKLTAHELSHTM 400 (420)
Q Consensus 376 ~~C----~~C~~~f~~~~~l~~H~~~H~~ 400 (420)
|.| ..|++.+.+...+..|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 789 9999999999999999998775
No 75
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=82.51 E-value=0.68 Score=44.56 Aligned_cols=54 Identities=26% Similarity=0.473 Sum_probs=34.5
Q ss_pred ccccCCCccccCCHHHHHccccc-cCCCC--Cceecc--cccccccChHHHHHHhhccC
Q psy3231 205 RFKCPCCERIFTSETRMRNHIDM-KHADE--NLFKCK--KCLKVFSDEIKFHLHGRAHA 258 (420)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~-~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~ 258 (420)
++.|..|...|.....|..|.+. .|.++ .++.|+ .|++.|.....+..|...|.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHT 347 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCccccc
Confidence 56677777777777777777642 56666 666666 56666666666666655554
No 76
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.48 E-value=1 Score=29.00 Aligned_cols=12 Identities=50% Similarity=1.157 Sum_probs=6.7
Q ss_pred CCCcccCCccCC
Q psy3231 312 HGNPYMCNHCFL 323 (420)
Q Consensus 312 h~~~~~C~~C~~ 323 (420)
++++|.|+.||.
T Consensus 47 ~g~~Y~Cp~CGF 58 (61)
T COG2888 47 LGNPYRCPKCGF 58 (61)
T ss_pred cCCceECCCcCc
Confidence 345666666654
No 77
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.91 E-value=1.1 Score=33.40 Aligned_cols=24 Identities=29% Similarity=0.533 Sum_probs=12.3
Q ss_pred ccccccchhccCChhHHHHHHhhC
Q psy3231 289 AYVCNYCYDSFETKSTLVDHFFHH 312 (420)
Q Consensus 289 ~~~C~~C~~~f~~~~~l~~H~~~h 312 (420)
.|.|+.|...|-..-+...|...|
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ceeCCCCCCccccccchhhhhhcc
Confidence 355555555555555555554444
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=80.03 E-value=0.82 Score=26.09 Aligned_cols=11 Identities=18% Similarity=0.504 Sum_probs=6.2
Q ss_pred ccccccccccC
Q psy3231 376 QKCRYCQRMFR 386 (420)
Q Consensus 376 ~~C~~C~~~f~ 386 (420)
|.|..||+.+.
T Consensus 3 ~~C~~CG~i~~ 13 (34)
T cd00729 3 WVCPVCGYIHE 13 (34)
T ss_pred EECCCCCCEeE
Confidence 55666665543
No 79
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=78.78 E-value=0.26 Score=42.25 Aligned_cols=11 Identities=27% Similarity=0.470 Sum_probs=5.2
Q ss_pred cccccchhccC
Q psy3231 290 YVCNYCYDSFE 300 (420)
Q Consensus 290 ~~C~~C~~~f~ 300 (420)
..||.||.++.
T Consensus 49 ~vCP~CgyA~~ 59 (214)
T PF09986_consen 49 WVCPHCGYAAF 59 (214)
T ss_pred EECCCCCCccc
Confidence 34555554443
No 80
>KOG2186|consensus
Probab=77.33 E-value=1.5 Score=37.54 Aligned_cols=45 Identities=20% Similarity=0.617 Sum_probs=21.2
Q ss_pred cccccccccccCchHHHHHHhhccCCCccccccccccccChHHHHHHH
Q psy3231 124 YKCKLCARMYRYKWNLKAHLKMHKGPKIFTCAQCDKAFSLKSNLSKHV 171 (420)
Q Consensus 124 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 171 (420)
|.|..||....- ..+..|+...++ .-|.|-.|+..|.. .+...|.
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhh
Confidence 445555544442 234445544444 34555555555544 4444444
No 81
>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=76.76 E-value=1.4 Score=33.03 Aligned_cols=30 Identities=30% Similarity=0.651 Sum_probs=15.7
Q ss_pred cccccchhccCChhHHHHHHhhCCCcccCCccCCcCCCc
Q psy3231 290 YVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLMFPDE 328 (420)
Q Consensus 290 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~ 328 (420)
..|+.||.+|.... ..|..|+.||..|.-.
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 45666666655432 1455555555555444
No 82
>PF12907 zf-met2: Zinc-binding
Probab=76.25 E-value=2.8 Score=24.91 Aligned_cols=32 Identities=28% Similarity=0.572 Sum_probs=21.3
Q ss_pred ccCcchhhcC---CCHHHHHHHHHhhcCCCCcccc
Q psy3231 261 YRCSECEKRF---ATEDIMRQHFRNYHNKEDAYVC 292 (420)
Q Consensus 261 ~~C~~C~~~f---~~~~~l~~H~~~~H~~~~~~~C 292 (420)
++|.+|-..| .+...|..|....|....+-.|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~C 36 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEEC 36 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHc
Confidence 4677777444 5567788888877876544444
No 83
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=76.14 E-value=1.8 Score=28.03 Aligned_cols=11 Identities=45% Similarity=1.165 Sum_probs=5.9
Q ss_pred CCcccCCccCC
Q psy3231 313 GNPYMCNHCFL 323 (420)
Q Consensus 313 ~~~~~C~~C~~ 323 (420)
+++|.|+.||.
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 35555555554
No 84
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=74.69 E-value=1.7 Score=25.39 Aligned_cols=7 Identities=43% Similarity=0.990 Sum_probs=2.6
Q ss_pred cccchhc
Q psy3231 292 CNYCYDS 298 (420)
Q Consensus 292 C~~C~~~ 298 (420)
|+.|+..
T Consensus 5 CP~C~~~ 11 (38)
T TIGR02098 5 CPNCKTS 11 (38)
T ss_pred CCCCCCE
Confidence 3333333
No 85
>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=74.43 E-value=1.8 Score=32.34 Aligned_cols=15 Identities=27% Similarity=0.439 Sum_probs=8.0
Q ss_pred ccccccccccccCCh
Q psy3231 374 TLQKCRYCQRMFRNE 388 (420)
Q Consensus 374 ~~~~C~~C~~~f~~~ 388 (420)
.|-.|++||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 344466666665544
No 86
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=74.37 E-value=1.1 Score=38.42 Aligned_cols=12 Identities=25% Similarity=0.631 Sum_probs=8.2
Q ss_pred ccccccccccCC
Q psy3231 340 FTCPFCQRKYKI 351 (420)
Q Consensus 340 ~~C~~C~~~f~~ 351 (420)
..|+.||.++..
T Consensus 49 ~vCP~CgyA~~~ 60 (214)
T PF09986_consen 49 WVCPHCGYAAFE 60 (214)
T ss_pred EECCCCCCcccc
Confidence 467777777664
No 87
>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=72.29 E-value=1.3 Score=26.34 Aligned_cols=9 Identities=33% Similarity=0.811 Sum_probs=3.5
Q ss_pred cCCccCCcC
Q psy3231 317 MCNHCFLMF 325 (420)
Q Consensus 317 ~C~~C~~~f 325 (420)
+|..||..|
T Consensus 7 ~C~~Cg~~f 15 (41)
T smart00834 7 RCEDCGHTF 15 (41)
T ss_pred EcCCCCCEE
Confidence 334444333
No 88
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=72.23 E-value=1.8 Score=35.01 Aligned_cols=12 Identities=33% Similarity=0.598 Sum_probs=6.1
Q ss_pred CCCCccccccch
Q psy3231 285 NKEDAYVCNYCY 296 (420)
Q Consensus 285 ~~~~~~~C~~C~ 296 (420)
.++.|-+||+||
T Consensus 145 ~ge~P~~CPiCg 156 (166)
T COG1592 145 EGEAPEVCPICG 156 (166)
T ss_pred cCCCCCcCCCCC
Confidence 334555555555
No 89
>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=71.96 E-value=4.2 Score=21.55 Aligned_cols=20 Identities=35% Similarity=0.838 Sum_probs=12.9
Q ss_pred cccccccccCChhHHHHHHHH
Q psy3231 341 TCPFCQRKYKIEKHLEKHIES 361 (420)
Q Consensus 341 ~C~~C~~~f~~~~~l~~H~~~ 361 (420)
.|++|++.+ ....++.|+..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 3 QCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHHH
Confidence 467777776 45666666654
No 90
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=71.47 E-value=1.2 Score=26.84 Aligned_cols=10 Identities=40% Similarity=0.943 Sum_probs=4.2
Q ss_pred ccCCccCCcC
Q psy3231 316 YMCNHCFLMF 325 (420)
Q Consensus 316 ~~C~~C~~~f 325 (420)
|.|..||..|
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 3444444444
No 91
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=69.95 E-value=3.6 Score=23.82 Aligned_cols=7 Identities=29% Similarity=1.042 Sum_probs=2.8
Q ss_pred ccccccc
Q psy3231 378 CRYCQRM 384 (420)
Q Consensus 378 C~~C~~~ 384 (420)
|+.|+..
T Consensus 28 C~~C~~~ 34 (36)
T PF13717_consen 28 CSKCGHV 34 (36)
T ss_pred CCCCCCE
Confidence 4444333
No 92
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=69.70 E-value=2.2 Score=26.02 Aligned_cols=26 Identities=12% Similarity=0.077 Sum_probs=13.9
Q ss_pred ccccccccccCChhHHHHHHhhhcCCcccccccceee
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATVS 412 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~~ 412 (420)
|.|..||..|... ...+..|+.||.-
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 5566666655433 2345556666543
No 93
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=69.06 E-value=3.6 Score=23.98 Aligned_cols=12 Identities=33% Similarity=0.924 Sum_probs=6.0
Q ss_pred ccCCCccccCCH
Q psy3231 207 KCPCCERIFTSE 218 (420)
Q Consensus 207 ~C~~C~~~f~~~ 218 (420)
.||.|+..|.-.
T Consensus 4 ~CP~C~~~f~v~ 15 (37)
T PF13719_consen 4 TCPNCQTRFRVP 15 (37)
T ss_pred ECCCCCceEEcC
Confidence 455555555443
No 94
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=68.13 E-value=1.9 Score=27.30 Aligned_cols=9 Identities=33% Similarity=0.711 Sum_probs=3.6
Q ss_pred cCCccCCcC
Q psy3231 317 MCNHCFLMF 325 (420)
Q Consensus 317 ~C~~C~~~f 325 (420)
.|..||..|
T Consensus 7 ~C~~Cg~~f 15 (52)
T TIGR02605 7 RCTACGHRF 15 (52)
T ss_pred EeCCCCCEe
Confidence 344444433
No 95
>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=66.99 E-value=2.7 Score=23.60 Aligned_cols=7 Identities=43% Similarity=1.241 Sum_probs=2.6
Q ss_pred ccccccc
Q psy3231 341 TCPFCQR 347 (420)
Q Consensus 341 ~C~~C~~ 347 (420)
+|+.||.
T Consensus 19 rC~~CG~ 25 (32)
T PF03604_consen 19 RCPECGH 25 (32)
T ss_dssp SBSSSS-
T ss_pred ECCcCCC
Confidence 3444443
No 96
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=66.44 E-value=2.1 Score=26.38 Aligned_cols=7 Identities=43% Similarity=1.554 Sum_probs=2.9
Q ss_pred ccccccc
Q psy3231 341 TCPFCQR 347 (420)
Q Consensus 341 ~C~~C~~ 347 (420)
.|+.||.
T Consensus 23 ~Cp~CG~ 29 (46)
T PRK00398 23 RCPYCGY 29 (46)
T ss_pred ECCCCCC
Confidence 3444443
No 97
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=65.81 E-value=2.6 Score=33.82 Aligned_cols=11 Identities=18% Similarity=0.748 Sum_probs=5.0
Q ss_pred ccccccccccC
Q psy3231 340 FTCPFCQRKYK 350 (420)
Q Consensus 340 ~~C~~C~~~f~ 350 (420)
++|+.||++|.
T Consensus 29 ~~c~~c~~~f~ 39 (154)
T PRK00464 29 RECLACGKRFT 39 (154)
T ss_pred eeccccCCcce
Confidence 44444444444
No 98
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=64.91 E-value=2.5 Score=33.84 Aligned_cols=35 Identities=20% Similarity=0.281 Sum_probs=19.8
Q ss_pred ccccccccccccCChhHHHH-HHhhhcCCcccccccceeeE
Q psy3231 374 TLQKCRYCQRMFRNEDKLTA-HELSHTMEKTFYRNVATVSV 413 (420)
Q Consensus 374 ~~~~C~~C~~~f~~~~~l~~-H~~~H~~~~~~~c~~c~~~~ 413 (420)
..|.|+.|+..|+...++.. . .+..|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d-----~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLD-----MDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcC-----CCCcEECCCCCCEE
Confidence 45677777777765444332 1 12337777777654
No 99
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=62.74 E-value=4.6 Score=30.82 Aligned_cols=30 Identities=20% Similarity=0.235 Sum_probs=14.9
Q ss_pred cccccchhccCChhHHHHHHhhCCCcccCCccCCcCCCc
Q psy3231 290 YVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLMFPDE 328 (420)
Q Consensus 290 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~f~~~ 328 (420)
..|+.||++|.... ..|..|+.||..|...
T Consensus 10 r~Cp~cg~kFYDLn---------k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDLN---------RRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccccC---------CCCccCCCcCCccCcc
Confidence 45555555555432 1455555555555433
No 100
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=62.57 E-value=4.3 Score=32.46 Aligned_cols=35 Identities=14% Similarity=0.336 Sum_probs=16.8
Q ss_pred CccccccchhccCChhHHHH-HHhhCCCcccCCccCCcC
Q psy3231 288 DAYVCNYCYDSFETKSTLVD-HFFHHGNPYMCNHCFLMF 325 (420)
Q Consensus 288 ~~~~C~~C~~~f~~~~~l~~-H~~~h~~~~~C~~C~~~f 325 (420)
.-|.|+.|+..|.....+.. . ..+.|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d---~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLD---MDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcC---CCCcEECCCCCCEE
Confidence 34666666666654333222 1 12335666665543
No 101
>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=61.15 E-value=3.4 Score=33.46 Aligned_cols=30 Identities=10% Similarity=0.058 Sum_probs=19.1
Q ss_pred ccccccccccccCChhHHHHHHhhhcCCcccccccceee
Q psy3231 374 TLQKCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATVS 412 (420)
Q Consensus 374 ~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~~ 412 (420)
.-|.|+.|+..|+...++. .-|.|+.||..
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 3466777777777666664 24677777654
No 102
>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=59.98 E-value=9.4 Score=23.14 Aligned_cols=26 Identities=35% Similarity=0.722 Sum_probs=13.8
Q ss_pred CCccccccCccccCC----HHHHHHHHHHh
Q psy3231 92 ERKFKCEMCPKSFDH----KSNIRRHMAAT 117 (420)
Q Consensus 92 ~~~~~C~~C~~~f~~----~~~l~~H~~~~ 117 (420)
.....|..|++.+.. .+.|..|++..
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~ 43 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKK 43 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhh
Confidence 344667777777655 36677776433
No 103
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=59.20 E-value=6 Score=24.88 Aligned_cols=8 Identities=25% Similarity=0.978 Sum_probs=3.0
Q ss_pred CCccCCcC
Q psy3231 318 CNHCFLMF 325 (420)
Q Consensus 318 C~~C~~~f 325 (420)
|.+||..+
T Consensus 4 C~~CgyiY 11 (50)
T cd00730 4 CRICGYIY 11 (50)
T ss_pred CCCCCeEE
Confidence 33333333
No 104
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=58.98 E-value=6.4 Score=30.06 Aligned_cols=15 Identities=20% Similarity=0.208 Sum_probs=8.6
Q ss_pred ccccccccccccCCh
Q psy3231 374 TLQKCRYCQRMFRNE 388 (420)
Q Consensus 374 ~~~~C~~C~~~f~~~ 388 (420)
.|-.|++||..|...
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 344566666666444
No 105
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=58.41 E-value=3.8 Score=33.92 Aligned_cols=29 Identities=14% Similarity=0.218 Sum_probs=17.9
Q ss_pred cccccccccccCChhHHHHHHhhhcCCcccccccceee
Q psy3231 375 LQKCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATVS 412 (420)
Q Consensus 375 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~~ 412 (420)
-|.|+.|+..|+...++. .-|.|+.||..
T Consensus 117 ~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred EEECCCCCcEEeHHHHhh---------cCCcCCCCCCC
Confidence 466777776666666652 24667777653
No 106
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=57.65 E-value=7.3 Score=24.43 Aligned_cols=22 Identities=32% Similarity=0.771 Sum_probs=13.1
Q ss_pred cccccccccCCh-----hHHHHHHh-hh
Q psy3231 377 KCRYCQRMFRNE-----DKLTAHEL-SH 398 (420)
Q Consensus 377 ~C~~C~~~f~~~-----~~l~~H~~-~H 398 (420)
.|.+|++.+... +.|.+|++ +|
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 466666666544 46666666 44
No 107
>PHA00626 hypothetical protein
Probab=57.57 E-value=5.1 Score=25.47 Aligned_cols=16 Identities=13% Similarity=0.096 Sum_probs=13.2
Q ss_pred cccccccccccccCCh
Q psy3231 373 KTLQKCRYCQRMFRNE 388 (420)
Q Consensus 373 ~~~~~C~~C~~~f~~~ 388 (420)
...|+|+.||+.|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 3579999999999764
No 108
>KOG2272|consensus
Probab=57.52 E-value=6.7 Score=33.61 Aligned_cols=114 Identities=19% Similarity=0.376 Sum_probs=55.0
Q ss_pred CceecccccccccChHHHHHHhhc---------c---CCCccCcchhhcCCCHHHHHHHHHhhcCCCCccccccchhccC
Q psy3231 233 NLFKCKKCLKVFSDEIKFHLHGRA---------H---AKFYRCSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCYDSFE 300 (420)
Q Consensus 233 ~~~~C~~C~~~f~~~~~l~~H~~~---------h---~~~~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~ 300 (420)
.-|.|++|.+...+...+..-.+. - ...|.|..|...-.. ..|.---...| ..-|+|..|++...
T Consensus 98 ~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~-~~l~fr~d~yH--~yHFkCt~C~keL~ 174 (332)
T KOG2272|consen 98 ACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDE-QPLTFRGDPYH--PYHFKCTTCGKELT 174 (332)
T ss_pred ccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccc-ccccccCCCCC--ccceeccccccccc
Confidence 347888888877665544432221 1 135777777432222 21111101111 12378888887766
Q ss_pred ChhHHHHH----HhhCCCcccCCccCCcCCC-----chhhhcccCCCcccccccccccC
Q psy3231 301 TKSTLVDH----FFHHGNPYMCNHCFLMFPD-----EKNLRNHECTSCFTCPFCQRKYK 350 (420)
Q Consensus 301 ~~~~l~~H----~~~h~~~~~C~~C~~~f~~-----~~~l~~H~~~~~~~C~~C~~~f~ 350 (420)
+.+.-..- ++-| ..+.+++||..-.- ...|-.|--+..|.|..|.+.|-
T Consensus 175 sdaRevk~eLyClrCh-D~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFl 232 (332)
T KOG2272|consen 175 SDAREVKGELYCLRCH-DKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFL 232 (332)
T ss_pred chhhhhccceeccccc-cccCCcccccccCchHHHHHHHhccccchhheeehhcCCccc
Confidence 54321111 0111 22445555443222 12334443345688999999885
No 109
>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=57.27 E-value=5.8 Score=33.80 Aligned_cols=26 Identities=35% Similarity=0.685 Sum_probs=19.9
Q ss_pred CccCcchhhcCCCHHHHHHHHHhhcC
Q psy3231 260 FYRCSECEKRFATEDIMRQHFRNYHN 285 (420)
Q Consensus 260 ~~~C~~C~~~f~~~~~l~~H~~~~H~ 285 (420)
.|.|++|+|.|.....+..|+.+.|.
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred EECCCCCCcccCChHHHHHHHhhcCH
Confidence 48888899999999999999988886
No 110
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=57.20 E-value=9.2 Score=33.92 Aligned_cols=26 Identities=23% Similarity=0.451 Sum_probs=22.5
Q ss_pred ccccccccccccCChhHHHHHHhhhc
Q psy3231 374 TLQKCRYCQRMFRNEDKLTAHELSHT 399 (420)
Q Consensus 374 ~~~~C~~C~~~f~~~~~l~~H~~~H~ 399 (420)
..|.|+.|...|-..-+.-.|...|-
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHhh
Confidence 57999999999999999999987763
No 111
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=55.83 E-value=4.2 Score=27.83 Aligned_cols=12 Identities=25% Similarity=0.830 Sum_probs=6.1
Q ss_pred cccc--ccccccCC
Q psy3231 376 QKCR--YCQRMFRN 387 (420)
Q Consensus 376 ~~C~--~C~~~f~~ 387 (420)
+.|. .||.+|+.
T Consensus 28 ~qC~N~eCg~tF~t 41 (72)
T PRK09678 28 HQCQNVNCSATFIT 41 (72)
T ss_pred eecCCCCCCCEEEE
Confidence 3455 55555544
No 112
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=55.63 E-value=7.2 Score=27.50 Aligned_cols=31 Identities=19% Similarity=0.410 Sum_probs=16.3
Q ss_pred CcccCCccCCcCCCchhhhcccCCCcccccccccccC
Q psy3231 314 NPYMCNHCFLMFPDEKNLRNHECTSCFTCPFCQRKYK 350 (420)
Q Consensus 314 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~C~~C~~~f~ 350 (420)
.+|.|+.|++.-.. -..+..+.|..||..|.
T Consensus 34 ~~~~Cp~C~~~~Vk------R~a~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRTTVK------RIATGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCccee------eeccCeEEcCCCCCeec
Confidence 45666666654111 11224566666666665
No 113
>KOG2186|consensus
Probab=55.57 E-value=7.5 Score=33.49 Aligned_cols=45 Identities=20% Similarity=0.553 Sum_probs=23.8
Q ss_pred ccCcchhhcCCCHHHHHHHHHhhcCCCCccccccchhccCChhHHHHHH
Q psy3231 261 YRCSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCYDSFETKSTLVDHF 309 (420)
Q Consensus 261 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~ 309 (420)
|.|.+||....... |.+|+..-++ .-|.|-.|+..|.. .++..|.
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn--~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN--AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC--CeeEEeeccccccc-chhhhhh
Confidence 45555655554433 4446555333 44666666666655 4555553
No 114
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=54.25 E-value=8.7 Score=39.35 Aligned_cols=10 Identities=20% Similarity=0.716 Sum_probs=6.7
Q ss_pred ccCCccCCcC
Q psy3231 316 YMCNHCFLMF 325 (420)
Q Consensus 316 ~~C~~C~~~f 325 (420)
..|..||..+
T Consensus 436 l~C~~Cg~v~ 445 (730)
T COG1198 436 LLCRDCGYIA 445 (730)
T ss_pred eecccCCCcc
Confidence 4577777765
No 115
>KOG2807|consensus
Probab=53.27 E-value=17 Score=32.65 Aligned_cols=27 Identities=22% Similarity=0.435 Sum_probs=21.6
Q ss_pred cccccccccccccCChhHHHHHHhhhc
Q psy3231 373 KTLQKCRYCQRMFRNEDKLTAHELSHT 399 (420)
Q Consensus 373 ~~~~~C~~C~~~f~~~~~l~~H~~~H~ 399 (420)
...|.|+.|.-.|-..-+.-.|...|-
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred CCcEEchhccceeeccchHHHHhhhhc
Confidence 356889999999988888888877763
No 116
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=53.08 E-value=9.3 Score=29.44 Aligned_cols=10 Identities=40% Similarity=0.840 Sum_probs=4.1
Q ss_pred ccccchhccC
Q psy3231 291 VCNYCYDSFE 300 (420)
Q Consensus 291 ~C~~C~~~f~ 300 (420)
+|..||+.|.
T Consensus 3 ~Ct~Cg~~f~ 12 (131)
T PF09845_consen 3 QCTKCGRVFE 12 (131)
T ss_pred ccCcCCCCcC
Confidence 3444444443
No 117
>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=52.85 E-value=4.7 Score=34.73 Aligned_cols=39 Identities=18% Similarity=0.477 Sum_probs=21.3
Q ss_pred CCCccccccccccccCchHHHHHHhhc--cCCCccccccccc
Q psy3231 120 LQKKYKCKLCARMYRYKWNLKAHLKMH--KGPKIFTCAQCDK 159 (420)
Q Consensus 120 ~~~~~~C~~C~~~f~~~~~l~~H~~~h--~~~~~~~C~~C~~ 159 (420)
+.+.|.|.+|+.-+- ..+-..|+..- .....|+|..|++
T Consensus 139 GGrif~CsfC~~flC-EDDQFEHQAsCQvLe~E~~KC~SCNr 179 (314)
T PF06524_consen 139 GGRIFKCSFCDNFLC-EDDQFEHQASCQVLESETFKCQSCNR 179 (314)
T ss_pred CCeEEEeecCCCeee-ccchhhhhhhhhhhhccccccccccc
Confidence 446788888865433 23333454332 1234577777765
No 118
>PF14353 CpXC: CpXC protein
Probab=52.30 E-value=1.9 Score=33.62 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=11.0
Q ss_pred cccCCccCCcCCCchhhhccc
Q psy3231 315 PYMCNHCFLMFPDEKNLRNHE 335 (420)
Q Consensus 315 ~~~C~~C~~~f~~~~~l~~H~ 335 (420)
.|.|+.||..|.-...+.-|-
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D 58 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHD 58 (128)
T ss_pred EEECCCCCCceecCCCEEEEc
Confidence 455555555555544444443
No 119
>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=52.16 E-value=14 Score=29.90 Aligned_cols=12 Identities=8% Similarity=0.467 Sum_probs=5.3
Q ss_pred cccccccccccC
Q psy3231 124 YKCKLCARMYRY 135 (420)
Q Consensus 124 ~~C~~C~~~f~~ 135 (420)
|.|+.|+..|..
T Consensus 110 Y~Cp~c~~r~tf 121 (158)
T TIGR00373 110 FICPNMCVRFTF 121 (158)
T ss_pred EECCCCCcEeeH
Confidence 444444444443
No 120
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=50.91 E-value=8.8 Score=31.16 Aligned_cols=24 Identities=29% Similarity=0.616 Sum_probs=15.9
Q ss_pred ccccCCCccccCCHHHHHccccccCCCCCceecccccc
Q psy3231 205 RFKCPCCERIFTSETRMRNHIDMKHADENLFKCKKCLK 242 (420)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~ 242 (420)
.|.|++||+. +.++.|-.|++||.
T Consensus 134 ~~vC~vCGy~--------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT--------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc--------------ccCCCCCcCCCCCC
Confidence 5778888753 33466777777763
No 121
>PF15269 zf-C2H2_7: Zinc-finger
Probab=49.98 E-value=10 Score=22.74 Aligned_cols=23 Identities=22% Similarity=0.258 Sum_probs=18.8
Q ss_pred cccccccccccCChhHHHHHHhh
Q psy3231 375 LQKCRYCQRMFRNEDKLTAHELS 397 (420)
Q Consensus 375 ~~~C~~C~~~f~~~~~l~~H~~~ 397 (420)
.|+|-.|.++...++.|-.||+.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 47888888888888888888864
No 122
>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=48.36 E-value=9.3 Score=29.74 Aligned_cols=25 Identities=20% Similarity=0.313 Sum_probs=15.1
Q ss_pred ccccccccccCChhHHHHHHhhhcCCcc
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELSHTMEKT 403 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~H~~~~~ 403 (420)
..|-.||+.|... ++|++.|+|-.|
T Consensus 73 i~clecGk~~k~L---krHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-S-H
T ss_pred eEEccCCcccchH---HHHHHHccCCCH
Confidence 4688888888754 888888877544
No 123
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=47.38 E-value=12 Score=38.45 Aligned_cols=40 Identities=23% Similarity=0.550 Sum_probs=25.5
Q ss_pred ccCcchhhcCCCHHHHHHHHHhhcCCCCccccccchhccCChhHHHHHHhhCCCcccCCccCCc
Q psy3231 261 YRCSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLM 324 (420)
Q Consensus 261 ~~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~ 324 (420)
++|+.|+..+ +.|...+...|.+||..- ..|..|+.||..
T Consensus 445 ~~Cp~Cd~~l-----------t~H~~~~~L~CH~Cg~~~-------------~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPL-----------TLHKATGQLRCHYCGYQE-------------PIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcce-----------EEecCCCeeEeCCCCCCC-------------CCCCCCCCCCCC
Confidence 3577776442 235555668888888641 257778888876
No 124
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=47.09 E-value=7.8 Score=24.17 Aligned_cols=11 Identities=36% Similarity=0.640 Sum_probs=7.0
Q ss_pred ccccccccccc
Q psy3231 375 LQKCRYCQRMF 385 (420)
Q Consensus 375 ~~~C~~C~~~f 385 (420)
.|+|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 46666666666
No 125
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=45.76 E-value=18 Score=29.95 Aligned_cols=13 Identities=31% Similarity=0.973 Sum_probs=5.5
Q ss_pred ccccccccccccC
Q psy3231 151 IFTCAQCDKAFSL 163 (420)
Q Consensus 151 ~~~C~~C~~~f~~ 163 (420)
-|.|+.|+..|+.
T Consensus 117 ~Y~Cp~C~~rytf 129 (178)
T PRK06266 117 FFFCPNCHIRFTF 129 (178)
T ss_pred EEECCCCCcEEeH
Confidence 3444444444433
No 126
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=45.67 E-value=12 Score=19.10 Aligned_cols=6 Identities=33% Similarity=0.938 Sum_probs=2.2
Q ss_pred CCccCC
Q psy3231 318 CNHCFL 323 (420)
Q Consensus 318 C~~C~~ 323 (420)
|+.||.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 333333
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=44.17 E-value=6.4 Score=33.95 Aligned_cols=25 Identities=16% Similarity=0.155 Sum_probs=15.6
Q ss_pred CccccccchhccCChhHHHHHHhhC
Q psy3231 288 DAYVCNYCYDSFETKSTLVDHFFHH 312 (420)
Q Consensus 288 ~~~~C~~C~~~f~~~~~l~~H~~~h 312 (420)
+++.||.|+........|..-.++|
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCcccccccceeeeecc
Confidence 5666777776666666665555555
No 128
>KOG2593|consensus
Probab=43.39 E-value=19 Score=33.82 Aligned_cols=35 Identities=14% Similarity=0.178 Sum_probs=20.0
Q ss_pred ccccccccccccCChhHHHHHHhhhcCCccccccccee
Q psy3231 374 TLQKCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATV 411 (420)
Q Consensus 374 ~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~ 411 (420)
.-|.|+.|.++|++..+++. .-.....|.|..|+-
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHh---hcccCceEEEecCCC
Confidence 45677777777766555443 222234567777764
No 129
>KOG3408|consensus
Probab=43.15 E-value=14 Score=27.94 Aligned_cols=24 Identities=25% Similarity=0.389 Sum_probs=20.3
Q ss_pred ccccccccccccCChhHHHHHHhh
Q psy3231 374 TLQKCRYCQRMFRNEDKLTAHELS 397 (420)
Q Consensus 374 ~~~~C~~C~~~f~~~~~l~~H~~~ 397 (420)
..|.|-.|.+-|.+..+|+.|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 567899999999999999999873
No 130
>KOG2071|consensus
Probab=42.65 E-value=15 Score=36.11 Aligned_cols=25 Identities=16% Similarity=0.341 Sum_probs=21.5
Q ss_pred ccceecchhhHHHHhhhhhhhhhcc
Q psy3231 3 LKTYTCDFCSAAFALKHSIADHIQT 27 (420)
Q Consensus 3 ~k~~~C~~C~~~f~~~~~l~~H~~~ 27 (420)
+.|..|..||.+|........||..
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~ 440 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDI 440 (579)
T ss_pred CCcchhcccccccccchhhhhHhhh
Confidence 4678999999999999888877776
No 131
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=41.90 E-value=17 Score=26.46 Aligned_cols=11 Identities=36% Similarity=0.839 Sum_probs=4.6
Q ss_pred cCCccCCcCCC
Q psy3231 317 MCNHCFLMFPD 327 (420)
Q Consensus 317 ~C~~C~~~f~~ 327 (420)
+|..||..|.+
T Consensus 4 ~CtrCG~vf~~ 14 (112)
T COG3364 4 QCTRCGEVFDD 14 (112)
T ss_pred eeccccccccc
Confidence 34444444443
No 132
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=41.65 E-value=17 Score=23.53 Aligned_cols=38 Identities=21% Similarity=0.454 Sum_probs=16.2
Q ss_pred cccccc--ccccccCchHHHHHHhhccCCCcccccc----ccccc
Q psy3231 123 KYKCKL--CARMYRYKWNLKAHLKMHKGPKIFTCAQ----CDKAF 161 (420)
Q Consensus 123 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~f 161 (420)
+..|+. |...+. ...|..|+...-..++..|+. |+..+
T Consensus 9 ~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~ 52 (60)
T PF02176_consen 9 PVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERV 52 (60)
T ss_dssp EEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EE
T ss_pred EeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCcc
Confidence 345555 333333 345556655444445555655 55544
No 133
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=41.56 E-value=23 Score=21.14 Aligned_cols=24 Identities=17% Similarity=0.476 Sum_probs=18.6
Q ss_pred ccccccccccC--ChhHHHHHHhhhc
Q psy3231 376 QKCRYCQRMFR--NEDKLTAHELSHT 399 (420)
Q Consensus 376 ~~C~~C~~~f~--~~~~l~~H~~~H~ 399 (420)
-.|+.||..+. ...+-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 46999998887 4677788888774
No 134
>KOG2272|consensus
Probab=41.05 E-value=16 Score=31.39 Aligned_cols=17 Identities=35% Similarity=1.157 Sum_probs=10.6
Q ss_pred CCCcccccccccccCCh
Q psy3231 336 CTSCFTCPFCQRKYKIE 352 (420)
Q Consensus 336 ~~~~~~C~~C~~~f~~~ 352 (420)
....|.|..|++....+
T Consensus 277 Cv~cf~Cs~Cdkkl~~K 293 (332)
T KOG2272|consen 277 CVECFSCSTCDKKLTQK 293 (332)
T ss_pred ccccccccccccccccc
Confidence 33567777777766544
No 135
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=40.31 E-value=24 Score=27.22 Aligned_cols=12 Identities=42% Similarity=0.952 Sum_probs=6.2
Q ss_pred ccccchhccCCh
Q psy3231 291 VCNYCYDSFETK 302 (420)
Q Consensus 291 ~C~~C~~~f~~~ 302 (420)
+||+|..+|++.
T Consensus 123 vCPvCkTSFKss 134 (140)
T PF05290_consen 123 VCPVCKTSFKSS 134 (140)
T ss_pred CCCccccccccc
Confidence 455555555543
No 136
>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=39.15 E-value=20 Score=21.02 Aligned_cols=22 Identities=23% Similarity=0.549 Sum_probs=9.8
Q ss_pred cccccccccccC-Ch-hHHHHHHh
Q psy3231 375 LQKCRYCQRMFR-NE-DKLTAHEL 396 (420)
Q Consensus 375 ~~~C~~C~~~f~-~~-~~l~~H~~ 396 (420)
.|-|++|+..|+ +. +.-+.|.+
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT-
T ss_pred CeecccccceecCCChHHHHHhhc
Confidence 477999999994 44 33377764
No 137
>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=38.64 E-value=17 Score=18.88 Aligned_cols=9 Identities=33% Similarity=0.969 Sum_probs=4.3
Q ss_pred CcccCCccC
Q psy3231 314 NPYMCNHCF 322 (420)
Q Consensus 314 ~~~~C~~C~ 322 (420)
.+|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 345555554
No 138
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=38.38 E-value=24 Score=19.97 Aligned_cols=24 Identities=29% Similarity=0.782 Sum_probs=17.2
Q ss_pred ccccccccccCChhHHHHHHHHhhc
Q psy3231 340 FTCPFCQRKYKIEKHLEKHIESCIQ 364 (420)
Q Consensus 340 ~~C~~C~~~f~~~~~l~~H~~~~~~ 364 (420)
+.|+.|++.. ....+..|+..|..
T Consensus 5 ~~C~nC~R~v-~a~RfA~HLekCmg 28 (33)
T PF08209_consen 5 VECPNCGRPV-AASRFAPHLEKCMG 28 (33)
T ss_dssp EE-TTTSSEE-EGGGHHHHHHHHTC
T ss_pred EECCCCcCCc-chhhhHHHHHHHHc
Confidence 6788898876 46778888887654
No 139
>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=37.96 E-value=21 Score=35.16 Aligned_cols=28 Identities=32% Similarity=0.577 Sum_probs=16.6
Q ss_pred cCCCCccccccchhccCChhHHHHHHhhCCCcccCCccCCc
Q psy3231 284 HNKEDAYVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLM 324 (420)
Q Consensus 284 H~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~ 324 (420)
|.......|.+||.... -|..|+.||..
T Consensus 235 h~~~~~l~Ch~Cg~~~~-------------~~~~Cp~C~s~ 262 (505)
T TIGR00595 235 HKKEGKLRCHYCGYQEP-------------IPKTCPQCGSE 262 (505)
T ss_pred ecCCCeEEcCCCcCcCC-------------CCCCCCCCCCC
Confidence 44555677777775432 34557777653
No 140
>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=37.59 E-value=27 Score=29.88 Aligned_cols=30 Identities=30% Similarity=0.669 Sum_probs=22.0
Q ss_pred ccCCccccccCccccCCHHHHHHHHHHhcC
Q psy3231 90 IQERKFKCEMCPKSFDHKSNIRRHMAATHD 119 (420)
Q Consensus 90 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 119 (420)
..+..|.|..|++.|....-++.|+...|.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 355678999999999999999999887674
No 141
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.06 E-value=30 Score=36.48 Aligned_cols=9 Identities=33% Similarity=0.722 Sum_probs=4.4
Q ss_pred ccccccccc
Q psy3231 340 FTCPFCQRK 348 (420)
Q Consensus 340 ~~C~~C~~~ 348 (420)
+.|+.||..
T Consensus 664 y~CPKCG~E 672 (1121)
T PRK04023 664 DECEKCGRE 672 (1121)
T ss_pred CcCCCCCCC
Confidence 345555544
No 142
>PRK04023 DNA polymerase II large subunit; Validated
Probab=36.19 E-value=29 Score=36.63 Aligned_cols=14 Identities=14% Similarity=0.152 Sum_probs=7.8
Q ss_pred CcccCCccCCcCCC
Q psy3231 314 NPYMCNHCFLMFPD 327 (420)
Q Consensus 314 ~~~~C~~C~~~f~~ 327 (420)
.++.|+.||..-..
T Consensus 662 ~~y~CPKCG~El~~ 675 (1121)
T PRK04023 662 EEDECEKCGREPTP 675 (1121)
T ss_pred CCCcCCCCCCCCCc
Confidence 34556666665433
No 143
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.10 E-value=14 Score=27.27 Aligned_cols=13 Identities=8% Similarity=0.225 Sum_probs=6.6
Q ss_pred ccccccccccccc
Q psy3231 373 KTLQKCRYCQRMF 385 (420)
Q Consensus 373 ~~~~~C~~C~~~f 385 (420)
..|..|++||++|
T Consensus 24 rdPiVsPytG~s~ 36 (129)
T COG4530 24 RDPIVSPYTGKSY 36 (129)
T ss_pred CCccccCcccccc
Confidence 3444555555555
No 144
>COG1773 Rubredoxin [Energy production and conversion]
Probab=34.20 E-value=21 Score=22.89 Aligned_cols=11 Identities=18% Similarity=0.754 Sum_probs=5.2
Q ss_pred cccccchhccC
Q psy3231 290 YVCNYCYDSFE 300 (420)
Q Consensus 290 ~~C~~C~~~f~ 300 (420)
|+|.+||..|.
T Consensus 4 ~~C~~CG~vYd 14 (55)
T COG1773 4 WRCSVCGYVYD 14 (55)
T ss_pred eEecCCceEec
Confidence 44444444443
No 145
>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=33.78 E-value=8.9 Score=20.71 Aligned_cols=20 Identities=25% Similarity=0.557 Sum_probs=11.7
Q ss_pred ccccccccccCChhHHHHHHh
Q psy3231 376 QKCRYCQRMFRNEDKLTAHEL 396 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~ 396 (420)
|.|-.|++.| ...+++.|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 3577788888 6666666654
No 146
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=33.47 E-value=15 Score=20.26 Aligned_cols=24 Identities=13% Similarity=0.209 Sum_probs=8.6
Q ss_pred cccccccccCChhHHHHHHhhhcCCccccccccee
Q psy3231 377 KCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATV 411 (420)
Q Consensus 377 ~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~ 411 (420)
+|+.|+-.++. .+...|.|+.|+.
T Consensus 4 ~Cp~C~se~~y-----------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E-----------E-SSSEEETTTTE
T ss_pred CCCCCCCccee-----------ccCCEEeCCcccc
Confidence 46666655544 2334566666654
No 147
>PRK14873 primosome assembly protein PriA; Provisional
Probab=32.59 E-value=26 Score=35.79 Aligned_cols=27 Identities=15% Similarity=0.363 Sum_probs=15.8
Q ss_pred cCCCCccccccchhccCChhHHHHHHhhCCCcccCCccCCc
Q psy3231 284 HNKEDAYVCNYCYDSFETKSTLVDHFFHHGNPYMCNHCFLM 324 (420)
Q Consensus 284 H~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~~ 324 (420)
|.......|.+||..- .|..|+.||..
T Consensus 405 h~~~~~l~Ch~CG~~~--------------~p~~Cp~Cgs~ 431 (665)
T PRK14873 405 PSAGGTPRCRWCGRAA--------------PDWRCPRCGSD 431 (665)
T ss_pred ecCCCeeECCCCcCCC--------------cCccCCCCcCC
Confidence 4444556777777531 24567777664
No 148
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=32.15 E-value=28 Score=18.29 Aligned_cols=6 Identities=33% Similarity=0.938 Sum_probs=2.5
Q ss_pred CCccCC
Q psy3231 318 CNHCFL 323 (420)
Q Consensus 318 C~~C~~ 323 (420)
|+.||.
T Consensus 5 Cp~Cg~ 10 (26)
T PF13248_consen 5 CPNCGA 10 (26)
T ss_pred CcccCC
Confidence 444444
No 149
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=31.14 E-value=23 Score=22.61 Aligned_cols=11 Identities=36% Similarity=1.102 Sum_probs=5.7
Q ss_pred cccccccccCC
Q psy3231 377 KCRYCQRMFRN 387 (420)
Q Consensus 377 ~C~~C~~~f~~ 387 (420)
+|+.|++.|..
T Consensus 7 ~C~~Cg~~~~~ 17 (54)
T PF14446_consen 7 KCPVCGKKFKD 17 (54)
T ss_pred cChhhCCcccC
Confidence 35555555543
No 150
>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=31.03 E-value=10 Score=23.91 Aligned_cols=26 Identities=23% Similarity=0.441 Sum_probs=15.4
Q ss_pred ccccccccccccCChhHHHHHHhhhc
Q psy3231 374 TLQKCRYCQRMFRNEDKLTAHELSHT 399 (420)
Q Consensus 374 ~~~~C~~C~~~f~~~~~l~~H~~~H~ 399 (420)
..|.|+.|...|=..=++-.|...|.
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CeEECCCCCCccccCcChhhhccccC
Confidence 56889998888888777777777664
No 151
>KOG2593|consensus
Probab=30.88 E-value=30 Score=32.55 Aligned_cols=38 Identities=21% Similarity=0.559 Sum_probs=22.8
Q ss_pred CCccccCCCccccCCHHHHHccccccCCCCCceecccccccc
Q psy3231 203 NRRFKCPCCERIFTSETRMRNHIDMKHADENLFKCKKCLKVF 244 (420)
Q Consensus 203 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f 244 (420)
...|.||.|++.|+....++. .-.....|.|..|+-..
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L----~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQL----LDNETGEFHCENCGGEL 163 (436)
T ss_pred cccccCCccccchhhhHHHHh----hcccCceEEEecCCCch
Confidence 345777777777776655542 22334557777776544
No 152
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=30.72 E-value=33 Score=21.47 Aligned_cols=21 Identities=14% Similarity=0.498 Sum_probs=11.7
Q ss_pred CccccccCccccCCHHHHHHH
Q psy3231 93 RKFKCEMCPKSFDHKSNIRRH 113 (420)
Q Consensus 93 ~~~~C~~C~~~f~~~~~l~~H 113 (420)
+.+.|..||..|.-...=+.-
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~f 23 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKF 23 (49)
T ss_pred eeEEcccCCCeEEEehhHHHH
Confidence 456677777766544433333
No 153
>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=29.88 E-value=63 Score=19.71 Aligned_cols=7 Identities=43% Similarity=1.065 Sum_probs=3.0
Q ss_pred cCCccCC
Q psy3231 317 MCNHCFL 323 (420)
Q Consensus 317 ~C~~C~~ 323 (420)
.|+.||.
T Consensus 20 ~CP~Cg~ 26 (46)
T PF12760_consen 20 VCPHCGS 26 (46)
T ss_pred CCCCCCC
Confidence 3444443
No 154
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=29.32 E-value=35 Score=32.92 Aligned_cols=29 Identities=24% Similarity=0.659 Sum_probs=25.0
Q ss_pred CCccCcchhhcCCCHHHHHHHHHhhcCCC
Q psy3231 259 KFYRCSECEKRFATEDIMRQHFRNYHNKE 287 (420)
Q Consensus 259 ~~~~C~~C~~~f~~~~~l~~H~~~~H~~~ 287 (420)
+-+.|+.|.+.|.+...+..|+...|.+.
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 45889999999999999999999888654
No 155
>KOG1842|consensus
Probab=29.28 E-value=37 Score=32.07 Aligned_cols=29 Identities=17% Similarity=0.330 Sum_probs=22.2
Q ss_pred CCccCcchhhcCCCHHHHHHHHHhhcCCC
Q psy3231 259 KFYRCSECEKRFATEDIMRQHFRNYHNKE 287 (420)
Q Consensus 259 ~~~~C~~C~~~f~~~~~l~~H~~~~H~~~ 287 (420)
.-|.||+|...|.+...|..|+...|.++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 45778888888888888888887777654
No 156
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=28.98 E-value=25 Score=22.51 Aligned_cols=7 Identities=29% Similarity=0.624 Sum_probs=2.9
Q ss_pred ccccchh
Q psy3231 291 VCNYCYD 297 (420)
Q Consensus 291 ~C~~C~~ 297 (420)
.|+.||.
T Consensus 4 ~CP~CG~ 10 (54)
T TIGR01206 4 ECPDCGA 10 (54)
T ss_pred CCCCCCC
Confidence 3444443
No 157
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=28.76 E-value=30 Score=24.62 Aligned_cols=13 Identities=38% Similarity=0.864 Sum_probs=5.8
Q ss_pred cccCCccCCcCCC
Q psy3231 315 PYMCNHCFLMFPD 327 (420)
Q Consensus 315 ~~~C~~C~~~f~~ 327 (420)
|-.|..||+.|.+
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 3444444444433
No 158
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=28.71 E-value=17 Score=26.42 Aligned_cols=9 Identities=22% Similarity=0.752 Sum_probs=4.0
Q ss_pred ccccccccc
Q psy3231 341 TCPFCQRKY 349 (420)
Q Consensus 341 ~C~~C~~~f 349 (420)
.|..||.+|
T Consensus 48 ~Cg~CGls~ 56 (104)
T COG4888 48 VCGNCGLSF 56 (104)
T ss_pred EcccCcceE
Confidence 344444444
No 159
>KOG0717|consensus
Probab=28.70 E-value=28 Score=33.08 Aligned_cols=21 Identities=33% Similarity=0.711 Sum_probs=14.7
Q ss_pred ccccccccccCChhHHHHHHh
Q psy3231 376 QKCRYCQRMFRNEDKLTAHEL 396 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~ 396 (420)
+.|..|+++|.+..+|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 557777777777777777764
No 160
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.65 E-value=11 Score=29.90 Aligned_cols=16 Identities=13% Similarity=-0.037 Sum_probs=11.6
Q ss_pred CCcccccccceeeEEe
Q psy3231 400 MEKTFYRNVATVSVCL 415 (420)
Q Consensus 400 ~~~~~~c~~c~~~~~~ 415 (420)
.+.|.+|..||+.|+|
T Consensus 65 ~~~PsYC~~CGkpyPW 80 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPW 80 (158)
T ss_pred CCCChhHHhCCCCCch
Confidence 3567778888877776
No 161
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=28.30 E-value=34 Score=31.10 Aligned_cols=55 Identities=20% Similarity=0.404 Sum_probs=0.0
Q ss_pred ccccccccccCChhHHHHHHHHhhccCCcccccc----------------------------------------------
Q psy3231 340 FTCPFCQRKYKIEKHLEKHIESCIQLNPTTTVLK---------------------------------------------- 373 (420)
Q Consensus 340 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~---------------------------------------------- 373 (420)
+.|..|++-|.....+..|+..-..+........
T Consensus 239 ~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~~~v~~Ey~l~r~~kyl~d~~s~trs~V~r~la~ta~ER~aei~~l~r 318 (470)
T COG5188 239 VYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEEFVYSEYVLHRYLKYLGDPVSETRSLVLRSLAITAKERKAEISLLSR 318 (470)
T ss_pred eeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHHhCChhHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q ss_pred ------------------------------------------------------ccccccccc-cccCChhHHHHH
Q psy3231 374 ------------------------------------------------------TLQKCRYCQ-RMFRNEDKLTAH 394 (420)
Q Consensus 374 ------------------------------------------------------~~~~C~~C~-~~f~~~~~l~~H 394 (420)
..|.|.+|| +.+.-...+.+|
T Consensus 319 ~~~~~at~S~e~EGaeq~d~eQ~DE~~~~k~fdmPLG~DG~PmP~WL~klhgLd~ef~CEICgNyvy~GR~~FdrH 394 (470)
T COG5188 319 RKKQPATKSSEKEGAEQVDGEQRDEHVSGKSFDMPLGPDGLPMPRWLCKLHGLDIEFECEICGNYVYYGRDRFDRH 394 (470)
T ss_pred HhhccCCCchhhcccccccccccchhhccCcccCCCCCCCCCCchHHHHhcCCCcceeeeecccccccchHHHHhh
No 162
>KOG4377|consensus
Probab=27.92 E-value=40 Score=31.44 Aligned_cols=24 Identities=25% Similarity=0.499 Sum_probs=16.7
Q ss_pred ccc--ccccccccChHHHHHHHHHhc
Q psy3231 152 FTC--AQCDKAFSLKSNLSKHVRHHM 175 (420)
Q Consensus 152 ~~C--~~C~~~f~~~~~l~~H~~~h~ 175 (420)
|.| +.|+..+-++.++..|+++|.
T Consensus 272 yhcl~e~C~ykr~~k~DvirH~~~hk 297 (480)
T KOG4377|consen 272 YHCLNEYCFYKRGQKNDVIRHVEIHK 297 (480)
T ss_pred hcccCccccccccchhhhHHHHHHHh
Confidence 555 457776666777888877765
No 163
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=27.91 E-value=21 Score=36.02 Aligned_cols=56 Identities=25% Similarity=0.474 Sum_probs=36.1
Q ss_pred ccCCCccccCCHHHHHccccccCCCCCce-ecccccccccChHHHHHHhhccCCCccCcchhh
Q psy3231 207 KCPCCERIFTSETRMRNHIDMKHADENLF-KCKKCLKVFSDEIKFHLHGRAHAKFYRCSECEK 268 (420)
Q Consensus 207 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~C~~C~~ 268 (420)
.|..||-.|+-...|-.-. .++.-..| .|+.|.+.+.+..+. |.|..|..|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYDR--~nTsM~~F~lC~~C~~EY~dP~nR----RfHAQp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDR--ENTSMADFPLCPFCDKEYKDPLNR----RFHAQPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCCc--ccCccccCcCCHHHHHHhcCcccc----ccccccccCcccCC
Confidence 5888888887665554332 23333344 488888888776553 45566788888885
No 164
>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=27.73 E-value=26 Score=20.25 Aligned_cols=30 Identities=10% Similarity=0.107 Sum_probs=14.1
Q ss_pred cccccccccCChhHHHHHHhhhcCCcccccccceeeEE
Q psy3231 377 KCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATVSVC 414 (420)
Q Consensus 377 ~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~~~~ 414 (420)
.|+.||+.|. +..-....+-.|..||..+.
T Consensus 3 ~C~~Cg~~Yh--------~~~~pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 3 ICPKCGRIYH--------IEFNPPKVEGVCDNCGGELV 32 (36)
T ss_dssp EETTTTEEEE--------TTTB--SSTTBCTTTTEBEB
T ss_pred CcCCCCCccc--------cccCCCCCCCccCCCCCeeE
Confidence 3666666662 22222334455666665443
No 165
>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=27.42 E-value=23 Score=25.39 Aligned_cols=13 Identities=23% Similarity=0.812 Sum_probs=6.6
Q ss_pred CcccccccccccC
Q psy3231 338 SCFTCPFCQRKYK 350 (420)
Q Consensus 338 ~~~~C~~C~~~f~ 350 (420)
-.+.|..|++.|+
T Consensus 52 GIW~C~~C~~~~A 64 (90)
T PF01780_consen 52 GIWKCKKCGKKFA 64 (90)
T ss_dssp TEEEETTTTEEEE
T ss_pred EEeecCCCCCEEe
Confidence 3455555555543
No 166
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=27.35 E-value=28 Score=25.01 Aligned_cols=13 Identities=15% Similarity=0.582 Sum_probs=7.5
Q ss_pred CcccccccccccC
Q psy3231 338 SCFTCPFCQRKYK 350 (420)
Q Consensus 338 ~~~~C~~C~~~f~ 350 (420)
..+.|..|++.|+
T Consensus 53 GIW~C~~C~~~~A 65 (90)
T PTZ00255 53 GIWRCKGCKKTVA 65 (90)
T ss_pred EEEEcCCCCCEEe
Confidence 3455666666654
No 167
>KOG4124|consensus
Probab=26.85 E-value=12 Score=33.93 Aligned_cols=50 Identities=24% Similarity=0.573 Sum_probs=33.3
Q ss_pred CCccCcc--hhhcCCCHHHHHHHHHhhcCC------------------CCccccccchhccCChhHHHHH
Q psy3231 259 KFYRCSE--CEKRFATEDIMRQHFRNYHNK------------------EDAYVCNYCYDSFETKSTLVDH 308 (420)
Q Consensus 259 ~~~~C~~--C~~~f~~~~~l~~H~~~~H~~------------------~~~~~C~~C~~~f~~~~~l~~H 308 (420)
++|+|++ |.+.+.....|..|...-|.. .++|+|++|.++++....|..|
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 6788854 888888888888876554431 3556777777666666555554
No 168
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.80 E-value=51 Score=35.87 Aligned_cols=7 Identities=29% Similarity=0.838 Sum_probs=2.9
Q ss_pred eeccccc
Q psy3231 235 FKCKKCL 241 (420)
Q Consensus 235 ~~C~~C~ 241 (420)
+.|+.||
T Consensus 668 rkCPkCG 674 (1337)
T PRK14714 668 RRCPSCG 674 (1337)
T ss_pred EECCCCC
Confidence 3344444
No 169
>KOG0717|consensus
Probab=26.66 E-value=35 Score=32.51 Aligned_cols=21 Identities=33% Similarity=0.608 Sum_probs=19.3
Q ss_pred ccccccccccCChhHHHHHHh
Q psy3231 376 QKCRYCQRMFRNEDKLTAHEL 396 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~ 396 (420)
..|..|+.+|.++.-|-.|+.
T Consensus 461 ~~C~tCr~~FdSRnkLF~Hlk 481 (508)
T KOG0717|consen 461 ISCTTCRESFDSRNKLFAHLK 481 (508)
T ss_pred HhhhhhhhhccchhHHHHHhh
Confidence 569999999999999999997
No 170
>KOG1280|consensus
Probab=26.22 E-value=62 Score=29.55 Aligned_cols=28 Identities=21% Similarity=0.294 Sum_probs=19.8
Q ss_pred CccCcchhhcCCCHHHHHHHHHhhcCCC
Q psy3231 260 FYRCSECEKRFATEDIMRQHFRNYHNKE 287 (420)
Q Consensus 260 ~~~C~~C~~~f~~~~~l~~H~~~~H~~~ 287 (420)
-|.|++|+..=.+...|..|+...|...
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda 106 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEA 106 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCccc
Confidence 3777777777777777777777767543
No 171
>KOG2807|consensus
Probab=26.09 E-value=75 Score=28.80 Aligned_cols=20 Identities=10% Similarity=0.285 Sum_probs=12.6
Q ss_pred CCccCcchhhcCCCHHHHHH
Q psy3231 259 KFYRCSECEKRFATEDIMRQ 278 (420)
Q Consensus 259 ~~~~C~~C~~~f~~~~~l~~ 278 (420)
-|-.|++|+-+......|.+
T Consensus 289 LP~eCpiC~ltLVss~hLAR 308 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLAR 308 (378)
T ss_pred CCccCCccceeEecchHHHH
Confidence 35567777766666666654
No 172
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=25.83 E-value=37 Score=21.36 Aligned_cols=9 Identities=22% Similarity=0.692 Sum_probs=3.8
Q ss_pred ccccccccc
Q psy3231 340 FTCPFCQRK 348 (420)
Q Consensus 340 ~~C~~C~~~ 348 (420)
+.|..||.+
T Consensus 38 ~~C~~Cgyt 46 (50)
T PRK00432 38 WHCGKCGYT 46 (50)
T ss_pred EECCCcCCE
Confidence 344444443
No 173
>KOG4167|consensus
Probab=25.35 E-value=18 Score=36.38 Aligned_cols=27 Identities=26% Similarity=0.473 Sum_probs=24.7
Q ss_pred ccccccccccccCChhHHHHHHhhhcC
Q psy3231 374 TLQKCRYCQRMFRNEDKLTAHELSHTM 400 (420)
Q Consensus 374 ~~~~C~~C~~~f~~~~~l~~H~~~H~~ 400 (420)
..|-|..|++.|....++..||++|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 568999999999999999999999864
No 174
>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=25.17 E-value=28 Score=25.04 Aligned_cols=13 Identities=31% Similarity=0.782 Sum_probs=7.5
Q ss_pred CcccccccccccC
Q psy3231 338 SCFTCPFCQRKYK 350 (420)
Q Consensus 338 ~~~~C~~C~~~f~ 350 (420)
..+.|..|++.|+
T Consensus 52 GIW~C~~C~~~~A 64 (91)
T TIGR00280 52 GIWTCRKCGAKFA 64 (91)
T ss_pred EEEEcCCCCCEEe
Confidence 3455666666654
No 175
>KOG1842|consensus
Probab=24.09 E-value=31 Score=32.57 Aligned_cols=28 Identities=29% Similarity=0.682 Sum_probs=20.1
Q ss_pred ccccCCCccccCCHHHHHccccccCCCC
Q psy3231 205 RFKCPCCERIFTSETRMRNHIDMKHADE 232 (420)
Q Consensus 205 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 232 (420)
.|.||+|...|.+...|..|....|.++
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 4677777777777777777776666654
No 176
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=23.80 E-value=33 Score=30.56 Aligned_cols=47 Identities=19% Similarity=0.412 Sum_probs=24.9
Q ss_pred CcchhhcCCCHHHHHHHHHhhcCCCCccccccchhccCChhHHHHHHhhC
Q psy3231 263 CSECEKRFATEDIMRQHFRNYHNKEDAYVCNYCYDSFETKSTLVDHFFHH 312 (420)
Q Consensus 263 C~~C~~~f~~~~~l~~H~~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~h 312 (420)
|-.|.-.|+.... |-...-+....|.|+.|...|-..-+...|...|
T Consensus 365 Cf~CQ~~fp~~~~---~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 365 CFVCQGPFPKPPV---SPFDESTSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceeccCCCCCCCC---CcccccccccceechhhhhhhhhhhHHHHHHHHh
Confidence 6666666654331 1000112233577777777777666666665555
No 177
>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=23.77 E-value=49 Score=32.72 Aligned_cols=18 Identities=22% Similarity=0.589 Sum_probs=8.5
Q ss_pred hhcccCCCcccccccccc
Q psy3231 331 LRNHECTSCFTCPFCQRK 348 (420)
Q Consensus 331 l~~H~~~~~~~C~~C~~~ 348 (420)
|.-|.......|..||..
T Consensus 232 l~~h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 232 LTYHKKEGKLRCHYCGYQ 249 (505)
T ss_pred eEEecCCCeEEcCCCcCc
Confidence 444444444455555544
No 178
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=23.66 E-value=51 Score=20.55 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=3.3
Q ss_pred cccccccc
Q psy3231 340 FTCPFCQR 347 (420)
Q Consensus 340 ~~C~~C~~ 347 (420)
+.|..||+
T Consensus 38 ~~CGkCgy 45 (51)
T COG1998 38 WACGKCGY 45 (51)
T ss_pred eEeccccc
Confidence 33444443
No 179
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=23.63 E-value=34 Score=19.65 Aligned_cols=12 Identities=17% Similarity=0.429 Sum_probs=4.6
Q ss_pred CcccCCccCCcC
Q psy3231 314 NPYMCNHCFLMF 325 (420)
Q Consensus 314 ~~~~C~~C~~~f 325 (420)
.+..|+.||-.+
T Consensus 20 ~~isC~~CGPr~ 31 (35)
T PF07503_consen 20 QFISCTNCGPRY 31 (35)
T ss_dssp TT--BTTCC-SC
T ss_pred cCccCCCCCCCE
Confidence 344455555444
No 180
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=23.55 E-value=19 Score=22.19 Aligned_cols=6 Identities=0% Similarity=-0.053 Sum_probs=2.8
Q ss_pred ceeeEE
Q psy3231 409 ATVSVC 414 (420)
Q Consensus 409 c~~~~~ 414 (420)
||-.|.
T Consensus 33 Cg~tfv 38 (47)
T PF04606_consen 33 CGHTFV 38 (47)
T ss_pred CCCEEE
Confidence 444444
No 181
>KOG4167|consensus
Probab=23.53 E-value=36 Score=34.34 Aligned_cols=25 Identities=24% Similarity=0.475 Sum_probs=23.0
Q ss_pred cceecchhhHHHHhhhhhhhhhccc
Q psy3231 4 KTYTCDFCSAAFALKHSIADHIQTE 28 (420)
Q Consensus 4 k~~~C~~C~~~f~~~~~l~~H~~~~ 28 (420)
..|.|.+|++.|-.-.++..||++|
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHH
Confidence 4699999999999999999999993
No 182
>KOG4124|consensus
Probab=23.45 E-value=20 Score=32.56 Aligned_cols=19 Identities=16% Similarity=0.134 Sum_probs=11.8
Q ss_pred hhHHHHhhhhhhhhhcccC
Q psy3231 11 CSAAFALKHSIADHIQTEH 29 (420)
Q Consensus 11 C~~~f~~~~~l~~H~~~~h 29 (420)
||.-|.+...+..|+-..|
T Consensus 19 ~g~Hf~~~~~~~f~I~~~s 37 (442)
T KOG4124|consen 19 NGNHFNSIHATSFGISPQS 37 (442)
T ss_pred cccccchhhhhhcCcCccc
Confidence 6666666666666665534
No 183
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=23.45 E-value=47 Score=21.17 Aligned_cols=9 Identities=33% Similarity=1.010 Sum_probs=3.9
Q ss_pred ccccccccc
Q psy3231 339 CFTCPFCQR 347 (420)
Q Consensus 339 ~~~C~~C~~ 347 (420)
|+.|+.|.+
T Consensus 28 PlyCpKCK~ 36 (55)
T PF14205_consen 28 PLYCPKCKQ 36 (55)
T ss_pred cccCCCCCc
Confidence 444444443
No 184
>PRK05580 primosome assembly protein PriA; Validated
Probab=23.40 E-value=48 Score=34.15 Aligned_cols=34 Identities=18% Similarity=0.422 Sum_probs=18.4
Q ss_pred ccCCccCCcCCC---chhhhcccCCCccccccccccc
Q psy3231 316 YMCNHCFLMFPD---EKNLRNHECTSCFTCPFCQRKY 349 (420)
Q Consensus 316 ~~C~~C~~~f~~---~~~l~~H~~~~~~~C~~C~~~f 349 (420)
..|..||..... ...|.-|.......|..||+..
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQE 418 (679)
T ss_pred eEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCC
Confidence 457777765422 2245555555555666666553
No 185
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.33 E-value=42 Score=34.41 Aligned_cols=31 Identities=19% Similarity=0.340 Sum_probs=14.2
Q ss_pred cCCccCCcCCCc---hhhhcccCCCccccccccc
Q psy3231 317 MCNHCFLMFPDE---KNLRNHECTSCFTCPFCQR 347 (420)
Q Consensus 317 ~C~~C~~~f~~~---~~l~~H~~~~~~~C~~C~~ 347 (420)
.|..||..+... ..|.-|.......|..||+
T Consensus 385 ~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 385 ACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred EhhhCcCeeECCCCCCceeEecCCCeeECCCCcC
Confidence 455555544221 2344444444455555554
No 186
>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=22.63 E-value=59 Score=31.41 Aligned_cols=29 Identities=28% Similarity=0.525 Sum_probs=25.4
Q ss_pred CccccccCccccCCHHHHHHHHHHhcCCC
Q psy3231 93 RKFKCEMCPKSFDHKSNIRRHMAATHDLQ 121 (420)
Q Consensus 93 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 121 (420)
+-+.|+.|.+.|.+...+..|+...|.+.
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 35789999999999999999999888654
No 187
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=22.31 E-value=51 Score=19.50 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=10.7
Q ss_pred CccccccccccccChHHHH
Q psy3231 150 KIFTCAQCDKAFSLKSNLS 168 (420)
Q Consensus 150 ~~~~C~~C~~~f~~~~~l~ 168 (420)
....|+.|+-.+-+...|.
T Consensus 18 ~id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 18 EIDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEEECCCCCeEEccHHHHH
Confidence 3455666666555555554
No 188
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.30 E-value=49 Score=20.63 Aligned_cols=11 Identities=27% Similarity=0.633 Sum_probs=5.4
Q ss_pred ccccccccccC
Q psy3231 340 FTCPFCQRKYK 350 (420)
Q Consensus 340 ~~C~~C~~~f~ 350 (420)
+.|+.||+.+.
T Consensus 21 ~vC~~Cg~~~~ 31 (52)
T smart00661 21 FVCRKCGYEEP 31 (52)
T ss_pred EECCcCCCeEE
Confidence 44555555443
No 189
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=22.23 E-value=48 Score=25.64 Aligned_cols=25 Identities=20% Similarity=0.194 Sum_probs=18.2
Q ss_pred ccccccccccCChhHHHHHHhhhcCCcc
Q psy3231 376 QKCRYCQRMFRNEDKLTAHELSHTMEKT 403 (420)
Q Consensus 376 ~~C~~C~~~f~~~~~l~~H~~~H~~~~~ 403 (420)
..|-.+|+.|. +|++|+.+|.|-.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 35888888885 57888888877544
No 190
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.08 E-value=77 Score=24.68 Aligned_cols=12 Identities=17% Similarity=0.741 Sum_probs=6.5
Q ss_pred cccccccccccC
Q psy3231 339 CFTCPFCQRKYK 350 (420)
Q Consensus 339 ~~~C~~C~~~f~ 350 (420)
.|.|..|++.|.
T Consensus 53 RyrC~~C~~tf~ 64 (129)
T COG3677 53 RYKCKSCGSTFT 64 (129)
T ss_pred ccccCCcCccee
Confidence 455555555554
No 191
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=21.92 E-value=39 Score=18.36 Aligned_cols=12 Identities=17% Similarity=0.454 Sum_probs=4.9
Q ss_pred cccccccccccc
Q psy3231 374 TLQKCRYCQRMF 385 (420)
Q Consensus 374 ~~~~C~~C~~~f 385 (420)
..|.|..|++.+
T Consensus 14 ~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 14 WFYRCSECDFDL 25 (30)
T ss_dssp -EEE-TTT----
T ss_pred ceEECccCCCcc
Confidence 468888888765
No 192
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=21.84 E-value=36 Score=27.05 Aligned_cols=33 Identities=15% Similarity=0.273 Sum_probs=15.2
Q ss_pred cccccccccccCChhHHHHHHhhhcCCcccccccceee
Q psy3231 375 LQKCRYCQRMFRNEDKLTAHELSHTMEKTFYRNVATVS 412 (420)
Q Consensus 375 ~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~c~~c~~~ 412 (420)
+|.|. |+..|-+. ++|-.+-.|+ .|.|..|+..
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 45555 55553322 3343333444 5555555543
No 193
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.63 E-value=33 Score=20.33 Aligned_cols=8 Identities=25% Similarity=0.704 Sum_probs=3.1
Q ss_pred cccccccc
Q psy3231 376 QKCRYCQR 383 (420)
Q Consensus 376 ~~C~~C~~ 383 (420)
|.|..|+.
T Consensus 29 y~C~~C~~ 36 (40)
T smart00440 29 YVCTKCGH 36 (40)
T ss_pred EEeCCCCC
Confidence 33333333
No 194
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=21.10 E-value=40 Score=19.84 Aligned_cols=14 Identities=43% Similarity=0.776 Sum_probs=11.0
Q ss_pred cccccccccccCCh
Q psy3231 375 LQKCRYCQRMFRNE 388 (420)
Q Consensus 375 ~~~C~~C~~~f~~~ 388 (420)
+++|..|+..|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 67899898888654
No 195
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.52 E-value=19 Score=36.31 Aligned_cols=37 Identities=19% Similarity=0.379 Sum_probs=18.2
Q ss_pred cccccchhccCChhHHHHHHhhCCCcc-cCCccCCcCCCchhh
Q psy3231 290 YVCNYCYDSFETKSTLVDHFFHHGNPY-MCNHCFLMFPDEKNL 331 (420)
Q Consensus 290 ~~C~~C~~~f~~~~~l~~H~~~h~~~~-~C~~C~~~f~~~~~l 331 (420)
-.|+.|-+...+.++-..+ .|| .|+.||-.|+-...|
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~-----YPF~~CT~CGPRfTIi~al 139 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYL-----YPFINCTNCGPRFTIIEAL 139 (750)
T ss_pred hhhHHHHHHhcCCCCccee-----ccccccCCCCcceeeeccC
Confidence 3466665555444331111 233 266666666655554
No 196
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=20.34 E-value=23 Score=24.17 Aligned_cols=11 Identities=27% Similarity=0.434 Sum_probs=4.6
Q ss_pred ceecccccccc
Q psy3231 234 LFKCKKCLKVF 244 (420)
Q Consensus 234 ~~~C~~C~~~f 244 (420)
...|..|+...
T Consensus 41 ~v~Cg~C~~~~ 51 (71)
T PF05495_consen 41 RVICGKCRTEQ 51 (71)
T ss_dssp EEEETTT--EE
T ss_pred CeECCCCCCcc
Confidence 45555555444
No 197
>KOG3408|consensus
Probab=20.28 E-value=57 Score=24.73 Aligned_cols=25 Identities=20% Similarity=0.452 Sum_probs=22.5
Q ss_pred cceecchhhHHHHhhhhhhhhhccc
Q psy3231 4 KTYTCDFCSAAFALKHSIADHIQTE 28 (420)
Q Consensus 4 k~~~C~~C~~~f~~~~~l~~H~~~~ 28 (420)
--|.|-+|.+-|.+...|..|.++.
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhcc
Confidence 4589999999999999999998863
No 198
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=20.08 E-value=38 Score=24.31 Aligned_cols=13 Identities=23% Similarity=0.715 Sum_probs=7.3
Q ss_pred CcccccccccccC
Q psy3231 338 SCFTCPFCQRKYK 350 (420)
Q Consensus 338 ~~~~C~~C~~~f~ 350 (420)
..+.|..|++.|+
T Consensus 53 GIW~C~~C~~~~A 65 (90)
T PRK03976 53 GIWECRKCGAKFA 65 (90)
T ss_pred EEEEcCCCCCEEe
Confidence 3455666666554
No 199
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=20.01 E-value=20 Score=25.28 Aligned_cols=11 Identities=18% Similarity=0.963 Sum_probs=3.9
Q ss_pred ccccccccccC
Q psy3231 340 FTCPFCQRKYK 350 (420)
Q Consensus 340 ~~C~~C~~~f~ 350 (420)
..|..||..|.
T Consensus 47 ~~C~~Cg~~~~ 57 (81)
T PF05129_consen 47 LSCRVCGESFQ 57 (81)
T ss_dssp EEESSS--EEE
T ss_pred EEecCCCCeEE
Confidence 34444444443
Done!