Query psy6628
Match_columns 132
No_of_seqs 129 out of 1031
Neff 11.3
Searched_HMMs 46136
Date Fri Aug 16 23:03:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6628.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6628hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 7.8E-30 1.7E-34 157.0 6.1 107 9-125 159-265 (279)
2 KOG2462|consensus 100.0 2.3E-29 4.9E-34 155.0 5.8 117 9-132 128-244 (279)
3 KOG1074|consensus 99.7 3.8E-19 8.1E-24 123.7 1.9 53 75-127 605-657 (958)
4 KOG3576|consensus 99.7 1.6E-18 3.4E-23 103.3 2.6 113 9-129 115-238 (267)
5 KOG1074|consensus 99.7 1.2E-18 2.7E-23 121.2 2.3 56 76-131 880-935 (958)
6 KOG3623|consensus 99.7 1.9E-18 4.1E-23 119.0 1.6 111 9-125 208-331 (1007)
7 KOG3608|consensus 99.7 4.3E-17 9.4E-22 104.3 4.2 80 44-127 264-345 (467)
8 KOG3576|consensus 99.6 2.9E-17 6.4E-22 97.9 1.0 82 43-128 117-198 (267)
9 KOG3623|consensus 99.6 2.1E-16 4.6E-21 109.1 2.0 78 42-123 893-970 (1007)
10 KOG3608|consensus 99.5 4.3E-14 9.3E-19 90.8 6.7 111 11-129 263-378 (467)
11 PHA00733 hypothetical protein 99.3 2.8E-12 6.2E-17 73.2 4.8 84 41-129 38-125 (128)
12 PLN03086 PRLI-interacting fact 99.2 5.4E-11 1.2E-15 82.1 7.5 106 9-129 451-566 (567)
13 PHA02768 hypothetical protein; 99.2 1.5E-11 3.2E-16 59.0 2.0 43 75-119 5-47 (55)
14 PHA00733 hypothetical protein 99.0 3.8E-10 8.2E-15 64.5 4.4 84 10-100 39-124 (128)
15 PF13465 zf-H2C2_2: Zinc-finge 99.0 1.3E-10 2.9E-15 47.9 1.6 26 90-115 1-26 (26)
16 PHA00616 hypothetical protein 99.0 3E-10 6.5E-15 52.0 1.5 29 103-131 1-29 (44)
17 PLN03086 PRLI-interacting fact 98.9 1.9E-09 4.2E-14 74.7 4.6 78 44-131 454-541 (567)
18 PHA02768 hypothetical protein; 98.9 8.4E-10 1.8E-14 53.0 1.9 43 11-62 5-47 (55)
19 KOG3993|consensus 98.5 1.7E-08 3.8E-13 66.9 0.4 108 12-128 268-381 (500)
20 PF13465 zf-H2C2_2: Zinc-finge 98.5 3.8E-08 8.1E-13 40.5 1.3 25 61-86 1-25 (26)
21 PHA00732 hypothetical protein 98.5 6.5E-08 1.4E-12 50.6 2.4 46 44-98 2-47 (79)
22 PHA00616 hypothetical protein 98.5 4E-08 8.6E-13 45.0 1.4 39 75-113 1-39 (44)
23 KOG3993|consensus 98.5 2.3E-08 5E-13 66.3 0.3 114 11-127 295-482 (500)
24 PF05605 zf-Di19: Drought indu 98.5 3.8E-07 8.2E-12 44.4 4.2 51 75-128 2-54 (54)
25 PF00096 zf-C2H2: Zinc finger, 98.4 2.9E-07 6.4E-12 36.7 2.2 23 12-34 1-23 (23)
26 PF00096 zf-C2H2: Zinc finger, 98.4 1.6E-07 3.5E-12 37.4 1.2 22 104-125 1-22 (23)
27 PF09237 GAGA: GAGA factor; I 98.3 5.1E-07 1.1E-11 42.3 2.0 33 99-131 20-52 (54)
28 PF13894 zf-C2H2_4: C2H2-type 98.3 4.2E-07 9.2E-12 36.4 1.6 24 104-127 1-24 (24)
29 PHA00732 hypothetical protein 98.2 1.5E-06 3.2E-11 45.5 2.5 43 11-66 1-44 (79)
30 PF05605 zf-Di19: Drought indu 98.2 5E-06 1.1E-10 40.4 4.1 49 11-67 2-50 (54)
31 PF13894 zf-C2H2_4: C2H2-type 98.2 2.4E-06 5.2E-11 34.1 2.5 24 12-35 1-24 (24)
32 PF13912 zf-C2H2_6: C2H2-type 98.2 6.7E-07 1.5E-11 37.1 0.8 26 103-128 1-26 (27)
33 PF13912 zf-C2H2_6: C2H2-type 98.1 1.8E-06 3.8E-11 35.7 1.6 25 11-35 1-25 (27)
34 COG5189 SFP1 Putative transcri 98.0 2.2E-06 4.7E-11 55.4 0.7 52 73-124 347-419 (423)
35 PF09237 GAGA: GAGA factor; I 98.0 1.2E-05 2.6E-10 37.8 2.8 33 4-36 17-49 (54)
36 PF12756 zf-C2H2_2: C2H2 type 97.9 9.7E-06 2.1E-10 44.3 2.1 73 13-98 1-73 (100)
37 PF12756 zf-C2H2_2: C2H2 type 97.8 9.6E-06 2.1E-10 44.3 1.7 70 51-126 4-73 (100)
38 smart00355 ZnF_C2H2 zinc finge 97.7 3.3E-05 7.1E-10 31.2 1.9 23 104-126 1-23 (26)
39 PF13909 zf-H2C2_5: C2H2-type 97.6 3.7E-05 8.1E-10 30.7 1.6 24 104-128 1-24 (24)
40 smart00355 ZnF_C2H2 zinc finge 97.6 7.3E-05 1.6E-09 30.1 2.0 24 12-35 1-24 (26)
41 COG5189 SFP1 Putative transcri 97.6 2.3E-05 5E-10 50.8 0.5 70 9-96 347-419 (423)
42 PF12874 zf-met: Zinc-finger o 97.5 4.1E-05 8.9E-10 30.9 0.8 22 104-125 1-22 (25)
43 PF12874 zf-met: Zinc-finger o 97.3 0.0002 4.2E-09 28.8 1.8 23 12-34 1-23 (25)
44 PRK04860 hypothetical protein; 97.2 0.00019 4E-09 42.8 1.5 38 75-116 119-156 (160)
45 PF13909 zf-H2C2_5: C2H2-type 97.1 0.00069 1.5E-08 26.9 2.5 23 12-35 1-23 (24)
46 PF12171 zf-C2H2_jaz: Zinc-fin 97.0 0.00013 2.8E-09 30.1 -0.2 22 104-125 2-23 (27)
47 PF13913 zf-C2HC_2: zinc-finge 96.8 0.0012 2.6E-08 26.6 1.7 21 104-125 3-23 (25)
48 PF12171 zf-C2H2_jaz: Zinc-fin 96.7 0.00035 7.6E-09 28.7 -0.1 22 12-33 2-23 (27)
49 KOG2231|consensus 96.7 0.0043 9.3E-08 44.7 4.8 106 12-128 100-237 (669)
50 smart00451 ZnF_U1 U1-like zinc 96.2 0.0031 6.8E-08 27.4 1.3 23 103-125 3-25 (35)
51 COG4049 Uncharacterized protei 95.7 0.0068 1.5E-07 29.1 1.3 29 8-36 14-42 (65)
52 KOG2893|consensus 95.7 0.0035 7.5E-08 39.5 0.3 41 78-122 13-53 (341)
53 COG4049 Uncharacterized protei 95.6 0.0081 1.8E-07 28.8 1.4 29 99-127 13-41 (65)
54 cd00350 rubredoxin_like Rubred 95.6 0.0074 1.6E-07 26.0 1.2 24 76-111 2-25 (33)
55 smart00451 ZnF_U1 U1-like zinc 95.4 0.02 4.3E-07 24.7 2.2 23 11-33 3-25 (35)
56 KOG4173|consensus 95.1 0.014 3E-07 36.0 1.5 82 41-127 77-170 (253)
57 PRK04860 hypothetical protein; 95.1 0.03 6.5E-07 33.5 3.0 37 44-88 120-156 (160)
58 KOG1146|consensus 94.5 0.012 2.5E-07 45.5 0.3 25 101-125 516-540 (1406)
59 COG1592 Rubrerythrin [Energy p 93.9 0.036 7.7E-07 33.3 1.4 25 74-111 133-157 (166)
60 COG5236 Uncharacterized conser 93.1 0.16 3.4E-06 34.1 3.4 79 12-97 152-242 (493)
61 COG5048 FOG: Zn-finger [Genera 92.8 0.02 4.3E-07 39.2 -0.9 56 75-130 289-350 (467)
62 TIGR00622 ssl1 transcription f 92.8 0.31 6.8E-06 27.3 3.9 24 75-98 81-104 (112)
63 KOG4173|consensus 92.8 0.03 6.5E-07 34.6 -0.1 75 12-96 80-167 (253)
64 KOG1146|consensus 92.7 0.033 7E-07 43.3 -0.0 109 12-129 1229-1354(1406)
65 cd00729 rubredoxin_SM Rubredox 92.6 0.071 1.5E-06 23.1 1.0 24 76-111 3-26 (34)
66 PF02892 zf-BED: BED zinc fing 92.1 0.13 2.9E-06 23.6 1.7 28 100-127 13-44 (45)
67 PF04959 ARS2: Arsenite-resist 92.0 0.083 1.8E-06 33.2 1.2 30 101-130 75-104 (214)
68 KOG2893|consensus 91.0 0.059 1.3E-06 34.2 -0.2 46 14-70 13-58 (341)
69 PF05443 ROS_MUCR: ROS/MUCR tr 90.8 0.13 2.7E-06 29.8 1.0 27 101-130 70-96 (132)
70 PF09538 FYDLN_acid: Protein o 90.7 0.18 3.9E-06 28.1 1.6 30 44-88 10-39 (108)
71 KOG2186|consensus 90.7 0.14 3E-06 32.8 1.2 46 44-96 4-49 (276)
72 PF12907 zf-met2: Zinc-binding 90.6 0.068 1.5E-06 24.1 -0.1 27 104-130 2-31 (40)
73 KOG2482|consensus 89.9 0.42 9.2E-06 32.1 2.9 49 76-124 280-355 (423)
74 PF09986 DUF2225: Uncharacteri 89.9 0.049 1.1E-06 34.3 -1.3 14 103-116 48-61 (214)
75 smart00614 ZnF_BED BED zinc fi 89.2 0.3 6.6E-06 23.1 1.5 22 104-125 19-45 (50)
76 PF13717 zinc_ribbon_4: zinc-r 89.2 0.27 5.8E-06 21.6 1.2 11 75-85 25-35 (36)
77 smart00734 ZnF_Rad18 Rad18-lik 89.0 0.47 1E-05 19.2 1.8 19 13-32 3-21 (26)
78 PF12013 DUF3505: Protein of u 88.6 0.33 7.1E-06 27.1 1.6 25 104-128 81-109 (109)
79 COG2888 Predicted Zn-ribbon RN 88.5 0.68 1.5E-05 22.7 2.4 9 75-83 50-58 (61)
80 PRK00398 rpoP DNA-directed RNA 88.4 0.2 4.4E-06 23.2 0.6 8 104-111 22-29 (46)
81 KOG2482|consensus 87.6 1.4 3E-05 29.8 4.1 25 104-128 280-304 (423)
82 PF06524 NOA36: NOA36 protein; 86.3 0.4 8.7E-06 31.0 1.2 41 4-47 135-175 (314)
83 KOG2785|consensus 85.9 0.81 1.8E-05 31.2 2.4 79 44-125 4-90 (390)
84 TIGR02605 CxxC_CxxC_SSSS putat 85.6 0.23 5E-06 23.6 -0.1 11 44-57 6-16 (52)
85 COG5048 FOG: Zn-finger [Genera 85.5 0.29 6.3E-06 33.5 0.3 61 44-107 290-355 (467)
86 PF13719 zinc_ribbon_5: zinc-r 83.5 1 2.3E-05 19.8 1.5 10 76-85 26-35 (37)
87 TIGR00373 conserved hypothetic 82.9 1.3 2.9E-05 26.5 2.3 32 73-113 107-138 (158)
88 PF07754 DUF1610: Domain of un 82.7 0.87 1.9E-05 18.1 1.0 11 9-19 14-24 (24)
89 KOG4167|consensus 82.6 0.28 6.1E-06 36.2 -0.7 28 9-36 790-817 (907)
90 smart00659 RPOLCX RNA polymera 82.3 0.9 1.9E-05 20.9 1.1 8 76-83 20-27 (44)
91 PF13878 zf-C2H2_3: zinc-finge 81.6 1.7 3.8E-05 19.6 1.9 23 104-126 14-38 (41)
92 PRK00464 nrdR transcriptional 81.5 0.28 6.1E-06 29.2 -0.9 13 76-88 29-41 (154)
93 TIGR02300 FYDLN_acid conserved 81.3 1.2 2.7E-05 25.5 1.6 30 44-88 10-39 (129)
94 PRK14890 putative Zn-ribbon RN 80.3 1.8 3.9E-05 21.3 1.8 9 75-83 48-56 (59)
95 TIGR02098 MJ0042_CXXC MJ0042 f 79.9 1.4 3.1E-05 19.3 1.3 7 77-83 27-33 (38)
96 COG3357 Predicted transcriptio 79.8 1.3 2.8E-05 23.8 1.3 31 74-114 57-87 (97)
97 PF10571 UPF0547: Uncharacteri 79.7 1.1 2.3E-05 18.1 0.8 11 12-22 15-25 (26)
98 PRK06266 transcription initiat 79.5 1.9 4E-05 26.5 2.1 31 74-113 116-146 (178)
99 COG1997 RPL43A Ribosomal prote 78.5 1.1 2.4E-05 23.9 0.9 11 103-113 53-63 (89)
100 PF04780 DUF629: Protein of un 76.0 2.1 4.6E-05 30.3 1.8 26 102-127 56-81 (466)
101 KOG2231|consensus 75.9 11 0.00024 28.2 5.3 90 23-124 161-260 (669)
102 smart00531 TFIIE Transcription 74.9 6.2 0.00014 23.3 3.4 14 43-59 99-112 (147)
103 smart00834 CxxC_CXXC_SSSS Puta 74.8 1.7 3.6E-05 19.3 0.8 14 11-24 5-18 (41)
104 PF05191 ADK_lid: Adenylate ki 73.6 1.2 2.5E-05 19.6 0.1 8 77-84 23-30 (36)
105 COG5236 Uncharacterized conser 73.1 4.4 9.5E-05 27.6 2.7 75 45-128 222-306 (493)
106 PF13453 zf-TFIIB: Transcripti 73.0 7.1 0.00015 17.4 2.7 12 51-62 24-35 (41)
107 COG1996 RPC10 DNA-directed RNA 72.7 1.7 3.8E-05 20.5 0.6 8 76-83 25-32 (49)
108 PHA00626 hypothetical protein 72.3 1.8 3.9E-05 21.0 0.6 15 101-115 21-35 (59)
109 KOG2186|consensus 72.3 3 6.5E-05 27.0 1.7 46 12-67 4-49 (276)
110 PRK09678 DNA-binding transcrip 71.7 1.3 2.9E-05 22.8 0.1 16 73-88 25-42 (72)
111 PF04959 ARS2: Arsenite-resist 70.4 1.7 3.6E-05 27.5 0.3 27 73-99 75-101 (214)
112 KOG2785|consensus 70.3 5.3 0.00011 27.5 2.6 52 74-125 165-242 (390)
113 KOG4118|consensus 70.2 2.3 4.9E-05 21.3 0.7 27 104-130 39-65 (74)
114 PRK03824 hypA hydrogenase nick 70.0 1.7 3.6E-05 25.4 0.2 15 74-88 69-83 (135)
115 PF09723 Zn-ribbon_8: Zinc rib 69.8 2.4 5.3E-05 19.2 0.7 14 11-24 5-18 (42)
116 PF15269 zf-C2H2_7: Zinc-finge 68.1 3.2 7E-05 19.1 0.9 21 104-124 21-41 (54)
117 COG4957 Predicted transcriptio 67.1 2.6 5.7E-05 24.5 0.6 22 104-128 77-98 (148)
118 PF13451 zf-trcl: Probable zin 67.1 3.5 7.6E-05 19.5 1.0 14 9-22 2-15 (49)
119 PF04423 Rad50_zn_hook: Rad50 66.3 2.3 5E-05 20.4 0.3 11 105-115 22-32 (54)
120 PTZ00255 60S ribosomal protein 66.1 2.2 4.7E-05 23.0 0.2 11 103-113 54-64 (90)
121 smart00154 ZnF_AN1 AN1-like Zi 66.1 3.8 8.2E-05 18.3 0.9 14 11-24 12-25 (39)
122 PF08274 PhnA_Zn_Ribbon: PhnA 66.1 2.1 4.6E-05 18.0 0.1 7 104-110 20-26 (30)
123 KOG3408|consensus 66.0 4.1 8.9E-05 23.2 1.2 26 100-125 54-79 (129)
124 PF03604 DNA_RNApol_7kD: DNA d 65.5 3.1 6.7E-05 17.7 0.6 8 76-83 18-25 (32)
125 PF02176 zf-TRAF: TRAF-type zi 65.4 3.2 6.9E-05 20.1 0.7 27 88-114 23-53 (60)
126 PF02891 zf-MIZ: MIZ/SP-RING z 64.1 3.6 7.7E-05 19.5 0.7 9 103-111 41-49 (50)
127 KOG2807|consensus 62.8 14 0.0003 25.1 3.3 25 102-126 344-368 (378)
128 PLN02294 cytochrome c oxidase 62.8 3.6 7.7E-05 25.0 0.7 13 9-21 139-151 (174)
129 PF06397 Desulfoferrod_N: Desu 62.3 5.2 0.00011 17.6 1.0 13 9-21 4-16 (36)
130 COG1655 Uncharacterized protei 62.0 1.3 2.9E-05 28.2 -1.2 8 104-111 63-70 (267)
131 KOG0717|consensus 60.7 4.2 9E-05 28.8 0.8 22 104-125 293-314 (508)
132 TIGR00280 L37a ribosomal prote 59.2 2.9 6.2E-05 22.6 -0.1 10 76-85 54-63 (91)
133 PF01780 Ribosomal_L37ae: Ribo 59.2 1.8 3.9E-05 23.3 -0.9 10 104-113 54-63 (90)
134 KOG2593|consensus 58.1 4.8 0.0001 28.2 0.7 17 9-25 126-142 (436)
135 KOG1842|consensus 56.7 6.6 0.00014 27.8 1.2 26 75-100 15-40 (505)
136 PF09845 DUF2072: Zn-ribbon co 56.3 5.3 0.00012 23.2 0.6 15 11-25 1-15 (131)
137 PF10013 DUF2256: Uncharacteri 56.0 5 0.00011 18.3 0.4 12 105-116 10-21 (42)
138 PF08790 zf-LYAR: LYAR-type C2 56.0 1.7 3.7E-05 17.9 -1.0 8 78-85 3-10 (28)
139 COG3364 Zn-ribbon containing p 55.7 7.1 0.00015 21.6 1.0 16 10-25 1-16 (112)
140 PF10276 zf-CHCC: Zinc-finger 55.3 3.6 7.8E-05 18.5 -0.1 12 102-113 28-39 (40)
141 PF13824 zf-Mss51: Zinc-finger 53.9 12 0.00025 18.2 1.5 10 74-83 13-22 (55)
142 KOG4124|consensus 53.6 2.9 6.2E-05 28.5 -0.8 48 74-121 348-416 (442)
143 COG0068 HypF Hydrogenase matur 53.0 5.2 0.00011 30.0 0.3 55 51-113 128-183 (750)
144 KOG1842|consensus 52.9 8.4 0.00018 27.3 1.2 26 11-36 15-40 (505)
145 COG2331 Uncharacterized protei 51.9 11 0.00025 19.6 1.3 31 11-55 12-42 (82)
146 PF01428 zf-AN1: AN1-like Zinc 51.7 6.3 0.00014 17.9 0.4 15 10-24 12-26 (43)
147 PRK03976 rpl37ae 50S ribosomal 51.3 4.4 9.6E-05 21.9 -0.2 10 76-85 55-64 (90)
148 smart00440 ZnF_C2C2 C2C2 Zinc 50.3 1.5 3.2E-05 19.7 -1.8 9 76-84 29-37 (40)
149 PF07975 C1_4: TFIIH C1-like d 50.3 3.2 6.8E-05 19.9 -0.8 25 74-98 20-44 (51)
150 PF14353 CpXC: CpXC protein 50.2 9.3 0.0002 21.9 1.0 13 11-23 38-50 (128)
151 COG4338 Uncharacterized protei 49.8 7.4 0.00016 18.2 0.4 12 14-25 15-26 (54)
152 TIGR00100 hypA hydrogenase nic 49.7 7.8 0.00017 21.9 0.6 25 75-111 70-94 (115)
153 cd00924 Cyt_c_Oxidase_Vb Cytoc 49.2 9.3 0.0002 21.0 0.8 18 97-115 74-91 (97)
154 KOG2907|consensus 49.1 6.7 0.00015 22.1 0.3 40 76-115 75-114 (116)
155 TIGR00319 desulf_FeS4 desulfof 49.1 11 0.00025 15.9 1.0 13 9-21 5-17 (34)
156 COG5151 SSL1 RNA polymerase II 48.9 14 0.0003 25.0 1.7 26 101-126 386-411 (421)
157 PF07800 DUF1644: Protein of u 48.3 61 0.0013 19.7 5.2 53 74-127 79-132 (162)
158 cd00974 DSRD Desulforedoxin (D 48.2 12 0.00025 15.9 0.9 12 10-21 3-14 (34)
159 KOG4727|consensus 47.3 13 0.00027 22.8 1.2 22 11-32 75-96 (193)
160 PF06220 zf-U1: U1 zinc finger 47.2 14 0.0003 16.3 1.1 22 103-124 3-26 (38)
161 PRK12380 hydrogenase nickel in 46.5 10 0.00022 21.4 0.8 25 75-111 70-94 (113)
162 KOG1280|consensus 46.4 26 0.00055 24.1 2.6 38 8-47 76-113 (381)
163 PTZ00448 hypothetical protein; 45.8 16 0.00036 25.2 1.7 23 11-33 314-336 (373)
164 COG5188 PRP9 Splicing factor 3 45.7 10 0.00022 26.1 0.7 24 102-125 237-260 (470)
165 COG1773 Rubredoxin [Energy pro 45.1 11 0.00023 18.4 0.6 13 11-23 3-15 (55)
166 cd00730 rubredoxin Rubredoxin; 45.1 9.7 0.00021 18.1 0.5 12 12-23 2-13 (50)
167 COG4530 Uncharacterized protei 44.9 12 0.00026 21.0 0.8 14 74-87 25-38 (129)
168 KOG2071|consensus 44.4 18 0.00039 26.7 1.8 27 101-127 416-442 (579)
169 PF00301 Rubredoxin: Rubredoxi 44.0 11 0.00024 17.6 0.6 12 12-23 2-13 (47)
170 PRK00432 30S ribosomal protein 43.3 13 0.00029 17.6 0.8 10 103-112 37-46 (50)
171 COG1594 RPB9 DNA-directed RNA 43.3 4.5 9.7E-05 22.9 -1.0 13 102-114 99-111 (113)
172 TIGR01206 lysW lysine biosynth 42.9 11 0.00023 18.3 0.4 11 11-21 2-12 (54)
173 KOG4167|consensus 42.8 6.9 0.00015 29.5 -0.3 26 102-127 791-816 (907)
174 COG4391 Uncharacterized protei 42.7 13 0.00028 18.5 0.7 44 68-115 17-60 (62)
175 TIGR00686 phnA alkylphosphonat 41.9 11 0.00024 21.1 0.4 12 76-87 20-31 (109)
176 PF04780 DUF629: Protein of un 41.2 29 0.00063 25.0 2.4 25 11-35 57-81 (466)
177 PF04810 zf-Sec23_Sec24: Sec23 40.6 4 8.8E-05 18.2 -1.2 9 102-110 23-31 (40)
178 KOG2636|consensus 40.6 23 0.00049 25.3 1.8 29 96-124 394-423 (497)
179 smart00586 ZnF_DBF Zinc finger 40.5 19 0.0004 17.1 1.0 21 101-124 3-23 (49)
180 KOG0717|consensus 40.2 21 0.00045 25.6 1.6 22 12-33 293-314 (508)
181 PF08792 A2L_zn_ribbon: A2L zi 39.5 19 0.00041 15.4 0.9 13 10-22 20-32 (33)
182 PRK00564 hypA hydrogenase nick 39.0 14 0.00029 21.1 0.5 13 75-87 71-83 (117)
183 KOG2071|consensus 38.5 23 0.00051 26.1 1.7 28 8-35 415-442 (579)
184 PF14803 Nudix_N_2: Nudix N-te 38.0 12 0.00025 16.2 0.1 7 14-20 3-9 (34)
185 PF01363 FYVE: FYVE zinc finge 37.9 19 0.00041 18.0 0.9 12 76-87 26-37 (69)
186 PF07282 OrfB_Zn_ribbon: Putat 37.2 53 0.0011 16.3 2.5 12 12-23 29-40 (69)
187 PF01155 HypA: Hydrogenase exp 37.1 12 0.00025 21.1 0.1 25 76-112 71-95 (113)
188 PF12760 Zn_Tnp_IS1595: Transp 36.6 10 0.00023 17.4 -0.2 8 75-82 37-44 (46)
189 COG3677 Transposase and inacti 36.5 19 0.00041 20.9 0.8 14 101-114 51-64 (129)
190 PF07535 zf-DBF: DBF zinc fing 35.9 31 0.00067 16.3 1.4 21 101-124 3-23 (49)
191 PF03884 DUF329: Domain of unk 35.3 20 0.00044 17.6 0.7 11 12-22 3-13 (57)
192 PF03811 Zn_Tnp_IS1: InsA N-te 35.2 7 0.00015 17.1 -0.8 8 74-81 28-35 (36)
193 PF06676 DUF1178: Protein of u 35.2 28 0.00061 20.8 1.4 48 44-96 6-53 (148)
194 PRK03681 hypA hydrogenase nick 35.1 13 0.00028 21.0 0.0 12 75-86 70-81 (114)
195 COG4888 Uncharacterized Zn rib 35.0 23 0.00049 19.6 0.9 16 8-23 19-34 (104)
196 PF07295 DUF1451: Protein of u 35.0 14 0.00031 21.9 0.2 28 74-111 111-138 (146)
197 COG1675 TFA1 Transcription ini 35.0 30 0.00064 21.4 1.5 7 104-110 133-139 (176)
198 TIGR00627 tfb4 transcription f 34.7 28 0.00061 23.2 1.5 24 76-113 256-279 (279)
199 PRK14873 primosome assembly pr 34.4 22 0.00047 26.9 1.1 11 102-112 421-431 (665)
200 KOG2857|consensus 33.9 21 0.00045 21.1 0.7 22 103-124 17-38 (157)
201 PHA02998 RNA polymerase subuni 33.3 6.2 0.00013 24.2 -1.5 14 102-115 170-183 (195)
202 PF11672 DUF3268: Protein of u 33.3 18 0.00039 20.1 0.4 7 104-110 32-38 (102)
203 PF01286 XPA_N: XPA protein N- 33.2 18 0.00039 15.7 0.3 12 105-116 5-16 (34)
204 PTZ00043 cytochrome c oxidase 33.1 19 0.00041 23.1 0.5 17 7-23 177-193 (268)
205 COG5216 Uncharacterized conser 33.1 23 0.00049 17.5 0.7 29 44-82 23-51 (67)
206 PF08271 TF_Zn_Ribbon: TFIIB z 32.9 24 0.00051 15.9 0.7 9 12-20 1-9 (43)
207 PF04438 zf-HIT: HIT zinc fing 32.9 44 0.00096 13.9 1.5 16 9-24 11-26 (30)
208 PLN03238 probable histone acet 32.8 30 0.00066 23.2 1.4 22 75-96 48-69 (290)
209 PF13821 DUF4187: Domain of un 32.5 25 0.00054 17.1 0.8 18 102-119 26-43 (55)
210 PF11931 DUF3449: Domain of un 31.3 16 0.00035 22.9 0.0 9 102-110 100-108 (196)
211 TIGR03831 YgiT_finger YgiT-typ 31.3 22 0.00047 15.9 0.4 11 12-22 33-43 (46)
212 PF02591 DUF164: Putative zinc 30.7 38 0.00083 16.2 1.3 12 9-20 44-55 (56)
213 COG2879 Uncharacterized small 30.7 43 0.00093 16.8 1.4 16 116-131 25-40 (65)
214 PLN03238 probable histone acet 30.6 69 0.0015 21.6 2.8 25 8-32 45-69 (290)
215 PRK01343 zinc-binding protein; 30.6 31 0.00068 16.9 0.9 12 11-22 9-20 (57)
216 PF14369 zf-RING_3: zinc-finge 30.4 24 0.00051 15.3 0.5 10 13-22 23-32 (35)
217 PLN02748 tRNA dimethylallyltra 29.6 40 0.00086 24.4 1.7 24 74-97 417-441 (468)
218 PF05495 zf-CHY: CHY zinc fing 29.4 9.6 0.00021 19.5 -1.0 9 103-111 61-69 (71)
219 cd00065 FYVE FYVE domain; Zinc 29.3 45 0.00098 15.7 1.4 12 76-87 19-30 (57)
220 PRK10220 hypothetical protein; 29.2 40 0.00087 19.0 1.3 11 13-23 5-15 (111)
221 COG5112 UFD2 U1-like Zn-finger 29.1 28 0.00061 19.5 0.7 24 102-125 54-77 (126)
222 PRK05452 anaerobic nitric oxid 29.1 19 0.00041 25.9 0.1 39 73-111 423-466 (479)
223 PRK00420 hypothetical protein; 29.1 31 0.00066 19.6 0.9 12 75-86 40-51 (112)
224 PF05129 Elf1: Transcription e 28.9 23 0.0005 18.7 0.4 9 10-18 21-29 (81)
225 KOG1994|consensus 28.9 20 0.00044 23.0 0.2 24 100-123 236-259 (268)
226 PF01927 Mut7-C: Mut7-C RNAse 28.4 23 0.0005 20.9 0.3 39 76-114 92-135 (147)
227 COG1198 PriA Primosomal protei 28.4 14 0.0003 28.2 -0.7 8 14-21 438-445 (730)
228 PF14311 DUF4379: Domain of un 27.9 27 0.00058 16.7 0.4 17 102-118 27-43 (55)
229 KOG0320|consensus 27.6 30 0.00065 21.4 0.7 15 102-116 166-180 (187)
230 PF08209 Sgf11: Sgf11 (transcr 27.3 44 0.00096 14.3 1.0 11 11-21 4-14 (33)
231 PRK00762 hypA hydrogenase nick 27.3 22 0.00047 20.5 0.1 31 75-111 70-100 (124)
232 PF14255 Cys_rich_CPXG: Cystei 27.3 30 0.00065 16.6 0.5 10 105-114 2-11 (52)
233 KOG2272|consensus 27.0 67 0.0015 21.2 2.2 16 73-88 219-234 (332)
234 TIGR03830 CxxCG_CxxCG_HTH puta 27.0 70 0.0015 18.0 2.2 22 11-32 31-52 (127)
235 COG1656 Uncharacterized conser 26.5 66 0.0014 19.7 2.0 10 51-60 135-144 (165)
236 PF02748 PyrI_C: Aspartate car 26.5 35 0.00077 16.3 0.7 16 8-23 32-47 (52)
237 PF05741 zf-nanos: Nanos RNA b 26.3 24 0.00053 17.2 0.1 9 12-20 34-42 (55)
238 PF05290 Baculo_IE-1: Baculovi 26.2 29 0.00064 20.3 0.5 58 10-90 79-136 (140)
239 smart00064 FYVE Protein presen 26.0 43 0.00094 16.6 1.1 29 44-88 11-39 (68)
240 TIGR03829 YokU_near_AblA uncha 26.0 48 0.001 18.0 1.2 20 12-31 36-55 (89)
241 PF10263 SprT-like: SprT-like 25.5 27 0.00059 20.6 0.3 32 75-114 123-154 (157)
242 PRK08222 hydrogenase 4 subunit 24.9 50 0.0011 20.4 1.3 21 101-121 112-132 (181)
243 PF13248 zf-ribbon_3: zinc-rib 24.8 28 0.0006 13.7 0.2 6 14-19 19-24 (26)
244 PF12773 DZR: Double zinc ribb 24.3 51 0.0011 15.1 1.1 8 77-84 31-38 (50)
245 PF01215 COX5B: Cytochrome c o 24.3 22 0.00049 20.9 -0.2 18 97-115 107-124 (136)
246 smart00132 LIM Zinc-binding do 24.0 36 0.00077 14.1 0.5 11 12-22 28-38 (39)
247 PF14354 Lar_restr_allev: Rest 23.8 36 0.00077 16.5 0.5 8 12-19 4-11 (61)
248 PF12230 PRP21_like_P: Pre-mRN 23.8 26 0.00057 22.4 0.0 27 9-36 166-192 (229)
249 COG4306 Uncharacterized protei 23.6 64 0.0014 18.7 1.5 61 22-88 21-81 (160)
250 PLN00104 MYST -like histone ac 23.4 41 0.00088 24.2 0.8 25 101-125 196-220 (450)
251 PF11789 zf-Nse: Zinc-finger o 23.2 30 0.00065 16.8 0.1 30 75-108 24-53 (57)
252 PF14787 zf-CCHC_5: GAG-polypr 23.1 45 0.00097 14.7 0.7 13 13-25 4-16 (36)
253 PF14690 zf-ISL3: zinc-finger 22.9 45 0.00097 15.0 0.7 9 103-111 2-10 (47)
254 PTZ00064 histone acetyltransfe 22.6 48 0.001 24.2 1.1 25 101-125 278-302 (552)
255 COG0675 Transposase and inacti 22.6 43 0.00094 22.4 0.9 11 76-86 323-333 (364)
256 PF03107 C1_2: C1 domain; Int 22.6 43 0.00092 13.7 0.5 10 104-113 1-10 (30)
257 PF14375 Cys_rich_CWC: Cystein 22.5 50 0.0011 15.5 0.8 11 14-24 1-11 (50)
258 smart00661 RPOL9 RNA polymeras 22.4 52 0.0011 15.2 0.9 13 10-22 19-31 (52)
259 PF14447 Prok-RING_4: Prokaryo 22.4 44 0.00095 16.3 0.6 11 12-22 40-50 (55)
260 PF07649 C1_3: C1-like domain; 22.3 57 0.0012 13.2 0.9 12 10-21 14-25 (30)
261 COG3091 SprT Zn-dependent meta 22.1 31 0.00067 20.7 0.1 34 74-112 116-149 (156)
262 PLN03239 histone acetyltransfe 21.5 93 0.002 21.6 2.2 25 9-33 104-128 (351)
263 COG1885 Uncharacterized protei 21.0 50 0.0011 18.4 0.7 13 12-24 50-62 (115)
264 COG1998 RPS31 Ribosomal protei 20.9 45 0.00097 15.9 0.5 9 103-111 37-45 (51)
265 KOG0562|consensus 20.3 94 0.002 19.1 1.8 29 101-129 151-179 (184)
266 PF13696 zf-CCHC_2: Zinc knuck 20.2 43 0.00093 14.3 0.3 11 10-20 7-17 (32)
267 COG3024 Uncharacterized protei 20.1 59 0.0013 16.4 0.8 13 11-23 7-19 (65)
No 1
>KOG2462|consensus
Probab=99.96 E-value=7.8e-30 Score=157.04 Aligned_cols=107 Identities=31% Similarity=0.646 Sum_probs=89.2
Q ss_pred ceeeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccCh
Q psy6628 9 RVVFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSK 88 (132)
Q Consensus 9 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~ 88 (132)
.+.+.|+.||++|.+..+|..|+++|.. +..|. +||+.|...+.|+.|+ +.|+|+|||.|..|+++|.+.
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~l------~c~C~---iCGKaFSRPWLLQGHi-RTHTGEKPF~C~hC~kAFADR 228 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHTL------PCECG---ICGKAFSRPWLLQGHI-RTHTGEKPFSCPHCGKAFADR 228 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccCC------Ccccc---cccccccchHHhhccc-ccccCCCCccCCcccchhcch
Confidence 5567788888888888888888888753 27777 8888888888888888 778888888888888888888
Q ss_pred hhHHHHHHHhcCCCCccCCCchhccccchHHHHHHHh
Q psy6628 89 YDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 89 ~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
++|+.||++|.+.|.|+|+.|+|.|+..+.|.+|...
T Consensus 229 SNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 229 SNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred HHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 8888888888888888888888888888888888754
No 2
>KOG2462|consensus
Probab=99.96 E-value=2.3e-29 Score=155.03 Aligned_cols=117 Identities=29% Similarity=0.631 Sum_probs=107.3
Q ss_pred ceeeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccCh
Q psy6628 9 RVVFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSK 88 (132)
Q Consensus 9 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~ 88 (132)
...|.|++||+.+....+|.+|..+|....+. ..+.|+ .|++.|.....|..|+ ++|+ -+++|.+||+.|...
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~-ka~~C~---~C~K~YvSmpALkMHi-rTH~--l~c~C~iCGKaFSRP 200 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSK-KAFSCK---YCGKVYVSMPALKMHI-RTHT--LPCECGICGKAFSRP 200 (279)
T ss_pred CCceeccccccccccccccchhhccccccccc-ccccCC---CCCceeeehHHHhhHh-hccC--CCcccccccccccch
Confidence 34599999999999999999999999876644 448999 9999999999999998 6676 578999999999999
Q ss_pred hhHHHHHHHhcCCCCccCCCchhccccchHHHHHHHhhhhhccC
Q psy6628 89 YDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRHRRSLHQMYEQ 132 (132)
Q Consensus 89 ~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 132 (132)
+.|..|+++|+|||||.|+.|++.|+++++|+.|+..|.+.|+|
T Consensus 201 WLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~ 244 (279)
T KOG2462|consen 201 WLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKH 244 (279)
T ss_pred HHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccc
Confidence 99999999999999999999999999999999999999988875
No 3
>KOG1074|consensus
Probab=99.75 E-value=3.8e-19 Score=123.69 Aligned_cols=53 Identities=30% Similarity=0.636 Sum_probs=49.8
Q ss_pred CccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccccchHHHHHHHhhh
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRHRRSLH 127 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 127 (132)
|-+|..|.+++.-.+.|..|.++|+||+||+|.+|++.|+.+.+|+.|+.+|-
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccc
Confidence 45899999999999999999999999999999999999999999999998753
No 4
>KOG3576|consensus
Probab=99.73 E-value=1.6e-18 Score=103.27 Aligned_cols=113 Identities=30% Similarity=0.588 Sum_probs=97.9
Q ss_pred ceeeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccCh
Q psy6628 9 RVVFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSK 88 (132)
Q Consensus 9 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~ 88 (132)
...|+|.+|++.|.-.+-|.+|+.-|... . .+.|. .|++.|.+...|.+|+ +.|+|.+||.|..|+++|...
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~v---k-r~lct---~cgkgfndtfdlkrh~-rthtgvrpykc~~c~kaftqr 186 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDV---K-RHLCT---FCGKGFNDTFDLKRHT-RTHTGVRPYKCSLCEKAFTQR 186 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHH---H-HHHHh---hccCcccchhhhhhhh-ccccCccccchhhhhHHHHhh
Confidence 44699999999999999999999888752 2 38998 8999999999999998 789999999999999999999
Q ss_pred hhHHHHHHH-h----------cCCCCccCCCchhccccchHHHHHHHhhhhh
Q psy6628 89 YDHKIHSRV-H----------TGEKPYACEFCPLTFRHSSHLFRHRRSLHQM 129 (132)
Q Consensus 89 ~~l~~h~~~-h----------~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 129 (132)
..|..|.+. | ..++.|.|..||.+-.....+..|++.+|..
T Consensus 187 csleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 187 CSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred ccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 999999763 2 2468899999999888888888898887753
No 5
>KOG1074|consensus
Probab=99.73 E-value=1.2e-18 Score=121.19 Aligned_cols=56 Identities=34% Similarity=0.595 Sum_probs=52.3
Q ss_pred ccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccccchHHHHHHHhhhhhcc
Q psy6628 76 YQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRHRRSLHQMYE 131 (132)
Q Consensus 76 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 131 (132)
..|.+|++.|...+.|..|+++|+++|||.|.+|++.|..+.+|+.|+..|+...|
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCC
Confidence 47999999999999999999999999999999999999999999999998876543
No 6
>KOG3623|consensus
Probab=99.71 E-value=1.9e-18 Score=119.02 Aligned_cols=111 Identities=32% Similarity=0.687 Sum_probs=96.3
Q ss_pred ceeeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCC-------------CCC
Q psy6628 9 RVVFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQK-------------EKP 75 (132)
Q Consensus 9 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~-------------~~~ 75 (132)
....+|++|++.+.....|.+|+...+.. ..+.|.|. .|..+|.+...|.+|+ ..|.. .+.
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhek--ne~nfsC~---lCsytFAyRtQLErhm-~~hkpg~dqa~sltqsa~lRK 281 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEK--NEPNFSCM---LCSYTFAYRTQLERHM-QLHKPGGDQAISLTQSALLRK 281 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhh--CCCCCcch---hhhhhhhhHHHHHHHH-HhhcCCCcccccccchhhhcc
Confidence 34578999999999999999999866543 33458999 9999999999999998 55532 367
Q ss_pred ccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccccchHHHHHHHh
Q psy6628 76 YQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 76 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
|+|..|+++|+++-.|+.|+++|.|||||.|+-|++.|+...++-.|+..
T Consensus 282 FKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 282 FKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred ccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 99999999999999999999999999999999999999999988888754
No 7
>KOG3608|consensus
Probab=99.67 E-value=4.3e-17 Score=104.33 Aligned_cols=80 Identities=31% Similarity=0.708 Sum_probs=64.1
Q ss_pred cccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhHHHHHHHhcCCCCccCCC--chhccccchHHHH
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEF--CPLTFRHSSHLFR 121 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~--C~~~f~~~~~l~~ 121 (132)
|+|+ .|+......++|..|++..|...|||+|+.|.+.+...+.|.+|...|. +..|+|.. |..+|.+...+++
T Consensus 264 ykCp---lCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~ 339 (467)
T KOG3608|consen 264 YKCP---LCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRR 339 (467)
T ss_pred cccc---ccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHH
Confidence 7787 8888888888888898778888999999999999999999999988776 56666654 6666666666666
Q ss_pred HHHhhh
Q psy6628 122 HRRSLH 127 (132)
Q Consensus 122 H~~~~~ 127 (132)
|.+.+|
T Consensus 340 H~~evh 345 (467)
T KOG3608|consen 340 HFLEVH 345 (467)
T ss_pred HHHHhc
Confidence 666555
No 8
>KOG3576|consensus
Probab=99.65 E-value=2.9e-17 Score=97.89 Aligned_cols=82 Identities=35% Similarity=0.746 Sum_probs=77.5
Q ss_pred ccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccccchHHHHH
Q psy6628 43 RFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRH 122 (132)
Q Consensus 43 ~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H 122 (132)
.+.|. .|++.|.....|.+|+ .-|...+.+.|..||+.|....+|++|+++|+|.+||+|..|++.|+++.+|..|
T Consensus 117 ~ftCr---vCgK~F~lQRmlnrh~-kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 117 SFTCR---VCGKKFGLQRMLNRHL-KCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred eeeee---hhhhhhhHHHHHHHHh-hhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHH
Confidence 48888 9999999999999999 6788889999999999999999999999999999999999999999999999999
Q ss_pred HHhhhh
Q psy6628 123 RRSLHQ 128 (132)
Q Consensus 123 ~~~~~~ 128 (132)
++..||
T Consensus 193 l~kvhg 198 (267)
T KOG3576|consen 193 LKKVHG 198 (267)
T ss_pred HHHHcC
Confidence 988776
No 9
>KOG3623|consensus
Probab=99.61 E-value=2.1e-16 Score=109.13 Aligned_cols=78 Identities=36% Similarity=0.787 Sum_probs=72.6
Q ss_pred CccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccccchHHHH
Q psy6628 42 PRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFR 121 (132)
Q Consensus 42 ~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~ 121 (132)
..|.|. .|++.|.-.++|.+|. =.|+|++||+|..|.++|+.+-.|..|.+.|.|||||+|..|++.|+...+.-+
T Consensus 893 gmyaCD---qCDK~FqKqSSLaRHK-YEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQ 968 (1007)
T KOG3623|consen 893 GMYACD---QCDKAFQKQSSLARHK-YEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQ 968 (1007)
T ss_pred ccchHH---HHHHHHHhhHHHHHhh-hhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHh
Confidence 349999 9999999999999996 779999999999999999999999999999999999999999999999988888
Q ss_pred HH
Q psy6628 122 HR 123 (132)
Q Consensus 122 H~ 123 (132)
|+
T Consensus 969 HM 970 (1007)
T KOG3623|consen 969 HM 970 (1007)
T ss_pred hh
Confidence 87
No 10
>KOG3608|consensus
Probab=99.52 E-value=4.3e-14 Score=90.83 Aligned_cols=111 Identities=29% Similarity=0.578 Sum_probs=96.7
Q ss_pred eeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCc--ccccccCh
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQ--CSKSFFSK 88 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~--C~~~~~~~ 88 (132)
-|+|+.|+++....+.|..|++..+.. +.| |+|. .|+..+.....|..|. ..|. +..|.|.. |..++.+.
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~--dkp-fKCd---~Cd~~c~~esdL~kH~-~~HS-~~~y~C~h~~C~~s~r~~ 334 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSK--DKP-FKCD---ECDTRCVRESDLAKHV-QVHS-KTVYQCEHPDCHYSVRTY 334 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhcc--CCC-cccc---chhhhhccHHHHHHHH-Hhcc-ccceecCCCCCcHHHHHH
Confidence 489999999999999999999987663 444 9999 9999999999999998 6787 56799988 99999999
Q ss_pred hhHHHHHHHhc-C--CCCccCCCchhccccchHHHHHHHhhhhh
Q psy6628 89 YDHKIHSRVHT-G--EKPYACEFCPLTFRHSSHLFRHRRSLHQM 129 (132)
Q Consensus 89 ~~l~~h~~~h~-~--~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 129 (132)
..+.+|+..++ | +-+|.|..|++.|++-.+|..|+...|+-
T Consensus 335 ~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f 378 (467)
T KOG3608|consen 335 TQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGF 378 (467)
T ss_pred HHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcc
Confidence 99999997654 3 45799999999999999999999887763
No 11
>PHA00733 hypothetical protein
Probab=99.33 E-value=2.8e-12 Score=73.17 Aligned_cols=84 Identities=21% Similarity=0.388 Sum_probs=66.8
Q ss_pred CCccccCCCCCCcccccChHHHHhh--h--hhccCCCCCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccccc
Q psy6628 41 RPRFKCEGRGECDRVFTTRNMLNIH--I--KRDHQKEKPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHS 116 (132)
Q Consensus 41 ~~~~~c~~~~~c~~~~~~~~~l~~h--~--~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~ 116 (132)
...+.|. +|...|.....|..+ + ...+.+.++|.|..|++.|.....|..|+..+ +.++.|.+|++.|...
T Consensus 38 ~~~~~~~---~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 38 QKRLIRA---VVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNT 112 (128)
T ss_pred hhhHHHH---HHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCH
Confidence 3448888 788777766555444 1 02234578999999999999999999999876 4679999999999999
Q ss_pred hHHHHHHHhhhhh
Q psy6628 117 SHLFRHRRSLHQM 129 (132)
Q Consensus 117 ~~l~~H~~~~~~~ 129 (132)
..|..|+...|++
T Consensus 113 ~sL~~H~~~~h~~ 125 (128)
T PHA00733 113 DSTLDHVCKKHNI 125 (128)
T ss_pred HHHHHHHHHhcCc
Confidence 9999999887764
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.22 E-value=5.4e-11 Score=82.13 Aligned_cols=106 Identities=17% Similarity=0.400 Sum_probs=85.0
Q ss_pred ceeeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccC-
Q psy6628 9 RVVFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFS- 87 (132)
Q Consensus 9 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~- 87 (132)
++.+.|+.|++.|. ...|..|+.+++. ++.|+ |+..+ ....|..|+ ..+...+++.|..|+..+..
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~Hk------pv~Cp----Cg~~~-~R~~L~~H~-~thCp~Kpi~C~fC~~~v~~g 517 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFHE------PLQCP----CGVVL-EKEQMVQHQ-ASTCPLRLITCRFCGDMVQAG 517 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcCC------CccCC----CCCCc-chhHHHhhh-hccCCCCceeCCCCCCccccC
Confidence 44578999999996 6789999998752 38897 77554 567899998 77899999999999998852
Q ss_pred ---------hhhHHHHHHHhcCCCCccCCCchhccccchHHHHHHHhhhhh
Q psy6628 88 ---------KYDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRHRRSLHQM 129 (132)
Q Consensus 88 ---------~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 129 (132)
...|..|.... +.+++.|..|++.+..+ .+..|+...|.+
T Consensus 518 ~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~~ 566 (567)
T PLN03086 518 GSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAVHQK 566 (567)
T ss_pred ccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHhhcC
Confidence 34788898875 88999999999999876 567888777653
No 13
>PHA02768 hypothetical protein; Provisional
Probab=99.17 E-value=1.5e-11 Score=59.01 Aligned_cols=43 Identities=16% Similarity=0.360 Sum_probs=36.4
Q ss_pred CccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccccchHH
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHSSHL 119 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l 119 (132)
.|.|+.||+.|...+.|..|++.|+ ++++|..|++.|.+.+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 4788889999999999999998887 688888899988877765
No 14
>PHA00733 hypothetical protein
Probab=99.04 E-value=3.8e-10 Score=64.51 Aligned_cols=84 Identities=20% Similarity=0.256 Sum_probs=65.5
Q ss_pred eeeeCCCCccccCChhHHHHH--HHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccC
Q psy6628 10 VVFTCQVCSKIFSYENGLKAH--VRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFS 87 (132)
Q Consensus 10 ~~~~C~~C~~~f~~~~~l~~h--~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~ 87 (132)
+.+.|.+|.+.|.....|..+ +..+....+..+ |.|+ .|++.|.....|..|+ ..+ ..++.|..|++.|..
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kP-y~C~---~Cgk~Fss~s~L~~H~-r~h--~~~~~C~~CgK~F~~ 111 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSP-YVCP---LCLMPFSSSVSLKQHI-RYT--EHSKVCPVCGKEFRN 111 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCCCCC-ccCC---CCCCcCCCHHHHHHHH-hcC--CcCccCCCCCCccCC
Confidence 458899999998888877776 333322222444 9999 9999999999999998 544 357999999999999
Q ss_pred hhhHHHHHHHhcC
Q psy6628 88 KYDHKIHSRVHTG 100 (132)
Q Consensus 88 ~~~l~~h~~~h~~ 100 (132)
...|..|+...++
T Consensus 112 ~~sL~~H~~~~h~ 124 (128)
T PHA00733 112 TDSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHHhcC
Confidence 9999999876543
No 15
>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=99.03 E-value=1.3e-10 Score=47.94 Aligned_cols=26 Identities=46% Similarity=1.027 Sum_probs=21.8
Q ss_pred hHHHHHHHhcCCCCccCCCchhcccc
Q psy6628 90 DHKIHSRVHTGEKPYACEFCPLTFRH 115 (132)
Q Consensus 90 ~l~~h~~~h~~~~~~~C~~C~~~f~~ 115 (132)
+|..|++.|++++||.|++|++.|.+
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 16
>PHA00616 hypothetical protein
Probab=98.96 E-value=3e-10 Score=51.96 Aligned_cols=29 Identities=28% Similarity=0.502 Sum_probs=14.4
Q ss_pred CccCCCchhccccchHHHHHHHhhhhhcc
Q psy6628 103 PYACEFCPLTFRHSSHLFRHRRSLHQMYE 131 (132)
Q Consensus 103 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 131 (132)
||+|+.||+.|..+++|..|++.+||++|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 34455555555555555555555555443
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.91 E-value=1.9e-09 Score=74.65 Aligned_cols=78 Identities=19% Similarity=0.432 Sum_probs=61.9
Q ss_pred cccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccc---------
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFR--------- 114 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~--------- 114 (132)
+.|+ .|+..|. ...|..|+ ..+. +++.|+ |+..+ ....|..|+..|..++++.|+.|++.|.
T Consensus 454 ~~C~---~Cgk~f~-~s~LekH~-~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~ 524 (567)
T PLN03086 454 VHCE---KCGQAFQ-QGEMEKHM-KVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVR 524 (567)
T ss_pred ccCC---CCCCccc-hHHHHHHH-HhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchh
Confidence 5666 8999886 56789998 4453 789999 99765 5689999999999999999999999984
Q ss_pred -cchHHHHHHHhhhhhcc
Q psy6628 115 -HSSHLFRHRRSLHQMYE 131 (132)
Q Consensus 115 -~~~~l~~H~~~~~~~~~ 131 (132)
..+.|..|.... |.++
T Consensus 525 d~~s~Lt~HE~~C-G~rt 541 (567)
T PLN03086 525 DRLRGMSEHESIC-GSRT 541 (567)
T ss_pred hhhhhHHHHHHhc-CCcc
Confidence 235788998774 5543
No 18
>PHA02768 hypothetical protein; Provisional
Probab=98.90 E-value=8.4e-10 Score=52.99 Aligned_cols=43 Identities=19% Similarity=0.544 Sum_probs=32.7
Q ss_pred eeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHH
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNML 62 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l 62 (132)
.|+|+.||+.|....+|..|+++|.. +++|. .|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k------~~kc~---~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNT------NLKLS---NCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCC------cccCC---cccceeccccee
Confidence 47888888888888888888888762 27787 788887766543
No 19
>KOG3993|consensus
Probab=98.54 E-value=1.7e-08 Score=66.87 Aligned_cols=108 Identities=20% Similarity=0.413 Sum_probs=68.8
Q ss_pred eeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCcc-CCcc-cc-cccCh
Q psy6628 12 FTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQ-CSQC-SK-SFFSK 88 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~-c~~C-~~-~~~~~ 88 (132)
|.|..|-..|.+...|.+|...-.... .|.|+ +|++.|.-..+|..|. +=|.-..... -..- .+ .....
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~v----EYrCP---EC~KVFsCPANLASHR-RWHKPR~eaa~a~~~P~k~~~~~r 339 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHV----EYRCP---ECDKVFSCPANLASHR-RWHKPRPEAAKAGSPPPKQAVETR 339 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEe----eecCC---cccccccCchhhhhhh-cccCCchhhhhcCCCChhhhhhhh
Confidence 789999999999999999987544322 38999 8999999999999886 4342111000 0000 00 00000
Q ss_pred hhHHHHHH---HhcCCCCccCCCchhccccchHHHHHHHhhhh
Q psy6628 89 YDHKIHSR---VHTGEKPYACEFCPLTFRHSSHLFRHRRSLHQ 128 (132)
Q Consensus 89 ~~l~~h~~---~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 128 (132)
.+.+-.. ....+..|.|..|+++|.....|++|+..|+.
T Consensus 340 -ae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 340 -AEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred -hhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 0000000 01224589999999999999999999988765
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.54 E-value=3.8e-08 Score=40.51 Aligned_cols=25 Identities=52% Similarity=0.975 Sum_probs=17.0
Q ss_pred HHHhhhhhccCCCCCccCCccccccc
Q psy6628 61 MLNIHIKRDHQKEKPYQCSQCSKSFF 86 (132)
Q Consensus 61 ~l~~h~~~~~~~~~~~~c~~C~~~~~ 86 (132)
+|..|+ ..|++++||.|+.|++.|.
T Consensus 1 ~l~~H~-~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHM-RTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHH-HHHSSSSSEEESSSSEEES
T ss_pred CHHHHh-hhcCCCCCCCCCCCcCeeC
Confidence 356676 5577777777777777664
No 21
>PHA00732 hypothetical protein
Probab=98.54 E-value=6.5e-08 Score=50.59 Aligned_cols=46 Identities=30% Similarity=0.512 Sum_probs=29.1
Q ss_pred cccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhHHHHHHHh
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHKIHSRVH 98 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h 98 (132)
|.|. .|++.|....+|..|++..|. ++.|+.|++.|. .+..|..+.
T Consensus 2 y~C~---~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 2 FKCP---ICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred ccCC---CCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 5666 777777777777777632343 246777777776 355566443
No 22
>PHA00616 hypothetical protein
Probab=98.54 E-value=4e-08 Score=45.03 Aligned_cols=39 Identities=23% Similarity=0.342 Sum_probs=28.1
Q ss_pred CccCCcccccccChhhHHHHHHHhcCCCCccCCCchhcc
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTF 113 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f 113 (132)
||+|..||+.|...+.+..|+..|++++++.|..--..|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeEEEEEE
Confidence 467788888888888888888888877777776543333
No 23
>KOG3993|consensus
Probab=98.51 E-value=2.3e-08 Score=66.31 Aligned_cols=114 Identities=24% Similarity=0.401 Sum_probs=69.4
Q ss_pred eeeCCCCccccCChhHHHHHHHhhcCC-----C------------------------CCCCccccCCCCCCcccccChHH
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRNKHGS-----S------------------------EERPRFKCEGRGECDRVFTTRNM 61 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~~~~~-----~------------------------~~~~~~~c~~~~~c~~~~~~~~~ 61 (132)
.|.|++|+++|..-.+|..|.+=|... . .+..-|.|. .|++.|....-
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~---~C~KkFrRqAY 371 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCH---TCGKKFRRQAY 371 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecH---HhhhhhHHHHH
Confidence 499999999999999999999866410 0 001126666 78888888777
Q ss_pred HHhhhhhccCCCCC----------------c-----------------------------cCCcccccccChhhHHHHHH
Q psy6628 62 LNIHIKRDHQKEKP----------------Y-----------------------------QCSQCSKSFFSKYDHKIHSR 96 (132)
Q Consensus 62 l~~h~~~~~~~~~~----------------~-----------------------------~c~~C~~~~~~~~~l~~h~~ 96 (132)
|..|+...+..... + .++.++..+..+..-..+..
T Consensus 372 LrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~r 451 (500)
T KOG3993|consen 372 LRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGR 451 (500)
T ss_pred HHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCCCCCCcccCCCCCcccc
Confidence 77775222211100 0 12223322222222222222
Q ss_pred HhcCCCCccCCCchhccccchHHHHHHHhhh
Q psy6628 97 VHTGEKPYACEFCPLTFRHSSHLFRHRRSLH 127 (132)
Q Consensus 97 ~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 127 (132)
.-..+.-|.|.+|...|.+...|.+|+...|
T Consensus 452 lg~~~q~f~~ky~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 452 LGIAEQGFTCKYCPATFYSSPGLTRHINKCH 482 (500)
T ss_pred ccchhhccccccchHhhhcCcchHhHhhhcC
Confidence 2223456899999999999999999987644
No 24
>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=98.48 E-value=3.8e-07 Score=44.37 Aligned_cols=51 Identities=27% Similarity=0.518 Sum_probs=33.6
Q ss_pred CccCCcccccccChhhHHHHHHHh-cC-CCCccCCCchhccccchHHHHHHHhhhh
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVH-TG-EKPYACEFCPLTFRHSSHLFRHRRSLHQ 128 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h-~~-~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 128 (132)
.|.|+.|++ ..+...|..|.... .. .+.+.||+|...+. .+|..|+..+|+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 367777777 45566777776543 32 24678888887554 478888877664
No 25
>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=98.40 E-value=2.9e-07 Score=36.66 Aligned_cols=23 Identities=39% Similarity=0.905 Sum_probs=19.9
Q ss_pred eeCCCCccccCChhHHHHHHHhh
Q psy6628 12 FTCQVCSKIFSYENGLKAHVRNK 34 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~~~~ 34 (132)
|+|+.|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 68999999999999999998763
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=98.38 E-value=1.6e-07 Score=37.45 Aligned_cols=22 Identities=41% Similarity=0.803 Sum_probs=17.8
Q ss_pred ccCCCchhccccchHHHHHHHh
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
|.|++|++.|...+.|..|++.
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 5688888888888888888876
No 27
>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=98.30 E-value=5.1e-07 Score=42.28 Aligned_cols=33 Identities=30% Similarity=0.480 Sum_probs=22.5
Q ss_pred cCCCCccCCCchhccccchHHHHHHHhhhhhcc
Q psy6628 99 TGEKPYACEFCPLTFRHSSHLFRHRRSLHQMYE 131 (132)
Q Consensus 99 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 131 (132)
..+.|..|++|+..+.+..+|++|++..|+.||
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 346788888888888888888888888888876
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=98.30 E-value=4.2e-07 Score=36.42 Aligned_cols=24 Identities=38% Similarity=0.796 Sum_probs=17.9
Q ss_pred ccCCCchhccccchHHHHHHHhhh
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRSLH 127 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~~~ 127 (132)
|.|++|++.|.+...|..|+..+|
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 578888888888888888887765
No 29
>PHA00732 hypothetical protein
Probab=98.18 E-value=1.5e-06 Score=45.49 Aligned_cols=43 Identities=30% Similarity=0.603 Sum_probs=35.8
Q ss_pred eeeCCCCccccCChhHHHHHHHh-hcCCCCCCCccccCCCCCCcccccChHHHHhhh
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRN-KHGSSEERPRFKCEGRGECDRVFTTRNMLNIHI 66 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~-~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~ 66 (132)
+|.|..|++.|.....|..|++. |.+ +.|+ .|++.|.. +..|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~-------~~C~---~CgKsF~~---l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL-------TKCP---VCNKSYRR---LNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC-------CccC---CCCCEeCC---hhhhh
Confidence 58899999999999999999985 432 5788 99999984 66676
No 30
>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=98.17 E-value=5e-06 Score=40.41 Aligned_cols=49 Identities=31% Similarity=0.513 Sum_probs=30.8
Q ss_pred eeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhh
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIK 67 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~ 67 (132)
.|.||.|++ ..+...|..|....+... ...+.|| +|...+. .+|..|+.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~--~~~v~CP---iC~~~~~--~~l~~Hl~ 50 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSE--SKNVVCP---ICSSRVT--DNLIRHLN 50 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCC--CCCccCC---Cchhhhh--hHHHHHHH
Confidence 477888888 445677888877655432 1237788 7766433 36666763
No 31
>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=98.17 E-value=2.4e-06 Score=34.12 Aligned_cols=24 Identities=38% Similarity=0.927 Sum_probs=18.9
Q ss_pred eeCCCCccccCChhHHHHHHHhhc
Q psy6628 12 FTCQVCSKIFSYENGLKAHVRNKH 35 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~~~~~ 35 (132)
|.|++|+..|.+...|..|+..++
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 689999999999999999988763
No 32
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=98.17 E-value=6.7e-07 Score=37.06 Aligned_cols=26 Identities=38% Similarity=0.680 Sum_probs=20.2
Q ss_pred CccCCCchhccccchHHHHHHHhhhh
Q psy6628 103 PYACEFCPLTFRHSSHLFRHRRSLHQ 128 (132)
Q Consensus 103 ~~~C~~C~~~f~~~~~l~~H~~~~~~ 128 (132)
||.|.+|++.|.....|..|++.|++
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 57788888888888888888877654
No 33
>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=98.11 E-value=1.8e-06 Score=35.75 Aligned_cols=25 Identities=36% Similarity=0.692 Sum_probs=21.2
Q ss_pred eeeCCCCccccCChhHHHHHHHhhc
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRNKH 35 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~~~ 35 (132)
+|+|..|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5889999999999999999987764
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.97 E-value=2.2e-06 Score=55.37 Aligned_cols=52 Identities=35% Similarity=0.756 Sum_probs=43.1
Q ss_pred CCCccCCc--ccccccChhhHHHHHHH-h------------------cCCCCccCCCchhccccchHHHHHHH
Q psy6628 73 EKPYQCSQ--CSKSFFSKYDHKIHSRV-H------------------TGEKPYACEFCPLTFRHSSHLFRHRR 124 (132)
Q Consensus 73 ~~~~~c~~--C~~~~~~~~~l~~h~~~-h------------------~~~~~~~C~~C~~~f~~~~~l~~H~~ 124 (132)
.|||.|++ |.+.+.+...|+-|+.. | ..+|||.|++|++.|.....|+-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 48999988 99999999999988763 2 12589999999999999999887753
No 35
>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=97.96 E-value=1.2e-05 Score=37.76 Aligned_cols=33 Identities=18% Similarity=0.402 Sum_probs=21.5
Q ss_pred cccccceeeeCCCCccccCChhHHHHHHHhhcC
Q psy6628 4 VHNIHRVVFTCQVCSKIFSYENGLKAHVRNKHG 36 (132)
Q Consensus 4 ~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~ 36 (132)
.+..++.+.+|++|+.++.+..+|++|+...++
T Consensus 17 ~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 17 SKSQSEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp CCCTTS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred HhhccCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 455677788888888888888888888877665
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.87 E-value=9.7e-06 Score=44.31 Aligned_cols=73 Identities=26% Similarity=0.508 Sum_probs=19.6
Q ss_pred eCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhHH
Q psy6628 13 TCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHK 92 (132)
Q Consensus 13 ~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l~ 92 (132)
.|..|+..|.+...|..|+...++. ..+ .. ..+.....+...+ . ..-...+.|..|++.|.+...|.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~-------~~~---~~-~~l~~~~~~~~~~-~-~~~~~~~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGF-------DIP---DQ-KYLVDPNRLLNYL-R-KKVKESFRCPYCNKTFRSREALQ 67 (100)
T ss_dssp -------------------------------------------------------------SSEEBSSSS-EESSHHHHH
T ss_pred Ccccccccccccccccccccccccc-------ccc---cc-ccccccccccccc-c-cccCCCCCCCccCCCCcCHHHHH
Confidence 4889999999999999998766652 111 01 1111222233332 1 11122578999998898888899
Q ss_pred HHHHHh
Q psy6628 93 IHSRVH 98 (132)
Q Consensus 93 ~h~~~h 98 (132)
.|+..+
T Consensus 68 ~Hm~~~ 73 (100)
T PF12756_consen 68 EHMRSK 73 (100)
T ss_dssp HHHHHT
T ss_pred HHHcCc
Confidence 998864
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.84 E-value=9.6e-06 Score=44.33 Aligned_cols=70 Identities=27% Similarity=0.429 Sum_probs=21.7
Q ss_pred CCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccccchHHHHHHHhh
Q psy6628 51 ECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRHRRSL 126 (132)
Q Consensus 51 ~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 126 (132)
.|+..|.....|..|+...|.-..+ ....+.....+..+..... ...+.|.+|++.|.+...|..|++.+
T Consensus 4 ~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 4 FCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ---------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccc-----ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 8999999999999998665643322 1111223333333333222 23799999999999999999999864
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.70 E-value=3.3e-05 Score=31.18 Aligned_cols=23 Identities=35% Similarity=0.621 Sum_probs=19.3
Q ss_pred ccCCCchhccccchHHHHHHHhh
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRSL 126 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~~ 126 (132)
|.|+.|++.|...+.|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 57888999999999999998754
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.64 E-value=3.7e-05 Score=30.73 Aligned_cols=24 Identities=33% Similarity=0.672 Sum_probs=17.2
Q ss_pred ccCCCchhccccchHHHHHHHhhhh
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRSLHQ 128 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~~~~ 128 (132)
|+|+.|+.... .+.|..|++.+|+
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 7788888887764
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.57 E-value=7.3e-05 Score=30.09 Aligned_cols=24 Identities=33% Similarity=0.834 Sum_probs=19.1
Q ss_pred eeCCCCccccCChhHHHHHHHhhc
Q psy6628 12 FTCQVCSKIFSYENGLKAHVRNKH 35 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~~~~~ 35 (132)
|.|+.|++.|.....|..|+..|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 568888888888888888887553
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.55 E-value=2.3e-05 Score=50.78 Aligned_cols=70 Identities=29% Similarity=0.525 Sum_probs=42.4
Q ss_pred ceeeeCCC--CccccCChhHHHHHHHhhcCCCCCCC-ccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccc
Q psy6628 9 RVVFTCQV--CSKIFSYENGLKAHVRNKHGSSEERP-RFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSF 85 (132)
Q Consensus 9 ~~~~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~~-~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~ 85 (132)
+++|+|++ |.+.+.+...|+=|+.--+. .... +-.-+ +--. ......|||+|.+|++.+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~--~~~~~~~p~p---~~~~-------------~F~~~~KPYrCevC~KRY 408 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQ--NQKLHENPSP---EKMN-------------IFSAKDKPYRCEVCDKRY 408 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhcccc--CcccCCCCCc---cccc-------------cccccCCceeccccchhh
Confidence 37788877 77777777777777532111 0000 00011 1101 123456899999999999
Q ss_pred cChhhHHHHHH
Q psy6628 86 FSKYDHKIHSR 96 (132)
Q Consensus 86 ~~~~~l~~h~~ 96 (132)
++...|+-|..
T Consensus 409 KNlNGLKYHr~ 419 (423)
T COG5189 409 KNLNGLKYHRK 419 (423)
T ss_pred ccCccceeccc
Confidence 99988888764
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.51 E-value=4.1e-05 Score=30.89 Aligned_cols=22 Identities=32% Similarity=0.736 Sum_probs=17.5
Q ss_pred ccCCCchhccccchHHHHHHHh
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
|.|.+|.+.|.+...+..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 5688888888888888888765
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.32 E-value=0.0002 Score=28.83 Aligned_cols=23 Identities=52% Similarity=1.051 Sum_probs=18.2
Q ss_pred eeCCCCccccCChhHHHHHHHhh
Q psy6628 12 FTCQVCSKIFSYENGLKAHVRNK 34 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~~~~ 34 (132)
|.|.+|++.|.+...|..|++.+
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 57888888888888888887643
No 44
>PRK04860 hypothetical protein; Provisional
Probab=97.20 E-value=0.00019 Score=42.79 Aligned_cols=38 Identities=34% Similarity=0.766 Sum_probs=32.9
Q ss_pred CccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccccc
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHS 116 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~ 116 (132)
+|.|. |+. ....+.+|.+++.++++|.|..|+..|...
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 987 666789999999999999999999988754
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.13 E-value=0.00069 Score=26.92 Aligned_cols=23 Identities=35% Similarity=0.736 Sum_probs=16.4
Q ss_pred eeCCCCccccCChhHHHHHHHhhc
Q psy6628 12 FTCQVCSKIFSYENGLKAHVRNKH 35 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~~~~~ 35 (132)
|.|+.|+.... ...|..|+..++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 67888888777 778888887754
No 46
>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=97.04 E-value=0.00013 Score=30.05 Aligned_cols=22 Identities=27% Similarity=0.635 Sum_probs=15.5
Q ss_pred ccCCCchhccccchHHHHHHHh
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
|.|.+|++.|.+...+..|++.
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 5677777777777777777654
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.78 E-value=0.0012 Score=26.61 Aligned_cols=21 Identities=24% Similarity=0.616 Sum_probs=15.0
Q ss_pred ccCCCchhccccchHHHHHHHh
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
..|+.|++.| ..+.|.+|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4688888888 56667777654
No 48
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.73 E-value=0.00035 Score=28.72 Aligned_cols=22 Identities=50% Similarity=0.969 Sum_probs=15.4
Q ss_pred eeCCCCccccCChhHHHHHHHh
Q psy6628 12 FTCQVCSKIFSYENGLKAHVRN 33 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~~~ 33 (132)
|.|..|++.|.+...+..|+..
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 5677777777777777766543
No 49
>KOG2231|consensus
Probab=96.67 E-value=0.0043 Score=44.75 Aligned_cols=106 Identities=25% Similarity=0.453 Sum_probs=64.6
Q ss_pred eeCCCCcccc---------------CChhHHHHHHHhhcCCCCCCCccccCCCC-------CCcccccChHHHHhhhhhc
Q psy6628 12 FTCQVCSKIF---------------SYENGLKAHVRNKHGSSEERPRFKCEGRG-------ECDRVFTTRNMLNIHIKRD 69 (132)
Q Consensus 12 ~~C~~C~~~f---------------~~~~~l~~h~~~~~~~~~~~~~~~c~~~~-------~c~~~~~~~~~l~~h~~~~ 69 (132)
+.|.+|+..| .....|+.|+..-+.. +.|..|. .+.+. .....|..|+..-
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~~------~~c~lC~~~~kif~~e~k~-Yt~~el~~h~~~g 172 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHKL------HLCSLCLQNLKIFINERKL-YTRAELNLHLMFG 172 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhhh------hccccccccceeeeeeeeh-ehHHHHHHHHhcC
Confidence 5677777665 3668899998544431 4444221 12222 2345567776322
Q ss_pred cCCCCC----ccCCcccccccChhhHHHHHHHhcCCCCccCCCc------hhccccchHHHHHHHhhhh
Q psy6628 70 HQKEKP----YQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFC------PLTFRHSSHLFRHRRSLHQ 128 (132)
Q Consensus 70 ~~~~~~----~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C------~~~f~~~~~l~~H~~~~~~ 128 (132)
-.++.. -.|..|...|.....|.+|+..++ |.|..| ...|.....|..|.+..|-
T Consensus 173 d~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~Hf 237 (669)
T KOG2231|consen 173 DPDDESCRGHPLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHF 237 (669)
T ss_pred CCccccccCCccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcCc
Confidence 221221 368889999999999999988654 455555 3466778888888877664
No 50
>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=96.18 E-value=0.0031 Score=27.39 Aligned_cols=23 Identities=22% Similarity=0.587 Sum_probs=19.1
Q ss_pred CccCCCchhccccchHHHHHHHh
Q psy6628 103 PYACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 103 ~~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
+|.|.+|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57899999999988888888764
No 51
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.69 E-value=0.0068 Score=29.11 Aligned_cols=29 Identities=24% Similarity=0.555 Sum_probs=23.5
Q ss_pred cceeeeCCCCccccCChhHHHHHHHhhcC
Q psy6628 8 HRVVFTCQVCSKIFSYENGLKAHVRNKHG 36 (132)
Q Consensus 8 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~ 36 (132)
++..+.||.||.+|....+..+|....++
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 66678899999999999889888876554
No 52
>KOG2893|consensus
Probab=95.66 E-value=0.0035 Score=39.45 Aligned_cols=41 Identities=22% Similarity=0.441 Sum_probs=24.0
Q ss_pred CCcccccccChhhHHHHHHHhcCCCCccCCCchhccccchHHHHH
Q psy6628 78 CSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRH 122 (132)
Q Consensus 78 c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H 122 (132)
|..|++.|..+..|.+|++. |.|+|.+|.+...+-..|..|
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceee
Confidence 55566666666666666653 446677776655444444444
No 53
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=95.60 E-value=0.0081 Score=28.85 Aligned_cols=29 Identities=31% Similarity=0.633 Sum_probs=18.7
Q ss_pred cCCCCccCCCchhccccchHHHHHHHhhh
Q psy6628 99 TGEKPYACEFCPLTFRHSSHLFRHRRSLH 127 (132)
Q Consensus 99 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 127 (132)
.||..+.|+.|++.|...-+..+|....|
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 45666777777777777666666655443
No 54
>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=95.60 E-value=0.0074 Score=26.03 Aligned_cols=24 Identities=25% Similarity=0.769 Sum_probs=14.5
Q ss_pred ccCCcccccccChhhHHHHHHHhcCCCCccCCCchh
Q psy6628 76 YQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPL 111 (132)
Q Consensus 76 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 111 (132)
|.|..||..+.... .++.|++|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 46677766653321 6677777764
No 55
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.37 E-value=0.02 Score=24.75 Aligned_cols=23 Identities=30% Similarity=0.723 Sum_probs=18.2
Q ss_pred eeeCCCCccccCChhHHHHHHHh
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRN 33 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~ 33 (132)
.|.|..|++.|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 47788888888888888888754
No 56
>KOG4173|consensus
Probab=95.10 E-value=0.014 Score=36.01 Aligned_cols=82 Identities=27% Similarity=0.466 Sum_probs=59.5
Q ss_pred CCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhHHHHHHH----------hcCCCCccCC--C
Q psy6628 41 RPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHKIHSRV----------HTGEKPYACE--F 108 (132)
Q Consensus 41 ~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~----------h~~~~~~~C~--~ 108 (132)
.+.+.|+.-+ |.++|........|..+.|. -.|.+|.+.|...--|-.|+.. ..|.-.|+|- .
T Consensus 77 ~~~~~cqvag-c~~~~d~lD~~E~hY~~~h~----~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEg 151 (253)
T KOG4173|consen 77 VPAFACQVAG-CCQVFDALDDYEHHYHTLHG----NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEG 151 (253)
T ss_pred cccccccccc-hHHHHhhhhhHHHhhhhccc----chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHh
Confidence 3457787554 77788877777888744443 3799999999988888888653 2355679994 4
Q ss_pred chhccccchHHHHHHHhhh
Q psy6628 109 CPLTFRHSSHLFRHRRSLH 127 (132)
Q Consensus 109 C~~~f~~~~~l~~H~~~~~ 127 (132)
|+-.|...-....|+-..|
T Consensus 152 Ct~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 152 CTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhhhhhhHHHHhc
Confidence 9999998888888875433
No 57
>PRK04860 hypothetical protein; Provisional
Probab=95.09 E-value=0.03 Score=33.53 Aligned_cols=37 Identities=24% Similarity=0.672 Sum_probs=27.0
Q ss_pred cccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccCh
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSK 88 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~ 88 (132)
|.|. |+. ...++..|. .+++++++|.|..|+..|...
T Consensus 120 Y~C~----C~~---~~~~~rrH~-ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 120 YRCK----CQE---HQLTVRRHN-RVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEcC----CCC---eeCHHHHHH-HHhcCCccEECCCCCceeEEe
Confidence 7774 654 445677887 778888888888888877654
No 58
>KOG1146|consensus
Probab=94.49 E-value=0.012 Score=45.49 Aligned_cols=25 Identities=32% Similarity=0.612 Sum_probs=20.0
Q ss_pred CCCccCCCchhccccchHHHHHHHh
Q psy6628 101 EKPYACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
.++|.|..|...++...+|-+|+..
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHH
Confidence 4678888888888888888888753
No 59
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=93.86 E-value=0.036 Score=33.31 Aligned_cols=25 Identities=32% Similarity=0.813 Sum_probs=20.2
Q ss_pred CCccCCcccccccChhhHHHHHHHhcCCCCccCCCchh
Q psy6628 74 KPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPL 111 (132)
Q Consensus 74 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 111 (132)
+.|.|.+||..+ .++.|.+||+|+.
T Consensus 133 ~~~vC~vCGy~~-------------~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYTH-------------EGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCcc-------------cCCCCCcCCCCCC
Confidence 369999998774 4578999999983
No 60
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.06 E-value=0.16 Score=34.13 Aligned_cols=79 Identities=23% Similarity=0.423 Sum_probs=40.3
Q ss_pred eeCCC--CccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCccccc------ChHHHHhhhhhccCCCCCc----cCC
Q psy6628 12 FTCQV--CSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFT------TRNMLNIHIKRDHQKEKPY----QCS 79 (132)
Q Consensus 12 ~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~------~~~~l~~h~~~~~~~~~~~----~c~ 79 (132)
|.||. |..+...-..|..|..+.++ .+.|..|..-.+.|+ ....|..|. .....+-.| .|.
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~------~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~-~~G~~e~GFKGHP~C~ 224 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG------FVLCSECIGNKKDFWNEIRLFRSSTLRDHK-NGGLEEEGFKGHPLCI 224 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC------cEEhHhhhcCcccCccceeeeecccccccc-cCCccccCcCCCchhh
Confidence 67776 66665556778888776554 144542211112222 223344443 222222112 466
Q ss_pred cccccccChhhHHHHHHH
Q psy6628 80 QCSKSFFSKYDHKIHSRV 97 (132)
Q Consensus 80 ~C~~~~~~~~~l~~h~~~ 97 (132)
.|..-|-....|.+|++.
T Consensus 225 FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 225 FCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hccceecChHHHHHHHHh
Confidence 677667677777777664
No 61
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.82 E-value=0.02 Score=39.17 Aligned_cols=56 Identities=32% Similarity=0.554 Sum_probs=43.8
Q ss_pred CccCCcccccccChhhHHHHHH--HhcCC--CCccCC--CchhccccchHHHHHHHhhhhhc
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSR--VHTGE--KPYACE--FCPLTFRHSSHLFRHRRSLHQMY 130 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~ 130 (132)
++.|..|...|.....+..|.. .|.++ +++.|+ .|++.|.....+..|...+.+..
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~ 350 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSIS 350 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCC
Confidence 5677778888888888888888 68888 888888 68888888888877776665543
No 62
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.77 E-value=0.31 Score=27.33 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=15.4
Q ss_pred CccCCcccccccChhhHHHHHHHh
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVH 98 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h 98 (132)
.|+|..|...|...-++..|...|
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ceeCCCCCCccccccchhhhhhcc
Confidence 466777777776666666665544
No 63
>KOG4173|consensus
Probab=92.76 E-value=0.03 Score=34.57 Aligned_cols=75 Identities=35% Similarity=0.690 Sum_probs=49.2
Q ss_pred eeCCC--CccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhcc---------CCCCCccCCc
Q psy6628 12 FTCQV--CSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDH---------QKEKPYQCSQ 80 (132)
Q Consensus 12 ~~C~~--C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~---------~~~~~~~c~~ 80 (132)
+.|++ |.++|....+...|-.+-++ ..|. .|.+.|+....|..|+...| .|..-|+|-+
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~-------~sCs---~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~Clv 149 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHG-------NSCS---FCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLV 149 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhccc-------chhH---HHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHH
Confidence 66776 55677666666666555444 5677 78888888877877764333 2344477755
Q ss_pred --ccccccChhhHHHHHH
Q psy6628 81 --CSKSFFSKYDHKIHSR 96 (132)
Q Consensus 81 --C~~~~~~~~~l~~h~~ 96 (132)
|+..|.....-..|+-
T Consensus 150 EgCt~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 150 EGCTEKFKTSRDRKDHMI 167 (253)
T ss_pred HhhhhhhhhhhhhhhHHH
Confidence 7777777766666653
No 64
>KOG1146|consensus
Probab=92.69 E-value=0.033 Score=43.26 Aligned_cols=109 Identities=18% Similarity=0.216 Sum_probs=69.1
Q ss_pred eeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhH
Q psy6628 12 FTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDH 91 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l 91 (132)
..|..|...|........+-.-........-.+.|. +|...+.....+. ++- ....|.|.+|...|.....+
T Consensus 1229 l~~~~~e~~f~~~~~~~~~a~~~~~~~~~sGe~~c~---~~~~~~~~~~~~~-~l~----~~~~~~~~~~~~~~~~~~~l 1300 (1406)
T KOG1146|consen 1229 LLPNALEQPFPQEPEPTATAPPKPPELPASGEGECG---AVDELLTPSFGIS-TLD----VTHRYLCRQCKMAFDGEAPL 1300 (1406)
T ss_pred ccHHhhhcCccCcccccccCCCCCCcCcCCCcchhh---hccccccCcccee-ecc----cchhHHHHHHHhhhcchhHH
Confidence 445556666655554433322111100111125666 7877777666555 442 23468999999999999999
Q ss_pred HHHHHHh-----------------cCCCCccCCCchhccccchHHHHHHHhhhhh
Q psy6628 92 KIHSRVH-----------------TGEKPYACEFCPLTFRHSSHLFRHRRSLHQM 129 (132)
Q Consensus 92 ~~h~~~h-----------------~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 129 (132)
..|.+.- ..-++| |..|...|.....|+.|+++.+.+
T Consensus 1301 ~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1301 TAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAHR 1354 (1406)
T ss_pred HHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhhc
Confidence 8887531 122456 999999999999999999875443
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=92.64 E-value=0.071 Score=23.11 Aligned_cols=24 Identities=25% Similarity=0.653 Sum_probs=14.9
Q ss_pred ccCCcccccccChhhHHHHHHHhcCCCCccCCCchh
Q psy6628 76 YQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPL 111 (132)
Q Consensus 76 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 111 (132)
|.|..||..+... +.|..|++|+.
T Consensus 3 ~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECC------------cCCCcCcCCCC
Confidence 6677777665332 24567777774
No 66
>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=92.07 E-value=0.13 Score=23.56 Aligned_cols=28 Identities=29% Similarity=0.586 Sum_probs=15.7
Q ss_pred CCCCccCCCchhcccc----chHHHHHHHhhh
Q psy6628 100 GEKPYACEFCPLTFRH----SSHLFRHRRSLH 127 (132)
Q Consensus 100 ~~~~~~C~~C~~~f~~----~~~l~~H~~~~~ 127 (132)
++.-..|..|++.+.. .+.|..|++..|
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 3455677777776654 477778875433
No 67
>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=92.00 E-value=0.083 Score=33.17 Aligned_cols=30 Identities=20% Similarity=0.418 Sum_probs=20.2
Q ss_pred CCCccCCCchhccccchHHHHHHHhhhhhc
Q psy6628 101 EKPYACEFCPLTFRHSSHLFRHRRSLHQMY 130 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 130 (132)
+.-|.|++|+|.|....-+++|+...|.++
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 345888888888888888888887776654
No 68
>KOG2893|consensus
Probab=91.01 E-value=0.059 Score=34.15 Aligned_cols=46 Identities=35% Similarity=0.636 Sum_probs=32.8
Q ss_pred CCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhcc
Q psy6628 14 CQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDH 70 (132)
Q Consensus 14 C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~ 70 (132)
|=.|++.|.+..-|.+|+...+ |+|. +|.+.......|..|..+.|
T Consensus 13 cwycnrefddekiliqhqkakh--------fkch---ichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAKH--------FKCH---ICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccccchhhhhhhhhhhcc--------ceee---eehhhhccCCCceeehhhhh
Confidence 6678899999999988887543 7888 77777665555666643334
No 69
>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=90.81 E-value=0.13 Score=29.85 Aligned_cols=27 Identities=30% Similarity=0.456 Sum_probs=13.2
Q ss_pred CCCccCCCchhccccchHHHHHHHhhhhhc
Q psy6628 101 EKPYACEFCPLTFRHSSHLFRHRRSLHQMY 130 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 130 (132)
+.-..|-+||+.|. .|.+|+..|||..
T Consensus 70 ~d~i~clecGk~~k---~LkrHL~~~~glt 96 (132)
T PF05443_consen 70 PDYIICLECGKKFK---TLKRHLRTHHGLT 96 (132)
T ss_dssp SS-EE-TBT--EES---BHHHHHHHTT-S-
T ss_pred cCeeEEccCCcccc---hHHHHHHHccCCC
Confidence 34466667777665 3467777776644
No 70
>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=90.69 E-value=0.18 Score=28.15 Aligned_cols=30 Identities=27% Similarity=0.685 Sum_probs=17.2
Q ss_pred cccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccCh
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSK 88 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~ 88 (132)
..|+ .||..|.... ..|..|+.||..|.-.
T Consensus 10 R~Cp---~CG~kFYDLn------------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCP---SCGAKFYDLN------------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCC---CCcchhccCC------------CCCccCCCCCCccCcc
Confidence 4566 6666666431 1355677777666544
No 71
>KOG2186|consensus
Probab=90.66 E-value=0.14 Score=32.77 Aligned_cols=46 Identities=24% Similarity=0.592 Sum_probs=28.1
Q ss_pred cccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhHHHHHH
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHKIHSR 96 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~ 96 (132)
|.|. .|+....-. .+..|+.+ -.+ ..|.|..|+..|.. .....|..
T Consensus 4 FtCn---vCgEsvKKp-~vekH~sr-Crn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCN---VCGESVKKP-QVEKHMSR-CRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehh---hhhhhcccc-chHHHHHh-ccC-CeeEEeeccccccc-chhhhhhh
Confidence 6677 777665543 35667633 333 45778888888766 44555544
No 72
>PF12907 zf-met2: Zinc-binding
Probab=90.62 E-value=0.068 Score=24.11 Aligned_cols=27 Identities=26% Similarity=0.503 Sum_probs=18.4
Q ss_pred ccCCCchhccc---cchHHHHHHHhhhhhc
Q psy6628 104 YACEFCPLTFR---HSSHLFRHRRSLHQMY 130 (132)
Q Consensus 104 ~~C~~C~~~f~---~~~~l~~H~~~~~~~~ 130 (132)
+.|.+|...|. ....|..|....|.+.
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 57888887664 4466888877666554
No 73
>KOG2482|consensus
Probab=89.91 E-value=0.42 Score=32.11 Aligned_cols=49 Identities=20% Similarity=0.320 Sum_probs=37.3
Q ss_pred ccCCcccccccChhhHHHHHHHhcC---------------------------CCCccCCCchhccccchHHHHHHH
Q psy6628 76 YQCSQCSKSFFSKYDHKIHSRVHTG---------------------------EKPYACEFCPLTFRHSSHLFRHRR 124 (132)
Q Consensus 76 ~~c~~C~~~~~~~~~l~~h~~~h~~---------------------------~~~~~C~~C~~~f~~~~~l~~H~~ 124 (132)
..|..|.....+...|..||+.-+. .+.-.|..|.-.|-....|..|+.
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~ 355 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMV 355 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcc
Confidence 5788898888888889999874221 123566778889999999999975
No 74
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=89.85 E-value=0.049 Score=34.26 Aligned_cols=14 Identities=14% Similarity=0.451 Sum_probs=9.8
Q ss_pred CccCCCchhccccc
Q psy6628 103 PYACEFCPLTFRHS 116 (132)
Q Consensus 103 ~~~C~~C~~~f~~~ 116 (132)
.+.||.||.+|...
T Consensus 48 V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 48 VWVCPHCGYAAFEE 61 (214)
T ss_pred EEECCCCCCccccc
Confidence 47888888766543
No 75
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=89.23 E-value=0.3 Score=23.05 Aligned_cols=22 Identities=36% Similarity=0.680 Sum_probs=14.3
Q ss_pred ccCCCchhccccc-----hHHHHHHHh
Q psy6628 104 YACEFCPLTFRHS-----SHLFRHRRS 125 (132)
Q Consensus 104 ~~C~~C~~~f~~~-----~~l~~H~~~ 125 (132)
-.|..|++.+... ++|.+|+..
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 4566676666543 577788774
No 76
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.16 E-value=0.27 Score=21.59 Aligned_cols=11 Identities=36% Similarity=1.014 Sum_probs=5.9
Q ss_pred CccCCcccccc
Q psy6628 75 PYQCSQCSKSF 85 (132)
Q Consensus 75 ~~~c~~C~~~~ 85 (132)
..+|..|+..|
T Consensus 25 ~v~C~~C~~~f 35 (36)
T PF13717_consen 25 KVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEe
Confidence 34566665544
No 77
>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=89.02 E-value=0.47 Score=19.16 Aligned_cols=19 Identities=32% Similarity=0.625 Sum_probs=13.1
Q ss_pred eCCCCccccCChhHHHHHHH
Q psy6628 13 TCQVCSKIFSYENGLKAHVR 32 (132)
Q Consensus 13 ~C~~C~~~f~~~~~l~~h~~ 32 (132)
.||+|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 588888877 4466666654
No 78
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=88.57 E-value=0.33 Score=27.06 Aligned_cols=25 Identities=28% Similarity=0.578 Sum_probs=20.4
Q ss_pred ccC----CCchhccccchHHHHHHHhhhh
Q psy6628 104 YAC----EFCPLTFRHSSHLFRHRRSLHQ 128 (132)
Q Consensus 104 ~~C----~~C~~~f~~~~~l~~H~~~~~~ 128 (132)
|.| ..|+..+.+...+.+|.+.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 777 7888888888888888888775
No 79
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.47 E-value=0.68 Score=22.74 Aligned_cols=9 Identities=44% Similarity=1.438 Sum_probs=5.0
Q ss_pred CccCCcccc
Q psy6628 75 PYQCSQCSK 83 (132)
Q Consensus 75 ~~~c~~C~~ 83 (132)
+|.|+.||.
T Consensus 50 ~Y~Cp~CGF 58 (61)
T COG2888 50 PYRCPKCGF 58 (61)
T ss_pred ceECCCcCc
Confidence 456666653
No 80
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.39 E-value=0.2 Score=23.22 Aligned_cols=8 Identities=25% Similarity=1.011 Sum_probs=3.7
Q ss_pred ccCCCchh
Q psy6628 104 YACEFCPL 111 (132)
Q Consensus 104 ~~C~~C~~ 111 (132)
..|+.||.
T Consensus 22 ~~Cp~CG~ 29 (46)
T PRK00398 22 VRCPYCGY 29 (46)
T ss_pred eECCCCCC
Confidence 44444443
No 81
>KOG2482|consensus
Probab=87.64 E-value=1.4 Score=29.82 Aligned_cols=25 Identities=28% Similarity=0.709 Sum_probs=21.0
Q ss_pred ccCCCchhccccchHHHHHHHhhhh
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRSLHQ 128 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~~~~ 128 (132)
.+|-.|....-....|..|++..|.
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe 304 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHE 304 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHH
Confidence 5888898888888899999988765
No 82
>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=86.34 E-value=0.4 Score=30.97 Aligned_cols=41 Identities=22% Similarity=0.475 Sum_probs=24.1
Q ss_pred cccccceeeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccC
Q psy6628 4 VHNIHRVVFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCE 47 (132)
Q Consensus 4 ~~~~~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~ 47 (132)
+|..+.++|.|..|..-+ ..-.--+|+..-.... .. .|+|.
T Consensus 135 vw~hGGrif~CsfC~~fl-CEDDQFEHQAsCQvLe-~E-~~KC~ 175 (314)
T PF06524_consen 135 VWDHGGRIFKCSFCDNFL-CEDDQFEHQASCQVLE-SE-TFKCQ 175 (314)
T ss_pred cccCCCeEEEeecCCCee-eccchhhhhhhhhhhh-cc-ccccc
Confidence 566788999999998743 3333344665432221 12 37776
No 83
>KOG2785|consensus
Probab=85.90 E-value=0.81 Score=31.22 Aligned_cols=79 Identities=22% Similarity=0.335 Sum_probs=44.8
Q ss_pred cccCCCCCCcccccChHHHHhhhhhccCC----CCCcc-CCcccccccChhhHHHH---HHHhcCCCCccCCCchhcccc
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKRDHQK----EKPYQ-CSQCSKSFFSKYDHKIH---SRVHTGEKPYACEFCPLTFRH 115 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~~~~~----~~~~~-c~~C~~~~~~~~~l~~h---~~~h~~~~~~~C~~C~~~f~~ 115 (132)
|+|. .|...|........|++..... .+... .++-...|...-....- .....++-++.|.+|.+.|..
T Consensus 4 ftC~---tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s 80 (390)
T KOG2785|consen 4 FTCN---TCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFAS 80 (390)
T ss_pred ceee---ceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccC
Confidence 8898 8999999887777777422111 01111 11111222111111000 111344568999999999999
Q ss_pred chHHHHHHHh
Q psy6628 116 SSHLFRHRRS 125 (132)
Q Consensus 116 ~~~l~~H~~~ 125 (132)
......|+..
T Consensus 81 ~~a~~~hl~S 90 (390)
T KOG2785|consen 81 PKAHENHLKS 90 (390)
T ss_pred hhhHHHHHHH
Confidence 9888888764
No 84
>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=85.58 E-value=0.23 Score=23.58 Aligned_cols=11 Identities=27% Similarity=1.099 Sum_probs=5.8
Q ss_pred cccCCCCCCccccc
Q psy6628 44 FKCEGRGECDRVFT 57 (132)
Q Consensus 44 ~~c~~~~~c~~~~~ 57 (132)
|.|. .|+..|.
T Consensus 6 y~C~---~Cg~~fe 16 (52)
T TIGR02605 6 YRCT---ACGHRFE 16 (52)
T ss_pred EEeC---CCCCEeE
Confidence 4555 5555554
No 85
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=85.45 E-value=0.29 Score=33.51 Aligned_cols=61 Identities=30% Similarity=0.556 Sum_probs=44.6
Q ss_pred cccCCCCCCcccccChHHHHhhhhh-ccCCC--CCccCC--cccccccChhhHHHHHHHhcCCCCccCC
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKR-DHQKE--KPYQCS--QCSKSFFSKYDHKIHSRVHTGEKPYACE 107 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~-~~~~~--~~~~c~--~C~~~~~~~~~l~~h~~~h~~~~~~~C~ 107 (132)
+.|. .|...|.....+..|... .|.++ +++.|. .|++.|.....+..|...|.+..+..+.
T Consensus 290 ~~~~---~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 290 IKSK---QCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred CCCc---cccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 5555 677777777777777732 67777 788888 6888888888888888877776665553
No 86
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=83.47 E-value=1 Score=19.79 Aligned_cols=10 Identities=30% Similarity=1.075 Sum_probs=4.7
Q ss_pred ccCCcccccc
Q psy6628 76 YQCSQCSKSF 85 (132)
Q Consensus 76 ~~c~~C~~~~ 85 (132)
.+|..|+..|
T Consensus 26 vrC~~C~~~f 35 (37)
T PF13719_consen 26 VRCPKCGHVF 35 (37)
T ss_pred EECCCCCcEe
Confidence 4455554443
No 87
>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=82.94 E-value=1.3 Score=26.52 Aligned_cols=32 Identities=13% Similarity=0.304 Sum_probs=19.8
Q ss_pred CCCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhcc
Q psy6628 73 EKPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTF 113 (132)
Q Consensus 73 ~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f 113 (132)
..-|.|+.|+..|.+...+. .-|.|+.||...
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 34566777777776665553 247777777543
No 88
>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=82.75 E-value=0.87 Score=18.05 Aligned_cols=11 Identities=36% Similarity=0.781 Sum_probs=8.5
Q ss_pred ceeeeCCCCcc
Q psy6628 9 RVVFTCQVCSK 19 (132)
Q Consensus 9 ~~~~~C~~C~~ 19 (132)
...|.||.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45699999984
No 89
>KOG4167|consensus
Probab=82.62 E-value=0.28 Score=36.23 Aligned_cols=28 Identities=25% Similarity=0.579 Sum_probs=24.6
Q ss_pred ceeeeCCCCccccCChhHHHHHHHhhcC
Q psy6628 9 RVVFTCQVCSKIFSYENGLKAHVRNKHG 36 (132)
Q Consensus 9 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~ 36 (132)
.-.|.|.+|+++|.....+..||..|..
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 3469999999999999999999998863
No 90
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.31 E-value=0.9 Score=20.95 Aligned_cols=8 Identities=25% Similarity=0.966 Sum_probs=3.8
Q ss_pred ccCCcccc
Q psy6628 76 YQCSQCSK 83 (132)
Q Consensus 76 ~~c~~C~~ 83 (132)
..|+.||.
T Consensus 20 irC~~CG~ 27 (44)
T smart00659 20 VRCRECGY 27 (44)
T ss_pred eECCCCCc
Confidence 44555543
No 91
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=81.63 E-value=1.7 Score=19.60 Aligned_cols=23 Identities=13% Similarity=0.348 Sum_probs=14.0
Q ss_pred ccCCCchhccc--cchHHHHHHHhh
Q psy6628 104 YACEFCPLTFR--HSSHLFRHRRSL 126 (132)
Q Consensus 104 ~~C~~C~~~f~--~~~~l~~H~~~~ 126 (132)
-.|+.|+..|. ...+-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 47777777665 345555665544
No 92
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.45 E-value=0.28 Score=29.24 Aligned_cols=13 Identities=31% Similarity=0.692 Sum_probs=8.0
Q ss_pred ccCCcccccccCh
Q psy6628 76 YQCSQCSKSFFSK 88 (132)
Q Consensus 76 ~~c~~C~~~~~~~ 88 (132)
++|+.||..|...
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 5666676666543
No 93
>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=81.26 E-value=1.2 Score=25.52 Aligned_cols=30 Identities=17% Similarity=0.256 Sum_probs=18.8
Q ss_pred cccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccCh
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSK 88 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~ 88 (132)
..|+ .|+..|.... ..|..|+.||..|.-.
T Consensus 10 r~Cp---~cg~kFYDLn------------k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICP---NTGSKFYDLN------------RRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCC---CcCccccccC------------CCCccCCCcCCccCcc
Confidence 5677 7777766431 2466777777776554
No 94
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=80.29 E-value=1.8 Score=21.32 Aligned_cols=9 Identities=44% Similarity=1.383 Sum_probs=5.6
Q ss_pred CccCCcccc
Q psy6628 75 PYQCSQCSK 83 (132)
Q Consensus 75 ~~~c~~C~~ 83 (132)
+|.|+.||.
T Consensus 48 ~Y~CP~CGF 56 (59)
T PRK14890 48 PYTCPKCGF 56 (59)
T ss_pred ceECCCCCC
Confidence 466766654
No 95
>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=79.92 E-value=1.4 Score=19.27 Aligned_cols=7 Identities=29% Similarity=1.303 Sum_probs=2.9
Q ss_pred cCCcccc
Q psy6628 77 QCSQCSK 83 (132)
Q Consensus 77 ~c~~C~~ 83 (132)
.|..|+.
T Consensus 27 ~C~~C~~ 33 (38)
T TIGR02098 27 RCGKCGH 33 (38)
T ss_pred ECCCCCC
Confidence 3444443
No 96
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=79.80 E-value=1.3 Score=23.83 Aligned_cols=31 Identities=26% Similarity=0.635 Sum_probs=21.4
Q ss_pred CCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccc
Q psy6628 74 KPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFR 114 (132)
Q Consensus 74 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~ 114 (132)
+|-.|..||..|... .-.+|-.|+.|.....
T Consensus 57 ~Pa~CkkCGfef~~~----------~ik~pSRCP~CKSE~I 87 (97)
T COG3357 57 RPARCKKCGFEFRDD----------KIKKPSRCPKCKSEWI 87 (97)
T ss_pred cChhhcccCcccccc----------ccCCcccCCcchhhcc
Confidence 567888898888662 1246788888875543
No 97
>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=79.73 E-value=1.1 Score=18.15 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=8.1
Q ss_pred eeCCCCccccC
Q psy6628 12 FTCQVCSKIFS 22 (132)
Q Consensus 12 ~~C~~C~~~f~ 22 (132)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 45888888774
No 98
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=79.45 E-value=1.9 Score=26.48 Aligned_cols=31 Identities=16% Similarity=0.388 Sum_probs=18.7
Q ss_pred CCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhcc
Q psy6628 74 KPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTF 113 (132)
Q Consensus 74 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f 113 (132)
..|.|+.|+..|.+...+. .-|.|+.||...
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 4466777777666655431 247777777543
No 99
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=78.50 E-value=1.1 Score=23.85 Aligned_cols=11 Identities=27% Similarity=0.772 Sum_probs=5.3
Q ss_pred CccCCCchhcc
Q psy6628 103 PYACEFCPLTF 113 (132)
Q Consensus 103 ~~~C~~C~~~f 113 (132)
.|.|..|+..|
T Consensus 53 IW~C~kCg~~f 63 (89)
T COG1997 53 IWKCRKCGAKF 63 (89)
T ss_pred eEEcCCCCCee
Confidence 34555554444
No 100
>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=75.98 E-value=2.1 Score=30.34 Aligned_cols=26 Identities=19% Similarity=0.470 Sum_probs=19.7
Q ss_pred CCccCCCchhccccchHHHHHHHhhh
Q psy6628 102 KPYACEFCPLTFRHSSHLFRHRRSLH 127 (132)
Q Consensus 102 ~~~~C~~C~~~f~~~~~l~~H~~~~~ 127 (132)
+.|.|+.|.+.|.....+..|+...|
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhh
Confidence 46778888888888888888876544
No 101
>KOG2231|consensus
Probab=75.86 E-value=11 Score=28.24 Aligned_cols=90 Identities=23% Similarity=0.349 Sum_probs=50.5
Q ss_pred ChhHHHHHHHhhcC-CCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCccc------ccccChhhHHHHH
Q psy6628 23 YENGLKAHVRNKHG-SSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCS------KSFFSKYDHKIHS 95 (132)
Q Consensus 23 ~~~~l~~h~~~~~~-~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~------~~~~~~~~l~~h~ 95 (132)
.+..|..|+..-.. .....--..|. .|...|.....|..|++..| +.|..|. .-|.+...|..|-
T Consensus 161 t~~el~~h~~~gd~d~~s~rGhp~C~---~C~~~fld~~el~rH~~~~h-----~~chfC~~~~~~neyy~~~~dLe~Hf 232 (669)
T KOG2231|consen 161 TRAELNLHLMFGDPDDESCRGHPLCK---FCHERFLDDDELYRHLRFDH-----EFCHFCDYKTGQNEYYNDYDDLEEHF 232 (669)
T ss_pred hHHHHHHHHhcCCCccccccCCccch---hhhhhhccHHHHHHhhccce-----eheeecCcccccchhcccchHHHHHh
Confidence 34667777654332 11111113566 88899999999999985433 4566663 3345556666666
Q ss_pred HHhcCCCCccCC--Cch-hccccchHHHHHHH
Q psy6628 96 RVHTGEKPYACE--FCP-LTFRHSSHLFRHRR 124 (132)
Q Consensus 96 ~~h~~~~~~~C~--~C~-~~f~~~~~l~~H~~ 124 (132)
+. ..|.|. .|. +.|.....+..+++
T Consensus 233 R~----~HflCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 233 RK----GHFLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred hh----cCccccccccccceeeehhHHHHHHH
Confidence 54 346776 454 34444434455554
No 102
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.94 E-value=6.2 Score=23.32 Aligned_cols=14 Identities=29% Similarity=0.764 Sum_probs=8.0
Q ss_pred ccccCCCCCCcccccCh
Q psy6628 43 RFKCEGRGECDRVFTTR 59 (132)
Q Consensus 43 ~~~c~~~~~c~~~~~~~ 59 (132)
.|.|+ .|+..|...
T Consensus 99 ~Y~Cp---~C~~~y~~~ 112 (147)
T smart00531 99 YYKCP---NCQSKYTFL 112 (147)
T ss_pred EEECc---CCCCEeeHH
Confidence 36666 566665543
No 103
>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=74.82 E-value=1.7 Score=19.25 Aligned_cols=14 Identities=21% Similarity=0.679 Sum_probs=10.6
Q ss_pred eeeCCCCccccCCh
Q psy6628 11 VFTCQVCSKIFSYE 24 (132)
Q Consensus 11 ~~~C~~C~~~f~~~ 24 (132)
.|.|+.||..|.-.
T Consensus 5 ~y~C~~Cg~~fe~~ 18 (41)
T smart00834 5 EYRCEDCGHTFEVL 18 (41)
T ss_pred EEEcCCCCCEEEEE
Confidence 48899999887543
No 104
>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=73.62 E-value=1.2 Score=19.58 Aligned_cols=8 Identities=25% Similarity=0.924 Sum_probs=3.9
Q ss_pred cCCccccc
Q psy6628 77 QCSQCSKS 84 (132)
Q Consensus 77 ~c~~C~~~ 84 (132)
.|+.||..
T Consensus 23 ~Cd~cg~~ 30 (36)
T PF05191_consen 23 VCDNCGGE 30 (36)
T ss_dssp BCTTTTEB
T ss_pred ccCCCCCe
Confidence 45555543
No 105
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=73.07 E-value=4.4 Score=27.64 Aligned_cols=75 Identities=28% Similarity=0.481 Sum_probs=43.6
Q ss_pred ccCCCCCCcccccChHHHHhhhhhccCCCCCccCCccccc----ccChhhHHHHHHHhcCCCCccCCC--ch----hccc
Q psy6628 45 KCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKS----FFSKYDHKIHSRVHTGEKPYACEF--CP----LTFR 114 (132)
Q Consensus 45 ~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~----~~~~~~l~~h~~~h~~~~~~~C~~--C~----~~f~ 114 (132)
.|. .|...|.....|..|++..| ++=+.|+.-+.. |.+...|..|.+ ...|.|.+ |. ..|.
T Consensus 222 ~C~---FC~~~FYdDDEL~~HcR~~H--E~ChICD~v~p~~~QYFK~Y~~Le~HF~----~~hy~ct~qtc~~~k~~vf~ 292 (493)
T COG5236 222 LCI---FCKIYFYDDDELRRHCRLRH--EACHICDMVGPIRYQYFKSYEDLEAHFR----NAHYCCTFQTCRVGKCYVFP 292 (493)
T ss_pred hhh---hccceecChHHHHHHHHhhh--hhhhhhhccCccchhhhhCHHHHHHHhh----cCceEEEEEEEecCcEEEec
Confidence 455 78888888888888874433 333344433221 444455555544 23366643 32 3567
Q ss_pred cchHHHHHHHhhhh
Q psy6628 115 HSSHLFRHRRSLHQ 128 (132)
Q Consensus 115 ~~~~l~~H~~~~~~ 128 (132)
+...|..|+-..|+
T Consensus 293 ~~~el~~h~~~~h~ 306 (493)
T COG5236 293 YHTELLEHLTRFHK 306 (493)
T ss_pred cHHHHHHHHHHHhh
Confidence 77788888766655
No 106
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=73.03 E-value=7.1 Score=17.44 Aligned_cols=12 Identities=17% Similarity=0.476 Sum_probs=5.6
Q ss_pred CCcccccChHHH
Q psy6628 51 ECDRVFTTRNML 62 (132)
Q Consensus 51 ~c~~~~~~~~~l 62 (132)
.|+-.+.....+
T Consensus 24 ~C~G~W~d~~el 35 (41)
T PF13453_consen 24 SCGGIWFDAGEL 35 (41)
T ss_pred CCCeEEccHHHH
Confidence 455554444433
No 107
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=72.73 E-value=1.7 Score=20.53 Aligned_cols=8 Identities=25% Similarity=0.957 Sum_probs=4.1
Q ss_pred ccCCcccc
Q psy6628 76 YQCSQCSK 83 (132)
Q Consensus 76 ~~c~~C~~ 83 (132)
..|+.||.
T Consensus 25 irCp~Cg~ 32 (49)
T COG1996 25 IRCPYCGS 32 (49)
T ss_pred eeCCCCCc
Confidence 45555553
No 108
>PHA00626 hypothetical protein
Probab=72.31 E-value=1.8 Score=21.02 Aligned_cols=15 Identities=20% Similarity=0.405 Sum_probs=11.3
Q ss_pred CCCccCCCchhcccc
Q psy6628 101 EKPYACEFCPLTFRH 115 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~ 115 (132)
...|.|+.|+..|+-
T Consensus 21 snrYkCkdCGY~ft~ 35 (59)
T PHA00626 21 SDDYVCCDCGYNDSK 35 (59)
T ss_pred CcceEcCCCCCeech
Confidence 356888888887763
No 109
>KOG2186|consensus
Probab=72.29 E-value=3 Score=27.03 Aligned_cols=46 Identities=26% Similarity=0.596 Sum_probs=34.0
Q ss_pred eeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhh
Q psy6628 12 FTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIK 67 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~ 67 (132)
|.|..||..... ..+..|+..-.+ ..|.|- .|+..|.. ..+..|..
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-----~~fSCI---DC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-----AYFSCI---DCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-----CeeEEe---eccccccc-chhhhhhh
Confidence 789999998765 456668876544 238898 89999987 56777764
No 110
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=71.71 E-value=1.3 Score=22.81 Aligned_cols=16 Identities=38% Similarity=0.798 Sum_probs=8.9
Q ss_pred CCCccCC--cccccccCh
Q psy6628 73 EKPYQCS--QCSKSFFSK 88 (132)
Q Consensus 73 ~~~~~c~--~C~~~~~~~ 88 (132)
++.++|. .||..|...
T Consensus 25 ~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 25 ERYHQCQNVNCSATFITY 42 (72)
T ss_pred eeeeecCCCCCCCEEEEE
Confidence 3445665 566666543
No 111
>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=70.41 E-value=1.7 Score=27.53 Aligned_cols=27 Identities=22% Similarity=0.327 Sum_probs=20.3
Q ss_pred CCCccCCcccccccChhhHHHHHHHhc
Q psy6628 73 EKPYQCSQCSKSFFSKYDHKIHSRVHT 99 (132)
Q Consensus 73 ~~~~~c~~C~~~~~~~~~l~~h~~~h~ 99 (132)
+..|.|.+|++.|.....+.+|+..-+
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 345899999999999999999987544
No 112
>KOG2785|consensus
Probab=70.32 E-value=5.3 Score=27.53 Aligned_cols=52 Identities=25% Similarity=0.362 Sum_probs=41.9
Q ss_pred CCccCCcccccccChhhHHHHHHHhcCC-----------------------CCccCCCch---hccccchHHHHHHHh
Q psy6628 74 KPYQCSQCSKSFFSKYDHKIHSRVHTGE-----------------------KPYACEFCP---LTFRHSSHLFRHRRS 125 (132)
Q Consensus 74 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~ 125 (132)
.|-.|..|+..+.....-..||..+++- .-+.|-.|. +.|.+....+.|+..
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 3467899999999999999999877651 236677777 999999999999864
No 113
>KOG4118|consensus
Probab=70.16 E-value=2.3 Score=21.33 Aligned_cols=27 Identities=15% Similarity=0.310 Sum_probs=15.6
Q ss_pred ccCCCchhccccchHHHHHHHhhhhhc
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRSLHQMY 130 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~~~~~~ 130 (132)
|.|.+|...-...-.+..|....|++.
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk~ 65 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPKE 65 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCCC
Confidence 566666655555555566665555443
No 114
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=70.00 E-value=1.7 Score=25.40 Aligned_cols=15 Identities=20% Similarity=0.581 Sum_probs=10.0
Q ss_pred CCccCCcccccccCh
Q psy6628 74 KPYQCSQCSKSFFSK 88 (132)
Q Consensus 74 ~~~~c~~C~~~~~~~ 88 (132)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 346788888776553
No 115
>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=69.80 E-value=2.4 Score=19.17 Aligned_cols=14 Identities=21% Similarity=0.653 Sum_probs=10.7
Q ss_pred eeeCCCCccccCCh
Q psy6628 11 VFTCQVCSKIFSYE 24 (132)
Q Consensus 11 ~~~C~~C~~~f~~~ 24 (132)
.|.|..||..|...
T Consensus 5 ey~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 5 EYRCEECGHEFEVL 18 (42)
T ss_pred EEEeCCCCCEEEEE
Confidence 48899999887554
No 116
>PF15269 zf-C2H2_7: Zinc-finger
Probab=68.14 E-value=3.2 Score=19.10 Aligned_cols=21 Identities=48% Similarity=0.991 Sum_probs=12.6
Q ss_pred ccCCCchhccccchHHHHHHH
Q psy6628 104 YACEFCPLTFRHSSHLFRHRR 124 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~ 124 (132)
|+|-.|......++.|-+|++
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 445556556666666666664
No 117
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=67.14 E-value=2.6 Score=24.48 Aligned_cols=22 Identities=23% Similarity=0.174 Sum_probs=11.3
Q ss_pred ccCCCchhccccchHHHHHHHhhhh
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRSLHQ 128 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~~~~ 128 (132)
..|-++|+.|. +|++|+..|++
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccC
Confidence 34445555554 45555555544
No 118
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=67.05 E-value=3.5 Score=19.51 Aligned_cols=14 Identities=29% Similarity=0.653 Sum_probs=8.4
Q ss_pred ceeeeCCCCccccC
Q psy6628 9 RVVFTCQVCSKIFS 22 (132)
Q Consensus 9 ~~~~~C~~C~~~f~ 22 (132)
++++.|..||..|.
T Consensus 2 Dk~l~C~dCg~~Fv 15 (49)
T PF13451_consen 2 DKTLTCKDCGAEFV 15 (49)
T ss_pred CeeEEcccCCCeEE
Confidence 45566666666553
No 119
>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=66.25 E-value=2.3 Score=20.36 Aligned_cols=11 Identities=18% Similarity=0.709 Sum_probs=6.0
Q ss_pred cCCCchhcccc
Q psy6628 105 ACEFCPLTFRH 115 (132)
Q Consensus 105 ~C~~C~~~f~~ 115 (132)
.||+|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 89999999874
No 120
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=66.13 E-value=2.2 Score=23.03 Aligned_cols=11 Identities=27% Similarity=0.600 Sum_probs=5.2
Q ss_pred CccCCCchhcc
Q psy6628 103 PYACEFCPLTF 113 (132)
Q Consensus 103 ~~~C~~C~~~f 113 (132)
.|.|..|++.|
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PTZ00255 54 IWRCKGCKKTV 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 34444444444
No 121
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=66.08 E-value=3.8 Score=18.28 Aligned_cols=14 Identities=36% Similarity=0.880 Sum_probs=11.4
Q ss_pred eeeCCCCccccCCh
Q psy6628 11 VFTCQVCSKIFSYE 24 (132)
Q Consensus 11 ~~~C~~C~~~f~~~ 24 (132)
+++|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78899999988653
No 122
>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=66.05 E-value=2.1 Score=17.96 Aligned_cols=7 Identities=29% Similarity=0.814 Sum_probs=2.9
Q ss_pred ccCCCch
Q psy6628 104 YACEFCP 110 (132)
Q Consensus 104 ~~C~~C~ 110 (132)
+.|+.|+
T Consensus 20 ~vCp~C~ 26 (30)
T PF08274_consen 20 LVCPECG 26 (30)
T ss_dssp EEETTTT
T ss_pred EeCCccc
Confidence 4444443
No 123
>KOG3408|consensus
Probab=65.97 E-value=4.1 Score=23.25 Aligned_cols=26 Identities=23% Similarity=0.423 Sum_probs=19.4
Q ss_pred CCCCccCCCchhccccchHHHHHHHh
Q psy6628 100 GEKPYACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 100 ~~~~~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
|...|.|-.|.+-|.+...|..|.+.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44457888888888888888888764
No 124
>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=65.46 E-value=3.1 Score=17.73 Aligned_cols=8 Identities=25% Similarity=1.120 Sum_probs=3.8
Q ss_pred ccCCcccc
Q psy6628 76 YQCSQCSK 83 (132)
Q Consensus 76 ~~c~~C~~ 83 (132)
..|..||.
T Consensus 18 irC~~CG~ 25 (32)
T PF03604_consen 18 IRCPECGH 25 (32)
T ss_dssp SSBSSSS-
T ss_pred EECCcCCC
Confidence 45555554
No 125
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=65.41 E-value=3.2 Score=20.10 Aligned_cols=27 Identities=15% Similarity=0.401 Sum_probs=13.7
Q ss_pred hhhHHHHHHHhcCCCCccCCC----chhccc
Q psy6628 88 KYDHKIHSRVHTGEKPYACEF----CPLTFR 114 (132)
Q Consensus 88 ~~~l~~h~~~h~~~~~~~C~~----C~~~f~ 114 (132)
...|..|....-..++..|+. |...+.
T Consensus 23 r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 23 RKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp CCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred HHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 345666666544456666666 665553
No 126
>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=64.15 E-value=3.6 Score=19.47 Aligned_cols=9 Identities=22% Similarity=0.873 Sum_probs=3.4
Q ss_pred CccCCCchh
Q psy6628 103 PYACEFCPL 111 (132)
Q Consensus 103 ~~~C~~C~~ 111 (132)
.|+|++|++
T Consensus 41 ~W~CPiC~~ 49 (50)
T PF02891_consen 41 KWKCPICNK 49 (50)
T ss_dssp --B-TTT--
T ss_pred CeECcCCcC
Confidence 388888865
No 127
>KOG2807|consensus
Probab=62.81 E-value=14 Score=25.15 Aligned_cols=25 Identities=28% Similarity=0.506 Sum_probs=15.9
Q ss_pred CCccCCCchhccccchHHHHHHHhh
Q psy6628 102 KPYACEFCPLTFRHSSHLFRHRRSL 126 (132)
Q Consensus 102 ~~~~C~~C~~~f~~~~~l~~H~~~~ 126 (132)
-.|.|..|...|-...+.-.|...|
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhh
Confidence 3477777777776666666665543
No 128
>PLN02294 cytochrome c oxidase subunit Vb
Probab=62.77 E-value=3.6 Score=25.01 Aligned_cols=13 Identities=38% Similarity=0.991 Sum_probs=6.5
Q ss_pred ceeeeCCCCcccc
Q psy6628 9 RVVFTCQVCSKIF 21 (132)
Q Consensus 9 ~~~~~C~~C~~~f 21 (132)
++++.|++||..|
T Consensus 139 Gkp~RCpeCG~~f 151 (174)
T PLN02294 139 GKSFECPVCTQYF 151 (174)
T ss_pred CCceeCCCCCCEE
Confidence 3445555555544
No 129
>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=62.28 E-value=5.2 Score=17.58 Aligned_cols=13 Identities=23% Similarity=0.779 Sum_probs=7.0
Q ss_pred ceeeeCCCCcccc
Q psy6628 9 RVVFTCQVCSKIF 21 (132)
Q Consensus 9 ~~~~~C~~C~~~f 21 (132)
.+.|+|..||...
T Consensus 4 ~~~YkC~~CGniV 16 (36)
T PF06397_consen 4 GEFYKCEHCGNIV 16 (36)
T ss_dssp TEEEE-TTT--EE
T ss_pred ccEEEccCCCCEE
Confidence 3568888888754
No 130
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.04 E-value=1.3 Score=28.20 Aligned_cols=8 Identities=25% Similarity=0.808 Sum_probs=5.6
Q ss_pred ccCCCchh
Q psy6628 104 YACEFCPL 111 (132)
Q Consensus 104 ~~C~~C~~ 111 (132)
+.||.|..
T Consensus 63 vvCP~C~y 70 (267)
T COG1655 63 VVCPICYY 70 (267)
T ss_pred EEcchhhH
Confidence 67777764
No 131
>KOG0717|consensus
Probab=60.70 E-value=4.2 Score=28.84 Aligned_cols=22 Identities=27% Similarity=0.582 Sum_probs=20.0
Q ss_pred ccCCCchhccccchHHHHHHHh
Q psy6628 104 YACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 104 ~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
+.|.+|.+.|.+...|.+|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 8899999999999999999754
No 132
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=59.24 E-value=2.9 Score=22.62 Aligned_cols=10 Identities=30% Similarity=1.182 Sum_probs=4.8
Q ss_pred ccCCcccccc
Q psy6628 76 YQCSQCSKSF 85 (132)
Q Consensus 76 ~~c~~C~~~~ 85 (132)
|.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (91)
T TIGR00280 54 WTCRKCGAKF 63 (91)
T ss_pred EEcCCCCCEE
Confidence 4454444444
No 133
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=59.24 E-value=1.8 Score=23.35 Aligned_cols=10 Identities=30% Similarity=0.932 Sum_probs=5.0
Q ss_pred ccCCCchhcc
Q psy6628 104 YACEFCPLTF 113 (132)
Q Consensus 104 ~~C~~C~~~f 113 (132)
|.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (90)
T PF01780_consen 54 WKCKKCGKKF 63 (90)
T ss_dssp EEETTTTEEE
T ss_pred eecCCCCCEE
Confidence 5555555444
No 134
>KOG2593|consensus
Probab=58.05 E-value=4.8 Score=28.20 Aligned_cols=17 Identities=18% Similarity=0.483 Sum_probs=9.4
Q ss_pred ceeeeCCCCccccCChh
Q psy6628 9 RVVFTCQVCSKIFSYEN 25 (132)
Q Consensus 9 ~~~~~C~~C~~~f~~~~ 25 (132)
...|.|+.|.+.|....
T Consensus 126 ~~~Y~Cp~C~kkyt~Le 142 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLE 142 (436)
T ss_pred cccccCCccccchhhhH
Confidence 34466666666665443
No 135
>KOG1842|consensus
Probab=56.74 E-value=6.6 Score=27.75 Aligned_cols=26 Identities=15% Similarity=0.149 Sum_probs=17.9
Q ss_pred CccCCcccccccChhhHHHHHHHhcC
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVHTG 100 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h~~ 100 (132)
.|.|+.|...|.+...|..|....+.
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcc
Confidence 36777777777777777777655443
No 136
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=56.31 E-value=5.3 Score=23.17 Aligned_cols=15 Identities=20% Similarity=0.669 Sum_probs=12.2
Q ss_pred eeeCCCCccccCChh
Q psy6628 11 VFTCQVCSKIFSYEN 25 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~ 25 (132)
|+.|..||++|.+..
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 578999999998764
No 137
>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=55.96 E-value=5 Score=18.28 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=9.1
Q ss_pred cCCCchhccccc
Q psy6628 105 ACEFCPLTFRHS 116 (132)
Q Consensus 105 ~C~~C~~~f~~~ 116 (132)
.|.+|++.|+.+
T Consensus 10 ~C~~C~rpf~WR 21 (42)
T PF10013_consen 10 ICPVCGRPFTWR 21 (42)
T ss_pred cCcccCCcchHH
Confidence 578888888754
No 138
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=55.95 E-value=1.7 Score=17.93 Aligned_cols=8 Identities=63% Similarity=1.456 Sum_probs=3.9
Q ss_pred CCcccccc
Q psy6628 78 CSQCSKSF 85 (132)
Q Consensus 78 c~~C~~~~ 85 (132)
|..|++.|
T Consensus 3 CiDC~~~F 10 (28)
T PF08790_consen 3 CIDCSKDF 10 (28)
T ss_dssp ETTTTEEE
T ss_pred eecCCCCc
Confidence 44455554
No 139
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=55.71 E-value=7.1 Score=21.58 Aligned_cols=16 Identities=19% Similarity=0.629 Sum_probs=12.9
Q ss_pred eeeeCCCCccccCChh
Q psy6628 10 VVFTCQVCSKIFSYEN 25 (132)
Q Consensus 10 ~~~~C~~C~~~f~~~~ 25 (132)
+++.|.-||.+|....
T Consensus 1 MpH~CtrCG~vf~~g~ 16 (112)
T COG3364 1 MPHQCTRCGEVFDDGS 16 (112)
T ss_pred CCceeccccccccccc
Confidence 3678999999998864
No 140
>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=55.31 E-value=3.6 Score=18.55 Aligned_cols=12 Identities=25% Similarity=0.974 Sum_probs=7.7
Q ss_pred CCccCCCchhcc
Q psy6628 102 KPYACEFCPLTF 113 (132)
Q Consensus 102 ~~~~C~~C~~~f 113 (132)
++..|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 356677777665
No 141
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=53.93 E-value=12 Score=18.25 Aligned_cols=10 Identities=20% Similarity=0.893 Sum_probs=5.0
Q ss_pred CCccCCcccc
Q psy6628 74 KPYQCSQCSK 83 (132)
Q Consensus 74 ~~~~c~~C~~ 83 (132)
..|.|+.||-
T Consensus 13 v~~~Cp~cGi 22 (55)
T PF13824_consen 13 VNFECPDCGI 22 (55)
T ss_pred cCCcCCCCCC
Confidence 3455555553
No 142
>KOG4124|consensus
Probab=53.57 E-value=2.9 Score=28.48 Aligned_cols=48 Identities=33% Similarity=0.739 Sum_probs=33.8
Q ss_pred CCccCCc--ccccccChhhHHHHHHH---------------hc----CCCCccCCCchhccccchHHHH
Q psy6628 74 KPYQCSQ--CSKSFFSKYDHKIHSRV---------------HT----GEKPYACEFCPLTFRHSSHLFR 121 (132)
Q Consensus 74 ~~~~c~~--C~~~~~~~~~l~~h~~~---------------h~----~~~~~~C~~C~~~f~~~~~l~~ 121 (132)
+++.|.+ |.+.+.....|..|-.. |. ..|+|.|++|.+.+.....|.-
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~ 416 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKY 416 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCc
Confidence 6778877 88888877777666432 11 2589999999998876655543
No 143
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=52.99 E-value=5.2 Score=30.02 Aligned_cols=55 Identities=22% Similarity=0.533 Sum_probs=35.4
Q ss_pred CCcccccChHHHHhhhhhccCCCCCc-cCCcccccccChhhHHHHHHHhcCCCCccCCCchhcc
Q psy6628 51 ECDRVFTTRNMLNIHIKRDHQKEKPY-QCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTF 113 (132)
Q Consensus 51 ~c~~~~~~~~~l~~h~~~~~~~~~~~-~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f 113 (132)
.||-+|+....|--.. ..+.-+.| -|+.|.+.+.+..+-+-| ..|..|+.||-..
T Consensus 128 ~CGPRfTIi~alPYDR--~nTsM~~F~lC~~C~~EY~dP~nRRfH------AQp~aCp~CGP~~ 183 (750)
T COG0068 128 NCGPRFTIIEALPYDR--ENTSMADFPLCPFCDKEYKDPLNRRFH------AQPIACPKCGPHL 183 (750)
T ss_pred CCCcceeeeccCCCCc--ccCccccCcCCHHHHHHhcCccccccc------cccccCcccCCCe
Confidence 8888888766554432 23333334 588898888776654333 3678899998533
No 144
>KOG1842|consensus
Probab=52.89 E-value=8.4 Score=27.26 Aligned_cols=26 Identities=23% Similarity=0.408 Sum_probs=23.4
Q ss_pred eeeCCCCccccCChhHHHHHHHhhcC
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRNKHG 36 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~~~~ 36 (132)
.|.||+|...|.+...|..|...-+.
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcc
Confidence 48999999999999999999987664
No 145
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.92 E-value=11 Score=19.58 Aligned_cols=31 Identities=26% Similarity=0.698 Sum_probs=18.6
Q ss_pred eeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCccc
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRV 55 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~ 55 (132)
.|+|..|+..| .+.+++. +.|.-.|+ .|+..
T Consensus 12 ~Y~c~~cg~~~----dvvq~~~-------ddplt~ce---~c~a~ 42 (82)
T COG2331 12 SYECTECGNRF----DVVQAMT-------DDPLTTCE---ECGAR 42 (82)
T ss_pred EEeecccchHH----HHHHhcc-------cCccccCh---hhChH
Confidence 48888888754 4444443 33335777 67643
No 146
>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=51.67 E-value=6.3 Score=17.88 Aligned_cols=15 Identities=33% Similarity=0.882 Sum_probs=9.3
Q ss_pred eeeeCCCCccccCCh
Q psy6628 10 VVFTCQVCSKIFSYE 24 (132)
Q Consensus 10 ~~~~C~~C~~~f~~~ 24 (132)
.++.|..|+..|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 578899999988543
No 147
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=51.26 E-value=4.4 Score=21.88 Aligned_cols=10 Identities=30% Similarity=1.238 Sum_probs=4.9
Q ss_pred ccCCcccccc
Q psy6628 76 YQCSQCSKSF 85 (132)
Q Consensus 76 ~~c~~C~~~~ 85 (132)
|.|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PRK03976 55 WECRKCGAKF 64 (90)
T ss_pred EEcCCCCCEE
Confidence 4455555444
No 148
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=50.34 E-value=1.5 Score=19.72 Aligned_cols=9 Identities=33% Similarity=1.224 Sum_probs=4.0
Q ss_pred ccCCccccc
Q psy6628 76 YQCSQCSKS 84 (132)
Q Consensus 76 ~~c~~C~~~ 84 (132)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 444444433
No 149
>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=50.32 E-value=3.2 Score=19.86 Aligned_cols=25 Identities=32% Similarity=0.743 Sum_probs=12.7
Q ss_pred CCccCCcccccccChhhHHHHHHHh
Q psy6628 74 KPYQCSQCSKSFFSKYDHKIHSRVH 98 (132)
Q Consensus 74 ~~~~c~~C~~~~~~~~~l~~h~~~h 98 (132)
..|+|+.|...|...-++..|...|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 3577888888777777766664444
No 150
>PF14353 CpXC: CpXC protein
Probab=50.23 E-value=9.3 Score=21.88 Aligned_cols=13 Identities=38% Similarity=0.922 Sum_probs=10.4
Q ss_pred eeeCCCCccccCC
Q psy6628 11 VFTCQVCSKIFSY 23 (132)
Q Consensus 11 ~~~C~~C~~~f~~ 23 (132)
.++||.||..|.-
T Consensus 38 ~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 38 SFTCPSCGHKFRL 50 (128)
T ss_pred EEECCCCCCceec
Confidence 5899999987743
No 151
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.76 E-value=7.4 Score=18.25 Aligned_cols=12 Identities=42% Similarity=1.137 Sum_probs=6.8
Q ss_pred CCCCccccCChh
Q psy6628 14 CQVCSKIFSYEN 25 (132)
Q Consensus 14 C~~C~~~f~~~~ 25 (132)
|+.|+..|..+.
T Consensus 15 CpvCqRPFsWRk 26 (54)
T COG4338 15 CPVCQRPFSWRK 26 (54)
T ss_pred hhhhcCchHHHH
Confidence 666666665443
No 152
>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=49.73 E-value=7.8 Score=21.93 Aligned_cols=25 Identities=28% Similarity=0.666 Sum_probs=16.4
Q ss_pred CccCCcccccccChhhHHHHHHHhcCCCCccCCCchh
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPL 111 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 111 (132)
.+.|..|+..|..... .+.||.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------LYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCCc------------CccCcCCcC
Confidence 3678888877654321 367888874
No 153
>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=49.22 E-value=9.3 Score=20.99 Aligned_cols=18 Identities=33% Similarity=0.739 Sum_probs=13.7
Q ss_pred HhcCCCCccCCCchhcccc
Q psy6628 97 VHTGEKPYACEFCPLTFRH 115 (132)
Q Consensus 97 ~h~~~~~~~C~~C~~~f~~ 115 (132)
.+.+ +|..|+.||..|..
T Consensus 74 l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 74 LEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EeCC-CceeCCCCCcEEEE
Confidence 3454 79999999988863
No 154
>KOG2907|consensus
Probab=49.07 E-value=6.7 Score=22.08 Aligned_cols=40 Identities=20% Similarity=0.415 Sum_probs=20.4
Q ss_pred ccCCcccccccChhhHHHHHHHhcCCCCccCCCchhcccc
Q psy6628 76 YQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRH 115 (132)
Q Consensus 76 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~ 115 (132)
..|+.||..=-....+.-.-.....-..|.|+.|+..|+.
T Consensus 75 ~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhhcccccCCceEEEEcCccceeeec
Confidence 4688887552221111111001112356999999988864
No 155
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=49.06 E-value=11 Score=15.95 Aligned_cols=13 Identities=38% Similarity=1.012 Sum_probs=9.9
Q ss_pred ceeeeCCCCcccc
Q psy6628 9 RVVFTCQVCSKIF 21 (132)
Q Consensus 9 ~~~~~C~~C~~~f 21 (132)
-+.|+|..||...
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 3478899998765
No 156
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=48.86 E-value=14 Score=24.99 Aligned_cols=26 Identities=31% Similarity=0.621 Sum_probs=18.1
Q ss_pred CCCccCCCchhccccchHHHHHHHhh
Q psy6628 101 EKPYACEFCPLTFRHSSHLFRHRRSL 126 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~H~~~~ 126 (132)
.-.|.|+.|...|-...+.-.|...|
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHHHHh
Confidence 34588888888887777776665443
No 157
>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=48.25 E-value=61 Score=19.68 Aligned_cols=53 Identities=23% Similarity=0.277 Sum_probs=32.8
Q ss_pred CCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccc-cchHHHHHHHhhh
Q psy6628 74 KPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFR-HSSHLFRHRRSLH 127 (132)
Q Consensus 74 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~-~~~~l~~H~~~~~ 127 (132)
....|++|......+.... ..+.+...|+-.|..=+=.|. +...|++|.+..|
T Consensus 79 ~~L~CPLCRG~V~GWtvve-~AR~~LN~K~RsC~~e~C~F~GtY~eLrKHar~~H 132 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVVE-PARRFLNAKKRSCSQESCSFSGTYSELRKHARSEH 132 (162)
T ss_pred ccccCccccCceeceEEch-HHHHHhccCCccCcccccccccCHHHHHHHHHhhC
Confidence 3467888876665554432 345555567777765333343 5678899987644
No 158
>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=48.20 E-value=12 Score=15.94 Aligned_cols=12 Identities=33% Similarity=1.104 Sum_probs=8.7
Q ss_pred eeeeCCCCcccc
Q psy6628 10 VVFTCQVCSKIF 21 (132)
Q Consensus 10 ~~~~C~~C~~~f 21 (132)
+.|+|..||...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 467888888764
No 159
>KOG4727|consensus
Probab=47.30 E-value=13 Score=22.76 Aligned_cols=22 Identities=18% Similarity=0.489 Sum_probs=19.3
Q ss_pred eeeCCCCccccCChhHHHHHHH
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVR 32 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~ 32 (132)
.|.|.+|+-++...-++..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 4899999999999988888874
No 160
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=47.23 E-value=14 Score=16.35 Aligned_cols=22 Identities=32% Similarity=0.643 Sum_probs=9.1
Q ss_pred CccCCCchhccc-cc-hHHHHHHH
Q psy6628 103 PYACEFCPLTFR-HS-SHLFRHRR 124 (132)
Q Consensus 103 ~~~C~~C~~~f~-~~-~~l~~H~~ 124 (132)
.|.|.+|...|+ +. +..+.|..
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT-
T ss_pred CeecccccceecCCChHHHHHhhc
Confidence 477888888884 33 34466654
No 161
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.53 E-value=10 Score=21.41 Aligned_cols=25 Identities=20% Similarity=0.347 Sum_probs=15.6
Q ss_pred CccCCcccccccChhhHHHHHHHhcCCCCccCCCchh
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPL 111 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 111 (132)
.+.|..|+..|.... ..+.||.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEEcccCCCEEecCC------------cCccCcCCCC
Confidence 357888886664421 3356888874
No 162
>KOG1280|consensus
Probab=46.44 E-value=26 Score=24.13 Aligned_cols=38 Identities=24% Similarity=0.421 Sum_probs=25.8
Q ss_pred cceeeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccC
Q psy6628 8 HRVVFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCE 47 (132)
Q Consensus 8 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~ 47 (132)
-+.-|+|++|++.-.....+..|....+.... +...|+
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~--~~~icp 113 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEAS--TSVICP 113 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccC--cceeee
Confidence 34469999999886677888888876554322 225566
No 163
>PTZ00448 hypothetical protein; Provisional
Probab=45.78 E-value=16 Score=25.22 Aligned_cols=23 Identities=26% Similarity=0.580 Sum_probs=19.8
Q ss_pred eeeCCCCccccCChhHHHHHHHh
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRN 33 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~ 33 (132)
.|+|..|+..|.+....+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 68899999999888888888765
No 164
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=45.68 E-value=10 Score=26.07 Aligned_cols=24 Identities=21% Similarity=0.251 Sum_probs=20.8
Q ss_pred CCccCCCchhccccchHHHHHHHh
Q psy6628 102 KPYACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 102 ~~~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
.-+.|++|++.|...+.+..|+..
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~g 260 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEG 260 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhh
Confidence 458899999999999999999864
No 165
>COG1773 Rubredoxin [Energy production and conversion]
Probab=45.12 E-value=11 Score=18.37 Aligned_cols=13 Identities=23% Similarity=0.818 Sum_probs=9.9
Q ss_pred eeeCCCCccccCC
Q psy6628 11 VFTCQVCSKIFSY 23 (132)
Q Consensus 11 ~~~C~~C~~~f~~ 23 (132)
.|.|..||.+|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 4788888888754
No 166
>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=45.11 E-value=9.7 Score=18.09 Aligned_cols=12 Identities=25% Similarity=1.038 Sum_probs=8.0
Q ss_pred eeCCCCccccCC
Q psy6628 12 FTCQVCSKIFSY 23 (132)
Q Consensus 12 ~~C~~C~~~f~~ 23 (132)
|.|..||.++..
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 567777776654
No 167
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.86 E-value=12 Score=21.00 Aligned_cols=14 Identities=21% Similarity=0.266 Sum_probs=8.5
Q ss_pred CCccCCcccccccC
Q psy6628 74 KPYQCSQCSKSFFS 87 (132)
Q Consensus 74 ~~~~c~~C~~~~~~ 87 (132)
.|..|+.||++|+.
T Consensus 25 dPiVsPytG~s~P~ 38 (129)
T COG4530 25 DPIVSPYTGKSYPR 38 (129)
T ss_pred CccccCcccccchH
Confidence 35666667766643
No 168
>KOG2071|consensus
Probab=44.38 E-value=18 Score=26.65 Aligned_cols=27 Identities=26% Similarity=0.503 Sum_probs=20.6
Q ss_pred CCCccCCCchhccccchHHHHHHHhhh
Q psy6628 101 EKPYACEFCPLTFRHSSHLFRHRRSLH 127 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~H~~~~~ 127 (132)
..|.+|..||..|........|+..|-
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 467888888888888877777776653
No 169
>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=44.04 E-value=11 Score=17.62 Aligned_cols=12 Identities=25% Similarity=0.977 Sum_probs=7.3
Q ss_pred eeCCCCccccCC
Q psy6628 12 FTCQVCSKIFSY 23 (132)
Q Consensus 12 ~~C~~C~~~f~~ 23 (132)
|.|..|+.++..
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 566667666543
No 170
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.33 E-value=13 Score=17.59 Aligned_cols=10 Identities=30% Similarity=0.740 Sum_probs=5.2
Q ss_pred CccCCCchhc
Q psy6628 103 PYACEFCPLT 112 (132)
Q Consensus 103 ~~~C~~C~~~ 112 (132)
.+.|..|+..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 4555555543
No 171
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=43.28 E-value=4.5 Score=22.87 Aligned_cols=13 Identities=31% Similarity=0.833 Sum_probs=9.5
Q ss_pred CCccCCCchhccc
Q psy6628 102 KPYACEFCPLTFR 114 (132)
Q Consensus 102 ~~~~C~~C~~~f~ 114 (132)
..|.|..||..|.
T Consensus 99 ~Fy~C~~Cg~~wr 111 (113)
T COG1594 99 RFYKCTRCGYRWR 111 (113)
T ss_pred EEEEecccCCEee
Confidence 4588888887765
No 172
>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=42.86 E-value=11 Score=18.28 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=7.9
Q ss_pred eeeCCCCcccc
Q psy6628 11 VFTCQVCSKIF 21 (132)
Q Consensus 11 ~~~C~~C~~~f 21 (132)
.++|+.||..+
T Consensus 2 ~~~CP~CG~~i 12 (54)
T TIGR01206 2 QFECPDCGAEI 12 (54)
T ss_pred ccCCCCCCCEE
Confidence 36788888755
No 173
>KOG4167|consensus
Probab=42.80 E-value=6.9 Score=29.52 Aligned_cols=26 Identities=15% Similarity=0.275 Sum_probs=22.3
Q ss_pred CCccCCCchhccccchHHHHHHHhhh
Q psy6628 102 KPYACEFCPLTFRHSSHLFRHRRSLH 127 (132)
Q Consensus 102 ~~~~C~~C~~~f~~~~~l~~H~~~~~ 127 (132)
..|.|.+|++.|--.-++..|++.|-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 46999999999988888889998874
No 174
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.75 E-value=13 Score=18.48 Aligned_cols=44 Identities=14% Similarity=0.193 Sum_probs=23.8
Q ss_pred hccCCCCCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhcccc
Q psy6628 68 RDHQKEKPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRH 115 (132)
Q Consensus 68 ~~~~~~~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~ 115 (132)
.++.+..++.|+--+-.+....-+.. . ..+.-..|++|+..|..
T Consensus 17 ~I~~~~~~l~C~g~~~p~~HPrV~L~---m-g~~gev~CPYC~t~y~l 60 (62)
T COG4391 17 TIEIGDLPLMCPGPEPPNDHPRVFLD---M-GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred EEEeCCeeEEcCCCCCCCCCCEEEEE---c-CCCCcEecCccccEEEe
Confidence 55666677777654433322211111 1 23455788899888764
No 175
>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=41.87 E-value=11 Score=21.12 Aligned_cols=12 Identities=17% Similarity=0.512 Sum_probs=8.0
Q ss_pred ccCCcccccccC
Q psy6628 76 YQCSQCSKSFFS 87 (132)
Q Consensus 76 ~~c~~C~~~~~~ 87 (132)
|.|+.|+..+..
T Consensus 20 ~iCpeC~~EW~~ 31 (109)
T TIGR00686 20 LICPSCLYEWNE 31 (109)
T ss_pred eECccccccccc
Confidence 677777766543
No 176
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=41.21 E-value=29 Score=24.98 Aligned_cols=25 Identities=32% Similarity=0.644 Sum_probs=22.0
Q ss_pred eeeCCCCccccCChhHHHHHHHhhc
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVRNKH 35 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~~~~ 35 (132)
-..|+.|.+.|.+...+..|+...+
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhh
Confidence 4789999999999999999998554
No 177
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=40.65 E-value=4 Score=18.23 Aligned_cols=9 Identities=44% Similarity=1.327 Sum_probs=3.7
Q ss_pred CCccCCCch
Q psy6628 102 KPYACEFCP 110 (132)
Q Consensus 102 ~~~~C~~C~ 110 (132)
+.|.|..|+
T Consensus 23 ~~w~C~~C~ 31 (40)
T PF04810_consen 23 KTWICNFCG 31 (40)
T ss_dssp TEEEETTT-
T ss_pred CEEECcCCC
Confidence 344444444
No 178
>KOG2636|consensus
Probab=40.59 E-value=23 Score=25.27 Aligned_cols=29 Identities=24% Similarity=0.568 Sum_probs=21.7
Q ss_pred HHhcCCCCccCCCch-hccccchHHHHHHH
Q psy6628 96 RVHTGEKPYACEFCP-LTFRHSSHLFRHRR 124 (132)
Q Consensus 96 ~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 124 (132)
+.|.-...|.|.+|| +++.-+-.+.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 446666778999998 77777778888863
No 179
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=40.50 E-value=19 Score=17.10 Aligned_cols=21 Identities=33% Similarity=0.515 Sum_probs=14.4
Q ss_pred CCCccCCCchhccccchHHHHHHH
Q psy6628 101 EKPYACEFCPLTFRHSSHLFRHRR 124 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~H~~ 124 (132)
.+|-.|..|...|. +|..|+.
T Consensus 3 ~k~GYCE~Cr~kfd---~l~~Hi~ 23 (49)
T smart00586 3 KKPGYCENCREKYD---DLETHLL 23 (49)
T ss_pred CCCcccccHhHHHh---hHHHHhc
Confidence 46778888888775 5556654
No 180
>KOG0717|consensus
Probab=40.18 E-value=21 Score=25.61 Aligned_cols=22 Identities=41% Similarity=0.729 Sum_probs=19.1
Q ss_pred eeCCCCccccCChhHHHHHHHh
Q psy6628 12 FTCQVCSKIFSYENGLKAHVRN 33 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~~~ 33 (132)
+.|.+|.+.|.+...+..|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7799999999999999887653
No 181
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=39.46 E-value=19 Score=15.38 Aligned_cols=13 Identities=23% Similarity=0.498 Sum_probs=8.9
Q ss_pred eeeeCCCCccccC
Q psy6628 10 VVFTCQVCSKIFS 22 (132)
Q Consensus 10 ~~~~C~~C~~~f~ 22 (132)
..+.|..|+.+|.
T Consensus 20 ~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 20 DYEVCIFCGSSFP 32 (33)
T ss_pred CeEEcccCCcEee
Confidence 3467888887764
No 182
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.04 E-value=14 Score=21.05 Aligned_cols=13 Identities=31% Similarity=0.797 Sum_probs=8.6
Q ss_pred CccCCcccccccC
Q psy6628 75 PYQCSQCSKSFFS 87 (132)
Q Consensus 75 ~~~c~~C~~~~~~ 87 (132)
.+.|..|+..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 3578888866644
No 183
>KOG2071|consensus
Probab=38.45 E-value=23 Score=26.09 Aligned_cols=28 Identities=14% Similarity=0.261 Sum_probs=23.0
Q ss_pred cceeeeCCCCccccCChhHHHHHHHhhc
Q psy6628 8 HRVVFTCQVCSKIFSYENGLKAHVRNKH 35 (132)
Q Consensus 8 ~~~~~~C~~C~~~f~~~~~l~~h~~~~~ 35 (132)
.+.+..|..||..|.+......||..|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 4556889999999999988888887775
No 184
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=38.04 E-value=12 Score=16.20 Aligned_cols=7 Identities=29% Similarity=0.857 Sum_probs=2.4
Q ss_pred CCCCccc
Q psy6628 14 CQVCSKI 20 (132)
Q Consensus 14 C~~C~~~ 20 (132)
|+.||..
T Consensus 3 C~~CG~~ 9 (34)
T PF14803_consen 3 CPQCGGP 9 (34)
T ss_dssp -TTT--B
T ss_pred cccccCh
Confidence 5666654
No 185
>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=37.92 E-value=19 Score=17.97 Aligned_cols=12 Identities=25% Similarity=0.725 Sum_probs=5.3
Q ss_pred ccCCcccccccC
Q psy6628 76 YQCSQCSKSFFS 87 (132)
Q Consensus 76 ~~c~~C~~~~~~ 87 (132)
+.|..||..|..
T Consensus 26 hhCr~CG~~vC~ 37 (69)
T PF01363_consen 26 HHCRNCGRVVCS 37 (69)
T ss_dssp EE-TTT--EEEC
T ss_pred EccCCCCCEECC
Confidence 456667766654
No 186
>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=37.19 E-value=53 Score=16.31 Aligned_cols=12 Identities=25% Similarity=0.396 Sum_probs=7.9
Q ss_pred eeCCCCccccCC
Q psy6628 12 FTCQVCSKIFSY 23 (132)
Q Consensus 12 ~~C~~C~~~f~~ 23 (132)
-.|+.||.....
T Consensus 29 q~C~~CG~~~~~ 40 (69)
T PF07282_consen 29 QTCPRCGHRNKK 40 (69)
T ss_pred cCccCccccccc
Confidence 457888876544
No 187
>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=37.06 E-value=12 Score=21.12 Aligned_cols=25 Identities=20% Similarity=0.578 Sum_probs=13.8
Q ss_pred ccCCcccccccChhhHHHHHHHhcCCCCccCCCchhc
Q psy6628 76 YQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLT 112 (132)
Q Consensus 76 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 112 (132)
+.|..|+..|.-.... +.||.|+..
T Consensus 71 ~~C~~Cg~~~~~~~~~------------~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFD------------FSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEECHHCC------------HH-SSSSSS
T ss_pred EECCCCCCEEecCCCC------------CCCcCCcCC
Confidence 5678888777553221 447777753
No 188
>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=36.56 E-value=10 Score=17.39 Aligned_cols=8 Identities=38% Similarity=1.294 Sum_probs=3.7
Q ss_pred CccCCccc
Q psy6628 75 PYQCSQCS 82 (132)
Q Consensus 75 ~~~c~~C~ 82 (132)
.|.|..|+
T Consensus 37 ~~~C~~C~ 44 (46)
T PF12760_consen 37 RYRCKACR 44 (46)
T ss_pred eEECCCCC
Confidence 34454443
No 189
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.51 E-value=19 Score=20.93 Aligned_cols=14 Identities=36% Similarity=0.842 Sum_probs=8.5
Q ss_pred CCCccCCCchhccc
Q psy6628 101 EKPYACEFCPLTFR 114 (132)
Q Consensus 101 ~~~~~C~~C~~~f~ 114 (132)
..-|.|+.|++.|.
T Consensus 51 ~qRyrC~~C~~tf~ 64 (129)
T COG3677 51 HQRYKCKSCGSTFT 64 (129)
T ss_pred ccccccCCcCccee
Confidence 34566666666665
No 190
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=35.85 E-value=31 Score=16.32 Aligned_cols=21 Identities=33% Similarity=0.653 Sum_probs=13.4
Q ss_pred CCCccCCCchhccccchHHHHHHH
Q psy6628 101 EKPYACEFCPLTFRHSSHLFRHRR 124 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~H~~ 124 (132)
.++-.|..|...|. +|..|+.
T Consensus 3 ~k~GYCE~C~~ky~---~l~~Hi~ 23 (49)
T PF07535_consen 3 KKPGYCENCRVKYD---DLEEHIQ 23 (49)
T ss_pred CCCccCccccchhh---hHHHHhC
Confidence 35567777777765 4566654
No 191
>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=35.28 E-value=20 Score=17.57 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=5.0
Q ss_pred eeCCCCccccC
Q psy6628 12 FTCQVCSKIFS 22 (132)
Q Consensus 12 ~~C~~C~~~f~ 22 (132)
..|++|++.+.
T Consensus 3 v~CP~C~k~~~ 13 (57)
T PF03884_consen 3 VKCPICGKPVE 13 (57)
T ss_dssp EE-TTT--EEE
T ss_pred ccCCCCCCeec
Confidence 46777777653
No 192
>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=35.19 E-value=7 Score=17.14 Aligned_cols=8 Identities=38% Similarity=1.410 Sum_probs=3.7
Q ss_pred CCccCCcc
Q psy6628 74 KPYQCSQC 81 (132)
Q Consensus 74 ~~~~c~~C 81 (132)
..|.|..|
T Consensus 28 qryrC~~C 35 (36)
T PF03811_consen 28 QRYRCKDC 35 (36)
T ss_pred EeEecCcC
Confidence 33555444
No 193
>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=35.17 E-value=28 Score=20.82 Aligned_cols=48 Identities=17% Similarity=0.252 Sum_probs=27.5
Q ss_pred cccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChhhHHHHHH
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHKIHSR 96 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~~l~~h~~ 96 (132)
+.|..-..-.-+|.+...+.... . .+-..|++||..-..+..+.-++.
T Consensus 6 L~C~~gH~FEgWF~ss~~fd~Q~-~----~glv~CP~Cgs~~V~K~lmAP~v~ 53 (148)
T PF06676_consen 6 LRCENGHEFEGWFRSSAAFDRQQ-A----RGLVSCPVCGSTEVSKALMAPAVA 53 (148)
T ss_pred EecCCCCccceecCCHHHHHHHH-H----cCCccCCCCCCCeEeeecCCCeec
Confidence 45642223445567777666554 2 234689999877666555444443
No 194
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=35.11 E-value=13 Score=21.03 Aligned_cols=12 Identities=17% Similarity=0.479 Sum_probs=7.8
Q ss_pred CccCCccccccc
Q psy6628 75 PYQCSQCSKSFF 86 (132)
Q Consensus 75 ~~~c~~C~~~~~ 86 (132)
.+.|..|+..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (114)
T PRK03681 70 ECWCETCQQYVT 81 (114)
T ss_pred EEEcccCCCeee
Confidence 357888876553
No 195
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.02 E-value=23 Score=19.62 Aligned_cols=16 Identities=25% Similarity=0.374 Sum_probs=11.6
Q ss_pred cceeeeCCCCccccCC
Q psy6628 8 HRVVFTCQVCSKIFSY 23 (132)
Q Consensus 8 ~~~~~~C~~C~~~f~~ 23 (132)
-++.|.|+.|+..-..
T Consensus 19 L~k~FtCp~Cghe~vs 34 (104)
T COG4888 19 LPKTFTCPRCGHEKVS 34 (104)
T ss_pred CCceEecCccCCeeee
Confidence 4567999999975433
No 196
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=34.98 E-value=14 Score=21.94 Aligned_cols=28 Identities=21% Similarity=0.454 Sum_probs=17.9
Q ss_pred CCccCCcccccccChhhHHHHHHHhcCCCCccCCCchh
Q psy6628 74 KPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPL 111 (132)
Q Consensus 74 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 111 (132)
..+.|..||...... + .+..-.|+.|+.
T Consensus 111 G~l~C~~Cg~~~~~~---------~-~~~l~~Cp~C~~ 138 (146)
T PF07295_consen 111 GTLVCENCGHEVELT---------H-PERLPPCPKCGH 138 (146)
T ss_pred ceEecccCCCEEEec---------C-CCcCCCCCCCCC
Confidence 457888888765332 2 235567888875
No 197
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=34.96 E-value=30 Score=21.38 Aligned_cols=7 Identities=29% Similarity=1.108 Sum_probs=3.5
Q ss_pred ccCCCch
Q psy6628 104 YACEFCP 110 (132)
Q Consensus 104 ~~C~~C~ 110 (132)
|.|+.||
T Consensus 133 F~Cp~Cg 139 (176)
T COG1675 133 FTCPKCG 139 (176)
T ss_pred CCCCCCC
Confidence 4555554
No 198
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.66 E-value=28 Score=23.21 Aligned_cols=24 Identities=25% Similarity=0.660 Sum_probs=14.4
Q ss_pred ccCCcccccccChhhHHHHHHHhcCCCCccCCCchhcc
Q psy6628 76 YQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTF 113 (132)
Q Consensus 76 ~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f 113 (132)
|.|+.|...|.. -|-.|+.|+..|
T Consensus 256 yvCs~Clsi~C~--------------~p~~C~~Cgt~f 279 (279)
T TIGR00627 256 FVCSVCLSVLCQ--------------YTPICKTCKTAF 279 (279)
T ss_pred EECCCccCCcCC--------------CCCCCCCCCCCC
Confidence 667777665543 233777777554
No 199
>PRK14873 primosome assembly protein PriA; Provisional
Probab=34.38 E-value=22 Score=26.86 Aligned_cols=11 Identities=18% Similarity=0.540 Sum_probs=7.2
Q ss_pred CCccCCCchhc
Q psy6628 102 KPYACEFCPLT 112 (132)
Q Consensus 102 ~~~~C~~C~~~ 112 (132)
.|+.|+.|+..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 35677777753
No 200
>KOG2857|consensus
Probab=33.88 E-value=21 Score=21.12 Aligned_cols=22 Identities=18% Similarity=0.498 Sum_probs=16.5
Q ss_pred CccCCCchhccccchHHHHHHH
Q psy6628 103 PYACEFCPLTFRHSSHLFRHRR 124 (132)
Q Consensus 103 ~~~C~~C~~~f~~~~~l~~H~~ 124 (132)
-|+|+.|...|-+...++.|+.
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hccCCCCCCccccchhhhhccC
Confidence 3788888877777777777765
No 201
>PHA02998 RNA polymerase subunit; Provisional
Probab=33.35 E-value=6.2 Score=24.21 Aligned_cols=14 Identities=29% Similarity=0.527 Sum_probs=10.3
Q ss_pred CCccCCCchhcccc
Q psy6628 102 KPYACEFCPLTFRH 115 (132)
Q Consensus 102 ~~~~C~~C~~~f~~ 115 (132)
..|.|..|+..|.-
T Consensus 170 ~FYkC~~CG~~wkp 183 (195)
T PHA02998 170 VRHACRDCKKHFKP 183 (195)
T ss_pred EEEEcCCCCCccCC
Confidence 34888889887753
No 202
>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=33.34 E-value=18 Score=20.10 Aligned_cols=7 Identities=43% Similarity=1.250 Sum_probs=3.3
Q ss_pred ccCCCch
Q psy6628 104 YACEFCP 110 (132)
Q Consensus 104 ~~C~~C~ 110 (132)
|.|.-|+
T Consensus 32 y~C~~C~ 38 (102)
T PF11672_consen 32 YVCTPCD 38 (102)
T ss_pred EECCCCC
Confidence 4454443
No 203
>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=33.20 E-value=18 Score=15.66 Aligned_cols=12 Identities=33% Similarity=0.714 Sum_probs=5.3
Q ss_pred cCCCchhccccc
Q psy6628 105 ACEFCPLTFRHS 116 (132)
Q Consensus 105 ~C~~C~~~f~~~ 116 (132)
.|..|++.|..+
T Consensus 5 ~C~eC~~~f~dS 16 (34)
T PF01286_consen 5 KCDECGKPFMDS 16 (34)
T ss_dssp E-TTT--EES-S
T ss_pred hHhHhCCHHHHH
Confidence 567777777654
No 204
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=33.12 E-value=19 Score=23.13 Aligned_cols=17 Identities=24% Similarity=0.696 Sum_probs=11.0
Q ss_pred ccceeeeCCCCccccCC
Q psy6628 7 IHRVVFTCQVCSKIFSY 23 (132)
Q Consensus 7 ~~~~~~~C~~C~~~f~~ 23 (132)
...++..|++||..|.-
T Consensus 177 rEGkpqRCpECGqVFKL 193 (268)
T PTZ00043 177 REGFLYRCGECDQIFML 193 (268)
T ss_pred cCCCCccCCCCCcEEEE
Confidence 34456777788777643
No 205
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=33.07 E-value=23 Score=17.46 Aligned_cols=29 Identities=24% Similarity=0.541 Sum_probs=17.4
Q ss_pred cccCCCCCCcccccChHHHHhhhhhccCCCCCccCCccc
Q psy6628 44 FKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCS 82 (132)
Q Consensus 44 ~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~ 82 (132)
|.|+ ||..|..... -...|++...|+.|.
T Consensus 23 yPCP----CGDRFeIsLe------Dl~~GE~VArCPSCS 51 (67)
T COG5216 23 YPCP----CGDRFEISLE------DLRNGEVVARCPSCS 51 (67)
T ss_pred ecCC----CCCEeEEEHH------HhhCCceEEEcCCce
Confidence 6776 8877765421 223456666777764
No 206
>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=32.94 E-value=24 Score=15.87 Aligned_cols=9 Identities=22% Similarity=0.767 Sum_probs=4.9
Q ss_pred eeCCCCccc
Q psy6628 12 FTCQVCSKI 20 (132)
Q Consensus 12 ~~C~~C~~~ 20 (132)
|.|+.|+..
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 356666653
No 207
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=32.85 E-value=44 Score=13.86 Aligned_cols=16 Identities=13% Similarity=0.445 Sum_probs=8.4
Q ss_pred ceeeeCCCCccccCCh
Q psy6628 9 RVVFTCQVCSKIFSYE 24 (132)
Q Consensus 9 ~~~~~C~~C~~~f~~~ 24 (132)
...|.|+.|+..+-+.
T Consensus 11 ~~kY~Cp~C~~~~CSl 26 (30)
T PF04438_consen 11 PAKYRCPRCGARYCSL 26 (30)
T ss_dssp EESEE-TTT--EESSH
T ss_pred CCEEECCCcCCceeCc
Confidence 3458888888776543
No 208
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=32.82 E-value=30 Score=23.15 Aligned_cols=22 Identities=27% Similarity=0.324 Sum_probs=12.7
Q ss_pred CccCCcccccccChhhHHHHHH
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSR 96 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~ 96 (132)
-|.|..|-+-|.....+.+|+.
T Consensus 48 lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 48 LYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred EEEcCCCcchhCCHHHHHHHHH
Confidence 3556666555556656655554
No 209
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=32.45 E-value=25 Score=17.05 Aligned_cols=18 Identities=17% Similarity=0.490 Sum_probs=8.2
Q ss_pred CCccCCCchhccccchHH
Q psy6628 102 KPYACEFCPLTFRHSSHL 119 (132)
Q Consensus 102 ~~~~C~~C~~~f~~~~~l 119 (132)
+-+.|-.||..|.+...|
T Consensus 26 ~~~YC~~Cg~~Y~d~~dL 43 (55)
T PF13821_consen 26 EHNYCFWCGTKYDDEEDL 43 (55)
T ss_pred hCceeeeeCCccCCHHHH
Confidence 334444455444444433
No 210
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=31.25 E-value=16 Score=22.93 Aligned_cols=9 Identities=44% Similarity=1.154 Sum_probs=0.0
Q ss_pred CCccCCCch
Q psy6628 102 KPYACEFCP 110 (132)
Q Consensus 102 ~~~~C~~C~ 110 (132)
+-|.|.+||
T Consensus 100 ~ey~CEICG 108 (196)
T PF11931_consen 100 VEYKCEICG 108 (196)
T ss_dssp ---------
T ss_pred CeeeeEeCC
Confidence 344555554
No 211
>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=31.25 E-value=22 Score=15.88 Aligned_cols=11 Identities=18% Similarity=0.764 Sum_probs=8.4
Q ss_pred eeCCCCccccC
Q psy6628 12 FTCQVCSKIFS 22 (132)
Q Consensus 12 ~~C~~C~~~f~ 22 (132)
+.|+.||..+-
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 57999998753
No 212
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=30.68 E-value=38 Score=16.19 Aligned_cols=12 Identities=25% Similarity=0.736 Sum_probs=8.2
Q ss_pred ceeeeCCCCccc
Q psy6628 9 RVVFTCQVCSKI 20 (132)
Q Consensus 9 ~~~~~C~~C~~~ 20 (132)
+....|+.||..
T Consensus 44 ~~i~~Cp~CgRi 55 (56)
T PF02591_consen 44 DEIVFCPNCGRI 55 (56)
T ss_pred CCeEECcCCCcc
Confidence 456778888764
No 213
>COG2879 Uncharacterized small protein [Function unknown]
Probab=30.67 E-value=43 Score=16.81 Aligned_cols=16 Identities=19% Similarity=0.158 Sum_probs=9.1
Q ss_pred chHHHHHHHhhhhhcc
Q psy6628 116 SSHLFRHRRSLHQMYE 131 (132)
Q Consensus 116 ~~~l~~H~~~~~~~~~ 131 (132)
.++...|++.+|+.+|
T Consensus 25 YdnYVehmr~~hPd~p 40 (65)
T COG2879 25 YDNYVEHMRKKHPDKP 40 (65)
T ss_pred HHHHHHHHHHhCcCCC
Confidence 3455566666666554
No 214
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=30.65 E-value=69 Score=21.55 Aligned_cols=25 Identities=20% Similarity=0.498 Sum_probs=22.6
Q ss_pred cceeeeCCCCccccCChhHHHHHHH
Q psy6628 8 HRVVFTCQVCSKIFSYENGLKAHVR 32 (132)
Q Consensus 8 ~~~~~~C~~C~~~f~~~~~l~~h~~ 32 (132)
.+..|.|..|-+-|.....|.+|+.
T Consensus 45 ~~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 45 CTKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CCeEEEcCCCcchhCCHHHHHHHHH
Confidence 3567999999999999999999987
No 215
>PRK01343 zinc-binding protein; Provisional
Probab=30.64 E-value=31 Score=16.94 Aligned_cols=12 Identities=25% Similarity=0.487 Sum_probs=9.5
Q ss_pred eeeCCCCccccC
Q psy6628 11 VFTCQVCSKIFS 22 (132)
Q Consensus 11 ~~~C~~C~~~f~ 22 (132)
.-.|++|++.+.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 467999999864
No 216
>PF14369 zf-RING_3: zinc-finger
Probab=30.36 E-value=24 Score=15.28 Aligned_cols=10 Identities=30% Similarity=0.720 Sum_probs=8.0
Q ss_pred eCCCCccccC
Q psy6628 13 TCQVCSKIFS 22 (132)
Q Consensus 13 ~C~~C~~~f~ 22 (132)
.|+.|+..|-
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 5999998774
No 217
>PLN02748 tRNA dimethylallyltransferase
Probab=29.60 E-value=40 Score=24.38 Aligned_cols=24 Identities=17% Similarity=0.439 Sum_probs=18.0
Q ss_pred CCccCCcccc-cccChhhHHHHHHH
Q psy6628 74 KPYQCSQCSK-SFFSKYDHKIHSRV 97 (132)
Q Consensus 74 ~~~~c~~C~~-~~~~~~~l~~h~~~ 97 (132)
+.|.|.+|+. .+.....|..|.+.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 4467888886 78888888888764
No 218
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=29.40 E-value=9.6 Score=19.49 Aligned_cols=9 Identities=44% Similarity=1.135 Sum_probs=4.8
Q ss_pred CccCCCchh
Q psy6628 103 PYACEFCPL 111 (132)
Q Consensus 103 ~~~C~~C~~ 111 (132)
.+.|+.|+.
T Consensus 61 ~~~C~~C~~ 69 (71)
T PF05495_consen 61 DYFCPICGL 69 (71)
T ss_dssp SEEETTTTE
T ss_pred CccCcCcCC
Confidence 455555553
No 219
>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=29.26 E-value=45 Score=15.70 Aligned_cols=12 Identities=33% Similarity=0.894 Sum_probs=7.8
Q ss_pred ccCCcccccccC
Q psy6628 76 YQCSQCSKSFFS 87 (132)
Q Consensus 76 ~~c~~C~~~~~~ 87 (132)
..|..||..|..
T Consensus 19 ~~Cr~Cg~~~C~ 30 (57)
T cd00065 19 HHCRNCGRIFCS 30 (57)
T ss_pred cccCcCcCCcCh
Confidence 457777777654
No 220
>PRK10220 hypothetical protein; Provisional
Probab=29.20 E-value=40 Score=19.00 Aligned_cols=11 Identities=27% Similarity=1.014 Sum_probs=6.9
Q ss_pred eCCCCccccCC
Q psy6628 13 TCQVCSKIFSY 23 (132)
Q Consensus 13 ~C~~C~~~f~~ 23 (132)
.||.|+..|.+
T Consensus 5 ~CP~C~seytY 15 (111)
T PRK10220 5 HCPKCNSEYTY 15 (111)
T ss_pred cCCCCCCcceE
Confidence 47777766544
No 221
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=29.14 E-value=28 Score=19.46 Aligned_cols=24 Identities=21% Similarity=0.397 Sum_probs=17.3
Q ss_pred CCccCCCchhccccchHHHHHHHh
Q psy6628 102 KPYACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 102 ~~~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
..+.|-.|.+-|.+...|..|.+.
T Consensus 54 GqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhcc
Confidence 346777788888877777777653
No 222
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=29.09 E-value=19 Score=25.91 Aligned_cols=39 Identities=18% Similarity=0.272 Sum_probs=20.7
Q ss_pred CCCccCCcccccccChhh-HHHHHH----HhcCCCCccCCCchh
Q psy6628 73 EKPYQCSQCSKSFFSKYD-HKIHSR----VHTGEKPYACEFCPL 111 (132)
Q Consensus 73 ~~~~~c~~C~~~~~~~~~-l~~h~~----~h~~~~~~~C~~C~~ 111 (132)
.+.|+|..|+..+.-... -..-+. ...-...|.||+|+.
T Consensus 423 ~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~ 466 (479)
T PRK05452 423 GPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSL 466 (479)
T ss_pred CCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCC
Confidence 345889999988754211 110010 001123589999984
No 223
>PRK00420 hypothetical protein; Validated
Probab=29.08 E-value=31 Score=19.58 Aligned_cols=12 Identities=17% Similarity=0.410 Sum_probs=7.2
Q ss_pred CccCCccccccc
Q psy6628 75 PYQCSQCSKSFF 86 (132)
Q Consensus 75 ~~~c~~C~~~~~ 86 (132)
...|+.||....
T Consensus 40 ~~~Cp~Cg~~~~ 51 (112)
T PRK00420 40 EVVCPVHGKVYI 51 (112)
T ss_pred ceECCCCCCeee
Confidence 356777776543
No 224
>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=28.87 E-value=23 Score=18.70 Aligned_cols=9 Identities=44% Similarity=1.202 Sum_probs=3.0
Q ss_pred eeeeCCCCc
Q psy6628 10 VVFTCQVCS 18 (132)
Q Consensus 10 ~~~~C~~C~ 18 (132)
+.|.|+.|+
T Consensus 21 ~~F~CPfC~ 29 (81)
T PF05129_consen 21 KVFDCPFCN 29 (81)
T ss_dssp S----TTT-
T ss_pred ceEcCCcCC
Confidence 458888888
No 225
>KOG1994|consensus
Probab=28.86 E-value=20 Score=23.01 Aligned_cols=24 Identities=25% Similarity=0.758 Sum_probs=19.8
Q ss_pred CCCCccCCCchhccccchHHHHHH
Q psy6628 100 GEKPYACEFCPLTFRHSSHLFRHR 123 (132)
Q Consensus 100 ~~~~~~C~~C~~~f~~~~~l~~H~ 123 (132)
....|.|-.||..|.+...|..|=
T Consensus 236 R~eh~YC~fCG~~y~~~edl~ehC 259 (268)
T KOG1994|consen 236 RSEHYYCFFCGIKYKDEEDLYEHC 259 (268)
T ss_pred hccceEEEEeccccCCHHHHHHhC
Confidence 345799999999999998887773
No 226
>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=28.45 E-value=23 Score=20.93 Aligned_cols=39 Identities=15% Similarity=0.310 Sum_probs=22.5
Q ss_pred ccCCcccccccChhhH--HHHH---HHhcCCCCccCCCchhccc
Q psy6628 76 YQCSQCSKSFFSKYDH--KIHS---RVHTGEKPYACEFCPLTFR 114 (132)
Q Consensus 76 ~~c~~C~~~~~~~~~l--~~h~---~~h~~~~~~~C~~C~~~f~ 114 (132)
-.|..|+..+.....- ..-. .....+..|.|+.|++.|=
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW 135 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYW 135 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEec
Confidence 4789998765432211 0000 1122356899999999884
No 227
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.44 E-value=14 Score=28.19 Aligned_cols=8 Identities=38% Similarity=0.899 Sum_probs=4.3
Q ss_pred CCCCcccc
Q psy6628 14 CQVCSKIF 21 (132)
Q Consensus 14 C~~C~~~f 21 (132)
|..||.++
T Consensus 438 C~~Cg~v~ 445 (730)
T COG1198 438 CRDCGYIA 445 (730)
T ss_pred cccCCCcc
Confidence 55555544
No 228
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=27.85 E-value=27 Score=16.66 Aligned_cols=17 Identities=18% Similarity=0.403 Sum_probs=11.7
Q ss_pred CCccCCCchhccccchH
Q psy6628 102 KPYACEFCPLTFRHSSH 118 (132)
Q Consensus 102 ~~~~C~~C~~~f~~~~~ 118 (132)
.-++|+.|+..|...-.
T Consensus 27 v~W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 27 VWWKCPKCGHEWKASVN 43 (55)
T ss_pred EEEECCCCCCeeEccHh
Confidence 34888888877765433
No 229
>KOG0320|consensus
Probab=27.61 E-value=30 Score=21.41 Aligned_cols=15 Identities=20% Similarity=0.521 Sum_probs=9.8
Q ss_pred CCccCCCchhccccc
Q psy6628 102 KPYACEFCPLTFRHS 116 (132)
Q Consensus 102 ~~~~C~~C~~~f~~~ 116 (132)
.-.+|+.|++....+
T Consensus 166 ~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 166 NTNKCPTCRKKITHK 180 (187)
T ss_pred hCCCCCCcccccchh
Confidence 446888888755443
No 230
>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=27.35 E-value=44 Score=14.32 Aligned_cols=11 Identities=18% Similarity=0.610 Sum_probs=5.2
Q ss_pred eeeCCCCcccc
Q psy6628 11 VFTCQVCSKIF 21 (132)
Q Consensus 11 ~~~C~~C~~~f 21 (132)
.+.|+.|++..
T Consensus 4 ~~~C~nC~R~v 14 (33)
T PF08209_consen 4 YVECPNCGRPV 14 (33)
T ss_dssp EEE-TTTSSEE
T ss_pred eEECCCCcCCc
Confidence 35566666543
No 231
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.34 E-value=22 Score=20.46 Aligned_cols=31 Identities=19% Similarity=0.365 Sum_probs=16.6
Q ss_pred CccCCcccccccChhhHHHHHHHhcCCCCccCCCchh
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPL 111 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 111 (132)
.+.| .|+..|.....-.. +. .-.+.||.|+.
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~----~~-~~~~~CP~Cgs 100 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEID----HY-AAVIECPVCGN 100 (124)
T ss_pred eEEe-eCcCcccccccchh----cc-ccCCcCcCCCC
Confidence 3679 89877654321000 00 01257999984
No 232
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=27.28 E-value=30 Score=16.61 Aligned_cols=10 Identities=20% Similarity=0.816 Sum_probs=6.6
Q ss_pred cCCCchhccc
Q psy6628 105 ACEFCPLTFR 114 (132)
Q Consensus 105 ~C~~C~~~f~ 114 (132)
.||+||..+.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 5777876553
No 233
>KOG2272|consensus
Probab=27.03 E-value=67 Score=21.19 Aligned_cols=16 Identities=25% Similarity=0.858 Sum_probs=11.2
Q ss_pred CCCccCCcccccccCh
Q psy6628 73 EKPYQCSQCSKSFFSK 88 (132)
Q Consensus 73 ~~~~~c~~C~~~~~~~ 88 (132)
.--|.|..|.+.|..-
T Consensus 219 veHFvCa~CekPFlGH 234 (332)
T KOG2272|consen 219 VEHFVCAKCEKPFLGH 234 (332)
T ss_pred hhheeehhcCCcccch
Confidence 3457888888887653
No 234
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=26.99 E-value=70 Score=17.98 Aligned_cols=22 Identities=14% Similarity=0.259 Sum_probs=15.7
Q ss_pred eeeCCCCccccCChhHHHHHHH
Q psy6628 11 VFTCQVCSKIFSYENGLKAHVR 32 (132)
Q Consensus 11 ~~~C~~C~~~f~~~~~l~~h~~ 32 (132)
.+.|+.||..+...........
T Consensus 31 ~~~C~~CGe~~~~~e~~~~~~~ 52 (127)
T TIGR03830 31 GWYCPACGEELLDPEESKRNSA 52 (127)
T ss_pred eeECCCCCCEEEcHHHHHHHHH
Confidence 4789999998877765554443
No 235
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=26.54 E-value=66 Score=19.68 Aligned_cols=10 Identities=10% Similarity=0.674 Sum_probs=4.7
Q ss_pred CCcccccChH
Q psy6628 51 ECDRVFTTRN 60 (132)
Q Consensus 51 ~c~~~~~~~~ 60 (132)
.|++.|...+
T Consensus 135 ~CgkiYW~Gs 144 (165)
T COG1656 135 KCGKIYWKGS 144 (165)
T ss_pred CCcccccCch
Confidence 4555544443
No 236
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=26.53 E-value=35 Score=16.31 Aligned_cols=16 Identities=19% Similarity=0.677 Sum_probs=9.6
Q ss_pred cceeeeCCCCccccCC
Q psy6628 8 HRVVFTCQVCSKIFSY 23 (132)
Q Consensus 8 ~~~~~~C~~C~~~f~~ 23 (132)
....|.|..|++.+..
T Consensus 32 ~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 32 EPIKLRCHYCERIITE 47 (52)
T ss_dssp TTCEEEETTT--EEEH
T ss_pred CCCEEEeeCCCCEecc
Confidence 4456889999887643
No 237
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=26.29 E-value=24 Score=17.17 Aligned_cols=9 Identities=22% Similarity=1.125 Sum_probs=2.5
Q ss_pred eeCCCCccc
Q psy6628 12 FTCQVCSKI 20 (132)
Q Consensus 12 ~~C~~C~~~ 20 (132)
|+|++||-+
T Consensus 34 y~Cp~CgAt 42 (55)
T PF05741_consen 34 YVCPICGAT 42 (55)
T ss_dssp ---TTT---
T ss_pred CcCCCCcCc
Confidence 778888764
No 238
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=26.19 E-value=29 Score=20.33 Aligned_cols=58 Identities=26% Similarity=0.449 Sum_probs=31.5
Q ss_pred eeeeCCCCccccCChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccChh
Q psy6628 10 VVFTCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKY 89 (132)
Q Consensus 10 ~~~~C~~C~~~f~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~~ 89 (132)
++|+|.+|..+.....-|. | -.|=+-.+|+.. ...|..+- ..++ .|++|..+|.+..
T Consensus 79 ~lYeCnIC~etS~ee~FLK-------------P-neCCgY~iCn~C---ya~LWK~~-~~yp-----vCPvCkTSFKss~ 135 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLK-------------P-NECCGYSICNAC---YANLWKFC-NLYP-----VCPVCKTSFKSSS 135 (140)
T ss_pred CceeccCcccccchhhcCC-------------c-ccccchHHHHHH---HHHHHHHc-ccCC-----CCCcccccccccc
Confidence 6799999999875543221 1 233111122222 23455554 3332 6888888887654
Q ss_pred h
Q psy6628 90 D 90 (132)
Q Consensus 90 ~ 90 (132)
.
T Consensus 136 ~ 136 (140)
T PF05290_consen 136 S 136 (140)
T ss_pred c
Confidence 3
No 239
>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 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=26.03 E-value=48 Score=17.97 Aligned_cols=20 Identities=15% Similarity=0.426 Sum_probs=14.9
Q ss_pred eeCCCCccccCChhHHHHHH
Q psy6628 12 FTCQVCSKIFSYENGLKAHV 31 (132)
Q Consensus 12 ~~C~~C~~~f~~~~~l~~h~ 31 (132)
..|+.||..+-+..-+..--
T Consensus 36 ~~C~~CGe~y~~dev~~eIE 55 (89)
T TIGR03829 36 ISCSHCGMEYQDDTTVKEIE 55 (89)
T ss_pred ccccCCCcEeecHHHHHHHH
Confidence 67999999987776554443
No 241
>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=25.48 E-value=27 Score=20.58 Aligned_cols=32 Identities=25% Similarity=0.629 Sum_probs=19.1
Q ss_pred CccCCcccccccChhhHHHHHHHhcCCCCccCCCchhccc
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFR 114 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~ 114 (132)
.|.|..|+..+.... .. ..+-|.|+.|+..+.
T Consensus 123 ~~~C~~C~~~~~r~~------~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYKRHR------RS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEeeeec------cc--chhhEECCCCCCEEE
Confidence 367888886663322 22 123388888886654
No 242
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=24.86 E-value=50 Score=20.36 Aligned_cols=21 Identities=14% Similarity=0.194 Sum_probs=15.9
Q ss_pred CCCccCCCchhccccchHHHH
Q psy6628 101 EKPYACEFCPLTFRHSSHLFR 121 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~ 121 (132)
.....|..||+.|.....+..
T Consensus 112 ~~~~~C~~Cg~~f~~~k~i~~ 132 (181)
T PRK08222 112 FHLQRCSRCERPFAPQKTVAL 132 (181)
T ss_pred cccCcCcccCCccCcHhHHHH
Confidence 357899999999986655543
No 243
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.78 E-value=28 Score=13.73 Aligned_cols=6 Identities=33% Similarity=1.143 Sum_probs=3.5
Q ss_pred CCCCcc
Q psy6628 14 CQVCSK 19 (132)
Q Consensus 14 C~~C~~ 19 (132)
|+.||.
T Consensus 19 C~~CG~ 24 (26)
T PF13248_consen 19 CPNCGA 24 (26)
T ss_pred ChhhCC
Confidence 666654
No 244
>PF12773 DZR: Double zinc ribbon
Probab=24.34 E-value=51 Score=15.13 Aligned_cols=8 Identities=25% Similarity=0.933 Sum_probs=3.7
Q ss_pred cCCccccc
Q psy6628 77 QCSQCSKS 84 (132)
Q Consensus 77 ~c~~C~~~ 84 (132)
.|..|+..
T Consensus 31 ~C~~Cg~~ 38 (50)
T PF12773_consen 31 ICPNCGAE 38 (50)
T ss_pred CCcCCcCC
Confidence 45555443
No 245
>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=24.26 E-value=22 Score=20.88 Aligned_cols=18 Identities=39% Similarity=0.855 Sum_probs=13.6
Q ss_pred HhcCCCCccCCCchhcccc
Q psy6628 97 VHTGEKPYACEFCPLTFRH 115 (132)
Q Consensus 97 ~h~~~~~~~C~~C~~~f~~ 115 (132)
.+.+ +|..|+.||..|..
T Consensus 107 l~~g-~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 107 LHKG-KPQRCPECGQVFKL 124 (136)
T ss_dssp EETT-SEEEETTTEEEEEE
T ss_pred EeCC-CccCCCCCCeEEEE
Confidence 3444 68999999998864
No 246
>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=24.01 E-value=36 Score=14.15 Aligned_cols=11 Identities=36% Similarity=0.969 Sum_probs=8.0
Q ss_pred eeCCCCccccC
Q psy6628 12 FTCQVCSKIFS 22 (132)
Q Consensus 12 ~~C~~C~~~f~ 22 (132)
|.|..|++.+.
T Consensus 28 f~C~~C~~~L~ 38 (39)
T smart00132 28 FKCSKCGKPLG 38 (39)
T ss_pred CCCcccCCcCc
Confidence 77888887653
No 247
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=23.78 E-value=36 Score=16.46 Aligned_cols=8 Identities=25% Similarity=0.841 Sum_probs=4.3
Q ss_pred eeCCCCcc
Q psy6628 12 FTCQVCSK 19 (132)
Q Consensus 12 ~~C~~C~~ 19 (132)
..||.||.
T Consensus 4 kPCPFCG~ 11 (61)
T PF14354_consen 4 KPCPFCGS 11 (61)
T ss_pred cCCCCCCC
Confidence 44666654
No 248
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=23.75 E-value=26 Score=22.38 Aligned_cols=27 Identities=11% Similarity=0.335 Sum_probs=0.0
Q ss_pred ceeeeCCCCccccCChhHHHHHHHhhcC
Q psy6628 9 RVVFTCQVCSKIFSYENGLKAHVRNKHG 36 (132)
Q Consensus 9 ~~~~~C~~C~~~f~~~~~l~~h~~~~~~ 36 (132)
.....||+||+..+. ..+..||++...
T Consensus 166 ~~~~~cPitGe~IP~-~e~~eHmRi~Ll 192 (229)
T PF12230_consen 166 EKMIICPITGEMIPA-DEMDEHMRIELL 192 (229)
T ss_dssp ----------------------------
T ss_pred ccccccccccccccc-cccccccccccc
Confidence 344678888886644 668888887653
No 249
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.63 E-value=64 Score=18.71 Aligned_cols=61 Identities=16% Similarity=0.244 Sum_probs=27.8
Q ss_pred CChhHHHHHHHhhcCCCCCCCccccCCCCCCcccccChHHHHhhhhhccCCCCCccCCcccccccCh
Q psy6628 22 SYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSK 88 (132)
Q Consensus 22 ~~~~~l~~h~~~~~~~~~~~~~~~c~~~~~c~~~~~~~~~l~~h~~~~~~~~~~~~c~~C~~~~~~~ 88 (132)
.+..+|.+-...+.+.. .-..|+ .|+........+..-+..-+.=+.|-.|.-||..|++-
T Consensus 21 dq~pel~eafcskcgea---ti~qcp---~csasirgd~~vegvlglg~dye~psfchncgs~fpwt 81 (160)
T COG4306 21 DQSPELMEAFCSKCGEA---TITQCP---ICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWT 81 (160)
T ss_pred cCCHHHHHHHHhhhchH---HHhcCC---ccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcH
Confidence 34455655555555532 224666 56544332221111110111123455677777777664
No 250
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=23.39 E-value=41 Score=24.16 Aligned_cols=25 Identities=36% Similarity=0.709 Sum_probs=21.1
Q ss_pred CCCccCCCchhccccchHHHHHHHh
Q psy6628 101 EKPYACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
...|.|..|-+-|.....|..|+..
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~ 220 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKK 220 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhc
Confidence 4678999999999999999999863
No 251
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=23.22 E-value=30 Score=16.84 Aligned_cols=30 Identities=13% Similarity=0.245 Sum_probs=11.8
Q ss_pred CccCCcccccccChhhHHHHHHHhcCCCCccCCC
Q psy6628 75 PYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEF 108 (132)
Q Consensus 75 ~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~ 108 (132)
|.....|+..|...+-+ ..+ ...+...|++
T Consensus 24 PV~s~~C~H~fek~aI~-~~i---~~~~~~~CPv 53 (57)
T PF11789_consen 24 PVKSKKCGHTFEKEAIL-QYI---QRNGSKRCPV 53 (57)
T ss_dssp EEEESSS--EEEHHHHH-HHC---TTTS-EE-SC
T ss_pred CcCcCCCCCeecHHHHH-HHH---HhcCCCCCCC
Confidence 44445566666544332 222 2234566665
No 252
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=23.12 E-value=45 Score=14.66 Aligned_cols=13 Identities=31% Similarity=0.779 Sum_probs=7.7
Q ss_pred eCCCCccccCChh
Q psy6628 13 TCQVCSKIFSYEN 25 (132)
Q Consensus 13 ~C~~C~~~f~~~~ 25 (132)
.|+-|++.|...+
T Consensus 4 ~CprC~kg~Hwa~ 16 (36)
T PF14787_consen 4 LCPRCGKGFHWAS 16 (36)
T ss_dssp C-TTTSSSCS-TT
T ss_pred cCcccCCCcchhh
Confidence 5788888775554
No 253
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=22.85 E-value=45 Score=15.00 Aligned_cols=9 Identities=33% Similarity=0.836 Sum_probs=6.5
Q ss_pred CccCCCchh
Q psy6628 103 PYACEFCPL 111 (132)
Q Consensus 103 ~~~C~~C~~ 111 (132)
|..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 567888884
No 254
>PTZ00064 histone acetyltransferase; Provisional
Probab=22.63 E-value=48 Score=24.24 Aligned_cols=25 Identities=28% Similarity=0.509 Sum_probs=21.7
Q ss_pred CCCccCCCchhccccchHHHHHHHh
Q psy6628 101 EKPYACEFCPLTFRHSSHLFRHRRS 125 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~H~~~ 125 (132)
+..|.|..|-+-|.....|.+|+..
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~ 302 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSR 302 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhc
Confidence 4679999999999999999999864
No 255
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.59 E-value=43 Score=22.35 Aligned_cols=11 Identities=18% Similarity=0.697 Sum_probs=5.4
Q ss_pred ccCCccccccc
Q psy6628 76 YQCSQCSKSFF 86 (132)
Q Consensus 76 ~~c~~C~~~~~ 86 (132)
+.|+.||..+.
T Consensus 323 ~~C~~cg~~~~ 333 (364)
T COG0675 323 FKCPRCGFVHD 333 (364)
T ss_pred EECCCCCCeeh
Confidence 45555554443
No 256
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=22.56 E-value=43 Score=13.70 Aligned_cols=10 Identities=20% Similarity=0.843 Sum_probs=5.5
Q ss_pred ccCCCchhcc
Q psy6628 104 YACEFCPLTF 113 (132)
Q Consensus 104 ~~C~~C~~~f 113 (132)
|.|.+|++..
T Consensus 1 ~~C~~C~~~~ 10 (30)
T PF03107_consen 1 FWCDVCRRKI 10 (30)
T ss_pred CCCCCCCCCc
Confidence 4566666543
No 257
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=22.46 E-value=50 Score=15.46 Aligned_cols=11 Identities=27% Similarity=0.730 Sum_probs=7.2
Q ss_pred CCCCccccCCh
Q psy6628 14 CQVCSKIFSYE 24 (132)
Q Consensus 14 C~~C~~~f~~~ 24 (132)
|+.||..|.-.
T Consensus 1 CP~Cg~~f~C~ 11 (50)
T PF14375_consen 1 CPRCGAPFECG 11 (50)
T ss_pred CCCCCCcCCCC
Confidence 66777776554
No 258
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.43 E-value=52 Score=15.17 Aligned_cols=13 Identities=23% Similarity=0.460 Sum_probs=10.0
Q ss_pred eeeeCCCCccccC
Q psy6628 10 VVFTCQVCSKIFS 22 (132)
Q Consensus 10 ~~~~C~~C~~~f~ 22 (132)
..+.|+.||..+.
T Consensus 19 ~~~vC~~Cg~~~~ 31 (52)
T smart00661 19 RRFVCRKCGYEEP 31 (52)
T ss_pred CEEECCcCCCeEE
Confidence 3788999997653
No 259
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=22.39 E-value=44 Score=16.29 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=6.0
Q ss_pred eeCCCCccccC
Q psy6628 12 FTCQVCSKIFS 22 (132)
Q Consensus 12 ~~C~~C~~~f~ 22 (132)
-.|+.|+..|.
T Consensus 40 ngCPfC~~~~~ 50 (55)
T PF14447_consen 40 NGCPFCGTPFE 50 (55)
T ss_pred cCCCCCCCccc
Confidence 34666665553
No 260
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=22.26 E-value=57 Score=13.21 Aligned_cols=12 Identities=17% Similarity=0.531 Sum_probs=5.2
Q ss_pred eeeeCCCCcccc
Q psy6628 10 VVFTCQVCSKIF 21 (132)
Q Consensus 10 ~~~~C~~C~~~f 21 (132)
..|.|.+|+..+
T Consensus 14 ~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 14 WFYRCSECDFDL 25 (30)
T ss_dssp -EEE-TTT----
T ss_pred ceEECccCCCcc
Confidence 678898887654
No 261
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=22.14 E-value=31 Score=20.73 Aligned_cols=34 Identities=32% Similarity=0.820 Sum_probs=20.8
Q ss_pred CCccCCcccccccChhhHHHHHHHhcCCCCccCCCchhc
Q psy6628 74 KPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLT 112 (132)
Q Consensus 74 ~~~~c~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 112 (132)
-+|.|. |+..+... .+|-..-.|+ .|.|..|+-.
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 357787 87765443 3344444555 7888888743
No 262
>PLN03239 histone acetyltransferase; Provisional
Probab=21.48 E-value=93 Score=21.63 Aligned_cols=25 Identities=16% Similarity=0.374 Sum_probs=22.1
Q ss_pred ceeeeCCCCccccCChhHHHHHHHh
Q psy6628 9 RVVFTCQVCSKIFSYENGLKAHVRN 33 (132)
Q Consensus 9 ~~~~~C~~C~~~f~~~~~l~~h~~~ 33 (132)
+..|.|..|-+-|.+...|.+|+..
T Consensus 104 ~~lYiCE~Clky~~~~~~l~~H~~~ 128 (351)
T PLN03239 104 DVLYVCEFSFGFFARKSELLRFQAK 128 (351)
T ss_pred ceEEEeccchhhhcCHHHHHHHHHh
Confidence 5789999999999999999999764
No 263
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.04 E-value=50 Score=18.44 Aligned_cols=13 Identities=23% Similarity=0.634 Sum_probs=9.7
Q ss_pred eeCCCCccccCCh
Q psy6628 12 FTCQVCSKIFSYE 24 (132)
Q Consensus 12 ~~C~~C~~~f~~~ 24 (132)
..||.||..|...
T Consensus 50 t~CP~Cg~~~e~~ 62 (115)
T COG1885 50 TSCPKCGEPFESA 62 (115)
T ss_pred ccCCCCCCcccee
Confidence 5699999877543
No 264
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=20.89 E-value=45 Score=15.87 Aligned_cols=9 Identities=33% Similarity=0.848 Sum_probs=4.9
Q ss_pred CccCCCchh
Q psy6628 103 PYACEFCPL 111 (132)
Q Consensus 103 ~~~C~~C~~ 111 (132)
.|.|..|+.
T Consensus 37 R~~CGkCgy 45 (51)
T COG1998 37 RWACGKCGY 45 (51)
T ss_pred eeEeccccc
Confidence 455555553
No 265
>KOG0562|consensus
Probab=20.34 E-value=94 Score=19.13 Aligned_cols=29 Identities=21% Similarity=0.171 Sum_probs=21.6
Q ss_pred CCCccCCCchhccccchHHHHHHHhhhhh
Q psy6628 101 EKPYACEFCPLTFRHSSHLFRHRRSLHQM 129 (132)
Q Consensus 101 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 129 (132)
+.+..|..|+..-..-+.|+.|++.+...
T Consensus 151 k~dLrC~~Cq~~~~~~~kLK~Hl~~~~~q 179 (184)
T KOG0562|consen 151 KEDLRCWRCQTFGPHFPKLKAHLREEYDQ 179 (184)
T ss_pred ccceeehhhhhcccccHHHHHHHHHHHhh
Confidence 45788999984445678899999877654
No 266
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=20.15 E-value=43 Score=14.29 Aligned_cols=11 Identities=18% Similarity=0.667 Sum_probs=8.0
Q ss_pred eeeeCCCCccc
Q psy6628 10 VVFTCQVCSKI 20 (132)
Q Consensus 10 ~~~~C~~C~~~ 20 (132)
..|.|..|++.
T Consensus 7 ~~Y~C~~C~~~ 17 (32)
T PF13696_consen 7 PGYVCHRCGQK 17 (32)
T ss_pred CCCEeecCCCC
Confidence 34888888874
No 267
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.08 E-value=59 Score=16.40 Aligned_cols=13 Identities=23% Similarity=0.698 Sum_probs=9.4
Q ss_pred eeeCCCCccccCC
Q psy6628 11 VFTCQVCSKIFSY 23 (132)
Q Consensus 11 ~~~C~~C~~~f~~ 23 (132)
.-+|+.||+....
T Consensus 7 ~v~CP~Cgkpv~w 19 (65)
T COG3024 7 TVPCPTCGKPVVW 19 (65)
T ss_pred cccCCCCCCcccc
Confidence 3579999987544
Done!