Query psy10278
Match_columns 110
No_of_seqs 113 out of 2258
Neff 11.1
Searched_HMMs 46136
Date Fri Aug 16 22:21:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10278.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10278hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2.8E-26 6E-31 137.0 5.5 98 2-102 169-266 (279)
2 KOG2462|consensus 99.9 3.8E-26 8.2E-31 136.4 5.0 103 2-107 138-243 (279)
3 KOG1074|consensus 99.7 1.6E-18 3.5E-23 116.4 1.3 55 51-105 605-659 (958)
4 KOG3576|consensus 99.7 3.9E-18 8.4E-23 98.7 -0.2 102 2-104 125-237 (267)
5 KOG3623|consensus 99.7 1.1E-17 2.3E-22 111.4 1.3 82 19-100 890-971 (1007)
6 KOG3576|consensus 99.7 3.7E-17 8.1E-22 94.6 2.3 86 20-105 114-199 (267)
7 KOG3623|consensus 99.7 9E-17 2E-21 107.1 3.9 101 2-102 218-332 (1007)
8 KOG1074|consensus 99.6 5.1E-16 1.1E-20 104.7 4.7 58 52-109 880-937 (958)
9 KOG3608|consensus 99.6 1.3E-14 2.9E-19 90.2 6.3 102 2-104 187-317 (467)
10 KOG3608|consensus 99.5 4.2E-14 9.1E-19 88.0 7.0 101 2-106 245-348 (467)
11 PHA00733 hypothetical protein 99.4 2.2E-13 4.8E-18 75.3 4.4 84 20-105 37-125 (128)
12 PHA02768 hypothetical protein; 99.2 1.1E-11 2.5E-16 57.9 1.9 44 51-96 5-48 (55)
13 PLN03086 PRLI-interacting fact 99.1 7.9E-10 1.7E-14 73.8 8.0 91 7-104 465-565 (567)
14 PF13465 zf-H2C2_2: Zinc-finge 99.0 1.9E-10 4.2E-15 46.3 2.5 26 66-91 1-26 (26)
15 PHA00733 hypothetical protein 99.0 1.3E-09 2.9E-14 60.3 5.7 64 9-76 61-124 (128)
16 PHA02768 hypothetical protein; 99.0 1.4E-10 3E-15 54.3 1.4 44 23-68 5-48 (55)
17 PLN03086 PRLI-interacting fact 99.0 2.6E-09 5.6E-14 71.4 6.6 77 21-102 451-537 (567)
18 KOG3993|consensus 98.9 3.8E-10 8.2E-15 72.1 -0.0 81 24-104 268-381 (500)
19 PF13465 zf-H2C2_2: Zinc-finge 98.8 4.2E-09 9.2E-14 42.4 2.2 25 9-34 1-25 (26)
20 PHA00616 hypothetical protein 98.7 7.7E-09 1.7E-13 46.2 1.3 31 52-82 2-32 (44)
21 PHA00616 hypothetical protein 98.6 1.4E-08 3E-13 45.4 1.4 33 23-55 1-33 (44)
22 PHA00732 hypothetical protein 98.5 1.3E-07 2.8E-12 48.1 3.4 45 23-73 1-46 (79)
23 PF05605 zf-Di19: Drought indu 98.4 1.1E-06 2.5E-11 41.5 4.3 49 52-103 3-53 (54)
24 KOG3993|consensus 98.4 1.7E-07 3.8E-12 60.3 1.7 71 3-74 276-379 (500)
25 PHA00732 hypothetical protein 98.3 5.5E-07 1.2E-11 45.8 2.9 47 51-103 1-48 (79)
26 PF00096 zf-C2H2: Zinc finger, 98.3 4.1E-07 8.8E-12 35.3 1.7 22 80-101 1-22 (23)
27 PF13912 zf-C2H2_6: C2H2-type 98.3 8.2E-07 1.8E-11 35.9 2.2 26 79-104 1-26 (27)
28 PF05605 zf-Di19: Drought indu 98.3 2.3E-06 4.9E-11 40.4 4.0 50 23-75 2-53 (54)
29 PF13894 zf-C2H2_4: C2H2-type 98.2 1.2E-06 2.6E-11 34.1 2.1 24 80-103 1-24 (24)
30 PF12756 zf-C2H2_2: C2H2 type 98.2 1.7E-06 3.7E-11 45.7 3.1 74 25-103 1-74 (100)
31 PF00096 zf-C2H2: Zinc finger, 98.1 2.2E-06 4.7E-11 33.2 1.2 22 24-45 1-22 (23)
32 COG5189 SFP1 Putative transcri 97.8 5.3E-06 1.1E-10 52.0 0.6 70 21-100 347-419 (423)
33 PF09237 GAGA: GAGA factor; I 97.8 3.4E-05 7.4E-10 35.4 2.6 33 75-107 20-52 (54)
34 PF13912 zf-C2H2_6: C2H2-type 97.8 1.2E-05 2.7E-10 32.3 1.0 24 23-46 1-24 (27)
35 PF13894 zf-C2H2_4: C2H2-type 97.8 2.1E-05 4.5E-10 30.4 1.6 23 24-46 1-23 (24)
36 PF12874 zf-met: Zinc-finger o 97.6 6.7E-05 1.4E-09 29.5 1.7 23 80-102 1-23 (25)
37 smart00355 ZnF_C2H2 zinc finge 97.5 8.1E-05 1.7E-09 29.1 2.0 23 80-102 1-23 (26)
38 PF12171 zf-C2H2_jaz: Zinc-fin 97.4 0.00011 2.4E-09 29.5 1.5 22 80-101 2-23 (27)
39 PRK04860 hypothetical protein; 97.3 0.00027 5.9E-09 40.7 2.9 38 51-92 119-156 (160)
40 PF13909 zf-H2C2_5: C2H2-type 97.3 0.00016 3.6E-09 28.1 1.5 24 80-104 1-24 (24)
41 smart00355 ZnF_C2H2 zinc finge 97.3 0.00025 5.5E-09 27.6 2.1 23 24-46 1-23 (26)
42 PF09237 GAGA: GAGA factor; I 97.3 8E-05 1.7E-09 34.2 0.4 29 50-78 23-51 (54)
43 PF12874 zf-met: Zinc-finger o 97.0 0.00031 6.8E-09 27.5 0.7 21 24-44 1-21 (25)
44 PRK04860 hypothetical protein; 96.9 0.00095 2.1E-08 38.5 2.7 37 23-63 119-155 (160)
45 PF12756 zf-C2H2_2: C2H2 type 96.4 0.0053 1.1E-07 32.1 3.0 66 3-74 8-73 (100)
46 PF13913 zf-C2HC_2: zinc-finge 96.3 0.0038 8.2E-08 24.5 1.7 19 81-100 4-22 (25)
47 smart00451 ZnF_U1 U1-like zinc 96.2 0.0056 1.2E-07 25.8 2.0 24 79-102 3-26 (35)
48 cd00350 rubredoxin_like Rubred 94.8 0.023 5.1E-07 23.8 1.5 10 24-33 2-11 (33)
49 PF09538 FYDLN_acid: Protein o 94.2 0.024 5.2E-07 30.6 1.0 14 51-64 26-39 (108)
50 COG5048 FOG: Zn-finger [Genera 94.0 0.019 4.2E-07 37.5 0.4 55 51-105 289-349 (467)
51 COG5048 FOG: Zn-finger [Genera 93.8 0.017 3.7E-07 37.8 -0.1 63 22-84 288-356 (467)
52 KOG1146|consensus 93.5 0.0096 2.1E-07 44.3 -1.7 83 16-102 458-541 (1406)
53 KOG2893|consensus 93.4 0.015 3.4E-07 35.6 -0.6 39 56-98 15-53 (341)
54 TIGR00622 ssl1 transcription f 93.2 0.3 6.4E-06 26.6 4.1 83 21-105 13-107 (112)
55 COG4049 Uncharacterized protei 93.1 0.043 9.4E-07 25.8 0.7 27 76-102 14-40 (65)
56 COG1592 Rubrerythrin [Energy p 92.1 0.1 2.2E-06 30.4 1.5 10 77-86 147-156 (166)
57 COG5189 SFP1 Putative transcri 92.0 0.091 2E-06 33.7 1.3 29 76-104 346-376 (423)
58 PF13719 zinc_ribbon_5: zinc-r 91.9 0.2 4.4E-06 21.5 2.0 32 53-89 4-35 (37)
59 KOG4173|consensus 91.9 0.08 1.7E-06 31.8 0.9 78 24-104 80-171 (253)
60 KOG2231|consensus 91.8 0.78 1.7E-05 32.6 5.7 47 53-103 184-236 (669)
61 PF09986 DUF2225: Uncharacteri 91.4 0.048 1E-06 33.1 -0.3 17 22-38 4-20 (214)
62 KOG2186|consensus 90.8 0.23 5E-06 30.8 2.2 49 24-75 4-52 (276)
63 KOG2231|consensus 90.5 1 2.2E-05 32.1 5.2 72 32-103 123-206 (669)
64 TIGR02300 FYDLN_acid conserved 90.4 0.16 3.4E-06 28.2 1.1 15 50-64 25-39 (129)
65 cd00729 rubredoxin_SM Rubredox 90.4 0.19 4.2E-06 21.2 1.2 10 24-33 3-12 (34)
66 KOG2186|consensus 90.1 0.29 6.3E-06 30.4 2.2 32 9-43 17-48 (276)
67 TIGR02098 MJ0042_CXXC MJ0042 f 90.0 0.33 7.2E-06 20.7 1.8 10 80-89 26-35 (38)
68 COG1997 RPL43A Ribosomal prote 89.1 0.27 5.8E-06 25.4 1.3 14 78-91 52-65 (89)
69 PRK00398 rpoP DNA-directed RNA 89.0 0.28 6E-06 22.1 1.2 8 80-87 22-29 (46)
70 TIGR00373 conserved hypothetic 89.0 0.63 1.4E-05 27.0 2.9 30 50-88 108-137 (158)
71 TIGR00373 conserved hypothetic 89.0 0.66 1.4E-05 26.9 3.0 34 19-61 105-138 (158)
72 PF13717 zinc_ribbon_4: zinc-r 88.8 0.53 1.1E-05 20.1 2.0 11 79-89 25-35 (36)
73 COG2888 Predicted Zn-ribbon RN 88.8 0.39 8.4E-06 23.0 1.6 33 50-87 26-58 (61)
74 PF02892 zf-BED: BED zinc fing 88.6 0.58 1.3E-05 20.7 2.1 25 77-101 14-42 (45)
75 smart00659 RPOLCX RNA polymera 88.5 0.56 1.2E-05 21.1 2.0 10 52-61 3-12 (44)
76 smart00531 TFIIE Transcription 88.4 1.5 3.2E-05 25.0 4.2 37 49-89 97-133 (147)
77 TIGR02605 CxxC_CxxC_SSSS putat 88.1 0.16 3.5E-06 23.4 0.1 13 24-36 6-18 (52)
78 PRK14890 putative Zn-ribbon RN 87.5 0.76 1.6E-05 22.0 2.2 32 50-87 24-56 (59)
79 smart00614 ZnF_BED BED zinc fi 87.3 0.59 1.3E-05 21.4 1.8 22 80-101 19-45 (50)
80 smart00834 CxxC_CXXC_SSSS Puta 87.3 0.2 4.4E-06 21.7 0.2 13 24-36 6-18 (41)
81 PRK06266 transcription initiat 86.0 0.97 2.1E-05 26.8 2.6 29 51-88 117-145 (178)
82 PRK00464 nrdR transcriptional 85.7 0.18 3.9E-06 29.1 -0.5 13 52-64 29-41 (154)
83 KOG2482|consensus 85.3 2.3 4.9E-05 28.0 4.1 25 80-104 196-220 (423)
84 PF06524 NOA36: NOA36 protein; 85.3 0.52 1.1E-05 29.6 1.2 81 19-100 138-230 (314)
85 PF04959 ARS2: Arsenite-resist 84.9 0.75 1.6E-05 28.1 1.8 30 76-105 74-103 (214)
86 PF05443 ROS_MUCR: ROS/MUCR tr 84.1 0.81 1.8E-05 25.7 1.6 27 77-106 70-96 (132)
87 PF14353 CpXC: CpXC protein 84.1 0.16 3.5E-06 28.2 -1.2 12 25-36 3-14 (128)
88 PTZ00255 60S ribosomal protein 83.9 0.57 1.2E-05 24.5 0.9 14 78-91 53-66 (90)
89 PF12013 DUF3505: Protein of u 83.3 1.2 2.6E-05 24.0 2.0 25 80-104 81-109 (109)
90 smart00734 ZnF_Rad18 Rad18-lik 82.1 1.5 3.2E-05 17.2 1.6 18 81-99 3-20 (26)
91 PF05290 Baculo_IE-1: Baculovi 82.0 0.44 9.4E-06 26.7 0.0 59 18-93 75-135 (140)
92 PRK09678 DNA-binding transcrip 81.3 0.49 1.1E-05 23.7 0.0 15 77-91 25-41 (72)
93 TIGR00280 L37a ribosomal prote 81.2 0.65 1.4E-05 24.3 0.5 13 78-90 52-64 (91)
94 PF02176 zf-TRAF: TRAF-type zi 80.9 1.4 3.1E-05 20.7 1.6 40 51-91 9-54 (60)
95 PF08790 zf-LYAR: LYAR-type C2 80.4 0.45 9.9E-06 19.2 -0.2 19 80-99 1-19 (28)
96 KOG4167|consensus 79.6 0.38 8.2E-06 34.4 -0.9 26 79-104 792-817 (907)
97 PF01780 Ribosomal_L37ae: Ribo 79.6 0.47 1E-05 24.8 -0.3 12 79-90 53-64 (90)
98 KOG2785|consensus 79.3 3.3 7.2E-05 27.5 3.2 24 79-102 217-243 (390)
99 PF04959 ARS2: Arsenite-resist 78.0 1.4 2.9E-05 27.0 1.2 27 21-47 75-101 (214)
100 PF07754 DUF1610: Domain of un 78.0 1.2 2.7E-05 17.2 0.7 8 79-86 16-23 (24)
101 COG5236 Uncharacterized conser 78.0 1.4 3E-05 29.0 1.3 21 53-73 222-242 (493)
102 KOG2893|consensus 77.8 0.61 1.3E-05 28.9 -0.3 45 21-70 9-53 (341)
103 PF03604 DNA_RNApol_7kD: DNA d 77.4 1.2 2.5E-05 18.6 0.6 8 80-87 18-25 (32)
104 PHA00626 hypothetical protein 77.4 1.7 3.7E-05 20.5 1.2 15 78-92 22-36 (59)
105 PRK03976 rpl37ae 50S ribosomal 76.9 0.98 2.1E-05 23.6 0.4 13 78-90 53-65 (90)
106 KOG3408|consensus 75.9 2 4.4E-05 23.7 1.4 23 79-101 57-79 (129)
107 PF10571 UPF0547: Uncharacteri 75.9 1.5 3.3E-05 17.3 0.7 9 81-89 16-24 (26)
108 COG0068 HypF Hydrogenase matur 75.3 0.37 7.9E-06 34.4 -1.8 58 26-90 126-184 (750)
109 PF10013 DUF2256: Uncharacteri 75.2 2.3 5E-05 18.9 1.2 14 81-94 10-23 (42)
110 KOG1146|consensus 74.8 0.31 6.7E-06 37.0 -2.4 77 24-105 1261-1354(1406)
111 smart00154 ZnF_AN1 AN1-like Zi 73.9 2.1 4.5E-05 18.6 0.9 13 79-91 12-24 (39)
112 PF05191 ADK_lid: Adenylate ki 73.8 0.51 1.1E-05 20.2 -1.0 8 80-87 22-29 (36)
113 PF12013 DUF3505: Protein of u 73.3 3.1 6.7E-05 22.4 1.7 18 27-44 88-105 (109)
114 COG4530 Uncharacterized protei 72.8 1.8 3.9E-05 23.5 0.7 12 50-61 25-36 (129)
115 COG1996 RPC10 DNA-directed RNA 72.4 3.1 6.7E-05 19.2 1.3 10 24-33 7-16 (49)
116 PF15135 UPF0515: Uncharacteri 72.0 8.9 0.00019 24.2 3.6 58 22-92 111-168 (278)
117 PF09723 Zn-ribbon_8: Zinc rib 71.9 2.2 4.7E-05 18.8 0.8 13 80-92 6-18 (42)
118 KOG2907|consensus 71.7 5 0.00011 21.9 2.2 38 52-92 75-115 (116)
119 PF13878 zf-C2H2_3: zinc-finge 71.0 5.1 0.00011 17.6 1.9 23 24-46 14-38 (41)
120 KOG2785|consensus 71.0 6 0.00013 26.4 2.9 52 22-73 165-242 (390)
121 PRK03824 hypA hydrogenase nick 70.3 1.8 4E-05 24.4 0.5 12 52-63 71-82 (135)
122 COG5216 Uncharacterized conser 69.9 4.2 9.1E-05 19.4 1.5 30 24-59 23-52 (67)
123 PF12760 Zn_Tnp_IS1595: Transp 69.4 4.8 0.0001 18.0 1.7 9 78-86 36-44 (46)
124 PF01428 zf-AN1: AN1-like Zinc 68.8 2.2 4.7E-05 18.9 0.4 14 78-91 12-25 (43)
125 PF08274 PhnA_Zn_Ribbon: PhnA 68.5 2.7 5.9E-05 17.2 0.7 8 51-58 19-26 (30)
126 COG1198 PriA Primosomal protei 68.4 5.3 0.00011 29.1 2.4 49 24-88 436-484 (730)
127 PF13451 zf-trcl: Probable zin 68.0 2.8 6.1E-05 19.3 0.7 16 77-92 2-17 (49)
128 KOG2593|consensus 67.8 8.9 0.00019 26.1 3.2 36 48-86 125-160 (436)
129 PF04780 DUF629: Protein of un 67.1 4.8 0.0001 27.7 1.9 22 51-72 57-78 (466)
130 KOG2482|consensus 66.9 18 0.00038 24.1 4.3 66 8-73 129-217 (423)
131 PF14446 Prok-RING_1: Prokaryo 66.7 5.3 0.00011 18.8 1.5 26 24-61 6-31 (54)
132 PF15269 zf-C2H2_7: Zinc-finge 66.5 5.4 0.00012 17.9 1.4 22 80-101 21-42 (54)
133 TIGR00595 priA primosomal prot 64.4 8.3 0.00018 26.8 2.7 10 78-87 252-261 (505)
134 KOG4167|consensus 63.8 1.4 3.1E-05 31.7 -0.9 25 23-47 792-816 (907)
135 COG5236 Uncharacterized conser 62.9 15 0.00032 24.5 3.4 77 25-106 222-308 (493)
136 COG4338 Uncharacterized protei 60.1 4.4 9.5E-05 18.5 0.6 14 81-94 14-27 (54)
137 KOG1842|consensus 59.2 5.4 0.00012 27.2 1.1 22 52-73 16-37 (505)
138 PRK14873 primosome assembly pr 59.1 9.5 0.00021 27.6 2.3 11 78-88 421-431 (665)
139 COG4957 Predicted transcriptio 59.1 5.2 0.00011 22.7 0.8 22 80-104 77-98 (148)
140 PF04423 Rad50_zn_hook: Rad50 58.8 4.3 9.3E-05 18.8 0.4 12 81-92 22-33 (54)
141 PF13824 zf-Mss51: Zinc-finger 58.5 11 0.00024 17.8 1.8 8 51-58 14-21 (55)
142 PF12907 zf-met2: Zinc-binding 58.2 8.5 0.00018 16.9 1.3 27 80-106 2-31 (40)
143 PF01363 FYVE: FYVE zinc finge 58.1 7.7 0.00017 18.8 1.3 9 25-33 11-19 (69)
144 PF04780 DUF629: Protein of un 57.8 7.6 0.00017 26.8 1.6 26 23-48 57-83 (466)
145 PF13453 zf-TFIIB: Transcripti 57.5 11 0.00023 16.4 1.6 16 52-67 20-35 (41)
146 PRK00432 30S ribosomal protein 56.3 8.6 0.00019 17.7 1.2 12 78-89 36-47 (50)
147 PTZ00448 hypothetical protein; 56.2 8.8 0.00019 25.6 1.6 24 79-102 314-337 (373)
148 COG4888 Uncharacterized Zn rib 56.2 3 6.6E-05 22.3 -0.3 36 22-61 21-56 (104)
149 PRK05580 primosome assembly pr 55.5 14 0.00031 26.8 2.7 10 78-87 420-429 (679)
150 smart00064 FYVE Protein presen 55.0 9.1 0.0002 18.5 1.3 10 25-34 12-21 (68)
151 TIGR00416 sms DNA repair prote 54.9 9.7 0.00021 26.2 1.8 30 22-65 6-35 (454)
152 COG1675 TFA1 Transcription ini 54.6 23 0.0005 21.1 3.1 8 80-87 133-140 (176)
153 TIGR00100 hypA hydrogenase nic 54.5 7.3 0.00016 21.3 1.0 11 52-62 71-81 (115)
154 PF10276 zf-CHCC: Zinc-finger 54.4 7.1 0.00015 17.1 0.7 12 78-89 28-39 (40)
155 PF07282 OrfB_Zn_ribbon: Putat 54.2 25 0.00054 16.9 3.0 13 77-89 44-56 (69)
156 KOG1280|consensus 53.0 21 0.00045 23.8 2.9 23 51-73 79-101 (381)
157 PRK12380 hydrogenase nickel in 52.6 8.7 0.00019 21.0 1.1 10 52-61 71-80 (113)
158 smart00440 ZnF_C2C2 C2C2 Zinc 52.1 1.6 3.4E-05 19.1 -1.5 9 80-88 29-37 (40)
159 cd00065 FYVE FYVE domain; Zinc 51.7 15 0.00032 16.9 1.7 10 26-35 5-14 (57)
160 COG3091 SprT Zn-dependent meta 51.4 7.5 0.00016 22.5 0.7 34 49-87 115-148 (156)
161 PF14787 zf-CCHC_5: GAG-polypr 51.4 5.5 0.00012 17.0 0.1 16 81-96 4-19 (36)
162 KOG2923|consensus 51.1 16 0.00034 17.9 1.6 29 24-58 23-51 (67)
163 COG1655 Uncharacterized protei 50.9 3.4 7.4E-05 25.6 -0.7 25 20-44 16-40 (267)
164 PF15616 TerY-C: TerY-C metal 49.7 2.8 6.1E-05 23.6 -1.1 14 76-89 102-115 (131)
165 PRK11823 DNA repair protein Ra 49.6 13 0.00029 25.4 1.8 29 22-64 6-34 (446)
166 PLN02748 tRNA dimethylallyltra 49.6 13 0.00029 25.7 1.7 26 78-103 417-443 (468)
167 PF10083 DUF2321: Uncharacteri 48.7 3.3 7.2E-05 24.0 -1.0 17 77-93 66-82 (158)
168 PF07975 C1_4: TFIIH C1-like d 48.5 16 0.00034 17.0 1.4 16 51-66 21-36 (51)
169 TIGR00627 tfb4 transcription f 47.6 20 0.00042 23.1 2.2 25 51-89 255-279 (279)
170 cd01121 Sms Sms (bacterial rad 47.2 18 0.0004 24.2 2.1 10 24-33 1-10 (372)
171 COG3677 Transposase and inacti 46.5 11 0.00024 21.2 0.9 15 77-91 51-65 (129)
172 COG1326 Uncharacterized archae 46.5 37 0.0008 20.7 3.0 11 51-61 30-40 (201)
173 KOG0717|consensus 46.4 14 0.0003 25.6 1.4 22 80-101 293-314 (508)
174 PF14311 DUF4379: Domain of un 46.4 15 0.00033 17.0 1.3 10 52-61 29-38 (55)
175 KOG2807|consensus 45.5 43 0.00094 22.2 3.4 24 80-103 346-369 (378)
176 PRK00420 hypothetical protein; 45.5 20 0.00043 19.7 1.7 28 24-62 24-51 (112)
177 PRK04023 DNA polymerase II lar 44.4 29 0.00062 26.7 2.8 9 24-32 627-635 (1121)
178 KOG4118|consensus 44.4 9.5 0.00021 18.7 0.4 27 80-106 39-65 (74)
179 PLN02294 cytochrome c oxidase 44.0 15 0.00033 21.7 1.2 18 73-91 136-153 (174)
180 PRK00564 hypA hydrogenase nick 43.8 13 0.00028 20.4 0.9 12 52-63 72-83 (117)
181 COG2331 Uncharacterized protei 43.8 12 0.00026 19.0 0.7 10 24-33 13-22 (82)
182 COG1773 Rubredoxin [Energy pro 42.9 12 0.00026 17.7 0.6 12 79-90 3-14 (55)
183 PHA02998 RNA polymerase subuni 42.9 4.5 9.7E-05 24.1 -1.0 12 80-91 172-183 (195)
184 PF07503 zf-HYPF: HypF finger; 42.7 16 0.00036 15.4 0.9 13 78-90 20-32 (35)
185 PF08209 Sgf11: Sgf11 (transcr 42.5 15 0.00032 15.4 0.8 21 79-100 4-24 (33)
186 COG5112 UFD2 U1-like Zn-finger 41.6 15 0.00033 19.9 0.9 22 80-101 56-77 (126)
187 COG2879 Uncharacterized small 40.6 33 0.00072 16.7 1.9 18 90-107 23-40 (65)
188 PF02891 zf-MIZ: MIZ/SP-RING z 39.7 14 0.00031 16.9 0.5 8 24-31 42-49 (50)
189 PF11672 DUF3268: Protein of u 39.4 16 0.00035 19.7 0.8 10 23-32 2-11 (102)
190 COG3357 Predicted transcriptio 39.2 15 0.00032 19.4 0.6 27 22-58 57-83 (97)
191 PF01155 HypA: Hydrogenase exp 39.1 12 0.00026 20.4 0.3 13 52-64 71-83 (113)
192 PF08792 A2L_zn_ribbon: A2L zi 38.7 18 0.00038 15.1 0.7 10 80-89 22-31 (33)
193 cd00924 Cyt_c_Oxidase_Vb Cytoc 37.5 23 0.00049 18.9 1.2 17 73-90 74-90 (97)
194 PRK03681 hypA hydrogenase nick 37.0 19 0.00041 19.7 0.9 10 52-61 71-80 (114)
195 PF06676 DUF1178: Protein of u 36.9 26 0.00056 20.3 1.4 29 3-36 17-45 (148)
196 PF02591 DUF164: Putative zinc 36.7 50 0.0011 15.3 2.2 11 77-87 44-54 (56)
197 KOG0978|consensus 36.6 13 0.00028 27.0 0.3 21 78-98 677-697 (698)
198 TIGR03831 YgiT_finger YgiT-typ 36.5 23 0.00049 15.3 1.0 14 22-35 31-44 (46)
199 PLN03238 probable histone acet 36.2 60 0.0013 21.1 3.0 22 51-72 48-69 (290)
200 COG4306 Uncharacterized protei 35.8 14 0.00031 20.7 0.3 15 77-91 66-80 (160)
201 COG1066 Sms Predicted ATP-depe 35.4 24 0.00051 24.3 1.2 27 22-62 6-32 (456)
202 PRK14892 putative transcriptio 35.3 19 0.00042 19.3 0.7 34 23-63 21-54 (99)
203 COG1998 RPS31 Ribosomal protei 35.1 42 0.00092 15.5 1.7 10 79-88 37-46 (51)
204 cd00730 rubredoxin Rubredoxin; 35.1 20 0.00044 16.5 0.7 12 24-35 2-13 (50)
205 PRK00762 hypA hydrogenase nick 34.5 18 0.00039 20.1 0.5 12 52-64 71-82 (124)
206 PF01286 XPA_N: XPA protein N- 34.5 20 0.00042 15.2 0.5 12 80-91 4-15 (34)
207 KOG1088|consensus 34.4 25 0.00055 19.5 1.1 20 73-92 92-111 (124)
208 TIGR01206 lysW lysine biosynth 34.3 19 0.00042 16.9 0.6 11 80-90 3-13 (54)
209 COG3364 Zn-ribbon containing p 34.0 21 0.00047 19.2 0.7 15 22-36 1-15 (112)
210 COG1571 Predicted DNA-binding 33.9 35 0.00075 23.4 1.8 14 51-64 367-380 (421)
211 PF00301 Rubredoxin: Rubredoxi 33.7 24 0.00052 16.1 0.8 11 80-90 2-12 (47)
212 PF07800 DUF1644: Protein of u 33.4 1.1E+02 0.0023 18.1 3.8 53 51-105 80-134 (162)
213 KOG2071|consensus 33.3 35 0.00077 24.4 1.8 29 19-47 414-442 (579)
214 PF14354 Lar_restr_allev: Rest 33.3 28 0.00061 16.3 1.1 11 23-33 3-13 (61)
215 PF04606 Ogr_Delta: Ogr/Delta- 32.6 10 0.00022 17.1 -0.5 13 78-90 24-38 (47)
216 PRK12496 hypothetical protein; 32.6 31 0.00068 20.2 1.3 12 51-62 127-138 (164)
217 PF09845 DUF2072: Zn-ribbon co 32.2 26 0.00056 19.8 0.9 15 23-37 1-15 (131)
218 PF06397 Desulfoferrod_N: Desu 32.2 24 0.00052 15.1 0.6 12 78-89 5-16 (36)
219 COG1594 RPB9 DNA-directed RNA 32.0 12 0.00027 20.4 -0.3 11 80-90 101-111 (113)
220 COG0675 Transposase and inacti 31.3 65 0.0014 20.6 2.8 10 78-87 321-330 (364)
221 TIGR00143 hypF [NiFe] hydrogen 31.1 3.1 6.7E-05 30.2 -3.4 58 26-90 93-151 (711)
222 PTZ00303 phosphatidylinositol 30.8 39 0.00085 25.5 1.8 12 25-36 462-473 (1374)
223 KOG1994|consensus 30.6 31 0.00068 21.5 1.1 23 77-99 237-259 (268)
224 PF14634 zf-RING_5: zinc-RING 30.2 58 0.0013 14.1 2.2 10 77-86 34-43 (44)
225 PF14803 Nudix_N_2: Nudix N-te 30.0 31 0.00068 14.5 0.8 8 52-59 23-30 (34)
226 PRK03564 formate dehydrogenase 29.8 31 0.00068 22.6 1.1 11 23-33 187-197 (309)
227 PRK05978 hypothetical protein; 29.6 33 0.00071 19.9 1.1 10 81-90 54-63 (148)
228 PF01927 Mut7-C: Mut7-C RNAse 29.5 42 0.0009 19.2 1.5 36 24-62 92-135 (147)
229 PF09855 DUF2082: Nucleic-acid 29.4 24 0.00052 17.2 0.4 8 80-87 1-8 (64)
230 TIGR00686 phnA alkylphosphonat 29.4 29 0.00062 19.0 0.7 26 25-61 4-29 (109)
231 smart00647 IBR In Between Ring 29.0 44 0.00095 15.5 1.3 12 51-62 40-51 (64)
232 PRK05452 anaerobic nitric oxid 28.9 36 0.00078 23.7 1.3 17 48-64 422-438 (479)
233 PF14369 zf-RING_3: zinc-finge 28.5 28 0.00061 14.6 0.5 10 25-34 23-32 (35)
234 PF09963 DUF2197: Uncharacteri 28.5 24 0.00053 16.8 0.4 7 80-86 32-38 (56)
235 COG1579 Zn-ribbon protein, pos 28.4 58 0.0013 20.6 2.0 15 76-90 218-232 (239)
236 PF03966 Trm112p: Trm112p-like 28.1 32 0.00069 16.7 0.8 18 73-90 47-64 (68)
237 PF14205 Cys_rich_KTR: Cystein 28.1 26 0.00056 16.6 0.4 10 78-87 27-36 (55)
238 PF08271 TF_Zn_Ribbon: TFIIB z 27.8 35 0.00075 14.9 0.8 8 81-88 2-9 (43)
239 COG5151 SSL1 RNA polymerase II 27.8 42 0.0009 22.2 1.4 25 78-102 387-411 (421)
240 COG4896 Uncharacterized protei 27.4 52 0.0011 16.0 1.4 7 52-58 32-38 (68)
241 PRK10220 hypothetical protein; 27.3 35 0.00077 18.7 0.9 27 25-62 5-31 (111)
242 PRK14714 DNA polymerase II lar 27.2 61 0.0013 25.8 2.3 9 24-32 668-676 (1337)
243 PF14255 Cys_rich_CPXG: Cystei 26.5 35 0.00075 15.9 0.7 11 25-35 2-12 (52)
244 TIGR01384 TFS_arch transcripti 26.4 43 0.00092 17.7 1.1 26 25-62 2-27 (104)
245 PF01096 TFIIS_C: Transcriptio 26.3 36 0.00077 14.6 0.7 9 80-88 29-37 (39)
246 COG3478 Predicted nucleic-acid 26.0 37 0.00081 16.7 0.7 10 79-88 4-13 (68)
247 PF14690 zf-ISL3: zinc-finger 26.0 35 0.00076 14.9 0.6 9 79-87 2-10 (47)
248 KOG0402|consensus 25.9 42 0.00092 17.4 1.0 8 24-31 37-44 (92)
249 PF11290 DUF3090: Protein of u 25.6 1.1E+02 0.0024 18.3 2.8 11 25-35 156-166 (171)
250 KOG3507|consensus 25.6 46 0.00099 16.0 1.0 11 79-89 37-47 (62)
251 TIGR03829 YokU_near_AblA uncha 25.3 51 0.0011 17.4 1.2 23 22-44 34-56 (89)
252 PF12773 DZR: Double zinc ribb 24.7 47 0.001 14.8 1.0 8 52-59 30-37 (50)
253 PRK12722 transcriptional activ 24.7 61 0.0013 19.6 1.6 28 52-87 135-162 (187)
254 PTZ00043 cytochrome c oxidase 24.6 43 0.00094 21.0 1.0 31 21-54 179-209 (268)
255 PRK01343 zinc-binding protein; 24.2 45 0.00097 15.9 0.8 11 80-90 10-20 (57)
256 COG2956 Predicted N-acetylgluc 24.2 1.4E+02 0.0031 20.1 3.3 10 22-31 353-362 (389)
257 cd00974 DSRD Desulforedoxin (D 23.8 46 0.001 13.6 0.8 12 78-89 3-14 (34)
258 COG5188 PRP9 Splicing factor 3 23.8 30 0.00065 23.2 0.3 22 80-101 239-260 (470)
259 PLN03208 E3 ubiquitin-protein 23.6 1.8E+02 0.0038 17.9 3.4 54 22-91 17-80 (193)
260 PF01215 COX5B: Cytochrome c o 23.2 38 0.00081 19.4 0.5 17 73-90 107-123 (136)
261 PF10537 WAC_Acf1_DNA_bd: ATP- 23.2 1.4E+02 0.003 16.1 3.5 41 22-63 2-42 (102)
262 PF10263 SprT-like: SprT-like 22.9 46 0.001 18.9 0.9 32 51-90 123-154 (157)
263 TIGR01562 FdhE formate dehydro 22.8 82 0.0018 20.7 2.0 13 47-59 206-218 (305)
264 PF09297 zf-NADH-PPase: NADH p 22.8 34 0.00074 13.8 0.3 11 49-59 19-29 (32)
265 PRK08222 hydrogenase 4 subunit 22.7 67 0.0014 19.1 1.6 20 77-96 112-131 (181)
266 TIGR00319 desulf_FeS4 desulfof 22.7 51 0.0011 13.5 0.8 12 78-89 6-17 (34)
267 PRK12860 transcriptional activ 22.6 66 0.0014 19.5 1.5 27 52-86 135-161 (189)
268 PF03811 Zn_Tnp_IS1: InsA N-te 22.0 34 0.00073 14.6 0.2 6 80-85 30-35 (36)
269 KOG2636|consensus 21.8 79 0.0017 22.1 1.8 27 18-44 396-423 (497)
270 PLN03239 histone acetyltransfe 21.8 93 0.002 20.9 2.1 25 77-101 104-128 (351)
271 smart00132 LIM Zinc-binding do 21.8 41 0.00089 13.5 0.4 9 80-88 28-36 (39)
272 PLN00104 MYST -like histone ac 21.7 1.1E+02 0.0023 21.5 2.4 25 77-101 196-220 (450)
273 KOG2857|consensus 21.7 56 0.0012 18.8 1.0 22 23-44 17-38 (157)
274 TIGR03847 conserved hypothetic 21.6 1.5E+02 0.0033 17.8 2.8 11 25-35 158-168 (177)
275 KOG0696|consensus 21.4 26 0.00057 24.3 -0.3 59 20-87 70-129 (683)
276 COG4391 Uncharacterized protei 21.4 66 0.0014 15.6 1.1 13 78-90 47-59 (62)
277 TIGR00515 accD acetyl-CoA carb 21.3 74 0.0016 20.6 1.6 34 24-66 27-60 (285)
278 PF05876 Terminase_GpA: Phage 21.3 59 0.0013 23.2 1.3 40 52-91 201-241 (557)
279 PHA02942 putative transposase; 20.9 1E+02 0.0023 20.8 2.3 14 77-90 340-353 (383)
280 KOG3214|consensus 20.8 23 0.0005 19.0 -0.6 13 52-64 48-60 (109)
281 PF13821 DUF4187: Domain of un 20.8 76 0.0017 14.9 1.2 21 77-97 25-45 (55)
282 PTZ00064 histone acetyltransfe 20.8 1.3E+02 0.0028 21.5 2.7 25 77-101 278-302 (552)
283 PF05129 Elf1: Transcription e 20.5 46 0.001 17.0 0.5 10 77-86 20-29 (81)
284 PRK06260 threonine synthase; V 20.4 94 0.002 21.0 2.0 27 24-62 4-30 (397)
285 PRK04351 hypothetical protein; 20.3 69 0.0015 18.5 1.2 32 51-90 112-143 (149)
286 PRK14138 NAD-dependent deacety 20.2 1.7E+02 0.0038 18.3 3.1 13 52-64 120-132 (244)
287 KOG4602|consensus 20.1 36 0.00079 21.7 0.1 10 51-60 268-277 (318)
288 PF03884 DUF329: Domain of unk 20.1 50 0.0011 15.8 0.5 12 80-91 3-14 (57)
No 1
>KOG2462|consensus
Probab=99.93 E-value=2.8e-26 Score=137.01 Aligned_cols=98 Identities=40% Similarity=0.686 Sum_probs=55.0
Q ss_pred cchhcHHHHHHHHHHHhcCCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCcee
Q psy10278 2 NFYADIKCLKKHIREVHKRLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQ 81 (110)
Q Consensus 2 ~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~ 81 (110)
|.|.+...|+-|++ +|. .+..|.+||+.|..+=.|+.|+++|+||+||.|+.|++.|...++|..|+++|.+.++|+
T Consensus 169 K~YvSmpALkMHir-TH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~q 245 (279)
T KOG2462|consen 169 KVYVSMPALKMHIR-THT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQ 245 (279)
T ss_pred ceeeehHHHhhHhh-ccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcccc
Confidence 44555555555553 343 345555555555555555555555555555555555555555555555555555555555
Q ss_pred ccCCCcccccHHHHHhhhhhc
Q psy10278 82 CTFCSYSCTERFRLKDHTLAK 102 (110)
Q Consensus 82 C~~C~~~f~~~~~l~~H~~~~ 102 (110)
|..|+|+|+..+.|.+|..+.
T Consensus 246 C~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 246 CPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred CcchhhHHHHHHHHHHhhhhc
Confidence 555555555555555555443
No 2
>KOG2462|consensus
Probab=99.93 E-value=3.8e-26 Score=136.45 Aligned_cols=103 Identities=25% Similarity=0.520 Sum_probs=94.5
Q ss_pred cchhcHHHHHHHHHHHhc---CCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcCCCC
Q psy10278 2 NFYADIKCLKKHIREVHK---RLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHMPVK 78 (110)
Q Consensus 2 ~~f~~~~~l~~h~~~~~~---~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~ 78 (110)
|.|++...|.+|.+ .|- ..+.+.|+.|++.+.+-..|+.|+++|. .+.+|.+||+.|..+.-|+.|+++|+||+
T Consensus 138 k~ysT~snLsrHkQ-~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEK 214 (279)
T KOG2462|consen 138 KSYSTSSNLSRHKQ-THRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEK 214 (279)
T ss_pred cccccccccchhhc-ccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCC
Confidence 67889999999995 664 3456899999999999999999999997 57899999999999999999999999999
Q ss_pred ceeccCCCcccccHHHHHhhhhhcCCCCC
Q psy10278 79 KYQCTFCSYSCTERFRLKDHTLAKHNPGT 107 (110)
Q Consensus 79 p~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 107 (110)
||.|+.|+++|+.+++|+.||.+|.+.+.
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQTHS~~K~ 243 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQTHSDVKK 243 (279)
T ss_pred CccCCcccchhcchHHHHHHHHhhcCCcc
Confidence 99999999999999999999999998764
No 3
>KOG1074|consensus
Probab=99.71 E-value=1.6e-18 Score=116.40 Aligned_cols=55 Identities=22% Similarity=0.417 Sum_probs=51.0
Q ss_pred ceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccHHHHHhhhhhcCCC
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTERFRLKDHTLAKHNP 105 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~~l~~H~~~~~~~ 105 (110)
+..|.+|.+...=.+.|+-|.++|+|||||+|..||++|+.+.+|+.|+.+|-..
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~ 659 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAK 659 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccC
Confidence 4689999999999999999999999999999999999999999999999888643
No 4
>KOG3576|consensus
Probab=99.68 E-value=3.9e-18 Score=98.67 Aligned_cols=102 Identities=25% Similarity=0.473 Sum_probs=58.2
Q ss_pred cchhcHHHHHHHHHHHhcCCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcC------
Q psy10278 2 NFYADIKCLKKHIREVHKRLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHM------ 75 (110)
Q Consensus 2 ~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~------ 75 (110)
|.|.--.-|.+|++ .|...+.+.|..||+.|.....|++|+++|+|..||.|..|++.|.+.-.|..|++.-+
T Consensus 125 K~F~lQRmlnrh~k-ch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~y 203 (267)
T KOG3576|consen 125 KKFGLQRMLNRHLK-CHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQY 203 (267)
T ss_pred hhhhHHHHHHHHhh-hccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHH
Confidence 45555555556662 45555555666666666666666666666666666666666666666655655555221
Q ss_pred -----CCCceeccCCCcccccHHHHHhhhhhcCC
Q psy10278 76 -----PVKKYQCTFCSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 76 -----~~~p~~C~~C~~~f~~~~~l~~H~~~~~~ 104 (110)
.++-|.|..||.+-.....+..|++.+|.
T Consensus 204 aykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 204 AYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred HHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 13335666666665555566666655554
No 5
>KOG3623|consensus
Probab=99.67 E-value=1.1e-17 Score=111.44 Aligned_cols=82 Identities=21% Similarity=0.408 Sum_probs=77.7
Q ss_pred cCCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccHHHHHhh
Q psy10278 19 KRLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTERFRLKDH 98 (110)
Q Consensus 19 ~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~~l~~H 98 (110)
..+-.|.|..|+++|.-.++|.+|...|+|.+||.|.+|.+.|..+-.|..|.+.|.||+||.|.+|+|.|+...++.+|
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQH 969 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhh
Confidence 34557999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hh
Q psy10278 99 TL 100 (110)
Q Consensus 99 ~~ 100 (110)
|.
T Consensus 970 MN 971 (1007)
T KOG3623|consen 970 MN 971 (1007)
T ss_pred hc
Confidence 85
No 6
>KOG3576|consensus
Probab=99.66 E-value=3.7e-17 Score=94.63 Aligned_cols=86 Identities=29% Similarity=0.556 Sum_probs=80.5
Q ss_pred CCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccHHHHHhhh
Q psy10278 20 RLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTERFRLKDHT 99 (110)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~~l~~H~ 99 (110)
+...+.|.+|++.|.....|.+|++.|...+.+.|..||+.|...-.|..|.++|+|.+||+|..|+++|+++.+|..|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 44558999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCC
Q psy10278 100 LAKHNP 105 (110)
Q Consensus 100 ~~~~~~ 105 (110)
+.-|+-
T Consensus 194 ~kvhgv 199 (267)
T KOG3576|consen 194 KKVHGV 199 (267)
T ss_pred HHHcCc
Confidence 977763
No 7
>KOG3623|consensus
Probab=99.65 E-value=9e-17 Score=107.15 Aligned_cols=101 Identities=23% Similarity=0.462 Sum_probs=87.7
Q ss_pred cchhcHHHHHHHHHHHhc-CCCCccCCcccccccCchhHHHHHHhcCC-------------CCceeCCCCCCCcCChHHH
Q psy10278 2 NFYADIKCLKKHIREVHK-RLKPFQCPVCGFTTGRKATLQLHVRQHTR-------------EKPYACPTCEFKTGDHNVL 67 (110)
Q Consensus 2 ~~f~~~~~l~~h~~~~~~-~~~~~~C~~c~~~~~~~~~l~~h~~~~~~-------------~~~~~c~~c~~~~~~~~~l 67 (110)
+.|.+...|+.|+...|. .+..|.|..|..+|.....|.+|+..|-. .+.|+|..|++.|..+-.|
T Consensus 218 rgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHL 297 (1007)
T KOG3623|consen 218 RGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHL 297 (1007)
T ss_pred HHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHH
Confidence 356667789999976665 45559999999999999999999988743 2348999999999999999
Q ss_pred HHHHHhcCCCCceeccCCCcccccHHHHHhhhhhc
Q psy10278 68 RKHVQRHMPVKKYQCTFCSYSCTERFRLKDHTLAK 102 (110)
Q Consensus 68 ~~h~~~h~~~~p~~C~~C~~~f~~~~~l~~H~~~~ 102 (110)
..|+++|.||+||.|+-|+|.|+...++..||.+.
T Consensus 298 KEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSSK 332 (1007)
T KOG3623|consen 298 KEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSSK 332 (1007)
T ss_pred HhhheeecCCCCcCCcccccccccCCccccccccc
Confidence 99999999999999999999999999999998654
No 8
>KOG1074|consensus
Probab=99.62 E-value=5.1e-16 Score=104.68 Aligned_cols=58 Identities=24% Similarity=0.359 Sum_probs=54.0
Q ss_pred eeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccHHHHHhhhhhcCCCCCCC
Q psy10278 52 YACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTERFRLKDHTLAKHNPGTDG 109 (110)
Q Consensus 52 ~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~ 109 (110)
..|.+|++.|..++.|..|+++|++++||.|..|++.|+.+.+|+.||..|...++..
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~s 937 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPS 937 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCc
Confidence 5799999999999999999999999999999999999999999999999988766544
No 9
>KOG3608|consensus
Probab=99.55 E-value=1.3e-14 Score=90.19 Aligned_cols=102 Identities=28% Similarity=0.565 Sum_probs=80.9
Q ss_pred cchhcHHHHHHHHHHHhcCCCCccCCcccccccCchhHHHHHHhcCC----------------------------CCcee
Q psy10278 2 NFYADIKCLKKHIREVHKRLKPFQCPVCGFTTGRKATLQLHVRQHTR----------------------------EKPYA 53 (110)
Q Consensus 2 ~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~----------------------------~~~~~ 53 (110)
+.|.++..|..|++ .|++++..-|+.|+.-|.+...|..|.+..+. ...|.
T Consensus 187 ~~~~~k~~LreH~r-~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~yk 265 (467)
T KOG3608|consen 187 KHMGNKYRLREHIR-THSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYK 265 (467)
T ss_pred hhhccHHHHHHHHH-hcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhccc
Confidence 56777788888884 67877777777777777777777777654321 13588
Q ss_pred CCCCCCCcCChHHHHHHHH-hcCCCCceeccCCCcccccHHHHHhhhhhcCC
Q psy10278 54 CPTCEFKTGDHNVLRKHVQ-RHMPVKKYQCTFCSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 54 c~~c~~~~~~~~~l~~h~~-~h~~~~p~~C~~C~~~f~~~~~l~~H~~~~~~ 104 (110)
|+.|+-.....+.|..|++ .|...+||+|..|.+.|...+.|.+|..+|..
T Consensus 266 CplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~ 317 (467)
T KOG3608|consen 266 CPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSK 317 (467)
T ss_pred ccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccc
Confidence 9999999999999999999 68889999999999999999999999987763
No 10
>KOG3608|consensus
Probab=99.53 E-value=4.2e-14 Score=88.03 Aligned_cols=101 Identities=33% Similarity=0.675 Sum_probs=84.5
Q ss_pred cchhcHHHHHHHHHHHhcCCCCccCCcccccccCchhHHHHHH-hcCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCce
Q psy10278 2 NFYADIKCLKKHIREVHKRLKPFQCPVCGFTTGRKATLQLHVR-QHTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKY 80 (110)
Q Consensus 2 ~~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~-~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~ 80 (110)
|.|.+...|..|+. .|-. -|+|+.|.++....++|..|++ .|...+|++|..|+..+...+.|..|..+|. +..|
T Consensus 245 KrFaTeklL~~Hv~-rHvn--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y 320 (467)
T KOG3608|consen 245 KRFATEKLLKSHVV-RHVN--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVY 320 (467)
T ss_pred HHHhHHHHHHHHHH-Hhhh--cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccce
Confidence 67899999999984 4543 5899999999999999999998 5778899999999999999999999999887 5668
Q ss_pred eccC--CCcccccHHHHHhhhhhcCCCC
Q psy10278 81 QCTF--CSYSCTERFRLKDHTLAKHNPG 106 (110)
Q Consensus 81 ~C~~--C~~~f~~~~~l~~H~~~~~~~~ 106 (110)
.|.. |...|.+..+++.|++.+|..+
T Consensus 321 ~C~h~~C~~s~r~~~q~~~H~~evhEg~ 348 (467)
T KOG3608|consen 321 QCEHPDCHYSVRTYTQMRRHFLEVHEGN 348 (467)
T ss_pred ecCCCCCcHHHHHHHHHHHHHHHhccCC
Confidence 8866 8888888888888888777433
No 11
>PHA00733 hypothetical protein
Probab=99.43 E-value=2.2e-13 Score=75.25 Aligned_cols=84 Identities=20% Similarity=0.294 Sum_probs=69.6
Q ss_pred CCCCccCCcccccccCchhHHHH--HH---hcCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccHHH
Q psy10278 20 RLKPFQCPVCGFTTGRKATLQLH--VR---QHTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTERFR 94 (110)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~~l~~h--~~---~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~~ 94 (110)
..+++.|.+|...|.....+..+ +. .+.+.++|.|..|++.|.....|..|+..+ +.++.|..|++.|.....
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~s 114 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDS 114 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHH
Confidence 35568999999888877666655 11 233477999999999999999999999976 467999999999999999
Q ss_pred HHhhhhhcCCC
Q psy10278 95 LKDHTLAKHNP 105 (110)
Q Consensus 95 l~~H~~~~~~~ 105 (110)
|..|+...|+-
T Consensus 115 L~~H~~~~h~~ 125 (128)
T PHA00733 115 TLDHVCKKHNI 125 (128)
T ss_pred HHHHHHHhcCc
Confidence 99999988863
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.18 E-value=1.1e-11 Score=57.88 Aligned_cols=44 Identities=16% Similarity=0.301 Sum_probs=34.0
Q ss_pred ceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccHHHHH
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTERFRLK 96 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~~l~ 96 (110)
.|.|+.||+.|...+.|..|++.|+ +|++|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3678888888888888888888877 6788888888887666553
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.09 E-value=7.9e-10 Score=73.76 Aligned_cols=91 Identities=22% Similarity=0.421 Sum_probs=64.4
Q ss_pred HHHHHHHHHHHhcCCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCC----------hHHHHHHHHhcCC
Q psy10278 7 IKCLKKHIREVHKRLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGD----------HNVLRKHVQRHMP 76 (110)
Q Consensus 7 ~~~l~~h~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~----------~~~l~~h~~~h~~ 76 (110)
...|..|+. .+. .++.|+ |+..+ ....|..|+..|-+.+++.|+.|+..+.. ...|..|.... +
T Consensus 465 ~s~LekH~~-~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G 538 (567)
T PLN03086 465 QGEMEKHMK-VFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-G 538 (567)
T ss_pred hHHHHHHHH-hcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-C
Confidence 567788885 443 578888 88654 45778888777888888888888877741 34677787774 7
Q ss_pred CCceeccCCCcccccHHHHHhhhhhcCC
Q psy10278 77 VKKYQCTFCSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~~~l~~H~~~~~~ 104 (110)
.+++.|..|++.+..+ .+..|+...|.
T Consensus 539 ~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 539 SRTAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred CcceEccccCCeeeeh-hHHHHHHHhhc
Confidence 7888888888877654 56667665543
No 14
>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=99.05 E-value=1.9e-10 Score=46.33 Aligned_cols=26 Identities=35% Similarity=0.797 Sum_probs=21.6
Q ss_pred HHHHHHHhcCCCCceeccCCCccccc
Q psy10278 66 VLRKHVQRHMPVKKYQCTFCSYSCTE 91 (110)
Q Consensus 66 ~l~~h~~~h~~~~p~~C~~C~~~f~~ 91 (110)
+|..|++.|++++||.|+.|++.|..
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 46788889999999999999988863
No 15
>PHA00733 hypothetical protein
Probab=99.01 E-value=1.3e-09 Score=60.31 Aligned_cols=64 Identities=25% Similarity=0.529 Sum_probs=52.8
Q ss_pred HHHHHHHHHhcCCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcCC
Q psy10278 9 CLKKHIREVHKRLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHMP 76 (110)
Q Consensus 9 ~l~~h~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~ 76 (110)
.|..|+ .+.+++||.|+.|++.|.+...|..|+..+ ..++.|..|++.|.....|..|+...++
T Consensus 61 ~l~~~~--~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 61 YLYKLL--TSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HHHhhc--ccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 344454 245688999999999999999999999865 3478999999999999999999886553
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.01 E-value=1.4e-10 Score=54.25 Aligned_cols=44 Identities=18% Similarity=0.451 Sum_probs=39.4
Q ss_pred CccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHH
Q psy10278 23 PFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLR 68 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~ 68 (110)
.|.|+.||+.|.....|..|++.|+ +++.|..|++.|...+.|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 4899999999999999999999998 6899999999998776654
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.96 E-value=2.6e-09 Score=71.38 Aligned_cols=77 Identities=18% Similarity=0.487 Sum_probs=64.1
Q ss_pred CCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccc----------
Q psy10278 21 LKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCT---------- 90 (110)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~---------- 90 (110)
+..+.|+.|++.|. ...+..|+..++ +++.|+ |+..+ ....|..|+..|..++|+.|..|++.|.
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d 525 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRD 525 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhh
Confidence 34578999999996 577999999874 789999 99755 6689999999999999999999999985
Q ss_pred cHHHHHhhhhhc
Q psy10278 91 ERFRLKDHTLAK 102 (110)
Q Consensus 91 ~~~~l~~H~~~~ 102 (110)
..+.|..|....
T Consensus 526 ~~s~Lt~HE~~C 537 (567)
T PLN03086 526 RLRGMSEHESIC 537 (567)
T ss_pred hhhhHHHHHHhc
Confidence 245788888764
No 18
>KOG3993|consensus
Probab=98.86 E-value=3.8e-10 Score=72.07 Aligned_cols=81 Identities=20% Similarity=0.387 Sum_probs=55.9
Q ss_pred ccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcC----------------------------
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHM---------------------------- 75 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~---------------------------- 75 (110)
|.|.+|...|.....|.+|.-.-.....|.|+.|++.|.=..+|..|.+=|.
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 6666666666666666666443333345666666666666666666665441
Q ss_pred -----CCCceeccCCCcccccHHHHHhhhhhcCC
Q psy10278 76 -----PVKKYQCTFCSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 76 -----~~~p~~C~~C~~~f~~~~~l~~H~~~~~~ 104 (110)
.+..|.|..|++.|.....|++|+.+|+.
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 12359999999999999999999999885
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.81 E-value=4.2e-09 Score=42.36 Aligned_cols=25 Identities=40% Similarity=0.972 Sum_probs=18.8
Q ss_pred HHHHHHHHHhcCCCCccCCccccccc
Q psy10278 9 CLKKHIREVHKRLKPFQCPVCGFTTG 34 (110)
Q Consensus 9 ~l~~h~~~~~~~~~~~~C~~c~~~~~ 34 (110)
+|..|++ .|.+++||.|+.|++.|.
T Consensus 1 ~l~~H~~-~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMR-THTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHH-HHSSSSSEEESSSSEEES
T ss_pred CHHHHhh-hcCCCCCCCCCCCcCeeC
Confidence 4677885 688888888888887775
No 20
>PHA00616 hypothetical protein
Probab=98.69 E-value=7.7e-09 Score=46.22 Aligned_cols=31 Identities=16% Similarity=0.222 Sum_probs=16.6
Q ss_pred eeCCCCCCCcCChHHHHHHHHhcCCCCceec
Q psy10278 52 YACPTCEFKTGDHNVLRKHVQRHMPVKKYQC 82 (110)
Q Consensus 52 ~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C 82 (110)
|.|+.||+.|...+.+..|++.|+++.|+.|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 4555555555555555555555555555544
No 21
>PHA00616 hypothetical protein
Probab=98.64 E-value=1.4e-08 Score=45.43 Aligned_cols=33 Identities=18% Similarity=0.313 Sum_probs=30.7
Q ss_pred CccCCcccccccCchhHHHHHHhcCCCCceeCC
Q psy10278 23 PFQCPVCGFTTGRKATLQLHVRQHTREKPYACP 55 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~ 55 (110)
||+|+.||+.|...+.+..|++.|++++++.|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 689999999999999999999999999988775
No 22
>PHA00732 hypothetical protein
Probab=98.54 E-value=1.3e-07 Score=48.08 Aligned_cols=45 Identities=40% Similarity=0.775 Sum_probs=28.2
Q ss_pred CccCCcccccccCchhHHHHHHh-cCCCCceeCCCCCCCcCChHHHHHHHHh
Q psy10278 23 PFQCPVCGFTTGRKATLQLHVRQ-HTREKPYACPTCEFKTGDHNVLRKHVQR 73 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~-~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 73 (110)
||.|..|++.|.+...|..|++. |.+ +.|+.|++.|. .+..|...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---Chhhhhcc
Confidence 46677777777777777777663 432 36777777665 34455543
No 23
>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=98.38 E-value=1.1e-06 Score=41.46 Aligned_cols=49 Identities=29% Similarity=0.510 Sum_probs=20.8
Q ss_pred eeCCCCCCCcCChHHHHHHHHh-cCC-CCceeccCCCcccccHHHHHhhhhhcC
Q psy10278 52 YACPTCEFKTGDHNVLRKHVQR-HMP-VKKYQCTFCSYSCTERFRLKDHTLAKH 103 (110)
Q Consensus 52 ~~c~~c~~~~~~~~~l~~h~~~-h~~-~~p~~C~~C~~~f~~~~~l~~H~~~~~ 103 (110)
|.||.|++ ......|..|... |.. .+.+.|+.|...+. .+|..|+...|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 34445544 2233344444442 222 12345555544333 24555555444
No 24
>KOG3993|consensus
Probab=98.37 E-value=1.7e-07 Score=60.28 Aligned_cols=71 Identities=30% Similarity=0.416 Sum_probs=56.6
Q ss_pred chhcHHHHHHHHHHHhcCCCCccCCcccccccCchhHHHHHHhcCC---------------------------------C
Q psy10278 3 FYADIKCLKKHIREVHKRLKPFQCPVCGFTTGRKATLQLHVRQHTR---------------------------------E 49 (110)
Q Consensus 3 ~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~---------------------------------~ 49 (110)
.|.+...|.+|. -..+-..-|.|+.|++.|.-..+|..|.+.|-. .
T Consensus 276 kYeD~F~LAQHr-C~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~ 354 (500)
T KOG3993|consen 276 KYEDAFALAQHR-CPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSS 354 (500)
T ss_pred hhhhHHHHhhcc-CCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccC
Confidence 477778888886 334444459999999999999999999887721 1
Q ss_pred CceeCCCCCCCcCChHHHHHHHHhc
Q psy10278 50 KPYACPTCEFKTGDHNVLRKHVQRH 74 (110)
Q Consensus 50 ~~~~c~~c~~~~~~~~~l~~h~~~h 74 (110)
..|.|..|++.|.....|..|+.+|
T Consensus 355 gi~~C~~C~KkFrRqAYLrKHqlth 379 (500)
T KOG3993|consen 355 GIFSCHTCGKKFRRQAYLRKHQLTH 379 (500)
T ss_pred ceeecHHhhhhhHHHHHHHHhHHhh
Confidence 2488999999999999999997766
No 25
>PHA00732 hypothetical protein
Probab=98.34 E-value=5.5e-07 Score=45.76 Aligned_cols=47 Identities=30% Similarity=0.639 Sum_probs=37.5
Q ss_pred ceeCCCCCCCcCChHHHHHHHHh-cCCCCceeccCCCcccccHHHHHhhhhhcC
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQR-HMPVKKYQCTFCSYSCTERFRLKDHTLAKH 103 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~~-h~~~~p~~C~~C~~~f~~~~~l~~H~~~~~ 103 (110)
||.|..|++.|.....|..|++. |. ++.|+.|++.|.+ +..|..+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhcccC
Confidence 47899999999999999999984 54 3589999999984 667775544
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.32 E-value=4.1e-07 Score=35.33 Aligned_cols=22 Identities=32% Similarity=0.674 Sum_probs=18.5
Q ss_pred eeccCCCcccccHHHHHhhhhh
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLA 101 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~ 101 (110)
|.|+.|++.|.....|..|++.
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 5788888888888888888876
No 27
>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=98.28 E-value=8.2e-07 Score=35.85 Aligned_cols=26 Identities=15% Similarity=0.450 Sum_probs=22.5
Q ss_pred ceeccCCCcccccHHHHHhhhhhcCC
Q psy10278 79 KYQCTFCSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 79 p~~C~~C~~~f~~~~~l~~H~~~~~~ 104 (110)
||.|..|++.|.....|..|++.++.
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 68899999999999999999987764
No 28
>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=98.28 E-value=2.3e-06 Score=40.43 Aligned_cols=50 Identities=30% Similarity=0.649 Sum_probs=38.0
Q ss_pred CccCCcccccccCchhHHHHHH-hcCCC-CceeCCCCCCCcCChHHHHHHHHhcC
Q psy10278 23 PFQCPVCGFTTGRKATLQLHVR-QHTRE-KPYACPTCEFKTGDHNVLRKHVQRHM 75 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~-~~~~~-~~~~c~~c~~~~~~~~~l~~h~~~h~ 75 (110)
.|.||.|++ ..+...|..|.. .|..+ +.+.||+|...+. .+|..|+...+
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 566788999987 45553 5689999997544 48888887543
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=98.22 E-value=1.2e-06 Score=34.11 Aligned_cols=24 Identities=29% Similarity=0.693 Sum_probs=18.3
Q ss_pred eeccCCCcccccHHHHHhhhhhcC
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLAKH 103 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~~~ 103 (110)
|.|+.|++.|.....|..|+..+|
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 578888888888888888888765
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=98.21 E-value=1.7e-06 Score=45.69 Aligned_cols=74 Identities=20% Similarity=0.368 Sum_probs=22.3
Q ss_pred cCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccHHHHHhhhhhcC
Q psy10278 25 QCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTERFRLKDHTLAKH 103 (110)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~~l~~H~~~~~ 103 (110)
+|..|+..|.+...+..|+....+...- . ...+.....+...+.... ...+.|..|++.|.....|..|+..++
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~---~-~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP---D-QKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Cccccccccccccccccccccccccccc---c-cccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 4889999999999999998754432211 1 111122333333433222 237999999999999999999999764
No 31
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.06 E-value=2.2e-06 Score=33.20 Aligned_cols=22 Identities=36% Similarity=0.984 Sum_probs=13.4
Q ss_pred ccCCcccccccCchhHHHHHHh
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQ 45 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~ 45 (110)
|.|+.|++.|.....|..|++.
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 4566666666666666666554
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.83 E-value=5.3e-06 Score=52.00 Aligned_cols=70 Identities=27% Similarity=0.436 Sum_probs=42.1
Q ss_pred CCCccCCc--ccccccCchhHHHHHHh-cCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccHHHHHh
Q psy10278 21 LKPFQCPV--CGFTTGRKATLQLHVRQ-HTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTERFRLKD 97 (110)
Q Consensus 21 ~~~~~C~~--c~~~~~~~~~l~~h~~~-~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~~l~~ 97 (110)
++||+|++ |.+.+.....|+-|+.. |-..+...-+. ...+..+-...+||.|++|+|.+.....|.-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~----------p~~~~~F~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPS----------PEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCC----------ccccccccccCCceeccccchhhccCcccee
Confidence 46777766 77777777777766552 21111111110 0011111335689999999999999988888
Q ss_pred hhh
Q psy10278 98 HTL 100 (110)
Q Consensus 98 H~~ 100 (110)
|+.
T Consensus 417 Hr~ 419 (423)
T COG5189 417 HRK 419 (423)
T ss_pred ccc
Confidence 875
No 33
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.77 E-value=3.4e-05 Score=35.40 Aligned_cols=33 Identities=15% Similarity=0.267 Sum_probs=20.7
Q ss_pred CCCCceeccCCCcccccHHHHHhhhhhcCCCCC
Q psy10278 75 MPVKKYQCTFCSYSCTERFRLKDHTLAKHNPGT 107 (110)
Q Consensus 75 ~~~~p~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 107 (110)
..+.|-.|+.|+..+.+..+|+.|+...|...+
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 346778888888888888888888877776554
No 34
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.76 E-value=1.2e-05 Score=32.28 Aligned_cols=24 Identities=42% Similarity=0.805 Sum_probs=14.7
Q ss_pred CccCCcccccccCchhHHHHHHhc
Q psy10278 23 PFQCPVCGFTTGRKATLQLHVRQH 46 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~ 46 (110)
||.|..|+..|.+...|..|++.|
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 355666666666666666665544
No 35
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.75 E-value=2.1e-05 Score=30.40 Aligned_cols=23 Identities=48% Similarity=1.031 Sum_probs=13.1
Q ss_pred ccCCcccccccCchhHHHHHHhc
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQH 46 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~ 46 (110)
|.|+.|+..|.+...|..|+..+
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 45666666666666666666543
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.55 E-value=6.7e-05 Score=29.48 Aligned_cols=23 Identities=26% Similarity=0.592 Sum_probs=19.5
Q ss_pred eeccCCCcccccHHHHHhhhhhc
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLAK 102 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~~ 102 (110)
|.|..|++.|.....+..|++++
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 57889999999999999998754
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.55 E-value=8.1e-05 Score=29.11 Aligned_cols=23 Identities=26% Similarity=0.564 Sum_probs=16.0
Q ss_pred eeccCCCcccccHHHHHhhhhhc
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLAK 102 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~~ 102 (110)
+.|..|++.|.....+..|+..|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45777777777777777777643
No 38
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.40 E-value=0.00011 Score=29.49 Aligned_cols=22 Identities=23% Similarity=0.498 Sum_probs=19.5
Q ss_pred eeccCCCcccccHHHHHhhhhh
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLA 101 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~ 101 (110)
|.|..|++.|.....+..|+++
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 6799999999999999999875
No 39
>PRK04860 hypothetical protein; Provisional
Probab=97.31 E-value=0.00027 Score=40.73 Aligned_cols=38 Identities=24% Similarity=0.546 Sum_probs=32.1
Q ss_pred ceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccH
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTER 92 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~ 92 (110)
+|.|. |+. ....+..|.+.+.++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 58897 886 566778999999999999999999987643
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.31 E-value=0.00016 Score=28.08 Aligned_cols=24 Identities=42% Similarity=0.837 Sum_probs=16.6
Q ss_pred eeccCCCcccccHHHHHhhhhhcCC
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~~~~ 104 (110)
|.|+.|..... ...|..|++.+|+
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 57888887777 7788888877653
No 41
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.31 E-value=0.00025 Score=27.61 Aligned_cols=23 Identities=39% Similarity=0.883 Sum_probs=13.4
Q ss_pred ccCCcccccccCchhHHHHHHhc
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQH 46 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~ 46 (110)
|.|..|++.|.....+..|+..|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 34666666666666666665543
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=97.27 E-value=8e-05 Score=34.20 Aligned_cols=29 Identities=28% Similarity=0.522 Sum_probs=12.6
Q ss_pred CceeCCCCCCCcCChHHHHHHHHhcCCCC
Q psy10278 50 KPYACPTCEFKTGDHNVLRKHVQRHMPVK 78 (110)
Q Consensus 50 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~ 78 (110)
.|..|++|+..+.+..+|..|+...++.+
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 34555555555555555555555444443
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.98 E-value=0.00031 Score=27.48 Aligned_cols=21 Identities=29% Similarity=0.732 Sum_probs=14.1
Q ss_pred ccCCcccccccCchhHHHHHH
Q psy10278 24 FQCPVCGFTTGRKATLQLHVR 44 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~ 44 (110)
|.|.+|+..|.+...+..|++
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 456677777777777766665
No 44
>PRK04860 hypothetical protein; Provisional
Probab=96.94 E-value=0.00095 Score=38.53 Aligned_cols=37 Identities=27% Similarity=0.512 Sum_probs=31.9
Q ss_pred CccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCC
Q psy10278 23 PFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGD 63 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~ 63 (110)
+|.|. |+. ....+..|.+.+.++++|.|..|+..+..
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 58998 987 66778999999999999999999987754
No 45
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.35 E-value=0.0053 Score=32.14 Aligned_cols=66 Identities=17% Similarity=0.310 Sum_probs=21.2
Q ss_pred chhcHHHHHHHHHHHhcCCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhc
Q psy10278 3 FYADIKCLKKHIREVHKRLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRH 74 (110)
Q Consensus 3 ~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h 74 (110)
.|.+...|..|+...|.-..+ . ...+.....+........ ...+.|..|+..|.....|..|+..+
T Consensus 8 ~f~~~~~l~~H~~~~H~~~~~----~-~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 8 SFSSVDDLLQHMKKKHGFDIP----D-QKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccc----c-cccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 577888899999766654332 1 111112222333322221 22689999999999999999999964
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.33 E-value=0.0038 Score=24.54 Aligned_cols=19 Identities=26% Similarity=0.553 Sum_probs=12.0
Q ss_pred eccCCCcccccHHHHHhhhh
Q psy10278 81 QCTFCSYSCTERFRLKDHTL 100 (110)
Q Consensus 81 ~C~~C~~~f~~~~~l~~H~~ 100 (110)
.|+.|++.| ....|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 567777777 4456666654
No 47
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=96.17 E-value=0.0056 Score=25.81 Aligned_cols=24 Identities=21% Similarity=0.602 Sum_probs=18.7
Q ss_pred ceeccCCCcccccHHHHHhhhhhc
Q psy10278 79 KYQCTFCSYSCTERFRLKDHTLAK 102 (110)
Q Consensus 79 p~~C~~C~~~f~~~~~l~~H~~~~ 102 (110)
+|.|..|+..|.....+..|+...
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 577888888888888888887643
No 48
>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=94.81 E-value=0.023 Score=23.80 Aligned_cols=10 Identities=50% Similarity=1.557 Sum_probs=4.7
Q ss_pred ccCCcccccc
Q psy10278 24 FQCPVCGFTT 33 (110)
Q Consensus 24 ~~C~~c~~~~ 33 (110)
|.|..||..+
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 3455555443
No 49
>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=94.20 E-value=0.024 Score=30.64 Aligned_cols=14 Identities=29% Similarity=0.757 Sum_probs=7.0
Q ss_pred ceeCCCCCCCcCCh
Q psy10278 51 PYACPTCEFKTGDH 64 (110)
Q Consensus 51 ~~~c~~c~~~~~~~ 64 (110)
|..|+.||..|...
T Consensus 26 PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 26 PIVCPKCGTEFPPE 39 (108)
T ss_pred CccCCCCCCccCcc
Confidence 44555555554433
No 50
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.96 E-value=0.019 Score=37.53 Aligned_cols=55 Identities=22% Similarity=0.442 Sum_probs=36.1
Q ss_pred ceeCCCCCCCcCChHHHHHHHH--hcCCC--Cceecc--CCCcccccHHHHHhhhhhcCCC
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQ--RHMPV--KKYQCT--FCSYSCTERFRLKDHTLAKHNP 105 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~--~h~~~--~p~~C~--~C~~~f~~~~~l~~H~~~~~~~ 105 (110)
++.|..|...|.....+..|.. .|.++ +|+.|+ .|++.|.+...+..|...+.+.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCC
Confidence 4556666666666666666666 56666 677776 5777777766666666666553
No 51
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.76 E-value=0.017 Score=37.77 Aligned_cols=63 Identities=25% Similarity=0.597 Sum_probs=54.7
Q ss_pred CCccCCcccccccCchhHHHHHH--hcCCC--CceeCC--CCCCCcCChHHHHHHHHhcCCCCceeccC
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVR--QHTRE--KPYACP--TCEFKTGDHNVLRKHVQRHMPVKKYQCTF 84 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~--~~~~~--~~~~c~--~c~~~~~~~~~l~~h~~~h~~~~p~~C~~ 84 (110)
.++.|..|...|.....+..|.+ .|.++ +++.|+ .|++.|.....+..|...|.+..++.+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 36789999999999999999999 78888 899999 79999999999999999998877776643
No 52
>KOG1146|consensus
Probab=93.49 E-value=0.0096 Score=44.30 Aligned_cols=83 Identities=28% Similarity=0.508 Sum_probs=46.8
Q ss_pred HHhcCCCCccCCcccccccCchhHHHHHHh-cCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccHHH
Q psy10278 16 EVHKRLKPFQCPVCGFTTGRKATLQLHVRQ-HTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTERFR 94 (110)
Q Consensus 16 ~~~~~~~~~~C~~c~~~~~~~~~l~~h~~~-~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~~ 94 (110)
..+.-.+.+.|+.|+..+.....|-.|++. |..... ..|.. +...-.+..-...-.+-+||.|..|...++.+.+
T Consensus 458 ~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~---~~c~~-gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~ 533 (1406)
T KOG1146|consen 458 VLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS---AYCKA-GQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGN 533 (1406)
T ss_pred eeecccccccCCccchhhhhHHHhhhcccccccccch---hHhHh-ccccccccccccccCCCCcccceeeeeeeecchH
Confidence 334445667788888888887777777774 322211 11110 0000000000001123467899999999999999
Q ss_pred HHhhhhhc
Q psy10278 95 LKDHTLAK 102 (110)
Q Consensus 95 l~~H~~~~ 102 (110)
|..|+.+-
T Consensus 534 LsihlqS~ 541 (1406)
T KOG1146|consen 534 LSIHLQSD 541 (1406)
T ss_pred HHHHHHHH
Confidence 99998753
No 53
>KOG2893|consensus
Probab=93.43 E-value=0.015 Score=35.58 Aligned_cols=39 Identities=23% Similarity=0.458 Sum_probs=18.6
Q ss_pred CCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccHHHHHhh
Q psy10278 56 TCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTERFRLKDH 98 (110)
Q Consensus 56 ~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~~l~~H 98 (110)
.|++.|.....|++|++ .+.|+|-.|.+.....-.|..|
T Consensus 15 ycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 15 YCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 45555555555555544 2335555555443333344333
No 54
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.19 E-value=0.3 Score=26.61 Aligned_cols=83 Identities=19% Similarity=0.271 Sum_probs=51.5
Q ss_pred CCCccCCcccccccCchhHHHHHHhcCCCCc------------eeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcc
Q psy10278 21 LKPFQCPVCGFTTGRKATLQLHVRQHTREKP------------YACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYS 88 (110)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~------------~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~ 88 (110)
+-|-.|++|+-.+-+...|.+..-.-....+ ..|..|...|........ ..-.....|.|+.|...
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCc
Confidence 3477899999988888877755321111111 137788887765421110 00122346899999999
Q ss_pred cccHHHHHhhhhhcCCC
Q psy10278 89 CTERFRLKDHTLAKHNP 105 (110)
Q Consensus 89 f~~~~~l~~H~~~~~~~ 105 (110)
|--.-+.-.|-..|.-.
T Consensus 91 FC~dCD~fiHe~Lh~CP 107 (112)
T TIGR00622 91 FCVDCDVFVHESLHCCP 107 (112)
T ss_pred cccccchhhhhhccCCc
Confidence 98887777787766644
No 55
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.12 E-value=0.043 Score=25.78 Aligned_cols=27 Identities=15% Similarity=0.191 Sum_probs=14.5
Q ss_pred CCCceeccCCCcccccHHHHHhhhhhc
Q psy10278 76 PVKKYQCTFCSYSCTERFRLKDHTLAK 102 (110)
Q Consensus 76 ~~~p~~C~~C~~~f~~~~~l~~H~~~~ 102 (110)
||--+.|+-|+..|....++..|....
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 344455555666555555555555433
No 56
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=92.11 E-value=0.1 Score=30.45 Aligned_cols=10 Identities=20% Similarity=0.580 Sum_probs=5.1
Q ss_pred CCceeccCCC
Q psy10278 77 VKKYQCTFCS 86 (110)
Q Consensus 77 ~~p~~C~~C~ 86 (110)
+-|..||.||
T Consensus 147 e~P~~CPiCg 156 (166)
T COG1592 147 EAPEVCPICG 156 (166)
T ss_pred CCCCcCCCCC
Confidence 4445555554
No 57
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=91.96 E-value=0.091 Score=33.72 Aligned_cols=29 Identities=31% Similarity=0.535 Sum_probs=25.3
Q ss_pred CCCceeccC--CCcccccHHHHHhhhhhcCC
Q psy10278 76 PVKKYQCTF--CSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 76 ~~~p~~C~~--C~~~f~~~~~l~~H~~~~~~ 104 (110)
+++||+|++ |.|.+.....|.-|++-.|.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~ 376 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQ 376 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhcccc
Confidence 469999976 99999999999999987773
No 58
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=91.89 E-value=0.2 Score=21.51 Aligned_cols=32 Identities=19% Similarity=0.392 Sum_probs=14.4
Q ss_pred eCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCccc
Q psy10278 53 ACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSC 89 (110)
Q Consensus 53 ~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f 89 (110)
.|+.|+..|.-...- ...+.+...|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHH-----cccCCcEEECCCCCcEe
Confidence 455555555443321 11223345566665544
No 59
>KOG4173|consensus
Probab=91.87 E-value=0.08 Score=31.82 Aligned_cols=78 Identities=22% Similarity=0.376 Sum_probs=56.9
Q ss_pred ccCCc--ccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhc----------CCCCceec--cCCCccc
Q psy10278 24 FQCPV--CGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRH----------MPVKKYQC--TFCSYSC 89 (110)
Q Consensus 24 ~~C~~--c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h----------~~~~p~~C--~~C~~~f 89 (110)
+-|++ |...|.....+..|...-.+ -.|..|.+.|...--|..|+.-. -|.-.|.| ..|+..|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 66876 77788887777766553332 37899999998888888887642 23345888 4599999
Q ss_pred ccHHHHHhhhhhcCC
Q psy10278 90 TERFRLKDHTLAKHN 104 (110)
Q Consensus 90 ~~~~~l~~H~~~~~~ 104 (110)
........|+...|.
T Consensus 157 kT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 157 KTSRDRKDHMIRMHK 171 (253)
T ss_pred hhhhhhhhHHHHhcc
Confidence 988888888887664
No 60
>KOG2231|consensus
Probab=91.84 E-value=0.78 Score=32.64 Aligned_cols=47 Identities=23% Similarity=0.412 Sum_probs=27.3
Q ss_pred eCCCCCCCcCChHHHHHHHHhcCCCCceeccCC------CcccccHHHHHhhhhhcC
Q psy10278 53 ACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFC------SYSCTERFRLKDHTLAKH 103 (110)
Q Consensus 53 ~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C------~~~f~~~~~l~~H~~~~~ 103 (110)
.|..|...|.....+..|++.++ |.|..| .--|.....|..|.+..|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 56667667766666666666443 233333 234556666666666655
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=91.38 E-value=0.048 Score=33.11 Aligned_cols=17 Identities=41% Similarity=0.786 Sum_probs=11.8
Q ss_pred CCccCCcccccccCchh
Q psy10278 22 KPFQCPVCGFTTGRKAT 38 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~ 38 (110)
+...||+|+..|.++..
T Consensus 4 k~~~CPvC~~~F~~~~v 20 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKV 20 (214)
T ss_pred CceECCCCCCeeeeeEE
Confidence 44678888888877643
No 62
>KOG2186|consensus
Probab=90.82 E-value=0.23 Score=30.85 Aligned_cols=49 Identities=18% Similarity=0.444 Sum_probs=34.0
Q ss_pred ccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcC
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHM 75 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~ 75 (110)
|.|..||....-+. +-.|+..-.+ .-|.|..|+..|.. ..+..|..--+
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 67888888776654 4557776555 46888888888877 45566666433
No 63
>KOG2231|consensus
Probab=90.49 E-value=1 Score=32.07 Aligned_cols=72 Identities=21% Similarity=0.163 Sum_probs=45.3
Q ss_pred cccCchhHHHHHH-hcCCCCceeCCCCCCCc------CChHHHHHHHHhcCC-CC----ceeccCCCcccccHHHHHhhh
Q psy10278 32 TTGRKATLQLHVR-QHTREKPYACPTCEFKT------GDHNVLRKHVQRHMP-VK----KYQCTFCSYSCTERFRLKDHT 99 (110)
Q Consensus 32 ~~~~~~~l~~h~~-~~~~~~~~~c~~c~~~~------~~~~~l~~h~~~h~~-~~----p~~C~~C~~~f~~~~~l~~H~ 99 (110)
.|.+...|+.|+. .|-.-....|..-.+.| .....|..|+..... ++ .-.|..|..-|.....|..|+
T Consensus 123 ~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~ 202 (669)
T KOG2231|consen 123 EFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHL 202 (669)
T ss_pred chhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhh
Confidence 3447788999986 45433222232212222 334567777775332 22 146889999999999999999
Q ss_pred hhcC
Q psy10278 100 LAKH 103 (110)
Q Consensus 100 ~~~~ 103 (110)
+..|
T Consensus 203 ~~~h 206 (669)
T KOG2231|consen 203 RFDH 206 (669)
T ss_pred ccce
Confidence 9766
No 64
>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=90.44 E-value=0.16 Score=28.20 Aligned_cols=15 Identities=13% Similarity=0.140 Sum_probs=7.8
Q ss_pred CceeCCCCCCCcCCh
Q psy10278 50 KPYACPTCEFKTGDH 64 (110)
Q Consensus 50 ~~~~c~~c~~~~~~~ 64 (110)
.|..|+.||..|...
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 355566665554433
No 65
>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=90.43 E-value=0.19 Score=21.16 Aligned_cols=10 Identities=50% Similarity=1.560 Sum_probs=5.5
Q ss_pred ccCCcccccc
Q psy10278 24 FQCPVCGFTT 33 (110)
Q Consensus 24 ~~C~~c~~~~ 33 (110)
|.|..||..+
T Consensus 3 ~~C~~CG~i~ 12 (34)
T cd00729 3 WVCPVCGYIH 12 (34)
T ss_pred EECCCCCCEe
Confidence 5566666543
No 66
>KOG2186|consensus
Probab=90.09 E-value=0.29 Score=30.44 Aligned_cols=32 Identities=28% Similarity=0.486 Sum_probs=14.4
Q ss_pred HHHHHHHHHhcCCCCccCCcccccccCchhHHHHH
Q psy10278 9 CLKKHIREVHKRLKPFQCPVCGFTTGRKATLQLHV 43 (110)
Q Consensus 9 ~l~~h~~~~~~~~~~~~C~~c~~~~~~~~~l~~h~ 43 (110)
.+..|+- ...+ .-|.|-.|+..|.. .++..|.
T Consensus 17 ~vekH~s-rCrn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 17 QVEKHMS-RCRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred chHHHHH-hccC-CeeEEeeccccccc-chhhhhh
Confidence 3444552 2333 23455555555555 3344443
No 67
>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=89.99 E-value=0.33 Score=20.75 Aligned_cols=10 Identities=20% Similarity=0.507 Sum_probs=5.3
Q ss_pred eeccCCCccc
Q psy10278 80 YQCTFCSYSC 89 (110)
Q Consensus 80 ~~C~~C~~~f 89 (110)
..|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4555555544
No 68
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=89.07 E-value=0.27 Score=25.43 Aligned_cols=14 Identities=14% Similarity=0.458 Sum_probs=8.9
Q ss_pred CceeccCCCccccc
Q psy10278 78 KKYQCTFCSYSCTE 91 (110)
Q Consensus 78 ~p~~C~~C~~~f~~ 91 (110)
..|.|..|+..|+-
T Consensus 52 GIW~C~kCg~~fAG 65 (89)
T COG1997 52 GIWKCRKCGAKFAG 65 (89)
T ss_pred CeEEcCCCCCeecc
Confidence 45677777766653
No 69
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.02 E-value=0.28 Score=22.10 Aligned_cols=8 Identities=38% Similarity=1.530 Sum_probs=3.8
Q ss_pred eeccCCCc
Q psy10278 80 YQCTFCSY 87 (110)
Q Consensus 80 ~~C~~C~~ 87 (110)
+.|+.||.
T Consensus 22 ~~Cp~CG~ 29 (46)
T PRK00398 22 VRCPYCGY 29 (46)
T ss_pred eECCCCCC
Confidence 44555543
No 70
>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=88.98 E-value=0.63 Score=26.96 Aligned_cols=30 Identities=13% Similarity=0.398 Sum_probs=16.6
Q ss_pred CceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcc
Q psy10278 50 KPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYS 88 (110)
Q Consensus 50 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~ 88 (110)
.-|.|+.|+..|+....+. --|.|+.||-.
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 3466666666665554442 13666666643
No 71
>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=88.98 E-value=0.66 Score=26.89 Aligned_cols=34 Identities=18% Similarity=0.373 Sum_probs=25.7
Q ss_pred cCCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCc
Q psy10278 19 KRLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKT 61 (110)
Q Consensus 19 ~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 61 (110)
.+..-|.|+.|+..|.....+. ..|.|+.||...
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 3445699999999888776653 268999999743
No 72
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=88.83 E-value=0.53 Score=20.09 Aligned_cols=11 Identities=27% Similarity=0.643 Sum_probs=5.9
Q ss_pred ceeccCCCccc
Q psy10278 79 KYQCTFCSYSC 89 (110)
Q Consensus 79 p~~C~~C~~~f 89 (110)
...|+.|+..|
T Consensus 25 ~v~C~~C~~~f 35 (36)
T PF13717_consen 25 KVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEe
Confidence 45555555544
No 73
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.78 E-value=0.39 Score=22.97 Aligned_cols=33 Identities=18% Similarity=0.476 Sum_probs=18.7
Q ss_pred CceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCc
Q psy10278 50 KPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSY 87 (110)
Q Consensus 50 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~ 87 (110)
..|.|+.||..--.... +--.-..+|.|+.||.
T Consensus 26 v~F~CPnCGe~~I~Rc~-----~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCA-----KCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhh-----hHHHcCCceECCCcCc
Confidence 35788888854322211 1111246899998875
No 74
>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=88.61 E-value=0.58 Score=20.73 Aligned_cols=25 Identities=28% Similarity=0.430 Sum_probs=12.2
Q ss_pred CCceeccCCCcccccH----HHHHhhhhh
Q psy10278 77 VKKYQCTFCSYSCTER----FRLKDHTLA 101 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~----~~l~~H~~~ 101 (110)
+.-..|..|++.+... +.|..|++.
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 3445666676666543 566666643
No 75
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=88.50 E-value=0.56 Score=21.05 Aligned_cols=10 Identities=30% Similarity=0.866 Sum_probs=4.6
Q ss_pred eeCCCCCCCc
Q psy10278 52 YACPTCEFKT 61 (110)
Q Consensus 52 ~~c~~c~~~~ 61 (110)
|.|..|+..+
T Consensus 3 Y~C~~Cg~~~ 12 (44)
T smart00659 3 YICGECGREN 12 (44)
T ss_pred EECCCCCCEe
Confidence 4444444443
No 76
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.37 E-value=1.5 Score=25.05 Aligned_cols=37 Identities=22% Similarity=0.415 Sum_probs=21.7
Q ss_pred CCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCccc
Q psy10278 49 EKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSC 89 (110)
Q Consensus 49 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f 89 (110)
...|.|+.|+..|.....+.. ... ...|.|+.||...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEE
Confidence 345788888877764433211 112 3348888888654
No 77
>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=88.10 E-value=0.16 Score=23.41 Aligned_cols=13 Identities=23% Similarity=0.743 Sum_probs=7.9
Q ss_pred ccCCcccccccCc
Q psy10278 24 FQCPVCGFTTGRK 36 (110)
Q Consensus 24 ~~C~~c~~~~~~~ 36 (110)
|.|..|+..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (52)
T TIGR02605 6 YRCTACGHRFEVL 18 (52)
T ss_pred EEeCCCCCEeEEE
Confidence 5566666666544
No 78
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.52 E-value=0.76 Score=22.00 Aligned_cols=32 Identities=22% Similarity=0.597 Sum_probs=18.6
Q ss_pred CceeCCCCCCC-cCChHHHHHHHHhcCCCCceeccCCCc
Q psy10278 50 KPYACPTCEFK-TGDHNVLRKHVQRHMPVKKYQCTFCSY 87 (110)
Q Consensus 50 ~~~~c~~c~~~-~~~~~~l~~h~~~h~~~~p~~C~~C~~ 87 (110)
..|.|+.||.. ...-..-. . -..+|.|+.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~~CR----k--~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEKCR----K--QSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeechhHH----h--cCCceECCCCCC
Confidence 35788888875 22221111 1 136788988875
No 79
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=87.30 E-value=0.59 Score=21.39 Aligned_cols=22 Identities=18% Similarity=0.484 Sum_probs=11.8
Q ss_pred eeccCCCcccccH-----HHHHhhhhh
Q psy10278 80 YQCTFCSYSCTER-----FRLKDHTLA 101 (110)
Q Consensus 80 ~~C~~C~~~f~~~-----~~l~~H~~~ 101 (110)
-.|..|++.++.. +.|..|+..
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 4555565555433 456666653
No 80
>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=87.27 E-value=0.2 Score=21.70 Aligned_cols=13 Identities=31% Similarity=0.720 Sum_probs=7.1
Q ss_pred ccCCcccccccCc
Q psy10278 24 FQCPVCGFTTGRK 36 (110)
Q Consensus 24 ~~C~~c~~~~~~~ 36 (110)
|.|+.|+..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (41)
T smart00834 6 YRCEDCGHTFEVL 18 (41)
T ss_pred EEcCCCCCEEEEE
Confidence 4566666655443
No 81
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=86.04 E-value=0.97 Score=26.78 Aligned_cols=29 Identities=17% Similarity=0.589 Sum_probs=15.7
Q ss_pred ceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcc
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYS 88 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~ 88 (110)
-|.|+.|+..|+....+. --|.|+.||-.
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 456666666555544431 24666666643
No 82
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=85.65 E-value=0.18 Score=29.10 Aligned_cols=13 Identities=15% Similarity=0.378 Sum_probs=7.8
Q ss_pred eeCCCCCCCcCCh
Q psy10278 52 YACPTCEFKTGDH 64 (110)
Q Consensus 52 ~~c~~c~~~~~~~ 64 (110)
+.|+.||..|...
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 5666666666443
No 83
>KOG2482|consensus
Probab=85.30 E-value=2.3 Score=27.96 Aligned_cols=25 Identities=24% Similarity=0.579 Sum_probs=21.3
Q ss_pred eeccCCCcccccHHHHHhhhhhcCC
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~~~~ 104 (110)
+.|-.|.+.|..+..|+.||+....
T Consensus 196 ~~CLyCekifrdkntLkeHMrkK~H 220 (423)
T KOG2482|consen 196 LRCLYCEKIFRDKNTLKEHMRKKRH 220 (423)
T ss_pred heeeeeccccCCcHHHHHHHHhccC
Confidence 7899999999999999999985443
No 84
>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=85.28 E-value=0.52 Score=29.55 Aligned_cols=81 Identities=20% Similarity=0.288 Sum_probs=45.6
Q ss_pred cCCCCccCCcccccccCchhHHHHHHh--cCCCCceeCCCCCCCcCCh------HHHHHHHHh----cCCCCceeccCCC
Q psy10278 19 KRLKPFQCPVCGFTTGRKATLQLHVRQ--HTREKPYACPTCEFKTGDH------NVLRKHVQR----HMPVKKYQCTFCS 86 (110)
Q Consensus 19 ~~~~~~~C~~c~~~~~~~~~l~~h~~~--~~~~~~~~c~~c~~~~~~~------~~l~~h~~~----h~~~~p~~C~~C~ 86 (110)
.|.+.|.|.+|..-+..-. --.|+.+ -.....|.|..|++.-..+ ..-..|.+. ....+|+.|++|+
T Consensus 138 hGGrif~CsfC~~flCEDD-QFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg 216 (314)
T PF06524_consen 138 HGGRIFKCSFCDNFLCEDD-QFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCG 216 (314)
T ss_pred CCCeEEEeecCCCeeeccc-hhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCCC
Confidence 4566789999976444333 3345542 3344567887776543221 111234332 2345789999999
Q ss_pred cccccHHHHHhhhh
Q psy10278 87 YSCTERFRLKDHTL 100 (110)
Q Consensus 87 ~~f~~~~~l~~H~~ 100 (110)
.--..-..|..-.+
T Consensus 217 ~et~eTkdLSmStR 230 (314)
T PF06524_consen 217 YETQETKDLSMSTR 230 (314)
T ss_pred Ccccccccceeeee
Confidence 76665555544443
No 85
>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=84.88 E-value=0.75 Score=28.09 Aligned_cols=30 Identities=20% Similarity=0.428 Sum_probs=22.0
Q ss_pred CCCceeccCCCcccccHHHHHhhhhhcCCC
Q psy10278 76 PVKKYQCTFCSYSCTERFRLKDHTLAKHNP 105 (110)
Q Consensus 76 ~~~p~~C~~C~~~f~~~~~l~~H~~~~~~~ 105 (110)
.+..|.|+.|+|.|....-.++|+...|.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 344599999999999999999999887754
No 86
>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=84.13 E-value=0.81 Score=25.74 Aligned_cols=27 Identities=22% Similarity=0.285 Sum_probs=16.4
Q ss_pred CCceeccCCCcccccHHHHHhhhhhcCCCC
Q psy10278 77 VKKYQCTFCSYSCTERFRLKDHTLAKHNPG 106 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~~~l~~H~~~~~~~~ 106 (110)
+....|-+||+.|.. |..|+..||+-.
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCC
Confidence 344789999998886 488999987643
No 87
>PF14353 CpXC: CpXC protein
Probab=84.09 E-value=0.16 Score=28.17 Aligned_cols=12 Identities=33% Similarity=0.833 Sum_probs=7.1
Q ss_pred cCCcccccccCc
Q psy10278 25 QCPVCGFTTGRK 36 (110)
Q Consensus 25 ~C~~c~~~~~~~ 36 (110)
.|+.|+..|...
T Consensus 3 tCP~C~~~~~~~ 14 (128)
T PF14353_consen 3 TCPHCGHEFEFE 14 (128)
T ss_pred CCCCCCCeeEEE
Confidence 466676665543
No 88
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=83.86 E-value=0.57 Score=24.50 Aligned_cols=14 Identities=14% Similarity=0.468 Sum_probs=8.6
Q ss_pred CceeccCCCccccc
Q psy10278 78 KKYQCTFCSYSCTE 91 (110)
Q Consensus 78 ~p~~C~~C~~~f~~ 91 (110)
..|.|..|++.|+-
T Consensus 53 GIW~C~~C~~~~AG 66 (90)
T PTZ00255 53 GIWRCKGCKKTVAG 66 (90)
T ss_pred EEEEcCCCCCEEeC
Confidence 45666666666653
No 89
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=83.31 E-value=1.2 Score=23.99 Aligned_cols=25 Identities=24% Similarity=0.679 Sum_probs=23.2
Q ss_pred eec----cCCCcccccHHHHHhhhhhcCC
Q psy10278 80 YQC----TFCSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 80 ~~C----~~C~~~f~~~~~l~~H~~~~~~ 104 (110)
|.| ..|+....+...+..|...+|+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999998875
No 90
>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=82.06 E-value=1.5 Score=17.24 Aligned_cols=18 Identities=22% Similarity=0.462 Sum_probs=10.1
Q ss_pred eccCCCcccccHHHHHhhh
Q psy10278 81 QCTFCSYSCTERFRLKDHT 99 (110)
Q Consensus 81 ~C~~C~~~f~~~~~l~~H~ 99 (110)
.|+.|++.+ ....+..|+
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 466666665 334555554
No 91
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=82.04 E-value=0.44 Score=26.74 Aligned_cols=59 Identities=24% Similarity=0.453 Sum_probs=33.4
Q ss_pred hcCCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCC--hHHHHHHHHhcCCCCceeccCCCcccccHH
Q psy10278 18 HKRLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGD--HNVLRKHVQRHMPVKKYQCTFCSYSCTERF 93 (110)
Q Consensus 18 ~~~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~--~~~l~~h~~~h~~~~p~~C~~C~~~f~~~~ 93 (110)
....+.|+|.+|.++...+..| +|-.| ||..... -..|+.+-..+. .|+.|.-+|.+.+
T Consensus 75 F~d~~lYeCnIC~etS~ee~FL----------KPneC--CgY~iCn~Cya~LWK~~~~yp-----vCPvCkTSFKss~ 135 (140)
T PF05290_consen 75 FLDPKLYECNICKETSAEERFL----------KPNEC--CGYSICNACYANLWKFCNLYP-----VCPVCKTSFKSSS 135 (140)
T ss_pred ecCCCceeccCcccccchhhcC----------Ccccc--cchHHHHHHHHHHHHHcccCC-----CCCcccccccccc
Confidence 3456779999998876554433 23333 2222211 144555544443 6888888887543
No 92
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=81.30 E-value=0.49 Score=23.70 Aligned_cols=15 Identities=27% Similarity=0.425 Sum_probs=8.1
Q ss_pred CCceecc--CCCccccc
Q psy10278 77 VKKYQCT--FCSYSCTE 91 (110)
Q Consensus 77 ~~p~~C~--~C~~~f~~ 91 (110)
++.+.|. .||.+|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 4455555 56665543
No 93
>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=81.17 E-value=0.65 Score=24.32 Aligned_cols=13 Identities=15% Similarity=0.475 Sum_probs=8.0
Q ss_pred CceeccCCCcccc
Q psy10278 78 KKYQCTFCSYSCT 90 (110)
Q Consensus 78 ~p~~C~~C~~~f~ 90 (110)
..|.|..|++.|+
T Consensus 52 GIW~C~~C~~~~A 64 (91)
T TIGR00280 52 GIWTCRKCGAKFA 64 (91)
T ss_pred EEEEcCCCCCEEe
Confidence 3466666666665
No 94
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=80.89 E-value=1.4 Score=20.71 Aligned_cols=40 Identities=23% Similarity=0.649 Sum_probs=21.3
Q ss_pred ceeCCC--CCCCcCChHHHHHHHHhcCCCCceeccC----CCccccc
Q psy10278 51 PYACPT--CEFKTGDHNVLRKHVQRHMPVKKYQCTF----CSYSCTE 91 (110)
Q Consensus 51 ~~~c~~--c~~~~~~~~~l~~h~~~h~~~~p~~C~~----C~~~f~~ 91 (110)
+..|+. |...+ ....|..|+...-..++..|+. |+..+..
T Consensus 9 ~v~C~~~cc~~~i-~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 9 PVPCPNGCCNEMI-PRKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp EEE-TT--S-BEE-ECCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred EeeCCCCCcccce-eHHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 455655 33323 2346677877666667788888 7776654
No 95
>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=80.44 E-value=0.45 Score=19.16 Aligned_cols=19 Identities=32% Similarity=0.518 Sum_probs=11.4
Q ss_pred eeccCCCcccccHHHHHhhh
Q psy10278 80 YQCTFCSYSCTERFRLKDHT 99 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~ 99 (110)
|.|-.|++.|. ...+..|.
T Consensus 1 ~sCiDC~~~F~-~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDFD-GDSYKSHT 19 (28)
T ss_dssp EEETTTTEEEE-GGGTTT--
T ss_pred CeeecCCCCcC-cCCcCCCC
Confidence 57888888884 34444454
No 96
>KOG4167|consensus
Probab=79.64 E-value=0.38 Score=34.42 Aligned_cols=26 Identities=12% Similarity=0.199 Sum_probs=23.4
Q ss_pred ceeccCCCcccccHHHHHhhhhhcCC
Q psy10278 79 KYQCTFCSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 79 p~~C~~C~~~f~~~~~l~~H~~~~~~ 104 (110)
.|.|..|++.|..-.++..||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 49999999999999999999998863
No 97
>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=79.63 E-value=0.47 Score=24.79 Aligned_cols=12 Identities=17% Similarity=0.598 Sum_probs=8.2
Q ss_pred ceeccCCCcccc
Q psy10278 79 KYQCTFCSYSCT 90 (110)
Q Consensus 79 p~~C~~C~~~f~ 90 (110)
.|.|..|++.|+
T Consensus 53 IW~C~~C~~~~A 64 (90)
T PF01780_consen 53 IWKCKKCGKKFA 64 (90)
T ss_dssp EEEETTTTEEEE
T ss_pred EeecCCCCCEEe
Confidence 477777777665
No 98
>KOG2785|consensus
Probab=79.25 E-value=3.3 Score=27.53 Aligned_cols=24 Identities=21% Similarity=0.484 Sum_probs=20.5
Q ss_pred ceeccCCC---cccccHHHHHhhhhhc
Q psy10278 79 KYQCTFCS---YSCTERFRLKDHTLAK 102 (110)
Q Consensus 79 p~~C~~C~---~~f~~~~~l~~H~~~~ 102 (110)
-+.|-+|. +.|.+....++||...
T Consensus 217 ~~~CL~CN~~~~~f~sleavr~HM~~K 243 (390)
T KOG2785|consen 217 GFICLFCNELGRPFSSLEAVRAHMRDK 243 (390)
T ss_pred CceEEEeccccCcccccHHHHHHHhhc
Confidence 38888898 9999999999999843
No 99
>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=78.04 E-value=1.4 Score=27.01 Aligned_cols=27 Identities=19% Similarity=0.465 Sum_probs=20.7
Q ss_pred CCCccCCcccccccCchhHHHHHHhcC
Q psy10278 21 LKPFQCPVCGFTTGRKATLQLHVRQHT 47 (110)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~~ 47 (110)
+..|.|++|++.|.-...+..|+..-+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcC
Confidence 445999999999999999999998533
No 100
>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=78.02 E-value=1.2 Score=17.20 Aligned_cols=8 Identities=25% Similarity=1.028 Sum_probs=4.1
Q ss_pred ceeccCCC
Q psy10278 79 KYQCTFCS 86 (110)
Q Consensus 79 p~~C~~C~ 86 (110)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 35555554
No 101
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=77.96 E-value=1.4 Score=28.97 Aligned_cols=21 Identities=29% Similarity=0.524 Sum_probs=12.7
Q ss_pred eCCCCCCCcCChHHHHHHHHh
Q psy10278 53 ACPTCEFKTGDHNVLRKHVQR 73 (110)
Q Consensus 53 ~c~~c~~~~~~~~~l~~h~~~ 73 (110)
.|..|...|.....|..|.+.
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hhhhccceecChHHHHHHHHh
Confidence 456666666666666666553
No 102
>KOG2893|consensus
Probab=77.82 E-value=0.61 Score=28.90 Aligned_cols=45 Identities=27% Similarity=0.404 Sum_probs=29.8
Q ss_pred CCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHH
Q psy10278 21 LKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKH 70 (110)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h 70 (110)
++|| |=.|+..|..+.-|..|++ .+.|+|-+|-+...+.-.|..|
T Consensus 9 ~kpw-cwycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred CCce-eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 3454 7778889988887777765 3568898887644444344444
No 103
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=77.37 E-value=1.2 Score=18.58 Aligned_cols=8 Identities=25% Similarity=0.758 Sum_probs=3.5
Q ss_pred eeccCCCc
Q psy10278 80 YQCTFCSY 87 (110)
Q Consensus 80 ~~C~~C~~ 87 (110)
..|+.||.
T Consensus 18 irC~~CG~ 25 (32)
T PF03604_consen 18 IRCPECGH 25 (32)
T ss_dssp SSBSSSS-
T ss_pred EECCcCCC
Confidence 45555543
No 104
>PHA00626 hypothetical protein
Probab=77.35 E-value=1.7 Score=20.54 Aligned_cols=15 Identities=27% Similarity=0.747 Sum_probs=11.7
Q ss_pred CceeccCCCcccccH
Q psy10278 78 KKYQCTFCSYSCTER 92 (110)
Q Consensus 78 ~p~~C~~C~~~f~~~ 92 (110)
..|.|+.|+..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 568888898888754
No 105
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=76.89 E-value=0.98 Score=23.62 Aligned_cols=13 Identities=15% Similarity=0.519 Sum_probs=8.0
Q ss_pred CceeccCCCcccc
Q psy10278 78 KKYQCTFCSYSCT 90 (110)
Q Consensus 78 ~p~~C~~C~~~f~ 90 (110)
..|.|..|++.|+
T Consensus 53 GIW~C~~C~~~~A 65 (90)
T PRK03976 53 GIWECRKCGAKFA 65 (90)
T ss_pred EEEEcCCCCCEEe
Confidence 3466666666665
No 106
>KOG3408|consensus
Probab=75.92 E-value=2 Score=23.74 Aligned_cols=23 Identities=22% Similarity=0.394 Sum_probs=14.4
Q ss_pred ceeccCCCcccccHHHHHhhhhh
Q psy10278 79 KYQCTFCSYSCTERFRLKDHTLA 101 (110)
Q Consensus 79 p~~C~~C~~~f~~~~~l~~H~~~ 101 (110)
.|.|-.|.+-|.....|..|.++
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhc
Confidence 36666666666666666666654
No 107
>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=75.90 E-value=1.5 Score=17.25 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=4.6
Q ss_pred eccCCCccc
Q psy10278 81 QCTFCSYSC 89 (110)
Q Consensus 81 ~C~~C~~~f 89 (110)
.|+.||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 455555554
No 108
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=75.33 E-value=0.37 Score=34.36 Aligned_cols=58 Identities=22% Similarity=0.374 Sum_probs=36.0
Q ss_pred CCcccccccCchhHHHHHHhcCCCCce-eCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccc
Q psy10278 26 CPVCGFTTGRKATLQLHVRQHTREKPY-ACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCT 90 (110)
Q Consensus 26 C~~c~~~~~~~~~l~~h~~~~~~~~~~-~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~ 90 (110)
|..||-+|.....|- -.+.++.-..| .|+.|.+.|..+.+ .+.|. +|..|+.||....
T Consensus 126 CT~CGPRfTIi~alP-YDR~nTsM~~F~lC~~C~~EY~dP~n----RRfHA--Qp~aCp~CGP~~~ 184 (750)
T COG0068 126 CTNCGPRFTIIEALP-YDRENTSMADFPLCPFCDKEYKDPLN----RRFHA--QPIACPKCGPHLF 184 (750)
T ss_pred cCCCCcceeeeccCC-CCcccCccccCcCCHHHHHHhcCccc----ccccc--ccccCcccCCCeE
Confidence 777888887655431 11223332333 58888887777755 33453 7889999997543
No 109
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=75.16 E-value=2.3 Score=18.86 Aligned_cols=14 Identities=29% Similarity=0.520 Sum_probs=9.5
Q ss_pred eccCCCcccccHHH
Q psy10278 81 QCTFCSYSCTERFR 94 (110)
Q Consensus 81 ~C~~C~~~f~~~~~ 94 (110)
.|..|++.|+++..
T Consensus 10 ~C~~C~rpf~WRKK 23 (42)
T PF10013_consen 10 ICPVCGRPFTWRKK 23 (42)
T ss_pred cCcccCCcchHHHH
Confidence 57777777776543
No 110
>KOG1146|consensus
Probab=74.84 E-value=0.31 Score=36.98 Aligned_cols=77 Identities=14% Similarity=0.219 Sum_probs=51.1
Q ss_pred ccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhc-----------------CCCCceeccCCC
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRH-----------------MPVKKYQCTFCS 86 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h-----------------~~~~p~~C~~C~ 86 (110)
+.|..|.+.+.....+. ++. ...+|.|..|...|.....+..|.+.- ..-.+| |..|.
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~---~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~ 1335 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLD---VTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACE 1335 (1406)
T ss_pred chhhhccccccCcccee-ecc---cchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHH
Confidence 56777777766555443 322 233577777777777777777766421 112235 99999
Q ss_pred cccccHHHHHhhhhhcCCC
Q psy10278 87 YSCTERFRLKDHTLAKHNP 105 (110)
Q Consensus 87 ~~f~~~~~l~~H~~~~~~~ 105 (110)
..|.....|..|+++-+++
T Consensus 1336 ~~~~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1336 VLLSGREALQIHMRSSAHR 1354 (1406)
T ss_pred hhcchhHHHHHHHHHhhhc
Confidence 9999999999999865543
No 111
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=73.90 E-value=2.1 Score=18.61 Aligned_cols=13 Identities=15% Similarity=0.590 Sum_probs=10.8
Q ss_pred ceeccCCCccccc
Q psy10278 79 KYQCTFCSYSCTE 91 (110)
Q Consensus 79 p~~C~~C~~~f~~ 91 (110)
||.|..|+..|=.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 7899999988864
No 112
>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=73.77 E-value=0.51 Score=20.20 Aligned_cols=8 Identities=25% Similarity=0.451 Sum_probs=3.4
Q ss_pred eeccCCCc
Q psy10278 80 YQCTFCSY 87 (110)
Q Consensus 80 ~~C~~C~~ 87 (110)
-.|..||-
T Consensus 22 ~~Cd~cg~ 29 (36)
T PF05191_consen 22 GVCDNCGG 29 (36)
T ss_dssp TBCTTTTE
T ss_pred CccCCCCC
Confidence 34444443
No 113
>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=73.31 E-value=3.1 Score=22.37 Aligned_cols=18 Identities=44% Similarity=0.835 Sum_probs=8.5
Q ss_pred CcccccccCchhHHHHHH
Q psy10278 27 PVCGFTTGRKATLQLHVR 44 (110)
Q Consensus 27 ~~c~~~~~~~~~l~~h~~ 44 (110)
..|+....+...|..|.+
T Consensus 88 ~~C~y~~~~~~~m~~H~~ 105 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWR 105 (109)
T ss_pred CCCCcEeccHHHHHHHHH
Confidence 444444444444444444
No 114
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.79 E-value=1.8 Score=23.49 Aligned_cols=12 Identities=17% Similarity=0.193 Sum_probs=6.6
Q ss_pred CceeCCCCCCCc
Q psy10278 50 KPYACPTCEFKT 61 (110)
Q Consensus 50 ~~~~c~~c~~~~ 61 (110)
.|..|+.||+.|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 355555555555
No 115
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=72.44 E-value=3.1 Score=19.18 Aligned_cols=10 Identities=30% Similarity=1.039 Sum_probs=4.7
Q ss_pred ccCCcccccc
Q psy10278 24 FQCPVCGFTT 33 (110)
Q Consensus 24 ~~C~~c~~~~ 33 (110)
|.|..|+..+
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 4444444444
No 116
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=72.03 E-value=8.9 Score=24.16 Aligned_cols=58 Identities=17% Similarity=0.394 Sum_probs=29.0
Q ss_pred CCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccccH
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCTER 92 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~~~ 92 (110)
+.|-|..|...+.. +.........|..|.+.|..-..-. . -|---|.|+.|+..|...
T Consensus 111 rqFaC~~Cd~~WwR--------rvp~rKeVSRCr~C~~rYDPVP~dk---m--wG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 111 RQFACSSCDHMWWR--------RVPQRKEVSRCRKCRKRYDPVPCDK---M--WGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred eeeeccccchHHHh--------ccCcccccccccccccccCCCcccc---c--cceeeeecccccccchhh
Confidence 56888888654322 3222222345666666554332100 0 012237777777777643
No 117
>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=71.86 E-value=2.2 Score=18.80 Aligned_cols=13 Identities=23% Similarity=0.557 Sum_probs=9.9
Q ss_pred eeccCCCcccccH
Q psy10278 80 YQCTFCSYSCTER 92 (110)
Q Consensus 80 ~~C~~C~~~f~~~ 92 (110)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 6 YRCEECGHEFEVL 18 (42)
T ss_pred EEeCCCCCEEEEE
Confidence 7888898877643
No 118
>KOG2907|consensus
Probab=71.72 E-value=5 Score=21.95 Aligned_cols=38 Identities=26% Similarity=0.505 Sum_probs=20.5
Q ss_pred eeCCCCCCCcCChHHHHHHHHhcCCCC---ceeccCCCcccccH
Q psy10278 52 YACPTCEFKTGDHNVLRKHVQRHMPVK---KYQCTFCSYSCTER 92 (110)
Q Consensus 52 ~~c~~c~~~~~~~~~l~~h~~~h~~~~---p~~C~~C~~~f~~~ 92 (110)
..|+.||..=- .+..-+-....|. -|.|+.|+..|+..
T Consensus 75 ~kCpkCghe~m---~Y~T~QlRSADEGQTVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 75 HKCPKCGHEEM---SYHTLQLRSADEGQTVFYTCPKCKYKFTEN 115 (116)
T ss_pred ccCcccCCchh---hhhhhhcccccCCceEEEEcCccceeeecc
Confidence 46888874322 2222122223333 28999999888653
No 119
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=71.00 E-value=5.1 Score=17.57 Aligned_cols=23 Identities=30% Similarity=0.671 Sum_probs=15.5
Q ss_pred ccCCcccccccC--chhHHHHHHhc
Q psy10278 24 FQCPVCGFTTGR--KATLQLHVRQH 46 (110)
Q Consensus 24 ~~C~~c~~~~~~--~~~l~~h~~~~ 46 (110)
-.|+.|++.+.. +.....|.+-|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 479999998764 35556665544
No 120
>KOG2785|consensus
Probab=71.00 E-value=6 Score=26.40 Aligned_cols=52 Identities=15% Similarity=0.278 Sum_probs=40.4
Q ss_pred CCccCCcccccccCchhHHHHHHhcCCC-----------------------CceeCCCCC---CCcCChHHHHHHHHh
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVRQHTRE-----------------------KPYACPTCE---FKTGDHNVLRKHVQR 73 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~-----------------------~~~~c~~c~---~~~~~~~~l~~h~~~ 73 (110)
-|-.|-.|+..+.+...-..||..++|- ..+.|..|+ +.|.+......|+..
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 3456888999999998888998866551 346788887 888888888888873
No 121
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=70.34 E-value=1.8 Score=24.39 Aligned_cols=12 Identities=17% Similarity=0.346 Sum_probs=7.5
Q ss_pred eeCCCCCCCcCC
Q psy10278 52 YACPTCEFKTGD 63 (110)
Q Consensus 52 ~~c~~c~~~~~~ 63 (110)
+.|..|+..|..
T Consensus 71 ~~C~~CG~~~~~ 82 (135)
T PRK03824 71 LKCRNCGNEWSL 82 (135)
T ss_pred EECCCCCCEEec
Confidence 567777765544
No 122
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=69.87 E-value=4.2 Score=19.43 Aligned_cols=30 Identities=27% Similarity=0.674 Sum_probs=16.6
Q ss_pred ccCCcccccccCchhHHHHHHhcCCCCceeCCCCCC
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEF 59 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~ 59 (110)
|.|+ ||-.|...-. ....|+....|+.|+-
T Consensus 23 yPCP-CGDRFeIsLe-----Dl~~GE~VArCPSCSL 52 (67)
T COG5216 23 YPCP-CGDRFEISLE-----DLRNGEVVARCPSCSL 52 (67)
T ss_pred ecCC-CCCEeEEEHH-----HhhCCceEEEcCCceE
Confidence 4555 6666654321 2345666667777753
No 123
>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=69.39 E-value=4.8 Score=18.00 Aligned_cols=9 Identities=33% Similarity=1.165 Sum_probs=4.3
Q ss_pred CceeccCCC
Q psy10278 78 KKYQCTFCS 86 (110)
Q Consensus 78 ~p~~C~~C~ 86 (110)
..|.|..|+
T Consensus 36 ~~~~C~~C~ 44 (46)
T PF12760_consen 36 GRYRCKACR 44 (46)
T ss_pred CeEECCCCC
Confidence 335555554
No 124
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=68.78 E-value=2.2 Score=18.86 Aligned_cols=14 Identities=21% Similarity=0.555 Sum_probs=8.9
Q ss_pred CceeccCCCccccc
Q psy10278 78 KKYQCTFCSYSCTE 91 (110)
Q Consensus 78 ~p~~C~~C~~~f~~ 91 (110)
-|+.|..|+..|=.
T Consensus 12 ~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 12 LPFKCKHCGKSFCL 25 (43)
T ss_dssp SHEE-TTTS-EE-T
T ss_pred CCeECCCCCcccCc
Confidence 57899999988854
No 125
>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=68.52 E-value=2.7 Score=17.18 Aligned_cols=8 Identities=38% Similarity=1.144 Sum_probs=3.6
Q ss_pred ceeCCCCC
Q psy10278 51 PYACPTCE 58 (110)
Q Consensus 51 ~~~c~~c~ 58 (110)
.+.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34444443
No 126
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=68.39 E-value=5.3 Score=29.15 Aligned_cols=49 Identities=16% Similarity=0.445 Sum_probs=25.3
Q ss_pred ccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcc
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYS 88 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~ 88 (110)
..|..||..+.-+.- ...+..|-......|..|+.. ...|..|+.||..
T Consensus 436 l~C~~Cg~v~~Cp~C-d~~lt~H~~~~~L~CH~Cg~~---------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYIAECPNC-DSPLTLHKATGQLRCHYCGYQ---------------EPIPQSCPECGSE 484 (730)
T ss_pred eecccCCCcccCCCC-CcceEEecCCCeeEeCCCCCC---------------CCCCCCCCCCCCC
Confidence 346666665443210 011223444445666666532 2467888888854
No 127
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=68.02 E-value=2.8 Score=19.31 Aligned_cols=16 Identities=19% Similarity=0.262 Sum_probs=12.3
Q ss_pred CCceeccCCCcccccH
Q psy10278 77 VKKYQCTFCSYSCTER 92 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~ 92 (110)
.+++.|..||..|..-
T Consensus 2 Dk~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFT 17 (49)
T ss_pred CeeEEcccCCCeEEEe
Confidence 4678999999887643
No 128
>KOG2593|consensus
Probab=67.84 E-value=8.9 Score=26.09 Aligned_cols=36 Identities=22% Similarity=0.548 Sum_probs=22.1
Q ss_pred CCCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCC
Q psy10278 48 REKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCS 86 (110)
Q Consensus 48 ~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~ 86 (110)
....|.|+.|.+.|...-.+.- .....--|.|..|+
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCG 160 (436)
T ss_pred ccccccCCccccchhhhHHHHh---hcccCceEEEecCC
Confidence 4456888888888766544321 22223458888886
No 129
>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=67.09 E-value=4.8 Score=27.68 Aligned_cols=22 Identities=27% Similarity=0.572 Sum_probs=14.1
Q ss_pred ceeCCCCCCCcCChHHHHHHHH
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQ 72 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~ 72 (110)
-+.|+.|.+.|.....+..|+.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~ 78 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHME 78 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHH
Confidence 3566666666666666666666
No 130
>KOG2482|consensus
Probab=66.88 E-value=18 Score=24.08 Aligned_cols=66 Identities=21% Similarity=0.399 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhcCCCCccCCccccccc-CchhHHHHHH-hcC---C------------------CCceeCCCCCCCcCCh
Q psy10278 8 KCLKKHIREVHKRLKPFQCPVCGFTTG-RKATLQLHVR-QHT---R------------------EKPYACPTCEFKTGDH 64 (110)
Q Consensus 8 ~~l~~h~~~~~~~~~~~~C~~c~~~~~-~~~~l~~h~~-~~~---~------------------~~~~~c~~c~~~~~~~ 64 (110)
..|..+++..-......+|-.|...+. ..+.+..|+. .|. | -..+.|..|.+.|...
T Consensus 129 eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdk 208 (423)
T KOG2482|consen 129 EALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDK 208 (423)
T ss_pred HHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCc
Confidence 345556543222223356888877644 4466667765 332 1 1236899999999999
Q ss_pred HHHHHHHHh
Q psy10278 65 NVLRKHVQR 73 (110)
Q Consensus 65 ~~l~~h~~~ 73 (110)
..|..|++.
T Consensus 209 ntLkeHMrk 217 (423)
T KOG2482|consen 209 NTLKEHMRK 217 (423)
T ss_pred HHHHHHHHh
Confidence 999999983
No 131
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=66.72 E-value=5.3 Score=18.83 Aligned_cols=26 Identities=31% Similarity=0.704 Sum_probs=18.0
Q ss_pred ccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCc
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKT 61 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 61 (110)
-.|+.|+..|.... ....|+.|+..+
T Consensus 6 ~~C~~Cg~~~~~~d------------DiVvCp~Cgapy 31 (54)
T PF14446_consen 6 CKCPVCGKKFKDGD------------DIVVCPECGAPY 31 (54)
T ss_pred ccChhhCCcccCCC------------CEEECCCCCCcc
Confidence 46888888775433 246788888765
No 132
>PF15269 zf-C2H2_7: Zinc-finger
Probab=66.48 E-value=5.4 Score=17.94 Aligned_cols=22 Identities=32% Similarity=0.827 Sum_probs=14.9
Q ss_pred eeccCCCcccccHHHHHhhhhh
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLA 101 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~ 101 (110)
|+|-.|..+...++.|..||+.
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5566666666677777777764
No 133
>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=64.41 E-value=8.3 Score=26.82 Aligned_cols=10 Identities=20% Similarity=0.474 Sum_probs=6.3
Q ss_pred CceeccCCCc
Q psy10278 78 KKYQCTFCSY 87 (110)
Q Consensus 78 ~p~~C~~C~~ 87 (110)
-|..|+.|+.
T Consensus 252 ~~~~Cp~C~s 261 (505)
T TIGR00595 252 IPKTCPQCGS 261 (505)
T ss_pred CCCCCCCCCC
Confidence 4566777764
No 134
>KOG4167|consensus
Probab=63.78 E-value=1.4 Score=31.71 Aligned_cols=25 Identities=24% Similarity=0.473 Sum_probs=22.5
Q ss_pred CccCCcccccccCchhHHHHHHhcC
Q psy10278 23 PFQCPVCGFTTGRKATLQLHVRQHT 47 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~ 47 (110)
.|.|.+|++.|.-.-++..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999999999999998885
No 135
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=62.93 E-value=15 Score=24.47 Aligned_cols=77 Identities=22% Similarity=0.332 Sum_probs=50.5
Q ss_pred cCCcccccccCchhHHHHHHhcCCCCceeCCCCC----CCcCChHHHHHHHHhcCCCCceeccC--CC----cccccHHH
Q psy10278 25 QCPVCGFTTGRKATLQLHVRQHTREKPYACPTCE----FKTGDHNVLRKHVQRHMPVKKYQCTF--CS----YSCTERFR 94 (110)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~----~~~~~~~~l~~h~~~h~~~~p~~C~~--C~----~~f~~~~~ 94 (110)
.|..|...|.....|..|++.... +-+.|...+ ..|.....|..|.+. -.|.|++ |. ..|.....
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE-~ChICD~v~p~~~QYFK~Y~~Le~HF~~----~hy~ct~qtc~~~k~~vf~~~~e 296 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHE-ACHICDMVGPIRYQYFKSYEDLEAHFRN----AHYCCTFQTCRVGKCYVFPYHTE 296 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhh-hhhhhhccCccchhhhhCHHHHHHHhhc----CceEEEEEEEecCcEEEeccHHH
Confidence 589999999999999999985432 234443322 245555666666553 2355543 32 47888899
Q ss_pred HHhhhhhcCCCC
Q psy10278 95 LKDHTLAKHNPG 106 (110)
Q Consensus 95 l~~H~~~~~~~~ 106 (110)
|..|+...|+-+
T Consensus 297 l~~h~~~~h~~~ 308 (493)
T COG5236 297 LLEHLTRFHKVN 308 (493)
T ss_pred HHHHHHHHhhcc
Confidence 999998887643
No 136
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.08 E-value=4.4 Score=18.53 Aligned_cols=14 Identities=21% Similarity=0.491 Sum_probs=9.6
Q ss_pred eccCCCcccccHHH
Q psy10278 81 QCTFCSYSCTERFR 94 (110)
Q Consensus 81 ~C~~C~~~f~~~~~ 94 (110)
.|+.|++.|+++..
T Consensus 14 ICpvCqRPFsWRkK 27 (54)
T COG4338 14 ICPVCQRPFSWRKK 27 (54)
T ss_pred hhhhhcCchHHHHH
Confidence 57778877776543
No 137
>KOG1842|consensus
Probab=59.23 E-value=5.4 Score=27.23 Aligned_cols=22 Identities=23% Similarity=0.659 Sum_probs=12.3
Q ss_pred eeCCCCCCCcCChHHHHHHHHh
Q psy10278 52 YACPTCEFKTGDHNVLRKHVQR 73 (110)
Q Consensus 52 ~~c~~c~~~~~~~~~l~~h~~~ 73 (110)
+.||.|...|.....|..|.-.
T Consensus 16 flCPiC~~dl~~~~~L~~H~d~ 37 (505)
T KOG1842|consen 16 FLCPICLLDLPNLSALNDHLDV 37 (505)
T ss_pred ccCchHhhhhhhHHHHHHHHhh
Confidence 4555555555555555555553
No 138
>PRK14873 primosome assembly protein PriA; Provisional
Probab=59.13 E-value=9.5 Score=27.61 Aligned_cols=11 Identities=18% Similarity=0.739 Sum_probs=7.4
Q ss_pred CceeccCCCcc
Q psy10278 78 KKYQCTFCSYS 88 (110)
Q Consensus 78 ~p~~C~~C~~~ 88 (110)
.|+.|+.|+..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 36678888753
No 139
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=59.06 E-value=5.2 Score=22.66 Aligned_cols=22 Identities=18% Similarity=0.119 Sum_probs=11.8
Q ss_pred eeccCCCcccccHHHHHhhhhhcCC
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLAKHN 104 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~~~~ 104 (110)
..|-++|+.|. +|..|+.+|++
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccC
Confidence 45555555554 24555555554
No 140
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=58.81 E-value=4.3 Score=18.83 Aligned_cols=12 Identities=25% Similarity=0.672 Sum_probs=6.1
Q ss_pred eccCCCcccccH
Q psy10278 81 QCTFCSYSCTER 92 (110)
Q Consensus 81 ~C~~C~~~f~~~ 92 (110)
.|+.|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 889999888743
No 141
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=58.54 E-value=11 Score=17.84 Aligned_cols=8 Identities=38% Similarity=1.414 Sum_probs=3.9
Q ss_pred ceeCCCCC
Q psy10278 51 PYACPTCE 58 (110)
Q Consensus 51 ~~~c~~c~ 58 (110)
.|.|+.||
T Consensus 14 ~~~Cp~cG 21 (55)
T PF13824_consen 14 NFECPDCG 21 (55)
T ss_pred CCcCCCCC
Confidence 34555554
No 142
>PF12907 zf-met2: Zinc-binding
Probab=58.20 E-value=8.5 Score=16.91 Aligned_cols=27 Identities=30% Similarity=0.535 Sum_probs=16.1
Q ss_pred eeccCCCccc---ccHHHHHhhhhhcCCCC
Q psy10278 80 YQCTFCSYSC---TERFRLKDHTLAKHNPG 106 (110)
Q Consensus 80 ~~C~~C~~~f---~~~~~l~~H~~~~~~~~ 106 (110)
+.|..|..+| +....|..|-...|...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 3566666444 34556777776666554
No 143
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=58.08 E-value=7.7 Score=18.79 Aligned_cols=9 Identities=33% Similarity=0.947 Sum_probs=2.5
Q ss_pred cCCcccccc
Q psy10278 25 QCPVCGFTT 33 (110)
Q Consensus 25 ~C~~c~~~~ 33 (110)
.|..|+..|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 355555555
No 144
>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=57.79 E-value=7.6 Score=26.76 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=22.6
Q ss_pred CccCCcccccccCchhHHHHHH-hcCC
Q psy10278 23 PFQCPVCGFTTGRKATLQLHVR-QHTR 48 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~-~~~~ 48 (110)
-|.|+.|.+.|.....+..|+. .|.+
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 3789999999999999999998 4654
No 145
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=57.48 E-value=11 Score=16.36 Aligned_cols=16 Identities=31% Similarity=0.397 Sum_probs=7.8
Q ss_pred eeCCCCCCCcCChHHH
Q psy10278 52 YACPTCEFKTGDHNVL 67 (110)
Q Consensus 52 ~~c~~c~~~~~~~~~l 67 (110)
..|+.|+..+.....+
T Consensus 20 d~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGEL 35 (41)
T ss_pred EECCCCCeEEccHHHH
Confidence 4555555544444333
No 146
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=56.27 E-value=8.6 Score=17.71 Aligned_cols=12 Identities=25% Similarity=0.938 Sum_probs=7.1
Q ss_pred CceeccCCCccc
Q psy10278 78 KKYQCTFCSYSC 89 (110)
Q Consensus 78 ~p~~C~~C~~~f 89 (110)
.-+.|..|+..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 346677776543
No 147
>PTZ00448 hypothetical protein; Provisional
Probab=56.21 E-value=8.8 Score=25.60 Aligned_cols=24 Identities=17% Similarity=0.344 Sum_probs=21.1
Q ss_pred ceeccCCCcccccHHHHHhhhhhc
Q psy10278 79 KYQCTFCSYSCTERFRLKDHTLAK 102 (110)
Q Consensus 79 p~~C~~C~~~f~~~~~l~~H~~~~ 102 (110)
.|.|..|+..|......+.|+++-
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 588999999999888999998864
No 148
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=56.21 E-value=3 Score=22.26 Aligned_cols=36 Identities=25% Similarity=0.569 Sum_probs=18.8
Q ss_pred CCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCc
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKT 61 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 61 (110)
+.|.|+.|+..-.+...+..- .......|..|+..|
T Consensus 21 k~FtCp~Cghe~vs~ctvkk~----~~~g~~~Cg~CGls~ 56 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKKT----VNIGTAVCGNCGLSF 56 (104)
T ss_pred ceEecCccCCeeeeEEEEEec----CceeEEEcccCcceE
Confidence 347788887665544332211 122235677776655
No 149
>PRK05580 primosome assembly protein PriA; Validated
Probab=55.52 E-value=14 Score=26.78 Aligned_cols=10 Identities=20% Similarity=0.424 Sum_probs=5.6
Q ss_pred CceeccCCCc
Q psy10278 78 KKYQCTFCSY 87 (110)
Q Consensus 78 ~p~~C~~C~~ 87 (110)
.|..|+.|+.
T Consensus 420 ~~~~Cp~Cg~ 429 (679)
T PRK05580 420 IPKACPECGS 429 (679)
T ss_pred CCCCCCCCcC
Confidence 3456666654
No 150
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=54.94 E-value=9.7 Score=26.15 Aligned_cols=30 Identities=23% Similarity=0.519 Sum_probs=21.0
Q ss_pred CCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChH
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHN 65 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~ 65 (110)
..|.|..||..+..+ ...|+.|+.+-+...
T Consensus 6 ~~y~C~~Cg~~~~~~--------------~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 6 SKFVCQHCGADSPKW--------------QGKCPACHAWNTITE 35 (454)
T ss_pred CeEECCcCCCCCccc--------------cEECcCCCCccccch
Confidence 359999998765442 468999987665543
No 152
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=54.58 E-value=23 Score=21.13 Aligned_cols=8 Identities=25% Similarity=0.941 Sum_probs=4.1
Q ss_pred eeccCCCc
Q psy10278 80 YQCTFCSY 87 (110)
Q Consensus 80 ~~C~~C~~ 87 (110)
|.|+.||-
T Consensus 133 F~Cp~Cg~ 140 (176)
T COG1675 133 FTCPKCGE 140 (176)
T ss_pred CCCCCCCc
Confidence 55555553
No 153
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=54.54 E-value=7.3 Score=21.33 Aligned_cols=11 Identities=18% Similarity=0.604 Sum_probs=6.0
Q ss_pred eeCCCCCCCcC
Q psy10278 52 YACPTCEFKTG 62 (110)
Q Consensus 52 ~~c~~c~~~~~ 62 (110)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 45666665543
No 154
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=54.39 E-value=7.1 Score=17.13 Aligned_cols=12 Identities=17% Similarity=0.603 Sum_probs=8.1
Q ss_pred CceeccCCCccc
Q psy10278 78 KKYQCTFCSYSC 89 (110)
Q Consensus 78 ~p~~C~~C~~~f 89 (110)
.+..|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 356777777665
No 155
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=54.19 E-value=25 Score=16.95 Aligned_cols=13 Identities=15% Similarity=0.708 Sum_probs=7.4
Q ss_pred CCceeccCCCccc
Q psy10278 77 VKKYQCTFCSYSC 89 (110)
Q Consensus 77 ~~p~~C~~C~~~f 89 (110)
.+.|.|+.||...
T Consensus 44 ~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 44 GRVFTCPNCGFEM 56 (69)
T ss_pred cceEEcCCCCCEE
Confidence 3456666666553
No 156
>KOG1280|consensus
Probab=52.98 E-value=21 Score=23.76 Aligned_cols=23 Identities=22% Similarity=0.511 Sum_probs=15.1
Q ss_pred ceeCCCCCCCcCChHHHHHHHHh
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQR 73 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~~ 73 (110)
.|.|+.|+.+-.....+..|...
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s 101 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLS 101 (381)
T ss_pred cccCCcccccccchhHHHHHhhh
Confidence 46677777666666666666663
No 157
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=52.64 E-value=8.7 Score=20.97 Aligned_cols=10 Identities=20% Similarity=0.272 Sum_probs=5.3
Q ss_pred eeCCCCCCCc
Q psy10278 52 YACPTCEFKT 61 (110)
Q Consensus 52 ~~c~~c~~~~ 61 (110)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 4555665444
No 158
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=52.07 E-value=1.6 Score=19.07 Aligned_cols=9 Identities=44% Similarity=0.980 Sum_probs=4.1
Q ss_pred eeccCCCcc
Q psy10278 80 YQCTFCSYS 88 (110)
Q Consensus 80 ~~C~~C~~~ 88 (110)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 444444443
No 159
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=51.66 E-value=15 Score=16.91 Aligned_cols=10 Identities=30% Similarity=0.507 Sum_probs=5.4
Q ss_pred CCcccccccC
Q psy10278 26 CPVCGFTTGR 35 (110)
Q Consensus 26 C~~c~~~~~~ 35 (110)
|..|+..|..
T Consensus 5 C~~C~~~F~~ 14 (57)
T cd00065 5 CMGCGKPFTL 14 (57)
T ss_pred CcccCccccC
Confidence 5556555543
No 160
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=51.44 E-value=7.5 Score=22.51 Aligned_cols=34 Identities=24% Similarity=0.482 Sum_probs=20.0
Q ss_pred CCceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCc
Q psy10278 49 EKPYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSY 87 (110)
Q Consensus 49 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~ 87 (110)
.-+|.|. |+..+...- .|-..-.|+ -|.|..|+-
T Consensus 115 ~~~Y~C~-C~q~~l~~R---Rhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 115 TYPYRCQ-CQQHYLRIR---RHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred ceeEEee-cCCccchhh---hcccccccc-eEEeccCCc
Confidence 3468888 887753332 222233344 688988864
No 161
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=51.37 E-value=5.5 Score=17.04 Aligned_cols=16 Identities=13% Similarity=0.206 Sum_probs=8.9
Q ss_pred eccCCCcccccHHHHH
Q psy10278 81 QCTFCSYSCTERFRLK 96 (110)
Q Consensus 81 ~C~~C~~~f~~~~~l~ 96 (110)
.|+.|+++|-+.+..+
T Consensus 4 ~CprC~kg~Hwa~~C~ 19 (36)
T PF14787_consen 4 LCPRCGKGFHWASECR 19 (36)
T ss_dssp C-TTTSSSCS-TTT--
T ss_pred cCcccCCCcchhhhhh
Confidence 5788888887765543
No 162
>KOG2923|consensus
Probab=51.06 E-value=16 Score=17.88 Aligned_cols=29 Identities=28% Similarity=0.694 Sum_probs=14.5
Q ss_pred ccCCcccccccCchhHHHHHHhcCCCCceeCCCCC
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCE 58 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~ 58 (110)
|+|+ ||-.|..... ..-.|+....|+.|+
T Consensus 23 yPCp-CGDrf~It~e-----dL~~ge~Va~CpsCS 51 (67)
T KOG2923|consen 23 YPCP-CGDRFQITLE-----DLENGEDVARCPSCS 51 (67)
T ss_pred cCCC-CCCeeeecHH-----HHhCCCeeecCCCce
Confidence 4444 5655544321 223455556677665
No 163
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.92 E-value=3.4 Score=25.64 Aligned_cols=25 Identities=24% Similarity=0.482 Sum_probs=16.3
Q ss_pred CCCCccCCcccccccCchhHHHHHH
Q psy10278 20 RLKPFQCPVCGFTTGRKATLQLHVR 44 (110)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~~l~~h~~ 44 (110)
-++...||+|+..|..+...-..++
T Consensus 16 ~kk~ieCPvC~tkFkkeev~tgsiR 40 (267)
T COG1655 16 YKKTIECPVCNTKFKKEEVKTGSIR 40 (267)
T ss_pred hhceeccCcccchhhhhheecccee
Confidence 3455789999998877654433333
No 164
>PF15616 TerY-C: TerY-C metal binding domain
Probab=49.67 E-value=2.8 Score=23.59 Aligned_cols=14 Identities=14% Similarity=0.463 Sum_probs=10.2
Q ss_pred CCCceeccCCCccc
Q psy10278 76 PVKKYQCTFCSYSC 89 (110)
Q Consensus 76 ~~~p~~C~~C~~~f 89 (110)
++....|++|+..-
T Consensus 102 g~~~~~CPwCg~~g 115 (131)
T PF15616_consen 102 GEGEVTCPWCGNEG 115 (131)
T ss_pred CCCCEECCCCCCee
Confidence 44568999998753
No 165
>PRK11823 DNA repair protein RadA; Provisional
Probab=49.61 E-value=13 Score=25.42 Aligned_cols=29 Identities=21% Similarity=0.445 Sum_probs=19.6
Q ss_pred CCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCCh
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDH 64 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~ 64 (110)
..|.|..||..+..+ ...|+.|+.+-+..
T Consensus 6 ~~y~C~~Cg~~~~~~--------------~g~Cp~C~~w~t~~ 34 (446)
T PRK11823 6 TAYVCQECGAESPKW--------------LGRCPECGAWNTLV 34 (446)
T ss_pred CeEECCcCCCCCccc--------------CeeCcCCCCcccee
Confidence 358999998765432 35788888765443
No 166
>PLN02748 tRNA dimethylallyltransferase
Probab=49.57 E-value=13 Score=25.71 Aligned_cols=26 Identities=15% Similarity=0.404 Sum_probs=21.7
Q ss_pred CceeccCCCc-ccccHHHHHhhhhhcC
Q psy10278 78 KKYQCTFCSY-SCTERFRLKDHTLAKH 103 (110)
Q Consensus 78 ~p~~C~~C~~-~f~~~~~l~~H~~~~~ 103 (110)
+.|.|..|++ ++.....+..|+++..
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~ 443 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRG 443 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchH
Confidence 5588999997 8999999999988654
No 167
>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=48.72 E-value=3.3 Score=23.99 Aligned_cols=17 Identities=12% Similarity=0.061 Sum_probs=12.2
Q ss_pred CCceeccCCCcccccHH
Q psy10278 77 VKKYQCTFCSYSCTERF 93 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~~ 93 (110)
+.|.-|..||+.|+|-.
T Consensus 66 ~~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTE 82 (158)
T ss_pred CCChhHHhCCCCCchHH
Confidence 46777888888887643
No 168
>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=48.54 E-value=16 Score=17.03 Aligned_cols=16 Identities=25% Similarity=0.488 Sum_probs=6.0
Q ss_pred ceeCCCCCCCcCChHH
Q psy10278 51 PYACPTCEFKTGDHNV 66 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~ 66 (110)
.|.|+.|...|...-.
T Consensus 21 ~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCD 36 (51)
T ss_dssp EE--TTTT--B-HHHH
T ss_pred eEECCCCCCccccCcC
Confidence 4666666666654433
No 169
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=47.63 E-value=20 Score=23.09 Aligned_cols=25 Identities=16% Similarity=0.396 Sum_probs=15.6
Q ss_pred ceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCccc
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSC 89 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f 89 (110)
.|.|+.|...|... |-.|+.|+-.|
T Consensus 255 GyvCs~Clsi~C~~--------------p~~C~~Cgt~f 279 (279)
T TIGR00627 255 GFVCSVCLSVLCQY--------------TPICKTCKTAF 279 (279)
T ss_pred eEECCCccCCcCCC--------------CCCCCCCCCCC
Confidence 37777777666432 23677777654
No 170
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=47.21 E-value=18 Score=24.17 Aligned_cols=10 Identities=30% Similarity=1.275 Sum_probs=5.9
Q ss_pred ccCCcccccc
Q psy10278 24 FQCPVCGFTT 33 (110)
Q Consensus 24 ~~C~~c~~~~ 33 (110)
|.|..||...
T Consensus 1 ~~c~~cg~~~ 10 (372)
T cd01121 1 YVCSECGYVS 10 (372)
T ss_pred CCCCCCCCCC
Confidence 4566666544
No 171
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=46.50 E-value=11 Score=21.18 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=12.0
Q ss_pred CCceeccCCCccccc
Q psy10278 77 VKKYQCTFCSYSCTE 91 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~ 91 (110)
.+-|.|+.|++.|..
T Consensus 51 ~qRyrC~~C~~tf~~ 65 (129)
T COG3677 51 HQRYKCKSCGSTFTV 65 (129)
T ss_pred ccccccCCcCcceee
Confidence 456899999998863
No 172
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=46.47 E-value=37 Score=20.66 Aligned_cols=11 Identities=18% Similarity=0.407 Sum_probs=5.9
Q ss_pred ceeCCCCCCCc
Q psy10278 51 PYACPTCEFKT 61 (110)
Q Consensus 51 ~~~c~~c~~~~ 61 (110)
.+.|..||..+
T Consensus 30 lvrC~eCG~V~ 40 (201)
T COG1326 30 LVRCEECGTVH 40 (201)
T ss_pred EEEccCCCcEe
Confidence 34566666544
No 173
>KOG0717|consensus
Probab=46.41 E-value=14 Score=25.57 Aligned_cols=22 Identities=27% Similarity=0.514 Sum_probs=16.6
Q ss_pred eeccCCCcccccHHHHHhhhhh
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLA 101 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~ 101 (110)
+.|..|.++|.+...+..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6688888888887777777653
No 174
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=46.36 E-value=15 Score=16.98 Aligned_cols=10 Identities=30% Similarity=1.039 Sum_probs=4.6
Q ss_pred eeCCCCCCCc
Q psy10278 52 YACPTCEFKT 61 (110)
Q Consensus 52 ~~c~~c~~~~ 61 (110)
+.|+.|+..+
T Consensus 29 W~C~~Cgh~w 38 (55)
T PF14311_consen 29 WKCPKCGHEW 38 (55)
T ss_pred EECCCCCCee
Confidence 3455554433
No 175
>KOG2807|consensus
Probab=45.47 E-value=43 Score=22.21 Aligned_cols=24 Identities=17% Similarity=0.289 Sum_probs=15.0
Q ss_pred eeccCCCcccccHHHHHhhhhhcC
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLAKH 103 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~~~ 103 (110)
|.|..|...|--.-+...|-.-|.
T Consensus 346 y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred EEchhccceeeccchHHHHhhhhc
Confidence 677777777766665555554443
No 176
>PRK00420 hypothetical protein; Validated
Probab=45.45 E-value=20 Score=19.72 Aligned_cols=28 Identities=25% Similarity=0.430 Sum_probs=16.0
Q ss_pred ccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcC
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTG 62 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 62 (110)
-.||.|+..+... .. ....|+.|+....
T Consensus 24 ~~CP~Cg~pLf~l---------k~--g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFEL---------KD--GEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceec---------CC--CceECCCCCCeee
Confidence 4588887654321 11 2457888877443
No 177
>PRK04023 DNA polymerase II large subunit; Validated
Probab=44.40 E-value=29 Score=26.72 Aligned_cols=9 Identities=44% Similarity=1.150 Sum_probs=6.4
Q ss_pred ccCCccccc
Q psy10278 24 FQCPVCGFT 32 (110)
Q Consensus 24 ~~C~~c~~~ 32 (110)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 568888765
No 178
>KOG4118|consensus
Probab=44.35 E-value=9.5 Score=18.69 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=16.2
Q ss_pred eeccCCCcccccHHHHHhhhhhcCCCC
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLAKHNPG 106 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~~~~~~ 106 (110)
++|.+|--.-.....+..|....|...
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk~ 65 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPKE 65 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCCC
Confidence 566666655555556666666666544
No 179
>PLN02294 cytochrome c oxidase subunit Vb
Probab=44.02 E-value=15 Score=21.71 Aligned_cols=18 Identities=17% Similarity=0.390 Sum_probs=13.6
Q ss_pred hcCCCCceeccCCCccccc
Q psy10278 73 RHMPVKKYQCTFCSYSCTE 91 (110)
Q Consensus 73 ~h~~~~p~~C~~C~~~f~~ 91 (110)
.+. .+|..|++||..|.-
T Consensus 136 L~k-Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 136 LEK-GKSFECPVCTQYFEL 153 (174)
T ss_pred ecC-CCceeCCCCCCEEEE
Confidence 344 478999999998863
No 180
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=43.79 E-value=13 Score=20.42 Aligned_cols=12 Identities=17% Similarity=0.467 Sum_probs=7.4
Q ss_pred eeCCCCCCCcCC
Q psy10278 52 YACPTCEFKTGD 63 (110)
Q Consensus 52 ~~c~~c~~~~~~ 63 (110)
..|..|+..|..
T Consensus 72 ~~C~~Cg~~~~~ 83 (117)
T PRK00564 72 LECKDCSHVFKP 83 (117)
T ss_pred EEhhhCCCcccc
Confidence 467777765533
No 181
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.77 E-value=12 Score=19.01 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=6.2
Q ss_pred ccCCcccccc
Q psy10278 24 FQCPVCGFTT 33 (110)
Q Consensus 24 ~~C~~c~~~~ 33 (110)
|.|..|+..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 6666666654
No 182
>COG1773 Rubredoxin [Energy production and conversion]
Probab=42.95 E-value=12 Score=17.71 Aligned_cols=12 Identities=25% Similarity=1.099 Sum_probs=8.2
Q ss_pred ceeccCCCcccc
Q psy10278 79 KYQCTFCSYSCT 90 (110)
Q Consensus 79 p~~C~~C~~~f~ 90 (110)
.|.|..||..|-
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 467777777664
No 183
>PHA02998 RNA polymerase subunit; Provisional
Probab=42.94 E-value=4.5 Score=24.06 Aligned_cols=12 Identities=17% Similarity=0.348 Sum_probs=9.5
Q ss_pred eeccCCCccccc
Q psy10278 80 YQCTFCSYSCTE 91 (110)
Q Consensus 80 ~~C~~C~~~f~~ 91 (110)
|.|..|+..|.-
T Consensus 172 YkC~~CG~~wkp 183 (195)
T PHA02998 172 HACRDCKKHFKP 183 (195)
T ss_pred EEcCCCCCccCC
Confidence 889999887753
No 184
>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=42.69 E-value=16 Score=15.43 Aligned_cols=13 Identities=23% Similarity=0.467 Sum_probs=5.8
Q ss_pred CceeccCCCcccc
Q psy10278 78 KKYQCTFCSYSCT 90 (110)
Q Consensus 78 ~p~~C~~C~~~f~ 90 (110)
.+..|+.||..++
T Consensus 20 ~~isC~~CGPr~~ 32 (35)
T PF07503_consen 20 QFISCTNCGPRYS 32 (35)
T ss_dssp TT--BTTCC-SCC
T ss_pred cCccCCCCCCCEE
Confidence 3456777776543
No 185
>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=42.47 E-value=15 Score=15.40 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=12.9
Q ss_pred ceeccCCCcccccHHHHHhhhh
Q psy10278 79 KYQCTFCSYSCTERFRLKDHTL 100 (110)
Q Consensus 79 p~~C~~C~~~f~~~~~l~~H~~ 100 (110)
.+.|+.|++.+.. +-+..|+.
T Consensus 4 ~~~C~nC~R~v~a-~RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVAA-SRFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEEG-GGHHHHHH
T ss_pred eEECCCCcCCcch-hhhHHHHH
Confidence 4789999987653 34455553
No 186
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=41.59 E-value=15 Score=19.90 Aligned_cols=22 Identities=18% Similarity=0.256 Sum_probs=13.7
Q ss_pred eeccCCCcccccHHHHHhhhhh
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLA 101 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~ 101 (110)
+-|-+|.+-|.....|..|++.
T Consensus 56 hYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 56 HYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred eeeehhHHHHHHHHHHHHHhcc
Confidence 5566666666666666666653
No 187
>COG2879 Uncharacterized small protein [Function unknown]
Probab=40.59 E-value=33 Score=16.73 Aligned_cols=18 Identities=17% Similarity=0.135 Sum_probs=11.0
Q ss_pred ccHHHHHhhhhhcCCCCC
Q psy10278 90 TERFRLKDHTLAKHNPGT 107 (110)
Q Consensus 90 ~~~~~l~~H~~~~~~~~~ 107 (110)
+...++..|++.+|.+.+
T Consensus 23 pdYdnYVehmr~~hPd~p 40 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKP 40 (65)
T ss_pred CcHHHHHHHHHHhCcCCC
Confidence 355566667776666554
No 188
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=39.65 E-value=14 Score=16.90 Aligned_cols=8 Identities=38% Similarity=1.493 Sum_probs=2.5
Q ss_pred ccCCcccc
Q psy10278 24 FQCPVCGF 31 (110)
Q Consensus 24 ~~C~~c~~ 31 (110)
|.|++|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 66666653
No 189
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=39.45 E-value=16 Score=19.68 Aligned_cols=10 Identities=50% Similarity=1.255 Sum_probs=6.2
Q ss_pred CccCCccccc
Q psy10278 23 PFQCPVCGFT 32 (110)
Q Consensus 23 ~~~C~~c~~~ 32 (110)
|-.|+.|+..
T Consensus 2 p~~CpYCg~~ 11 (102)
T PF11672_consen 2 PIICPYCGGP 11 (102)
T ss_pred CcccCCCCCe
Confidence 4457777664
No 190
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=39.16 E-value=15 Score=19.36 Aligned_cols=27 Identities=37% Similarity=0.978 Sum_probs=19.1
Q ss_pred CCccCCcccccccCchhHHHHHHhcCCCCceeCCCCC
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCE 58 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~ 58 (110)
.|-.|..||+.|.... -.+|..|+.|.
T Consensus 57 ~Pa~CkkCGfef~~~~----------ik~pSRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRDDK----------IKKPSRCPKCK 83 (97)
T ss_pred cChhhcccCccccccc----------cCCcccCCcch
Confidence 5678999999987621 12466788874
No 191
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=39.07 E-value=12 Score=20.41 Aligned_cols=13 Identities=15% Similarity=0.419 Sum_probs=7.3
Q ss_pred eeCCCCCCCcCCh
Q psy10278 52 YACPTCEFKTGDH 64 (110)
Q Consensus 52 ~~c~~c~~~~~~~ 64 (110)
..|..|+..|...
T Consensus 71 ~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 71 ARCRDCGHEFEPD 83 (113)
T ss_dssp EEETTTS-EEECH
T ss_pred EECCCCCCEEecC
Confidence 4677777666444
No 192
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=38.74 E-value=18 Score=15.07 Aligned_cols=10 Identities=40% Similarity=0.836 Sum_probs=5.1
Q ss_pred eeccCCCccc
Q psy10278 80 YQCTFCSYSC 89 (110)
Q Consensus 80 ~~C~~C~~~f 89 (110)
+.|..|+..|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 4455555544
No 193
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=37.46 E-value=23 Score=18.92 Aligned_cols=17 Identities=18% Similarity=0.254 Sum_probs=13.3
Q ss_pred hcCCCCceeccCCCcccc
Q psy10278 73 RHMPVKKYQCTFCSYSCT 90 (110)
Q Consensus 73 ~h~~~~p~~C~~C~~~f~ 90 (110)
.+.+ +|..|..||.-|.
T Consensus 74 l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 74 LEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EeCC-CceeCCCCCcEEE
Confidence 4455 7999999998875
No 194
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=37.04 E-value=19 Score=19.69 Aligned_cols=10 Identities=30% Similarity=0.597 Sum_probs=6.6
Q ss_pred eeCCCCCCCc
Q psy10278 52 YACPTCEFKT 61 (110)
Q Consensus 52 ~~c~~c~~~~ 61 (110)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 5677777654
No 195
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=36.93 E-value=26 Score=20.29 Aligned_cols=29 Identities=24% Similarity=0.580 Sum_probs=14.7
Q ss_pred chhcHHHHHHHHHHHhcCCCCccCCcccccccCc
Q psy10278 3 FYADIKCLKKHIREVHKRLKPFQCPVCGFTTGRK 36 (110)
Q Consensus 3 ~f~~~~~l~~h~~~~~~~~~~~~C~~c~~~~~~~ 36 (110)
+|.+..++..... .| ...|++||..--.+
T Consensus 17 WF~ss~~fd~Q~~---~g--lv~CP~Cgs~~V~K 45 (148)
T PF06676_consen 17 WFRSSAAFDRQQA---RG--LVSCPVCGSTEVSK 45 (148)
T ss_pred ecCCHHHHHHHHH---cC--CccCCCCCCCeEee
Confidence 4555555555542 11 34577776554333
No 196
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=36.71 E-value=50 Score=15.30 Aligned_cols=11 Identities=18% Similarity=0.338 Sum_probs=5.9
Q ss_pred CCceeccCCCc
Q psy10278 77 VKKYQCTFCSY 87 (110)
Q Consensus 77 ~~p~~C~~C~~ 87 (110)
+....|+.|++
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 34455666654
No 197
>KOG0978|consensus
Probab=36.65 E-value=13 Score=27.05 Aligned_cols=21 Identities=14% Similarity=0.293 Sum_probs=15.5
Q ss_pred CceeccCCCcccccHHHHHhh
Q psy10278 78 KKYQCTFCSYSCTERFRLKDH 98 (110)
Q Consensus 78 ~p~~C~~C~~~f~~~~~l~~H 98 (110)
|.-+||.|+.+|.....+..|
T Consensus 677 RqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred hcCCCCCCCCCCCcccccccC
Confidence 445899999999877665544
No 198
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=36.48 E-value=23 Score=15.30 Aligned_cols=14 Identities=29% Similarity=0.603 Sum_probs=9.3
Q ss_pred CCccCCcccccccC
Q psy10278 22 KPFQCPVCGFTTGR 35 (110)
Q Consensus 22 ~~~~C~~c~~~~~~ 35 (110)
+.+.|+.||+.+.+
T Consensus 31 p~~~C~~CGE~~~~ 44 (46)
T TIGR03831 31 PALVCPQCGEEYLD 44 (46)
T ss_pred CccccccCCCEeeC
Confidence 34678888877644
No 199
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=36.19 E-value=60 Score=21.14 Aligned_cols=22 Identities=23% Similarity=0.433 Sum_probs=12.1
Q ss_pred ceeCCCCCCCcCChHHHHHHHH
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQ 72 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~ 72 (110)
-|.|..|-+.|.....+..|+.
T Consensus 48 lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 48 LYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred EEEcCCCcchhCCHHHHHHHHH
Confidence 3555555555555555555544
No 200
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.75 E-value=14 Score=20.66 Aligned_cols=15 Identities=13% Similarity=0.120 Sum_probs=7.4
Q ss_pred CCceeccCCCccccc
Q psy10278 77 VKKYQCTFCSYSCTE 91 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~ 91 (110)
+.|--|.-||+.|+|
T Consensus 66 e~psfchncgs~fpw 80 (160)
T COG4306 66 EPPSFCHNCGSRFPW 80 (160)
T ss_pred CCcchhhcCCCCCCc
Confidence 334445555555554
No 201
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=35.35 E-value=24 Score=24.29 Aligned_cols=27 Identities=26% Similarity=0.678 Sum_probs=17.9
Q ss_pred CCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcC
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTG 62 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 62 (110)
..|.|..||.....+ .-+|+.|+.+-+
T Consensus 6 t~f~C~~CG~~s~KW--------------~GkCp~Cg~Wns 32 (456)
T COG1066 6 TAFVCQECGYVSPKW--------------LGKCPACGAWNT 32 (456)
T ss_pred cEEEcccCCCCCccc--------------cccCCCCCCccc
Confidence 358899998765443 236888876543
No 202
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=35.32 E-value=19 Score=19.25 Aligned_cols=34 Identities=24% Similarity=0.515 Sum_probs=17.4
Q ss_pred CccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCC
Q psy10278 23 PFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGD 63 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~ 63 (110)
.+.|+.|+.. ...-.+ ..+.....|+.|+..+..
T Consensus 21 ~f~CP~Cge~-~v~v~~------~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 21 IFECPRCGKV-SISVKI------KKNIAIITCGNCGLYTEF 54 (99)
T ss_pred EeECCCCCCe-Eeeeec------CCCcceEECCCCCCccCE
Confidence 4778888732 111111 113334578888765543
No 203
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=35.08 E-value=42 Score=15.53 Aligned_cols=10 Identities=30% Similarity=1.162 Sum_probs=6.4
Q ss_pred ceeccCCCcc
Q psy10278 79 KYQCTFCSYS 88 (110)
Q Consensus 79 p~~C~~C~~~ 88 (110)
-+.|..|+.+
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 4667777654
No 204
>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=35.08 E-value=20 Score=16.52 Aligned_cols=12 Identities=25% Similarity=1.121 Sum_probs=8.4
Q ss_pred ccCCcccccccC
Q psy10278 24 FQCPVCGFTTGR 35 (110)
Q Consensus 24 ~~C~~c~~~~~~ 35 (110)
|.|..|+..+..
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 677777777654
No 205
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.54 E-value=18 Score=20.13 Aligned_cols=12 Identities=17% Similarity=0.578 Sum_probs=7.6
Q ss_pred eeCCCCCCCcCCh
Q psy10278 52 YACPTCEFKTGDH 64 (110)
Q Consensus 52 ~~c~~c~~~~~~~ 64 (110)
..| .|+..|...
T Consensus 71 ~~C-~Cg~~~~~~ 82 (124)
T PRK00762 71 IEC-ECGYEGVVD 82 (124)
T ss_pred EEe-eCcCccccc
Confidence 567 787666443
No 206
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=34.49 E-value=20 Score=15.16 Aligned_cols=12 Identities=17% Similarity=0.487 Sum_probs=5.9
Q ss_pred eeccCCCccccc
Q psy10278 80 YQCTFCSYSCTE 91 (110)
Q Consensus 80 ~~C~~C~~~f~~ 91 (110)
-.|..|++.|..
T Consensus 4 ~~C~eC~~~f~d 15 (34)
T PF01286_consen 4 PKCDECGKPFMD 15 (34)
T ss_dssp EE-TTT--EES-
T ss_pred chHhHhCCHHHH
Confidence 368888888864
No 207
>KOG1088|consensus
Probab=34.38 E-value=25 Score=19.47 Aligned_cols=20 Identities=5% Similarity=-0.082 Sum_probs=15.3
Q ss_pred hcCCCCceeccCCCcccccH
Q psy10278 73 RHMPVKKYQCTFCSYSCTER 92 (110)
Q Consensus 73 ~h~~~~p~~C~~C~~~f~~~ 92 (110)
.+..|....|+.||+.|.=.
T Consensus 92 ~~v~EG~l~CpetG~vfpI~ 111 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFPIS 111 (124)
T ss_pred hhhccceEecCCCCcEeecc
Confidence 45567778999999998744
No 208
>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=34.33 E-value=19 Score=16.90 Aligned_cols=11 Identities=18% Similarity=0.685 Sum_probs=7.1
Q ss_pred eeccCCCcccc
Q psy10278 80 YQCTFCSYSCT 90 (110)
Q Consensus 80 ~~C~~C~~~f~ 90 (110)
++|+.|+..+.
T Consensus 3 ~~CP~CG~~ie 13 (54)
T TIGR01206 3 FECPDCGAEIE 13 (54)
T ss_pred cCCCCCCCEEe
Confidence 56777776553
No 209
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=34.00 E-value=21 Score=19.22 Aligned_cols=15 Identities=33% Similarity=0.647 Sum_probs=10.7
Q ss_pred CCccCCcccccccCc
Q psy10278 22 KPFQCPVCGFTTGRK 36 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~ 36 (110)
+|+.|.-||..|..-
T Consensus 1 MpH~CtrCG~vf~~g 15 (112)
T COG3364 1 MPHQCTRCGEVFDDG 15 (112)
T ss_pred CCceecccccccccc
Confidence 366788888877764
No 210
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.95 E-value=35 Score=23.42 Aligned_cols=14 Identities=14% Similarity=0.645 Sum_probs=7.5
Q ss_pred ceeCCCCCCCcCCh
Q psy10278 51 PYACPTCEFKTGDH 64 (110)
Q Consensus 51 ~~~c~~c~~~~~~~ 64 (110)
-|.|+-|+..+...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 45666666554433
No 211
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=33.67 E-value=24 Score=16.05 Aligned_cols=11 Identities=45% Similarity=1.222 Sum_probs=7.0
Q ss_pred eeccCCCcccc
Q psy10278 80 YQCTFCSYSCT 90 (110)
Q Consensus 80 ~~C~~C~~~f~ 90 (110)
|.|..|+..+.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 56777776553
No 212
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=33.41 E-value=1.1e+02 Score=18.14 Aligned_cols=53 Identities=28% Similarity=0.567 Sum_probs=29.4
Q ss_pred ceeCCCCCCCcCChHHHHHHHHhcCCCCceeccC--CCcccccHHHHHhhhhhcCCC
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTF--CSYSCTERFRLKDHTLAKHNP 105 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~--C~~~f~~~~~l~~H~~~~~~~ 105 (110)
...|+.|.......... .--+.+...|+-.|.. |... .....|++|.+..|..
T Consensus 80 ~L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~ 134 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPS 134 (162)
T ss_pred cccCccccCceeceEEc-hHHHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCC
Confidence 46788876443332222 2234445556656644 4332 3667888888877754
No 213
>KOG2071|consensus
Probab=33.30 E-value=35 Score=24.38 Aligned_cols=29 Identities=24% Similarity=0.445 Sum_probs=23.2
Q ss_pred cCCCCccCCcccccccCchhHHHHHHhcC
Q psy10278 19 KRLKPFQCPVCGFTTGRKATLQLHVRQHT 47 (110)
Q Consensus 19 ~~~~~~~C~~c~~~~~~~~~l~~h~~~~~ 47 (110)
....|-.|..||.+|........||..|.
T Consensus 414 y~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 414 YKDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred ccCCcchhcccccccccchhhhhHhhhhh
Confidence 34567889999999999988887776664
No 214
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=33.27 E-value=28 Score=16.31 Aligned_cols=11 Identities=36% Similarity=0.887 Sum_probs=6.9
Q ss_pred CccCCcccccc
Q psy10278 23 PFQCPVCGFTT 33 (110)
Q Consensus 23 ~~~C~~c~~~~ 33 (110)
...||+||...
T Consensus 3 LkPCPFCG~~~ 13 (61)
T PF14354_consen 3 LKPCPFCGSAD 13 (61)
T ss_pred CcCCCCCCCcc
Confidence 34588886543
No 215
>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=32.65 E-value=10 Score=17.08 Aligned_cols=13 Identities=31% Similarity=0.496 Sum_probs=6.2
Q ss_pred CceeccC--CCcccc
Q psy10278 78 KKYQCTF--CSYSCT 90 (110)
Q Consensus 78 ~p~~C~~--C~~~f~ 90 (110)
.-+.|.- ||..|.
T Consensus 24 ~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 24 LYCQCTNPECGHTFV 38 (47)
T ss_pred EEEEECCCcCCCEEE
Confidence 3344532 555554
No 216
>PRK12496 hypothetical protein; Provisional
Probab=32.61 E-value=31 Score=20.21 Aligned_cols=12 Identities=25% Similarity=0.445 Sum_probs=7.6
Q ss_pred ceeCCCCCCCcC
Q psy10278 51 PYACPTCEFKTG 62 (110)
Q Consensus 51 ~~~c~~c~~~~~ 62 (110)
.+.|..|++.|.
T Consensus 127 ~~~C~gC~~~~~ 138 (164)
T PRK12496 127 RKVCKGCKKKYP 138 (164)
T ss_pred eEECCCCCcccc
Confidence 356777776664
No 217
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=32.24 E-value=26 Score=19.85 Aligned_cols=15 Identities=33% Similarity=0.704 Sum_probs=11.1
Q ss_pred CccCCcccccccCch
Q psy10278 23 PFQCPVCGFTTGRKA 37 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~ 37 (110)
|++|..|+..|..-+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 567888888887654
No 218
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=32.21 E-value=24 Score=15.10 Aligned_cols=12 Identities=25% Similarity=0.755 Sum_probs=6.3
Q ss_pred CceeccCCCccc
Q psy10278 78 KKYQCTFCSYSC 89 (110)
Q Consensus 78 ~p~~C~~C~~~f 89 (110)
+-|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 458899888654
No 219
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=32.04 E-value=12 Score=20.44 Aligned_cols=11 Identities=45% Similarity=1.162 Sum_probs=9.0
Q ss_pred eeccCCCcccc
Q psy10278 80 YQCTFCSYSCT 90 (110)
Q Consensus 80 ~~C~~C~~~f~ 90 (110)
|.|..||..+.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 89999988764
No 220
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.33 E-value=65 Score=20.62 Aligned_cols=10 Identities=20% Similarity=1.085 Sum_probs=5.0
Q ss_pred CceeccCCCc
Q psy10278 78 KKYQCTFCSY 87 (110)
Q Consensus 78 ~p~~C~~C~~ 87 (110)
+-|.|+.||.
T Consensus 321 r~~~C~~cg~ 330 (364)
T COG0675 321 RLFKCPRCGF 330 (364)
T ss_pred eeEECCCCCC
Confidence 3455555554
No 221
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=31.08 E-value=3.1 Score=30.17 Aligned_cols=58 Identities=22% Similarity=0.399 Sum_probs=33.5
Q ss_pred CCcccccccCchhHHHHHHhcCCCCce-eCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccc
Q psy10278 26 CPVCGFTTGRKATLQLHVRQHTREKPY-ACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCT 90 (110)
Q Consensus 26 C~~c~~~~~~~~~l~~h~~~~~~~~~~-~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~ 90 (110)
|..||-.|.....|-- .+..+.-..+ .|+.|.+.+..+.. .+.|. .+..|+.||....
T Consensus 93 Ct~CGPr~~i~~~lpy-dr~~t~m~~f~~C~~C~~ey~~p~~----rr~h~--~~~~C~~Cgp~l~ 151 (711)
T TIGR00143 93 CTHCGPRFTIIEALPY-DRENTSMADFPLCPDCAKEYKDPLD----RRFHA--QPIACPRCGPQLN 151 (711)
T ss_pred ccCCCCCeEEeecCCC-CCCCcCCCCCcCCHHHHHHhcCCcc----ccCCC--CCccCCCCCcEEE
Confidence 7888888876654321 1122222222 57777766655533 33443 6789999997653
No 222
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=30.76 E-value=39 Score=25.46 Aligned_cols=12 Identities=33% Similarity=0.689 Sum_probs=7.7
Q ss_pred cCCcccccccCc
Q psy10278 25 QCPVCGFTTGRK 36 (110)
Q Consensus 25 ~C~~c~~~~~~~ 36 (110)
.|..|+..|...
T Consensus 462 tC~~C~kkFfSl 473 (1374)
T PTZ00303 462 SCPSCGRAFISL 473 (1374)
T ss_pred cccCcCCccccc
Confidence 477777776543
No 223
>KOG1994|consensus
Probab=30.63 E-value=31 Score=21.55 Aligned_cols=23 Identities=26% Similarity=0.625 Sum_probs=18.9
Q ss_pred CCceeccCCCcccccHHHHHhhh
Q psy10278 77 VKKYQCTFCSYSCTERFRLKDHT 99 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~~~l~~H~ 99 (110)
...|-|-+||..|.....|..|=
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhC
Confidence 44589999999999988887764
No 224
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=30.16 E-value=58 Score=14.10 Aligned_cols=10 Identities=30% Similarity=0.810 Sum_probs=5.8
Q ss_pred CCceeccCCC
Q psy10278 77 VKKYQCTFCS 86 (110)
Q Consensus 77 ~~p~~C~~C~ 86 (110)
.....|+.|+
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 3455676665
No 225
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=29.98 E-value=31 Score=14.46 Aligned_cols=8 Identities=50% Similarity=1.559 Sum_probs=4.2
Q ss_pred eeCCCCCC
Q psy10278 52 YACPTCEF 59 (110)
Q Consensus 52 ~~c~~c~~ 59 (110)
+.|+.|+.
T Consensus 23 ~vC~~Cg~ 30 (34)
T PF14803_consen 23 LVCPACGF 30 (34)
T ss_dssp EEETTTTE
T ss_pred eECCCCCC
Confidence 45555553
No 226
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=29.77 E-value=31 Score=22.58 Aligned_cols=11 Identities=45% Similarity=0.945 Sum_probs=7.8
Q ss_pred CccCCcccccc
Q psy10278 23 PFQCPVCGFTT 33 (110)
Q Consensus 23 ~~~C~~c~~~~ 33 (110)
.-.||+||..-
T Consensus 187 ~~~CPvCGs~P 197 (309)
T PRK03564 187 RQFCPVCGSMP 197 (309)
T ss_pred CCCCCCCCCcc
Confidence 35699998653
No 227
>PRK05978 hypothetical protein; Provisional
Probab=29.61 E-value=33 Score=19.89 Aligned_cols=10 Identities=30% Similarity=0.747 Sum_probs=6.0
Q ss_pred eccCCCcccc
Q psy10278 81 QCTFCSYSCT 90 (110)
Q Consensus 81 ~C~~C~~~f~ 90 (110)
.|+.||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 5666665554
No 228
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=29.46 E-value=42 Score=19.17 Aligned_cols=36 Identities=17% Similarity=0.291 Sum_probs=19.8
Q ss_pred ccCCcccccccCchhHHH--------HHHhcCCCCceeCCCCCCCcC
Q psy10278 24 FQCPVCGFTTGRKATLQL--------HVRQHTREKPYACPTCEFKTG 62 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~--------h~~~~~~~~~~~c~~c~~~~~ 62 (110)
-.|..|+..+.....-.. ...... -+.|+.|++.|=
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~---f~~C~~C~kiyW 135 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDE---FWRCPGCGKIYW 135 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCe---EEECCCCCCEec
Confidence 569999887543221100 011222 468999998773
No 229
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=29.37 E-value=24 Score=17.24 Aligned_cols=8 Identities=38% Similarity=1.169 Sum_probs=4.9
Q ss_pred eeccCCCc
Q psy10278 80 YQCTFCSY 87 (110)
Q Consensus 80 ~~C~~C~~ 87 (110)
|.|++|+-
T Consensus 1 y~C~KCg~ 8 (64)
T PF09855_consen 1 YKCPKCGN 8 (64)
T ss_pred CCCCCCCC
Confidence 45666664
No 230
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=29.35 E-value=29 Score=18.96 Aligned_cols=26 Identities=23% Similarity=0.668 Sum_probs=14.4
Q ss_pred cCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCc
Q psy10278 25 QCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKT 61 (110)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~ 61 (110)
.||.|+..|..+ ....+.|+.|+...
T Consensus 4 ~CP~C~seytY~-----------dg~~~iCpeC~~EW 29 (109)
T TIGR00686 4 PCPKCNSEYTYH-----------DGTQLICPSCLYEW 29 (109)
T ss_pred cCCcCCCcceEe-----------cCCeeECccccccc
Confidence 477776555433 22346777776443
No 231
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=29.00 E-value=44 Score=15.49 Aligned_cols=12 Identities=33% Similarity=0.872 Sum_probs=5.8
Q ss_pred ceeCCCCCCCcC
Q psy10278 51 PYACPTCEFKTG 62 (110)
Q Consensus 51 ~~~c~~c~~~~~ 62 (110)
...|+.|+..|.
T Consensus 40 ~v~C~~C~~~fC 51 (64)
T smart00647 40 RVTCPKCGFSFC 51 (64)
T ss_pred eeECCCCCCeEC
Confidence 345555554443
No 232
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=28.86 E-value=36 Score=23.66 Aligned_cols=17 Identities=12% Similarity=0.362 Sum_probs=11.3
Q ss_pred CCCceeCCCCCCCcCCh
Q psy10278 48 REKPYACPTCEFKTGDH 64 (110)
Q Consensus 48 ~~~~~~c~~c~~~~~~~ 64 (110)
....|.|..|+..|...
T Consensus 422 ~~~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPA 438 (479)
T ss_pred CCCeEEECCCCeEECCC
Confidence 34557888888776554
No 233
>PF14369 zf-RING_3: zinc-finger
Probab=28.52 E-value=28 Score=14.63 Aligned_cols=10 Identities=30% Similarity=0.507 Sum_probs=8.2
Q ss_pred cCCccccccc
Q psy10278 25 QCPVCGFTTG 34 (110)
Q Consensus 25 ~C~~c~~~~~ 34 (110)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999998875
No 234
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=28.46 E-value=24 Score=16.76 Aligned_cols=7 Identities=43% Similarity=1.236 Sum_probs=3.3
Q ss_pred eeccCCC
Q psy10278 80 YQCTFCS 86 (110)
Q Consensus 80 ~~C~~C~ 86 (110)
|-|..|.
T Consensus 32 YmC~eC~ 38 (56)
T PF09963_consen 32 YMCDECK 38 (56)
T ss_pred eeChhHH
Confidence 4454443
No 235
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=28.39 E-value=58 Score=20.56 Aligned_cols=15 Identities=13% Similarity=0.301 Sum_probs=10.5
Q ss_pred CCCceeccCCCcccc
Q psy10278 76 PVKKYQCTFCSYSCT 90 (110)
Q Consensus 76 ~~~p~~C~~C~~~f~ 90 (110)
+..+..||.||+...
T Consensus 218 ~d~iv~CP~CgRILy 232 (239)
T COG1579 218 KDEIVFCPYCGRILY 232 (239)
T ss_pred CCCCccCCccchHHH
Confidence 556678888887543
No 236
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=28.15 E-value=32 Score=16.74 Aligned_cols=18 Identities=11% Similarity=0.242 Sum_probs=12.3
Q ss_pred hcCCCCceeccCCCcccc
Q psy10278 73 RHMPVKKYQCTFCSYSCT 90 (110)
Q Consensus 73 ~h~~~~p~~C~~C~~~f~ 90 (110)
.+..+.-..|+.|++.|.
T Consensus 47 ~~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 47 VEIVEGELICPECGREYP 64 (68)
T ss_dssp EETTTTEEEETTTTEEEE
T ss_pred ccccCCEEEcCCCCCEEe
Confidence 345566678888887764
No 237
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=28.09 E-value=26 Score=16.56 Aligned_cols=10 Identities=20% Similarity=0.421 Sum_probs=5.2
Q ss_pred CceeccCCCc
Q psy10278 78 KKYQCTFCSY 87 (110)
Q Consensus 78 ~p~~C~~C~~ 87 (110)
-|..|+.|..
T Consensus 27 fPlyCpKCK~ 36 (55)
T PF14205_consen 27 FPLYCPKCKQ 36 (55)
T ss_pred ccccCCCCCc
Confidence 3455555544
No 238
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=27.78 E-value=35 Score=14.86 Aligned_cols=8 Identities=25% Similarity=0.837 Sum_probs=4.3
Q ss_pred eccCCCcc
Q psy10278 81 QCTFCSYS 88 (110)
Q Consensus 81 ~C~~C~~~ 88 (110)
.|+.|+..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 45666543
No 239
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=27.75 E-value=42 Score=22.15 Aligned_cols=25 Identities=20% Similarity=0.440 Sum_probs=17.8
Q ss_pred CceeccCCCcccccHHHHHhhhhhc
Q psy10278 78 KKYQCTFCSYSCTERFRLKDHTLAK 102 (110)
Q Consensus 78 ~p~~C~~C~~~f~~~~~l~~H~~~~ 102 (110)
-.|.|+.|...|-...+.-.|-..|
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHh
Confidence 3488888888887777766665544
No 240
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.44 E-value=52 Score=15.97 Aligned_cols=7 Identities=71% Similarity=1.958 Sum_probs=3.1
Q ss_pred eeCCCCC
Q psy10278 52 YACPTCE 58 (110)
Q Consensus 52 ~~c~~c~ 58 (110)
|.|+.|.
T Consensus 32 ymC~eC~ 38 (68)
T COG4896 32 YMCPECE 38 (68)
T ss_pred EechhhH
Confidence 4444443
No 241
>PRK10220 hypothetical protein; Provisional
Probab=27.26 E-value=35 Score=18.65 Aligned_cols=27 Identities=26% Similarity=0.699 Sum_probs=15.8
Q ss_pred cCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcC
Q psy10278 25 QCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTG 62 (110)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 62 (110)
.|+.|...|... ....+.|+.|+.-..
T Consensus 5 ~CP~C~seytY~-----------d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 5 HCPKCNSEYTYE-----------DNGMYICPECAHEWN 31 (111)
T ss_pred cCCCCCCcceEc-----------CCCeEECCcccCcCC
Confidence 477777655433 223578888875443
No 242
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.23 E-value=61 Score=25.76 Aligned_cols=9 Identities=44% Similarity=1.191 Sum_probs=6.8
Q ss_pred ccCCccccc
Q psy10278 24 FQCPVCGFT 32 (110)
Q Consensus 24 ~~C~~c~~~ 32 (110)
+.|+.||..
T Consensus 668 rkCPkCG~~ 676 (1337)
T PRK14714 668 RRCPSCGTE 676 (1337)
T ss_pred EECCCCCCc
Confidence 678888864
No 243
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=26.46 E-value=35 Score=15.92 Aligned_cols=11 Identities=45% Similarity=0.945 Sum_probs=6.3
Q ss_pred cCCcccccccC
Q psy10278 25 QCPVCGFTTGR 35 (110)
Q Consensus 25 ~C~~c~~~~~~ 35 (110)
.||.||..+..
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 46666665443
No 244
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=26.37 E-value=43 Score=17.72 Aligned_cols=26 Identities=35% Similarity=0.925 Sum_probs=15.6
Q ss_pred cCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcC
Q psy10278 25 QCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTG 62 (110)
Q Consensus 25 ~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 62 (110)
.|+.|+..+... ...+.|+.|+....
T Consensus 2 fC~~Cg~~l~~~------------~~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPK------------NGVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccccC------------CCeEECcCCCCccc
Confidence 377777665321 12577888886544
No 245
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=26.28 E-value=36 Score=14.62 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=5.0
Q ss_pred eeccCCCcc
Q psy10278 80 YQCTFCSYS 88 (110)
Q Consensus 80 ~~C~~C~~~ 88 (110)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 555555554
No 246
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=26.03 E-value=37 Score=16.66 Aligned_cols=10 Identities=20% Similarity=0.883 Sum_probs=6.6
Q ss_pred ceeccCCCcc
Q psy10278 79 KYQCTFCSYS 88 (110)
Q Consensus 79 p~~C~~C~~~ 88 (110)
.++|+.||-.
T Consensus 4 ~~kCpKCgn~ 13 (68)
T COG3478 4 AFKCPKCGNT 13 (68)
T ss_pred cccCCCcCCc
Confidence 4568888753
No 247
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=25.98 E-value=35 Score=14.91 Aligned_cols=9 Identities=22% Similarity=0.715 Sum_probs=6.8
Q ss_pred ceeccCCCc
Q psy10278 79 KYQCTFCSY 87 (110)
Q Consensus 79 p~~C~~C~~ 87 (110)
|..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 567888884
No 248
>KOG0402|consensus
Probab=25.85 E-value=42 Score=17.39 Aligned_cols=8 Identities=38% Similarity=1.327 Sum_probs=5.3
Q ss_pred ccCCcccc
Q psy10278 24 FQCPVCGF 31 (110)
Q Consensus 24 ~~C~~c~~ 31 (110)
|.|+.||+
T Consensus 37 y~CsfCGK 44 (92)
T KOG0402|consen 37 YTCSFCGK 44 (92)
T ss_pred hhhhhcch
Confidence 66777665
No 249
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=25.64 E-value=1.1e+02 Score=18.26 Aligned_cols=11 Identities=36% Similarity=0.996 Sum_probs=6.9
Q ss_pred cCCcccccccC
Q psy10278 25 QCPVCGFTTGR 35 (110)
Q Consensus 25 ~C~~c~~~~~~ 35 (110)
.|+.|+....-
T Consensus 156 ~CPlCg~PlDP 166 (171)
T PF11290_consen 156 PCPLCGEPLDP 166 (171)
T ss_pred CCCCCCCCCCC
Confidence 47777765443
No 250
>KOG3507|consensus
Probab=25.56 E-value=46 Score=16.01 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=6.4
Q ss_pred ceeccCCCccc
Q psy10278 79 KYQCTFCSYSC 89 (110)
Q Consensus 79 p~~C~~C~~~f 89 (110)
.+.|.+||...
T Consensus 37 ~irCReCG~RI 47 (62)
T KOG3507|consen 37 VIRCRECGYRI 47 (62)
T ss_pred cEehhhcchHH
Confidence 46666666543
No 251
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=25.32 E-value=51 Score=17.35 Aligned_cols=23 Identities=17% Similarity=0.393 Sum_probs=16.2
Q ss_pred CCccCCcccccccCchhHHHHHH
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVR 44 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~ 44 (110)
+...|+.||+.+.+...+..-..
T Consensus 34 Pa~~C~~CGe~y~~dev~~eIE~ 56 (89)
T TIGR03829 34 PSISCSHCGMEYQDDTTVKEIED 56 (89)
T ss_pred CcccccCCCcEeecHHHHHHHHh
Confidence 34679999999888766554433
No 252
>PF12773 DZR: Double zinc ribbon
Probab=24.75 E-value=47 Score=14.77 Aligned_cols=8 Identities=38% Similarity=1.045 Sum_probs=3.9
Q ss_pred eeCCCCCC
Q psy10278 52 YACPTCEF 59 (110)
Q Consensus 52 ~~c~~c~~ 59 (110)
..|+.|+.
T Consensus 30 ~~C~~Cg~ 37 (50)
T PF12773_consen 30 KICPNCGA 37 (50)
T ss_pred CCCcCCcC
Confidence 34555554
No 253
>PRK12722 transcriptional activator FlhC; Provisional
Probab=24.66 E-value=61 Score=19.64 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=18.2
Q ss_pred eeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCc
Q psy10278 52 YACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSY 87 (110)
Q Consensus 52 ~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~ 87 (110)
..|..|+..|..... .....|.|+.|..
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHAH--------DPVGSFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCCC
Confidence 468888887753322 2235689999865
No 254
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=24.64 E-value=43 Score=20.97 Aligned_cols=31 Identities=16% Similarity=0.179 Sum_probs=18.8
Q ss_pred CCCccCCcccccccCchhHHHHHHhcCCCCceeC
Q psy10278 21 LKPFQCPVCGFTTGRKATLQLHVRQHTREKPYAC 54 (110)
Q Consensus 21 ~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c 54 (110)
.++..|+.||..|.-...+. ....|..|+.-
T Consensus 179 GkpqRCpECGqVFKLVr~~~---s~~dg~dp~~~ 209 (268)
T PTZ00043 179 GFLYRCGECDQIFMLVRVLY---SLPDGEDPFPN 209 (268)
T ss_pred CCCccCCCCCcEEEEEEEEe---ecCCCCCCCCC
Confidence 45788999999887643221 13445555543
No 255
>PRK01343 zinc-binding protein; Provisional
Probab=24.23 E-value=45 Score=15.94 Aligned_cols=11 Identities=27% Similarity=0.561 Sum_probs=6.6
Q ss_pred eeccCCCcccc
Q psy10278 80 YQCTFCSYSCT 90 (110)
Q Consensus 80 ~~C~~C~~~f~ 90 (110)
..|+.|++.+.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 45666666554
No 256
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=24.15 E-value=1.4e+02 Score=20.13 Aligned_cols=10 Identities=40% Similarity=1.308 Sum_probs=6.2
Q ss_pred CCccCCcccc
Q psy10278 22 KPFQCPVCGF 31 (110)
Q Consensus 22 ~~~~C~~c~~ 31 (110)
..|.|..||+
T Consensus 353 ~~YRC~~CGF 362 (389)
T COG2956 353 PRYRCQNCGF 362 (389)
T ss_pred CCceecccCC
Confidence 3466777765
No 257
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=23.79 E-value=46 Score=13.61 Aligned_cols=12 Identities=25% Similarity=0.830 Sum_probs=8.8
Q ss_pred CceeccCCCccc
Q psy10278 78 KKYQCTFCSYSC 89 (110)
Q Consensus 78 ~p~~C~~C~~~f 89 (110)
+-|+|..|+...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 358888888655
No 258
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=23.78 E-value=30 Score=23.19 Aligned_cols=22 Identities=14% Similarity=0.215 Sum_probs=15.2
Q ss_pred eeccCCCcccccHHHHHhhhhh
Q psy10278 80 YQCTFCSYSCTERFRLKDHTLA 101 (110)
Q Consensus 80 ~~C~~C~~~f~~~~~l~~H~~~ 101 (110)
+-|++|++-|...+.+..|+..
T Consensus 239 ~YC~~C~r~f~~~~VFe~Hl~g 260 (470)
T COG5188 239 VYCVKCGREFSRSKVFEYHLEG 260 (470)
T ss_pred eeeHhhhhHhhhhHHHHHHHhh
Confidence 6677777777776777777653
No 259
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=23.55 E-value=1.8e+02 Score=17.86 Aligned_cols=54 Identities=15% Similarity=0.272 Sum_probs=29.7
Q ss_pred CCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHHh----------cCCCCceeccCCCccccc
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQR----------HMPVKKYQCTFCSYSCTE 91 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~----------h~~~~p~~C~~C~~~f~~ 91 (110)
..+.|++|...+.. +.. ..|+-.|...-...+.... .....+..|+.|...++.
T Consensus 17 ~~~~CpICld~~~d---------------PVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 17 GDFDCNICLDQVRD---------------PVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CccCCccCCCcCCC---------------cEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 35889999765422 222 3467677666443321110 112345789999877654
No 260
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=23.19 E-value=38 Score=19.36 Aligned_cols=17 Identities=24% Similarity=0.381 Sum_probs=13.2
Q ss_pred hcCCCCceeccCCCcccc
Q psy10278 73 RHMPVKKYQCTFCSYSCT 90 (110)
Q Consensus 73 ~h~~~~p~~C~~C~~~f~ 90 (110)
.+.+ +|..|+.||..|.
T Consensus 107 l~~g-~~~RCpeCG~~fk 123 (136)
T PF01215_consen 107 LHKG-KPQRCPECGQVFK 123 (136)
T ss_dssp EETT-SEEEETTTEEEEE
T ss_pred EeCC-CccCCCCCCeEEE
Confidence 4444 6899999998875
No 261
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=23.18 E-value=1.4e+02 Score=16.10 Aligned_cols=41 Identities=10% Similarity=0.076 Sum_probs=27.1
Q ss_pred CCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCC
Q psy10278 22 KPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGD 63 (110)
Q Consensus 22 ~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~ 63 (110)
+.|.|+.-++.|.+...+...+... ..+.+.|...|+.-..
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y-~~~vwtC~~TGk~~LT 42 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILY-NQRVWTCEITGKSNLT 42 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHH-hCCeeEEecCCCCCCC
Confidence 4567788888888877777665543 3356788877764433
No 262
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=22.87 E-value=46 Score=18.88 Aligned_cols=32 Identities=28% Similarity=0.647 Sum_probs=18.9
Q ss_pred ceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccc
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCT 90 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~ 90 (110)
.|.|..|+..+..... . ....+.|+.|+-.+.
T Consensus 123 ~~~C~~C~~~~~r~~~------~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRHRR------S--KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeeecc------c--chhhEECCCCCCEEE
Confidence 4788888866533322 1 123378888885543
No 263
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=22.84 E-value=82 Score=20.69 Aligned_cols=13 Identities=23% Similarity=0.496 Sum_probs=7.7
Q ss_pred CCCCceeCCCCCC
Q psy10278 47 TREKPYACPTCEF 59 (110)
Q Consensus 47 ~~~~~~~c~~c~~ 59 (110)
.|.+-..|..|+.
T Consensus 206 ~G~RyL~CslC~t 218 (305)
T TIGR01562 206 TGLRYLSCSLCAT 218 (305)
T ss_pred CCceEEEcCCCCC
Confidence 3445566777753
No 264
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=22.80 E-value=34 Score=13.78 Aligned_cols=11 Identities=27% Similarity=0.751 Sum_probs=5.3
Q ss_pred CCceeCCCCCC
Q psy10278 49 EKPYACPTCEF 59 (110)
Q Consensus 49 ~~~~~c~~c~~ 59 (110)
+....|+.|+.
T Consensus 19 g~~r~C~~Cg~ 29 (32)
T PF09297_consen 19 GWARRCPSCGH 29 (32)
T ss_dssp SS-EEESSSS-
T ss_pred cCEeECCCCcC
Confidence 44556666654
No 265
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=22.69 E-value=67 Score=19.13 Aligned_cols=20 Identities=10% Similarity=0.288 Sum_probs=15.0
Q ss_pred CCceeccCCCcccccHHHHH
Q psy10278 77 VKKYQCTFCSYSCTERFRLK 96 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~~~l~ 96 (110)
-....|..||+.|.....+.
T Consensus 112 ~~~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 112 FHLQRCSRCERPFAPQKTVA 131 (181)
T ss_pred cccCcCcccCCccCcHhHHH
Confidence 35789999999998654443
No 266
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=22.66 E-value=51 Score=13.46 Aligned_cols=12 Identities=25% Similarity=0.814 Sum_probs=9.1
Q ss_pred CceeccCCCccc
Q psy10278 78 KKYQCTFCSYSC 89 (110)
Q Consensus 78 ~p~~C~~C~~~f 89 (110)
+-|+|..|+..+
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 468899988755
No 267
>PRK12860 transcriptional activator FlhC; Provisional
Probab=22.58 E-value=66 Score=19.53 Aligned_cols=27 Identities=22% Similarity=0.422 Sum_probs=17.6
Q ss_pred eeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCC
Q psy10278 52 YACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCS 86 (110)
Q Consensus 52 ~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~ 86 (110)
..|..|+..|..... .....|.|+.|.
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTHAH--------DLRHNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCC
Confidence 468888887753322 223568899886
No 268
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=21.95 E-value=34 Score=14.56 Aligned_cols=6 Identities=50% Similarity=1.547 Sum_probs=2.5
Q ss_pred eeccCC
Q psy10278 80 YQCTFC 85 (110)
Q Consensus 80 ~~C~~C 85 (110)
|.|..|
T Consensus 30 yrC~~C 35 (36)
T PF03811_consen 30 YRCKDC 35 (36)
T ss_pred EecCcC
Confidence 444433
No 269
>KOG2636|consensus
Probab=21.82 E-value=79 Score=22.05 Aligned_cols=27 Identities=19% Similarity=0.559 Sum_probs=17.9
Q ss_pred hcCCCCccCCccc-ccccCchhHHHHHH
Q psy10278 18 HKRLKPFQCPVCG-FTTGRKATLQLHVR 44 (110)
Q Consensus 18 ~~~~~~~~C~~c~-~~~~~~~~l~~h~~ 44 (110)
|.-...|.|.+|| +++.-...+.+|..
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 4444557788887 66666677777765
No 270
>PLN03239 histone acetyltransferase; Provisional
Probab=21.78 E-value=93 Score=20.93 Aligned_cols=25 Identities=16% Similarity=0.121 Sum_probs=19.6
Q ss_pred CCceeccCCCcccccHHHHHhhhhh
Q psy10278 77 VKKYQCTFCSYSCTERFRLKDHTLA 101 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~~~l~~H~~~ 101 (110)
..-|.|..|-+-|.....+..|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 3568888888888888888888753
No 271
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=21.78 E-value=41 Score=13.49 Aligned_cols=9 Identities=22% Similarity=0.981 Sum_probs=4.5
Q ss_pred eeccCCCcc
Q psy10278 80 YQCTFCSYS 88 (110)
Q Consensus 80 ~~C~~C~~~ 88 (110)
|.|..|+..
T Consensus 28 f~C~~C~~~ 36 (39)
T smart00132 28 FKCSKCGKP 36 (39)
T ss_pred CCCcccCCc
Confidence 455555544
No 272
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=21.74 E-value=1.1e+02 Score=21.47 Aligned_cols=25 Identities=28% Similarity=0.483 Sum_probs=20.0
Q ss_pred CCceeccCCCcccccHHHHHhhhhh
Q psy10278 77 VKKYQCTFCSYSCTERFRLKDHTLA 101 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~~~l~~H~~~ 101 (110)
..-|.|..|-+-|.....|..|+..
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhc
Confidence 3458888888888888888888863
No 273
>KOG2857|consensus
Probab=21.74 E-value=56 Score=18.84 Aligned_cols=22 Identities=18% Similarity=0.599 Sum_probs=19.4
Q ss_pred CccCCcccccccCchhHHHHHH
Q psy10278 23 PFQCPVCGFTTGRKATLQLHVR 44 (110)
Q Consensus 23 ~~~C~~c~~~~~~~~~l~~h~~ 44 (110)
.|+|+.|...+.+-.-++.|..
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hccCCCCCCccccchhhhhccC
Confidence 5999999999999999988865
No 274
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=21.61 E-value=1.5e+02 Score=17.78 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=6.9
Q ss_pred cCCcccccccC
Q psy10278 25 QCPVCGFTTGR 35 (110)
Q Consensus 25 ~C~~c~~~~~~ 35 (110)
.|+.|+....-
T Consensus 158 ~CPlCg~PldP 168 (177)
T TIGR03847 158 PCPLCGRPIDP 168 (177)
T ss_pred CCCCCCCCCCC
Confidence 47777765543
No 275
>KOG0696|consensus
Probab=21.40 E-value=26 Score=24.35 Aligned_cols=59 Identities=25% Similarity=0.467 Sum_probs=31.2
Q ss_pred CCCCccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHHHHHHHH-hcCCCCceeccCCCc
Q psy10278 20 RLKPFQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNVLRKHVQ-RHMPVKKYQCTFCSY 87 (110)
Q Consensus 20 ~~~~~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~-~h~~~~p~~C~~C~~ 87 (110)
|..-|+|.+|. +..|.+.|.- ..+.|+.=++.+.....-..|-- .|+-..|--|..||.
T Consensus 70 gKQGfQCqvC~--------fvvHkrChef-VtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCGs 129 (683)
T KOG0696|consen 70 GKQGFQCQVCC--------FVVHKRCHEF-VTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCGS 129 (683)
T ss_pred ccCceeeeEEe--------ehhhhhhcce-EEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHHH
Confidence 33346666664 3456565532 34667766666655544444433 444455555666654
No 276
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.39 E-value=66 Score=15.65 Aligned_cols=13 Identities=23% Similarity=0.644 Sum_probs=8.5
Q ss_pred CceeccCCCcccc
Q psy10278 78 KKYQCTFCSYSCT 90 (110)
Q Consensus 78 ~p~~C~~C~~~f~ 90 (110)
.-..|+.|+..|.
T Consensus 47 gev~CPYC~t~y~ 59 (62)
T COG4391 47 GEVVCPYCSTRYR 59 (62)
T ss_pred CcEecCccccEEE
Confidence 3467777777664
No 277
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=21.33 E-value=74 Score=20.64 Aligned_cols=34 Identities=26% Similarity=0.582 Sum_probs=19.7
Q ss_pred ccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcCChHH
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTGDHNV 66 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~~~~~ 66 (110)
.+|+.|+.....+. |. ..-+.|+.|+.-|.....
T Consensus 27 ~~c~~c~~~~~~~~-l~--------~~~~vc~~c~~h~rl~ar 60 (285)
T TIGR00515 27 TKCPKCGQVLYTKE-LE--------RNLEVCPKCDHHMRMDAR 60 (285)
T ss_pred eECCCCcchhhHHH-HH--------hhCCCCCCCCCcCcCCHH
Confidence 45888876554332 11 123578888877765544
No 278
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=21.33 E-value=59 Score=23.18 Aligned_cols=40 Identities=20% Similarity=0.414 Sum_probs=20.8
Q ss_pred eeCCCCCCCcCCh-HHHHHHHHhcCCCCceeccCCCccccc
Q psy10278 52 YACPTCEFKTGDH-NVLRKHVQRHMPVKKYQCTFCSYSCTE 91 (110)
Q Consensus 52 ~~c~~c~~~~~~~-~~l~~h~~~h~~~~p~~C~~C~~~f~~ 91 (110)
..|+.|+..+... ..+..........--|.|+.||.....
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 4788888776544 222110000111223888888877654
No 279
>PHA02942 putative transposase; Provisional
Probab=20.94 E-value=1e+02 Score=20.85 Aligned_cols=14 Identities=21% Similarity=0.757 Sum_probs=10.7
Q ss_pred CCceeccCCCcccc
Q psy10278 77 VKKYQCTFCSYSCT 90 (110)
Q Consensus 77 ~~p~~C~~C~~~f~ 90 (110)
.+.|.|+.||...-
T Consensus 340 ~r~f~C~~CG~~~d 353 (383)
T PHA02942 340 HRYFHCPSCGYEND 353 (383)
T ss_pred CCEEECCCCCCEeC
Confidence 46799999997653
No 280
>KOG3214|consensus
Probab=20.80 E-value=23 Score=19.03 Aligned_cols=13 Identities=23% Similarity=0.429 Sum_probs=8.0
Q ss_pred eeCCCCCCCcCCh
Q psy10278 52 YACPTCEFKTGDH 64 (110)
Q Consensus 52 ~~c~~c~~~~~~~ 64 (110)
..|.+|+..|...
T Consensus 48 ~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 48 ASCRICEESFQTT 60 (109)
T ss_pred eeeeehhhhhccc
Confidence 4677777666543
No 281
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=20.78 E-value=76 Score=14.91 Aligned_cols=21 Identities=14% Similarity=0.368 Sum_probs=14.9
Q ss_pred CCceeccCCCcccccHHHHHh
Q psy10278 77 VKKYQCTFCSYSCTERFRLKD 97 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~~~l~~ 97 (110)
..-+-|-+||-.|.....|..
T Consensus 25 ~~~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 25 EEHNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred hhCceeeeeCCccCCHHHHHh
Confidence 445678888888887766643
No 282
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.76 E-value=1.3e+02 Score=21.53 Aligned_cols=25 Identities=16% Similarity=0.073 Sum_probs=20.2
Q ss_pred CCceeccCCCcccccHHHHHhhhhh
Q psy10278 77 VKKYQCTFCSYSCTERFRLKDHTLA 101 (110)
Q Consensus 77 ~~p~~C~~C~~~f~~~~~l~~H~~~ 101 (110)
..-|.|..|-+-|.....|..|+..
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhc
Confidence 3458888888888888888888874
No 283
>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=20.51 E-value=46 Score=17.03 Aligned_cols=10 Identities=40% Similarity=1.222 Sum_probs=3.5
Q ss_pred CCceeccCCC
Q psy10278 77 VKKYQCTFCS 86 (110)
Q Consensus 77 ~~p~~C~~C~ 86 (110)
++.|.|+.|+
T Consensus 20 ~~~F~CPfC~ 29 (81)
T PF05129_consen 20 PKVFDCPFCN 29 (81)
T ss_dssp SS----TTT-
T ss_pred CceEcCCcCC
Confidence 3558888887
No 284
>PRK06260 threonine synthase; Validated
Probab=20.38 E-value=94 Score=20.99 Aligned_cols=27 Identities=30% Similarity=0.625 Sum_probs=17.0
Q ss_pred ccCCcccccccCchhHHHHHHhcCCCCceeCCCCCCCcC
Q psy10278 24 FQCPVCGFTTGRKATLQLHVRQHTREKPYACPTCEFKTG 62 (110)
Q Consensus 24 ~~C~~c~~~~~~~~~l~~h~~~~~~~~~~~c~~c~~~~~ 62 (110)
+.|..|+..+... ...+.|+.|+..+.
T Consensus 4 ~~C~~cg~~~~~~------------~~~~~Cp~cg~~l~ 30 (397)
T PRK06260 4 LKCIECGKEYDPD------------EIIYTCPECGGLLE 30 (397)
T ss_pred EEECCCCCCCCCC------------CccccCCCCCCeEE
Confidence 5788888766432 22467888875443
No 285
>PRK04351 hypothetical protein; Provisional
Probab=20.28 E-value=69 Score=18.53 Aligned_cols=32 Identities=25% Similarity=0.556 Sum_probs=20.7
Q ss_pred ceeCCCCCCCcCChHHHHHHHHhcCCCCceeccCCCcccc
Q psy10278 51 PYACPTCEFKTGDHNVLRKHVQRHMPVKKYQCTFCSYSCT 90 (110)
Q Consensus 51 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~p~~C~~C~~~f~ 90 (110)
.|.|..|+..+... +.+ ....|.|..|+-.+.
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~-n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRI-NTKRYRCGKCRGKLK 143 (149)
T ss_pred EEECCCCCCEeeee-------eec-CCCcEEeCCCCcEee
Confidence 48898898765332 122 236699999986554
No 286
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=20.21 E-value=1.7e+02 Score=18.32 Aligned_cols=13 Identities=23% Similarity=0.506 Sum_probs=8.2
Q ss_pred eeCCCCCCCcCCh
Q psy10278 52 YACPTCEFKTGDH 64 (110)
Q Consensus 52 ~~c~~c~~~~~~~ 64 (110)
..|..|+..+...
T Consensus 120 ~~C~~C~~~~~~~ 132 (244)
T PRK14138 120 YYCVRCGKRYTVE 132 (244)
T ss_pred eEECCCCCcccHH
Confidence 4677777766543
No 287
>KOG4602|consensus
Probab=20.12 E-value=36 Score=21.69 Aligned_cols=10 Identities=40% Similarity=1.175 Sum_probs=5.9
Q ss_pred ceeCCCCCCC
Q psy10278 51 PYACPTCEFK 60 (110)
Q Consensus 51 ~~~c~~c~~~ 60 (110)
.|.|++||..
T Consensus 268 ~YVCPiCGAT 277 (318)
T KOG4602|consen 268 SYVCPICGAT 277 (318)
T ss_pred hhcCcccccc
Confidence 3666666643
No 288
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=20.12 E-value=50 Score=15.76 Aligned_cols=12 Identities=17% Similarity=0.523 Sum_probs=5.0
Q ss_pred eeccCCCccccc
Q psy10278 80 YQCTFCSYSCTE 91 (110)
Q Consensus 80 ~~C~~C~~~f~~ 91 (110)
..|+.|++.+..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 357777776554
Done!