Query psy11761
Match_columns 198
No_of_seqs 130 out of 1813
Neff 9.8
Searched_HMMs 46136
Date Fri Aug 16 18:15:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11761.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11761hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 7.8E-27 1.7E-31 174.2 4.0 124 23-162 128-264 (279)
2 KOG2462|consensus 99.9 2.2E-25 4.7E-30 166.5 4.3 125 43-185 130-257 (279)
3 KOG3608|consensus 99.8 6E-22 1.3E-26 152.2 0.1 157 2-180 189-361 (467)
4 KOG1074|consensus 99.8 3.1E-20 6.8E-25 156.0 4.1 51 45-95 607-657 (958)
5 KOG1074|consensus 99.7 9.7E-18 2.1E-22 141.3 3.1 70 125-195 618-692 (958)
6 KOG3608|consensus 99.6 6.1E-17 1.3E-21 124.9 1.5 165 1-184 216-401 (467)
7 KOG3576|consensus 99.6 4.1E-17 8.8E-22 117.0 -0.4 111 43-166 117-237 (267)
8 KOG3576|consensus 99.6 7.7E-17 1.7E-21 115.6 -0.4 103 69-185 115-226 (267)
9 KOG3623|consensus 99.4 2.6E-14 5.6E-19 119.4 1.6 81 68-162 891-971 (1007)
10 PLN03086 PRLI-interacting fact 99.4 2.3E-13 5E-18 113.4 4.7 130 26-166 434-565 (567)
11 KOG3623|consensus 99.4 1E-13 2.2E-18 115.8 1.0 78 43-133 894-971 (1007)
12 PHA00733 hypothetical protein 99.1 6.4E-11 1.4E-15 81.6 2.5 94 57-166 26-124 (128)
13 PLN03086 PRLI-interacting fact 98.9 8.1E-10 1.8E-14 92.5 4.4 124 26-181 408-551 (567)
14 KOG3993|consensus 98.7 3.4E-09 7.5E-14 84.2 1.7 113 43-166 267-381 (500)
15 PHA00733 hypothetical protein 98.7 5.8E-09 1.2E-13 71.9 1.0 78 43-136 40-123 (128)
16 PHA02768 hypothetical protein; 98.6 1.6E-08 3.6E-13 58.1 2.0 39 71-111 5-43 (55)
17 PHA02768 hypothetical protein; 98.5 3.8E-08 8.2E-13 56.6 1.3 46 41-88 3-48 (55)
18 PHA00616 hypothetical protein 98.5 6.8E-08 1.5E-12 52.9 1.9 32 141-172 1-32 (44)
19 PF13465 zf-H2C2_2: Zinc-finge 98.5 6.3E-08 1.4E-12 47.6 1.1 25 86-110 1-25 (26)
20 PF13465 zf-H2C2_2: Zinc-finge 98.5 3.2E-08 6.9E-13 48.7 0.0 23 14-36 3-25 (26)
21 PHA00616 hypothetical protein 98.1 1.4E-06 3E-11 47.8 1.2 34 71-104 1-34 (44)
22 KOG3993|consensus 98.1 1.4E-06 3E-11 69.7 1.5 70 26-95 268-380 (500)
23 PHA00732 hypothetical protein 98.0 4E-06 8.6E-11 52.7 2.7 50 43-97 1-50 (79)
24 PHA00732 hypothetical protein 98.0 1.5E-06 3.3E-11 54.5 0.6 47 99-164 1-47 (79)
25 PF05605 zf-Di19: Drought indu 98.0 3.5E-06 7.5E-11 49.1 1.3 52 99-166 2-54 (54)
26 PF00096 zf-C2H2: Zinc finger, 97.9 4.8E-06 1E-10 39.5 1.3 23 142-164 1-23 (23)
27 PF13894 zf-C2H2_4: C2H2-type 97.8 1.4E-05 2.9E-10 38.1 1.8 24 142-165 1-24 (24)
28 PF13912 zf-C2H2_6: C2H2-type 97.7 1.9E-05 4.1E-10 39.0 1.4 26 141-166 1-26 (27)
29 COG5189 SFP1 Putative transcri 97.4 5.9E-05 1.3E-09 58.5 1.3 53 97-162 347-419 (423)
30 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00018 4E-09 47.0 2.5 73 73-164 1-73 (100)
31 PF09237 GAGA: GAGA factor; I 97.3 0.0003 6.4E-09 39.5 2.7 40 130-169 13-52 (54)
32 PF05605 zf-Di19: Drought indu 97.2 0.00038 8.3E-09 40.4 2.6 42 141-183 2-43 (54)
33 PF00096 zf-C2H2: Zinc finger, 97.0 0.0002 4.3E-09 33.7 0.5 21 73-93 2-22 (23)
34 smart00355 ZnF_C2H2 zinc finge 96.9 0.00066 1.4E-08 32.5 1.7 24 142-165 1-24 (26)
35 PF13912 zf-C2H2_6: C2H2-type 96.8 0.00061 1.3E-08 33.4 1.2 24 44-67 2-25 (27)
36 PF12756 zf-C2H2_2: C2H2 type 96.6 0.00046 1E-08 45.1 -0.2 77 45-139 1-77 (100)
37 PF13894 zf-C2H2_4: C2H2-type 96.6 0.001 2.2E-08 31.2 1.0 23 72-94 1-23 (24)
38 COG5189 SFP1 Putative transcri 96.5 0.0011 2.4E-08 51.6 1.4 25 68-92 395-419 (423)
39 PF13909 zf-H2C2_5: C2H2-type 96.4 0.0019 4.1E-08 30.6 1.3 24 142-166 1-24 (24)
40 PF12874 zf-met: Zinc-finger o 96.2 0.0024 5.3E-08 30.5 1.2 23 142-164 1-23 (25)
41 PF12171 zf-C2H2_jaz: Zinc-fin 95.9 0.004 8.7E-08 30.5 1.0 22 142-163 2-23 (27)
42 PF09237 GAGA: GAGA factor; I 95.8 0.0079 1.7E-07 33.9 2.1 33 67-99 20-52 (54)
43 smart00355 ZnF_C2H2 zinc finge 95.5 0.011 2.4E-07 28.0 1.6 23 72-94 1-23 (26)
44 PRK04860 hypothetical protein; 95.2 0.0095 2.1E-07 42.7 1.4 38 70-111 118-155 (160)
45 PF12874 zf-met: Zinc-finger o 94.6 0.012 2.6E-07 28.0 0.4 22 72-93 1-22 (25)
46 PRK04860 hypothetical protein; 94.5 0.013 2.8E-07 42.0 0.5 38 43-84 119-156 (160)
47 PRK14890 putative Zn-ribbon RN 94.2 0.046 1E-06 31.9 2.3 50 24-79 6-56 (59)
48 COG5048 FOG: Zn-finger [Genera 94.2 0.056 1.2E-06 44.3 3.7 62 43-104 289-356 (467)
49 PF13913 zf-C2HC_2: zinc-finge 94.1 0.034 7.3E-07 26.7 1.3 20 142-162 3-22 (25)
50 COG2888 Predicted Zn-ribbon RN 94.0 0.042 9.1E-07 32.0 1.8 50 25-79 9-58 (61)
51 PF12171 zf-C2H2_jaz: Zinc-fin 93.9 0.021 4.6E-07 27.8 0.5 21 72-92 2-22 (27)
52 PF13909 zf-H2C2_5: C2H2-type 93.8 0.022 4.8E-07 26.8 0.4 23 72-95 1-23 (24)
53 PRK00398 rpoP DNA-directed RNA 93.5 0.046 1E-06 30.4 1.4 29 25-53 3-31 (46)
54 KOG2231|consensus 93.3 0.066 1.4E-06 46.5 2.7 120 26-165 100-236 (669)
55 COG4049 Uncharacterized protei 93.2 0.047 1E-06 31.3 1.2 29 138-166 14-42 (65)
56 smart00451 ZnF_U1 U1-like zinc 93.0 0.072 1.6E-06 27.5 1.6 23 140-162 2-24 (35)
57 KOG2893|consensus 91.9 0.055 1.2E-06 40.8 0.4 44 45-92 12-55 (341)
58 KOG2893|consensus 91.8 0.03 6.5E-07 42.1 -1.1 48 101-166 12-59 (341)
59 COG5048 FOG: Zn-finger [Genera 91.7 0.12 2.6E-06 42.4 2.3 75 98-186 288-368 (467)
60 COG1997 RPL43A Ribosomal prote 91.2 0.13 2.8E-06 32.5 1.4 33 24-56 34-66 (89)
61 PF07754 DUF1610: Domain of un 91.1 0.16 3.5E-06 24.0 1.4 21 30-50 3-23 (24)
62 cd00350 rubredoxin_like Rubred 90.9 0.13 2.7E-06 26.4 1.0 24 26-51 2-25 (33)
63 PF10571 UPF0547: Uncharacteri 90.8 0.19 4.1E-06 24.3 1.5 24 27-54 2-25 (26)
64 KOG1146|consensus 90.4 0.18 3.9E-06 46.8 2.2 97 49-162 442-539 (1406)
65 PF09538 FYDLN_acid: Protein o 90.2 0.18 4E-06 33.6 1.5 30 100-154 10-39 (108)
66 cd00729 rubredoxin_SM Rubredox 89.9 0.16 3.5E-06 26.2 0.9 12 99-110 2-13 (34)
67 PF09986 DUF2225: Uncharacteri 89.1 0.18 3.9E-06 38.0 1.0 15 24-38 4-18 (214)
68 PF09538 FYDLN_acid: Protein o 89.0 0.27 5.7E-06 32.8 1.6 30 26-56 10-39 (108)
69 PF14369 zf-RING_3: zinc-finge 88.8 0.26 5.5E-06 25.7 1.2 30 25-54 2-32 (35)
70 KOG4173|consensus 88.5 0.11 2.4E-06 38.3 -0.4 81 70-166 78-171 (253)
71 smart00659 RPOLCX RNA polymera 88.1 0.31 6.6E-06 26.9 1.3 27 25-52 2-28 (44)
72 PF01780 Ribosomal_L37ae: Ribo 88.0 0.18 3.9E-06 32.2 0.3 31 25-55 35-65 (90)
73 COG1996 RPC10 DNA-directed RNA 87.8 0.25 5.3E-06 27.8 0.7 29 24-52 5-33 (49)
74 COG5236 Uncharacterized conser 87.3 0.54 1.2E-05 37.6 2.6 85 72-165 152-244 (493)
75 KOG2231|consensus 85.9 0.51 1.1E-05 41.3 2.0 82 74-165 118-206 (669)
76 PF03604 DNA_RNApol_7kD: DNA d 85.9 0.56 1.2E-05 23.9 1.4 25 26-51 1-25 (32)
77 PF09986 DUF2225: Uncharacteri 85.5 0.48 1E-05 35.7 1.5 14 98-111 4-17 (214)
78 TIGR00622 ssl1 transcription f 85.5 1.8 3.8E-05 29.0 4.0 102 26-165 2-105 (112)
79 PF12013 DUF3505: Protein of u 85.4 1.2 2.6E-05 29.6 3.3 27 140-166 79-109 (109)
80 COG1592 Rubrerythrin [Energy p 85.1 0.47 1E-05 34.1 1.2 25 98-149 133-157 (166)
81 PTZ00255 60S ribosomal protein 85.0 0.42 9.1E-06 30.6 0.8 33 24-56 35-67 (90)
82 TIGR00280 L37a ribosomal prote 84.3 0.42 9.1E-06 30.6 0.6 32 25-56 35-66 (91)
83 PF14353 CpXC: CpXC protein 84.2 0.33 7.1E-06 33.4 0.1 40 27-66 3-61 (128)
84 TIGR00622 ssl1 transcription f 84.1 1.2 2.7E-05 29.7 2.8 71 23-95 13-105 (112)
85 KOG1146|consensus 84.0 0.5 1.1E-05 44.1 1.1 100 44-173 1261-1360(1406)
86 KOG2186|consensus 83.9 0.43 9.3E-06 36.4 0.6 47 99-162 3-49 (276)
87 smart00834 CxxC_CXXC_SSSS Puta 83.3 0.55 1.2E-05 25.0 0.7 26 26-51 6-34 (41)
88 PRK03976 rpl37ae 50S ribosomal 82.0 0.55 1.2E-05 30.1 0.5 32 25-56 36-67 (90)
89 PF09723 Zn-ribbon_8: Zinc rib 82.0 0.59 1.3E-05 25.4 0.5 11 26-36 6-16 (42)
90 TIGR02300 FYDLN_acid conserved 81.6 0.84 1.8E-05 31.1 1.3 33 100-157 10-42 (129)
91 COG1592 Rubrerythrin [Energy p 78.5 1.1 2.4E-05 32.2 1.2 24 25-51 134-157 (166)
92 COG4049 Uncharacterized protei 77.0 0.66 1.4E-05 26.7 -0.3 32 92-136 10-41 (65)
93 TIGR02300 FYDLN_acid conserved 76.3 1.7 3.8E-05 29.6 1.5 30 26-56 10-39 (129)
94 COG1198 PriA Primosomal protei 76.0 1.5 3.2E-05 39.2 1.5 45 27-80 437-484 (730)
95 PF13719 zinc_ribbon_5: zinc-r 75.9 1.2 2.7E-05 23.4 0.6 27 27-53 4-35 (37)
96 TIGR02098 MJ0042_CXXC MJ0042 f 75.1 0.91 2E-05 23.8 -0.0 10 27-36 4-13 (38)
97 TIGR00373 conserved hypothetic 75.0 0.98 2.1E-05 32.3 0.1 10 71-80 128-137 (158)
98 smart00531 TFIIE Transcription 74.7 1 2.2E-05 31.8 0.1 36 43-82 99-134 (147)
99 PF02176 zf-TRAF: TRAF-type zi 74.5 1.4 2.9E-05 25.7 0.6 49 96-160 6-60 (60)
100 PF00301 Rubredoxin: Rubredoxi 74.5 1.6 3.5E-05 24.3 0.9 11 26-36 2-12 (47)
101 PF13240 zinc_ribbon_2: zinc-r 74.0 1.6 3.6E-05 20.3 0.7 20 28-51 2-21 (23)
102 TIGR01206 lysW lysine biosynth 73.7 2.1 4.5E-05 24.7 1.2 28 26-53 3-32 (54)
103 TIGR02605 CxxC_CxxC_SSSS putat 73.5 1.5 3.3E-05 24.8 0.6 11 44-54 6-16 (52)
104 smart00661 RPOL9 RNA polymeras 73.4 2.2 4.8E-05 24.0 1.3 28 28-55 3-32 (52)
105 PRK00464 nrdR transcriptional 73.2 1.3 2.8E-05 31.6 0.3 16 44-59 29-44 (154)
106 COG0068 HypF Hydrogenase matur 72.9 1.6 3.4E-05 38.5 0.8 77 26-108 102-182 (750)
107 PRK06266 transcription initiat 72.8 1.3 2.8E-05 32.4 0.3 31 43-82 117-147 (178)
108 COG3357 Predicted transcriptio 72.3 2.2 4.7E-05 27.3 1.1 27 25-51 58-84 (97)
109 PHA00626 hypothetical protein 72.2 2.8 6.1E-05 24.2 1.5 13 70-82 22-34 (59)
110 PF05191 ADK_lid: Adenylate ki 71.5 1.4 3E-05 23.1 0.1 16 139-154 19-34 (36)
111 PF02892 zf-BED: BED zinc fing 71.4 3.2 7E-05 22.5 1.6 27 138-164 13-43 (45)
112 cd00730 rubredoxin Rubredoxin; 71.3 2.7 5.9E-05 23.8 1.3 11 26-36 2-12 (50)
113 smart00734 ZnF_Rad18 Rad18-lik 70.9 3 6.6E-05 20.0 1.3 19 143-162 3-21 (26)
114 PF12013 DUF3505: Protein of u 70.4 4.1 8.9E-05 27.0 2.3 21 43-64 11-31 (109)
115 TIGR00373 conserved hypothetic 70.2 2.5 5.5E-05 30.2 1.3 32 138-180 106-137 (158)
116 PF09845 DUF2072: Zn-ribbon co 68.6 1.8 3.9E-05 29.7 0.2 27 25-51 1-27 (131)
117 PF13717 zinc_ribbon_4: zinc-r 68.1 2.1 4.6E-05 22.3 0.4 11 27-37 4-14 (36)
118 PF12773 DZR: Double zinc ribb 67.5 5.3 0.00012 22.2 2.0 9 46-54 15-23 (50)
119 PRK06266 transcription initiat 67.0 3.1 6.8E-05 30.4 1.2 32 139-181 115-146 (178)
120 PF06524 NOA36: NOA36 protein; 66.9 3.3 7.2E-05 31.9 1.3 26 69-94 207-232 (314)
121 PF07282 OrfB_Zn_ribbon: Putat 66.3 4 8.7E-05 24.5 1.4 29 27-55 30-58 (69)
122 PF08271 TF_Zn_Ribbon: TFIIB z 65.8 3.9 8.4E-05 22.1 1.2 28 26-53 1-29 (43)
123 COG5236 Uncharacterized conser 64.8 2.8 6.1E-05 33.7 0.6 78 73-165 222-305 (493)
124 KOG0402|consensus 64.2 2.9 6.3E-05 26.2 0.5 31 25-55 36-66 (92)
125 PF13248 zf-ribbon_3: zinc-rib 63.7 4.2 9.1E-05 19.4 0.9 23 26-52 3-25 (26)
126 PRK04023 DNA polymerase II lar 63.4 7.2 0.00016 36.0 3.0 22 25-52 626-647 (1121)
127 PF01286 XPA_N: XPA protein N- 62.8 3.9 8.5E-05 21.1 0.8 24 27-50 5-28 (34)
128 smart00614 ZnF_BED BED zinc fi 62.6 5.7 0.00012 22.3 1.5 24 140-163 17-45 (50)
129 KOG2907|consensus 60.8 2.9 6.3E-05 27.8 0.1 29 26-54 8-36 (116)
130 COG1773 Rubredoxin [Energy pro 60.6 4.9 0.00011 23.2 1.0 11 26-36 4-14 (55)
131 PF12760 Zn_Tnp_IS1595: Transp 60.5 7.7 0.00017 21.3 1.8 27 25-51 18-45 (46)
132 PF13453 zf-TFIIB: Transcripti 60.0 7.4 0.00016 20.8 1.6 33 28-60 2-36 (41)
133 PRK14714 DNA polymerase II lar 59.2 8.4 0.00018 36.5 2.7 35 26-81 668-702 (1337)
134 PF04959 ARS2: Arsenite-resist 58.5 2.6 5.7E-05 31.7 -0.5 31 138-168 74-104 (214)
135 KOG4173|consensus 58.4 2.8 6.2E-05 31.1 -0.3 65 44-111 80-158 (253)
136 PF07295 DUF1451: Protein of u 58.3 3.8 8.3E-05 28.9 0.4 36 17-52 100-139 (146)
137 COG5151 SSL1 RNA polymerase II 57.9 11 0.00023 30.1 2.7 26 139-164 386-411 (421)
138 COG3364 Zn-ribbon containing p 57.2 3.1 6.7E-05 27.2 -0.3 26 25-50 2-27 (112)
139 KOG2186|consensus 56.7 4.8 0.00011 30.9 0.7 46 44-92 4-49 (276)
140 TIGR00595 priA primosomal prot 56.5 7.1 0.00015 33.5 1.7 44 27-79 215-261 (505)
141 PRK00432 30S ribosomal protein 56.3 8.7 0.00019 21.7 1.5 26 27-53 22-47 (50)
142 PF05443 ROS_MUCR: ROS/MUCR tr 55.9 7.1 0.00015 27.0 1.3 26 139-167 70-95 (132)
143 PF08274 PhnA_Zn_Ribbon: PhnA 55.6 6.8 0.00015 19.6 0.9 24 27-51 4-27 (30)
144 COG4530 Uncharacterized protei 55.5 9.6 0.00021 25.3 1.8 33 100-158 10-42 (129)
145 COG1571 Predicted DNA-binding 54.8 7.8 0.00017 32.2 1.6 30 27-57 352-381 (421)
146 COG1198 PriA Primosomal protei 52.9 9.9 0.00021 34.2 2.0 23 127-150 462-484 (730)
147 PF01155 HypA: Hydrogenase exp 52.0 4.1 8.8E-05 27.4 -0.3 24 26-51 71-94 (113)
148 KOG1280|consensus 51.1 12 0.00026 30.2 2.1 43 139-181 77-119 (381)
149 smart00154 ZnF_AN1 AN1-like Zi 50.8 13 0.00027 19.8 1.5 13 43-55 12-24 (39)
150 PRK00420 hypothetical protein; 50.5 11 0.00024 25.3 1.6 30 25-55 23-52 (112)
151 PRK05580 primosome assembly pr 50.1 10 0.00022 33.9 1.7 46 26-80 382-430 (679)
152 PF01363 FYVE: FYVE zinc finge 50.0 10 0.00022 22.7 1.2 28 26-55 10-37 (69)
153 KOG4167|consensus 49.7 5.2 0.00011 35.5 -0.1 27 139-165 790-816 (907)
154 KOG4124|consensus 48.4 8.3 0.00018 31.1 0.8 23 139-161 396-418 (442)
155 PRK12496 hypothetical protein; 48.0 10 0.00023 27.3 1.2 13 99-111 127-139 (164)
156 PF07975 C1_4: TFIIH C1-like d 47.9 10 0.00022 21.6 0.9 20 71-90 21-40 (51)
157 COG1655 Uncharacterized protei 47.6 7.3 0.00016 29.6 0.4 17 23-39 17-33 (267)
158 PRK14873 primosome assembly pr 47.2 9.7 0.00021 33.9 1.1 44 27-80 385-431 (665)
159 PRK03564 formate dehydrogenase 47.2 17 0.00038 29.1 2.4 14 66-79 207-220 (309)
160 PRK03824 hypA hydrogenase nick 46.7 12 0.00027 26.0 1.4 13 43-55 70-82 (135)
161 PF10013 DUF2256: Uncharacteri 46.5 9.8 0.00021 20.6 0.7 16 143-158 10-25 (42)
162 KOG2785|consensus 46.5 8.3 0.00018 31.5 0.6 54 98-164 165-243 (390)
163 PF14803 Nudix_N_2: Nudix N-te 45.9 11 0.00024 19.4 0.8 25 28-52 3-31 (34)
164 PF15135 UPF0515: Uncharacteri 45.7 16 0.00036 28.0 2.0 11 100-110 156-166 (278)
165 PF05129 Elf1: Transcription e 45.7 8.2 0.00018 24.3 0.3 32 24-55 21-58 (81)
166 COG1998 RPS31 Ribosomal protei 45.3 14 0.00031 20.8 1.2 25 28-52 22-46 (51)
167 KOG2482|consensus 43.2 17 0.00036 29.4 1.7 24 141-164 195-218 (423)
168 PF14446 Prok-RING_1: Prokaryo 43.1 13 0.00029 21.4 0.9 12 100-111 6-17 (54)
169 PRK14559 putative protein seri 42.8 20 0.00043 31.8 2.4 23 27-53 3-25 (645)
170 PRK12380 hydrogenase nickel in 41.6 14 0.0003 24.8 1.0 10 26-35 71-80 (113)
171 KOG2593|consensus 40.8 18 0.0004 30.1 1.7 40 94-150 123-162 (436)
172 COG4957 Predicted transcriptio 40.1 12 0.00026 25.9 0.5 27 140-169 75-101 (148)
173 TIGR00100 hypA hydrogenase nic 39.8 14 0.0003 24.9 0.8 10 44-53 71-80 (115)
174 PF09082 DUF1922: Domain of un 39.6 12 0.00026 22.6 0.4 27 25-53 3-29 (68)
175 TIGR00686 phnA alkylphosphonat 38.8 20 0.00044 23.8 1.4 29 27-56 4-32 (109)
176 PF11781 RRN7: RNA polymerase 38.4 21 0.00046 18.6 1.2 27 24-51 7-33 (36)
177 COG4888 Uncharacterized Zn rib 38.2 12 0.00027 24.4 0.3 30 25-54 22-57 (104)
178 KOG1842|consensus 38.2 20 0.00042 30.1 1.5 28 140-167 14-41 (505)
179 KOG0978|consensus 37.9 13 0.00028 33.1 0.4 12 73-84 680-691 (698)
180 PRK10220 hypothetical protein; 37.6 24 0.00051 23.5 1.5 29 27-56 5-33 (111)
181 KOG2636|consensus 37.5 20 0.00044 30.0 1.5 25 138-162 398-423 (497)
182 PF00130 C1_1: Phorbol esters/ 37.2 24 0.00052 19.6 1.4 29 23-52 9-37 (53)
183 PRK09678 DNA-binding transcrip 36.8 12 0.00026 23.0 0.1 7 27-33 3-9 (72)
184 cd00065 FYVE FYVE domain; Zinc 36.3 22 0.00048 20.1 1.2 25 28-54 5-29 (57)
185 PF14599 zinc_ribbon_6: Zinc-r 35.4 16 0.00034 21.7 0.4 26 26-51 31-56 (61)
186 PF11023 DUF2614: Protein of u 34.4 26 0.00056 23.5 1.3 31 23-55 67-97 (114)
187 PRK03681 hypA hydrogenase nick 34.2 21 0.00045 24.0 0.9 10 26-35 71-80 (114)
188 PF01485 IBR: IBR domain; Int 33.7 29 0.00062 20.0 1.4 30 27-56 20-53 (64)
189 smart00440 ZnF_C2C2 C2C2 Zinc 33.4 19 0.00042 19.1 0.5 12 141-152 28-39 (40)
190 smart00778 Prim_Zn_Ribbon Zinc 33.1 36 0.00078 17.9 1.5 26 26-51 4-33 (37)
191 PF08792 A2L_zn_ribbon: A2L zi 32.9 31 0.00068 17.5 1.3 28 26-53 4-31 (33)
192 COG4338 Uncharacterized protei 32.9 14 0.00031 20.6 -0.0 17 142-158 13-29 (54)
193 PF13005 zf-IS66: zinc-finger 32.8 29 0.00064 18.8 1.3 10 27-36 4-13 (47)
194 COG3880 Modulator of heat shoc 32.8 8.3 0.00018 27.7 -1.2 32 25-56 74-105 (176)
195 PRK00564 hypA hydrogenase nick 32.4 20 0.00044 24.2 0.6 12 100-111 72-83 (117)
196 TIGR00143 hypF [NiFe] hydrogen 32.1 16 0.00035 32.8 0.2 78 26-109 69-150 (711)
197 PF05290 Baculo_IE-1: Baculovi 32.1 27 0.00058 24.2 1.2 11 101-111 123-133 (140)
198 KOG3408|consensus 32.0 34 0.00073 23.3 1.6 28 137-164 53-80 (129)
199 PF01096 TFIIS_C: Transcriptio 31.9 11 0.00025 19.9 -0.5 11 141-151 28-38 (39)
200 KOG2593|consensus 31.8 19 0.00041 30.0 0.5 31 23-53 126-163 (436)
201 PF03107 C1_2: C1 domain; Int 31.2 29 0.00063 17.0 1.0 22 26-50 1-22 (30)
202 COG3091 SprT Zn-dependent meta 31.2 21 0.00046 25.3 0.6 36 96-150 114-149 (156)
203 KOG2785|consensus 31.1 33 0.00072 28.1 1.7 51 43-93 166-242 (390)
204 PF10263 SprT-like: SprT-like 30.2 27 0.00059 24.5 1.1 31 43-81 123-153 (157)
205 KOG4167|consensus 29.5 12 0.00027 33.2 -0.9 26 71-96 792-817 (907)
206 PF08273 Prim_Zn_Ribbon: Zinc- 29.4 31 0.00067 18.5 0.9 25 26-50 4-33 (40)
207 PF01428 zf-AN1: AN1-like Zinc 28.3 19 0.0004 19.4 -0.1 15 140-154 12-26 (43)
208 smart00064 FYVE Protein presen 28.3 31 0.00067 20.4 0.9 12 100-111 11-22 (68)
209 PF04810 zf-Sec23_Sec24: Sec23 28.3 37 0.00079 18.0 1.1 14 138-151 21-34 (40)
210 TIGR00416 sms DNA repair prote 28.2 31 0.00067 29.3 1.2 25 24-52 6-30 (454)
211 PF04216 FdhE: Protein involve 28.0 18 0.00039 28.6 -0.2 10 100-109 173-182 (290)
212 PF09297 zf-NADH-PPase: NADH p 28.0 37 0.0008 16.9 1.0 24 28-51 6-29 (32)
213 PF04423 Rad50_zn_hook: Rad50 27.8 22 0.00047 20.2 0.2 12 143-154 22-33 (54)
214 TIGR01384 TFS_arch transcripti 27.8 38 0.00082 22.1 1.3 26 28-55 3-28 (104)
215 PF03119 DNA_ligase_ZBD: NAD-d 27.7 32 0.00069 16.7 0.7 19 28-46 2-20 (28)
216 PF08790 zf-LYAR: LYAR-type C2 27.2 20 0.00044 17.6 -0.0 11 100-110 1-11 (28)
217 TIGR03831 YgiT_finger YgiT-typ 26.9 26 0.00057 18.7 0.4 8 45-52 34-41 (46)
218 PRK11823 DNA repair protein Ra 26.8 38 0.00082 28.6 1.5 26 23-52 5-30 (446)
219 PF14690 zf-ISL3: zinc-finger 26.6 42 0.00091 18.1 1.2 9 25-33 2-10 (47)
220 PF02150 RNA_POL_M_15KD: RNA p 26.6 23 0.0005 18.2 0.1 9 45-53 22-30 (35)
221 PF07649 C1_3: C1-like domain; 26.5 36 0.00077 16.6 0.8 8 43-50 15-22 (30)
222 COG5188 PRP9 Splicing factor 3 26.1 38 0.00082 27.6 1.3 25 138-162 371-396 (470)
223 PF10276 zf-CHCC: Zinc-finger 25.6 26 0.00057 18.7 0.2 11 25-35 29-39 (40)
224 smart00731 SprT SprT homologue 25.2 44 0.00096 23.3 1.4 32 43-81 112-143 (146)
225 KOG0782|consensus 25.0 22 0.00047 30.9 -0.2 47 6-57 239-290 (1004)
226 COG0068 HypF Hydrogenase matur 24.9 30 0.00065 30.9 0.6 46 28-79 126-181 (750)
227 COG1645 Uncharacterized Zn-fin 24.7 41 0.0009 23.2 1.1 26 26-53 29-54 (131)
228 PRK00762 hypA hydrogenase nick 24.5 34 0.00074 23.3 0.7 12 43-55 70-81 (124)
229 COG1779 C4-type Zn-finger prot 24.4 33 0.00072 25.5 0.6 10 27-36 16-25 (201)
230 COG3677 Transposase and inacti 24.4 48 0.001 22.8 1.4 17 138-154 50-66 (129)
231 cd01121 Sms Sms (bacterial rad 24.1 43 0.00093 27.6 1.3 23 26-52 1-23 (372)
232 COG2331 Uncharacterized protei 23.7 28 0.00061 21.5 0.1 12 100-111 13-24 (82)
233 PRK11827 hypothetical protein; 23.7 61 0.0013 19.1 1.5 11 44-54 27-37 (60)
234 PRK12286 rpmF 50S ribosomal pr 23.5 73 0.0016 18.5 1.8 22 25-51 27-48 (57)
235 PRK05452 anaerobic nitric oxid 23.2 47 0.001 28.4 1.4 14 43-56 425-438 (479)
236 PF12907 zf-met2: Zinc-binding 23.0 67 0.0014 17.2 1.5 27 142-168 2-31 (40)
237 PF10083 DUF2321: Uncharacteri 23.0 23 0.00049 25.2 -0.4 18 68-85 65-82 (158)
238 KOG1280|consensus 22.9 70 0.0015 26.0 2.2 38 69-106 77-116 (381)
239 PRK11032 hypothetical protein; 22.9 40 0.00087 24.2 0.8 37 16-52 111-151 (160)
240 cd00924 Cyt_c_Oxidase_Vb Cytoc 22.9 30 0.00066 22.6 0.2 12 25-36 79-90 (97)
241 COG1675 TFA1 Transcription ini 22.7 29 0.00062 25.4 0.0 31 22-52 110-141 (176)
242 KOG4118|consensus 22.6 54 0.0012 19.6 1.1 31 141-171 38-68 (74)
243 PF04780 DUF629: Protein of un 22.4 61 0.0013 27.6 1.9 27 140-166 56-82 (466)
244 PF14206 Cys_rich_CPCC: Cystei 22.2 57 0.0012 20.3 1.3 9 26-34 2-10 (78)
245 PRK04351 hypothetical protein; 21.9 54 0.0012 23.2 1.3 33 43-83 112-144 (149)
246 smart00109 C1 Protein kinase C 21.9 62 0.0013 17.2 1.3 25 25-51 11-35 (49)
247 PRK08402 replication factor A; 21.8 52 0.0011 27.0 1.3 26 26-51 213-238 (355)
248 PF13878 zf-C2H2_3: zinc-finge 21.5 81 0.0018 16.8 1.7 24 141-164 13-38 (41)
249 COG4896 Uncharacterized protei 21.0 48 0.001 19.6 0.7 38 73-110 4-42 (68)
250 PF10122 Mu-like_Com: Mu-like 21.0 66 0.0014 18.2 1.2 27 26-52 5-33 (51)
251 PRK05978 hypothetical protein; 20.9 58 0.0013 23.1 1.3 9 45-53 54-62 (148)
252 PF02591 DUF164: Putative zinc 20.8 55 0.0012 18.6 1.0 14 20-33 41-54 (56)
253 PF11672 DUF3268: Protein of u 20.7 72 0.0016 21.0 1.6 11 98-108 1-11 (102)
254 KOG3214|consensus 20.6 73 0.0016 20.9 1.6 18 138-155 44-61 (109)
255 PF11931 DUF3449: Domain of un 20.4 34 0.00073 25.5 0.0 24 139-162 99-123 (196)
256 TIGR00595 priA primosomal prot 20.4 61 0.0013 27.9 1.5 10 43-52 253-262 (505)
257 PF06044 DRP: Dam-replacing fa 20.2 46 0.001 25.6 0.7 31 26-56 32-66 (254)
258 TIGR00340 zpr1_rel ZPR1-relate 20.2 48 0.001 23.9 0.7 12 43-54 28-39 (163)
259 TIGR02159 PA_CoA_Oxy4 phenylac 20.2 34 0.00073 24.1 -0.0 30 26-55 106-142 (146)
260 smart00132 LIM Zinc-binding do 20.1 60 0.0013 16.1 1.0 7 72-78 28-34 (39)
261 PF09963 DUF2197: Uncharacteri 20.0 46 0.001 19.3 0.5 36 73-108 4-40 (56)
262 KOG3507|consensus 20.0 60 0.0013 19.0 0.9 9 43-51 37-45 (62)
No 1
>KOG2462|consensus
Probab=99.93 E-value=7.8e-27 Score=174.20 Aligned_cols=124 Identities=33% Similarity=0.619 Sum_probs=105.4
Q ss_pred CCccccCcccchhhcccCCC-------------ceecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHH
Q psy11761 23 DNAYKCHQCQRLIFLSANAG-------------VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNT 89 (198)
Q Consensus 23 ~~~~~C~~C~~~f~~~~~~~-------------~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 89 (198)
..-|+|+.||+.+.+.++|. .+.|..|++.+.....|..|+++|+ .+..|.+||+.|+....|+-
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhc
Confidence 34588888998888877654 5678889998888888888888888 68888999999988888888
Q ss_pred hhhhcCCCCcccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhcChhHHHhhhh
Q psy11761 90 HQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHC 162 (198)
Q Consensus 90 H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~ 162 (198)
|+|+|+|||||.|+.|+++|.+ +++|+.|+.+|. +.|.|+|..|+|.|...+-|.+|..
T Consensus 206 HiRTHTGEKPF~C~hC~kAFAD-------------RSNLRAHmQTHS-~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFAD-------------RSNLRAHMQTHS-DVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred ccccccCCCCccCCcccchhcc-------------hHHHHHHHHhhc-CCccccCcchhhHHHHHHHHHHhhh
Confidence 9999999999999999999988 888888988888 6788999999999988888888864
No 2
>KOG2462|consensus
Probab=99.91 E-value=2.2e-25 Score=166.49 Aligned_cols=125 Identities=26% Similarity=0.448 Sum_probs=116.0
Q ss_pred ceecCccccccCChhHHhhcccCCCC---CCCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCccc
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMK---PRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTH 119 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~---~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~ 119 (198)
.|+|.+|++.+...++|.+|+.+|.. .+.+.|..|++.+..-..|..|+++|+ -+.+|.+||+.|.+
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSR-------- 199 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSR-------- 199 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccc--------
Confidence 68999999999999999999999853 678999999999999999999999999 57899999999998
Q ss_pred CCCcCcccccccccccccCCCCeeCCcchhhhcChhHHHhhhhhhCCCCCCCcccccccCCCcccc
Q psy11761 120 TPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHCHKHKQSCLPFISRLFGFDDGDKV 185 (198)
Q Consensus 120 ~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (198)
..-|..|+|+|+ |||||.|+.|+|.|..+++|+.||.+|.+.| .|.|..|++.++.+-
T Consensus 200 -----PWLLQGHiRTHT-GEKPF~C~hC~kAFADRSNLRAHmQTHS~~K--~~qC~~C~KsFsl~S 257 (279)
T KOG2462|consen 200 -----PWLLQGHIRTHT-GEKPFSCPHCGKAFADRSNLRAHMQTHSDVK--KHQCPRCGKSFALKS 257 (279)
T ss_pred -----hHHhhccccccc-CCCCccCCcccchhcchHHHHHHHHhhcCCc--cccCcchhhHHHHHH
Confidence 888999999999 9999999999999999999999999999999 788999998876553
No 3
>KOG3608|consensus
Probab=99.83 E-value=6e-22 Score=152.23 Aligned_cols=157 Identities=25% Similarity=0.457 Sum_probs=118.0
Q ss_pred CccccceeeeechhhhhhhCCCCccccCcccchhhcccCCC------------ceecCccccccCChhHHhhcccCCCCC
Q psy11761 2 FTQTPNLVLFSQQTLLCIHGNDNAYKCHQCQRLIFLSANAG------------VHKCEYCHKVFDQQSSLLSHNCPQMKP 69 (198)
Q Consensus 2 f~~~~~l~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~~~------------~~~C~~C~~~f~~~~~l~~H~~~h~~~ 69 (198)
|.++..|+ +|++.|++++...|+.||..|.++..+- +|.|..|.+.|.....|..|+..|.
T Consensus 189 ~~~k~~Lr-----eH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv-- 261 (467)
T KOG3608|consen 189 MGNKYRLR-----EHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV-- 261 (467)
T ss_pred hccHHHHH-----HHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh--
Confidence 55677888 9999999999999999999998765432 7888888888888888888877766
Q ss_pred CCccCccchhcccCchhHHHhhh-hcCCCCcccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCc--
Q psy11761 70 RPYKCDTCEKSFTNSQNLNTHQL-IHSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDR-- 146 (198)
Q Consensus 70 ~~~~C~~C~~~f~~~~~l~~H~~-~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~-- 146 (198)
.-|+|+.|+...+..++|..|++ .|...|||+|+.|++.|.+ .+.|.+|...|+ +..|.|+.
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~-------------esdL~kH~~~HS--~~~y~C~h~~ 326 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVR-------------ESDLAKHVQVHS--KTVYQCEHPD 326 (467)
T ss_pred hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhcc-------------HHHHHHHHHhcc--ccceecCCCC
Confidence 56788888888888888888877 4667788888888888887 666777776554 55666666
Q ss_pred chhhhcChhHHHhhhhhhC-CCCCCCcccccccCC
Q psy11761 147 CSQFFGDRMNLISHHCHKH-KQSCLPFISRLFGFD 180 (198)
Q Consensus 147 C~k~f~~~~~L~~H~~~~~-~~~~~~~~~~~~~~~ 180 (198)
|..+|.+..++++|++.++ |.-|.+|.|-.|..-
T Consensus 327 C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ 361 (467)
T KOG3608|consen 327 CHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRF 361 (467)
T ss_pred CcHHHHHHHHHHHHHHHhccCCCCCceeeecchhh
Confidence 6666666666677766555 555555555555443
No 4
>KOG1074|consensus
Probab=99.79 E-value=3.1e-20 Score=156.02 Aligned_cols=51 Identities=33% Similarity=0.705 Sum_probs=48.0
Q ss_pred ecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcC
Q psy11761 45 KCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHS 95 (198)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 95 (198)
+|-+|-+.+...+.|..|+++|+|++||+|.+|+++|..+.+|..|+..|.
T Consensus 607 qCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 607 QCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred ceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccc
Confidence 799999999999999999999999999999999999999999999987664
No 5
>KOG1074|consensus
Probab=99.69 E-value=9.7e-18 Score=141.26 Aligned_cols=70 Identities=17% Similarity=0.237 Sum_probs=59.4
Q ss_pred cccccccccccccCCCCeeCCcchhhhcChhHHHhhhhhhCCCCC--CCcccc---cccCCCcccchhcccceecC
Q psy11761 125 KSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHCHKHKQSC--LPFISR---LFGFDDGDKVAKFSGRVVDT 195 (198)
Q Consensus 125 ~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~~~~~--~~~~~~---~~~~~~~~~~~~~~~~~~~~ 195 (198)
.+.|.-|.+.|+ |++||+|.+||+.|+++.+|+.||-+|....| .++.|+ +|..++.+.+....+-.+..
T Consensus 618 ~saLqmHyrtHt-GERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQhIriH~ 692 (958)
T KOG1074|consen 618 PSALQMHYRTHT-GERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQHIRIHL 692 (958)
T ss_pred hhhhhhhhhccc-CcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccccccceEEeec
Confidence 468899999999 99999999999999999999999998865433 578899 99999988887776665544
No 6
>KOG3608|consensus
Probab=99.63 E-value=6.1e-17 Score=124.89 Aligned_cols=165 Identities=24% Similarity=0.434 Sum_probs=137.8
Q ss_pred CCccccceeeeechhhhhhh--CCCCccccCcccchhhcccCCC--------ceecCccccccCChhHHhhcccC-CCCC
Q psy11761 1 MFTQTPNLVLFSQQTLLCIH--GNDNAYKCHQCQRLIFLSANAG--------VHKCEYCHKVFDQQSSLLSHNCP-QMKP 69 (198)
Q Consensus 1 ~f~~~~~l~~~~~~~h~~~h--~~~~~~~C~~C~~~f~~~~~~~--------~~~C~~C~~~f~~~~~l~~H~~~-h~~~ 69 (198)
+|..+..|. .|++-. ....+|.|..|.+.|.+...|. -|+|+.|.++.+..++|..|++. |...
T Consensus 216 ~F~~~tkl~-----DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~d 290 (467)
T KOG3608|consen 216 LFRTKTKLF-----DHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKD 290 (467)
T ss_pred HhccccHHH-----HHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccC
Confidence 366677776 775443 3556999999999998866554 68999999999999999999886 5568
Q ss_pred CCccCccchhcccCchhHHHhhhhcCCCCcccCCc--CchhhhcccCCCcccCCCcCcccccccccccccCC--CCeeCC
Q psy11761 70 RPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTT--CDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFP--KPYQCD 145 (198)
Q Consensus 70 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~--C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~--~~~~C~ 145 (198)
+||+|+.|++.+....+|..|..+|+ +..|.|.. |...|.. ...+.+|++.++.|. -+|.|.
T Consensus 291 kpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~-------------~~q~~~H~~evhEg~np~~Y~CH 356 (467)
T KOG3608|consen 291 KPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRT-------------YTQMRRHFLEVHEGNNPILYACH 356 (467)
T ss_pred CCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHH-------------HHHHHHHHHHhccCCCCCceeee
Confidence 99999999999999999999999999 66799976 9999998 889999999887554 479999
Q ss_pred cchhhhcChhHHHhhhhhhC------CCCCCCcccccccCCCccc
Q psy11761 146 RCSQFFGDRMNLISHHCHKH------KQSCLPFISRLFGFDDGDK 184 (198)
Q Consensus 146 ~C~k~f~~~~~L~~H~~~~~------~~~~~~~~~~~~~~~~~~~ 184 (198)
.|++.|++..+|..|+...| |.+.|.|....-|++.-..
T Consensus 357 ~Cdr~ft~G~~L~~HL~kkH~f~~PsGh~RFtYk~~edG~mRLqt 401 (467)
T KOG3608|consen 357 CCDRFFTSGKSLSAHLMKKHGFRLPSGHKRFTYKVDEDGFMRLQT 401 (467)
T ss_pred cchhhhccchhHHHHHHHhhcccCCCCCCceeeeeccCceeeeee
Confidence 99999999999999987665 4666777777777765433
No 7
>KOG3576|consensus
Probab=99.62 E-value=4.1e-17 Score=117.05 Aligned_cols=111 Identities=27% Similarity=0.491 Sum_probs=68.4
Q ss_pred ceecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCC
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPT 122 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~ 122 (198)
.|.|.+|++.|....-|.+|+.-|...+.+.|..||+.|.+.-+|.+|+++|+|.+||.|..|++.|..
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq----------- 185 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ----------- 185 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh-----------
Confidence 456666666666666666666666666666666666666666666666666666666666666666665
Q ss_pred cCccccccccccccc----------CCCCeeCCcchhhhcChhHHHhhhhhhCC
Q psy11761 123 YTKSNLAQHSCMNSH----------FPKPYQCDRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 123 ~~~~~l~~H~~~~~~----------~~~~~~C~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
.-.|..|.+..+. ..+-|+|+.||..-.....+..|+..||.
T Consensus 186 --rcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 186 --RCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred --hccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 4444444433321 13456666666666666666666666654
No 8
>KOG3576|consensus
Probab=99.60 E-value=7.7e-17 Score=115.64 Aligned_cols=103 Identities=26% Similarity=0.515 Sum_probs=92.7
Q ss_pred CCCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcch
Q psy11761 69 PRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCS 148 (198)
Q Consensus 69 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~ 148 (198)
...|.|.+|++.|.-..-|.+|++-|.+.+.+.|..||+.|-+ .-+|++|+++|+ |-+||+|..|+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfnd-------------tfdlkrh~rtht-gvrpykc~~c~ 180 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFND-------------TFDLKRHTRTHT-GVRPYKCSLCE 180 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccc-------------hhhhhhhhcccc-Cccccchhhhh
Confidence 4568999999999999999999999999999999999999987 889999999999 89999999999
Q ss_pred hhhcChhHHHhhhhhhCCC---------CCCCcccccccCCCcccc
Q psy11761 149 QFFGDRMNLISHHCHKHKQ---------SCLPFISRLFGFDDGDKV 185 (198)
Q Consensus 149 k~f~~~~~L~~H~~~~~~~---------~~~~~~~~~~~~~~~~~~ 185 (198)
|+|+++.+|..|++..||. +..-|.|+.||+...+.-
T Consensus 181 kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e 226 (267)
T KOG3576|consen 181 KAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPE 226 (267)
T ss_pred HHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChh
Confidence 9999999999999888762 344678999999876543
No 9
>KOG3623|consensus
Probab=99.44 E-value=2.6e-14 Score=119.36 Aligned_cols=81 Identities=36% Similarity=0.773 Sum_probs=76.3
Q ss_pred CCCCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcc
Q psy11761 68 KPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRC 147 (198)
Q Consensus 68 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C 147 (198)
...+|.|+.|++.|--..+|.+|.-.|+|.+||.|.+|.++|.. +.+|..|+|.|. |+|||+|+.|
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKH-------------KHHLtEHkRLHS-GEKPfQCdKC 956 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKH-------------KHHLTEHKRLHS-GEKPFQCDKC 956 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhh-------------hhhhhhhhhhcc-CCCcchhhhh
Confidence 45689999999999999999999999999999999999999998 999999999999 8999999999
Q ss_pred hhhhcChhHHHhhhh
Q psy11761 148 SQFFGDRMNLISHHC 162 (198)
Q Consensus 148 ~k~f~~~~~L~~H~~ 162 (198)
+|+|....++.+||.
T Consensus 957 lKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 957 LKRFSHSGSYSQHMN 971 (1007)
T ss_pred hhhcccccchHhhhc
Confidence 999999999999985
No 10
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.40 E-value=2.3e-13 Score=113.38 Aligned_cols=130 Identities=17% Similarity=0.356 Sum_probs=102.7
Q ss_pred cccCc--ccchhhcccCCCceecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcCCCCcccCC
Q psy11761 26 YKCHQ--CQRLIFLSANAGVHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCT 103 (198)
Q Consensus 26 ~~C~~--C~~~f~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~ 103 (198)
..|+. |+..|....-...+.|+.|++.|. ...|..|+..++ .++.|+ |+..+ ....|..|+.+|.+.+++.|+
T Consensus 434 V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~ 508 (567)
T PLN03086 434 VVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCR 508 (567)
T ss_pred eeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCC
Confidence 45875 999887777777889999999996 577999999886 789999 99765 568899999999999999999
Q ss_pred cCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhcChhHHHhhhhhhCC
Q psy11761 104 TCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 104 ~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
.|++.|....++.+ .....+.|..|.... +.+++.|..||+.+..+ .+..|+...|.
T Consensus 509 fC~~~v~~g~~~~d---~~d~~s~Lt~HE~~C--G~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 509 FCGDMVQAGGSAMD---VRDRLRGMSEHESIC--GSRTAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred CCCCccccCccccc---hhhhhhhHHHHHHhc--CCcceEccccCCeeeeh-hHHHHHHHhhc
Confidence 99999853111000 000145788998886 68999999999999888 88999877664
No 11
>KOG3623|consensus
Probab=99.37 E-value=1e-13 Score=115.84 Aligned_cols=78 Identities=37% Similarity=0.800 Sum_probs=74.2
Q ss_pred ceecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCC
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPT 122 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~ 122 (198)
+|.|.+|.+.|...++|.+|.=-|+|.+||.|.+|.++|..+..|..|+|.|.|+|||.|+.|+++|..
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSH----------- 962 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSH----------- 962 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhccc-----------
Confidence 799999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCccccccccc
Q psy11761 123 YTKSNLAQHSC 133 (198)
Q Consensus 123 ~~~~~l~~H~~ 133 (198)
...+.+||.
T Consensus 963 --SGSYSQHMN 971 (1007)
T KOG3623|consen 963 --SGSYSQHMN 971 (1007)
T ss_pred --ccchHhhhc
Confidence 677777773
No 12
>PHA00733 hypothetical protein
Probab=99.07 E-value=6.4e-11 Score=81.58 Aligned_cols=94 Identities=20% Similarity=0.357 Sum_probs=70.1
Q ss_pred hHHhhcccCCCCCCCccCccchhcccCchhHHHh--h---hhcCCCCcccCCcCchhhhcccCCCcccCCCcCccccccc
Q psy11761 57 SSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTH--Q---LIHSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQH 131 (198)
Q Consensus 57 ~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H--~---~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H 131 (198)
.+|..+-..-...+++.|.+|...|.....|..+ + ..+.+.+||.|+.|++.|.+ .+.|..|
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss-------------~s~L~~H 92 (128)
T PHA00733 26 EELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSS-------------SVSLKQH 92 (128)
T ss_pred HHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCC-------------HHHHHHH
Confidence 3443332223335678899998888776555544 1 12345789999999999998 8889999
Q ss_pred ccccccCCCCeeCCcchhhhcChhHHHhhhhhhCC
Q psy11761 132 SCMNSHFPKPYQCDRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 132 ~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
++.+ +.++.|+.|++.|.....|..|+...|+
T Consensus 93 ~r~h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 93 IRYT---EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred HhcC---CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 9865 3579999999999999999999988775
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.94 E-value=8.1e-10 Score=92.48 Aligned_cols=124 Identities=18% Similarity=0.374 Sum_probs=91.2
Q ss_pred cccCcccchhhcccCCC--------ceecCc--cccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcC
Q psy11761 26 YKCHQCQRLIFLSANAG--------VHKCEY--CHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHS 95 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~--------~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 95 (198)
..|+.|.+......-.. .-.|+. |+..|.. ..+..| +.|+.|++.|. ...+..|+..++
T Consensus 408 V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r-~el~~H---------~~C~~Cgk~f~-~s~LekH~~~~H 476 (567)
T PLN03086 408 VECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRV-EEAKNH---------VHCEKCGQAFQ-QGEMEKHMKVFH 476 (567)
T ss_pred EECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeec-cccccC---------ccCCCCCCccc-hHHHHHHHHhcC
Confidence 46888887654432211 235774 8887733 334444 48999999996 577999999975
Q ss_pred CCCcccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhcC----------hhHHHhhhhhhC
Q psy11761 96 GIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGD----------RMNLISHHCHKH 165 (198)
Q Consensus 96 ~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~----------~~~L~~H~~~~~ 165 (198)
+++.|+ ||+.+ . +..|..|...+. ..+++.|+.|++.|.. .+.|..|....
T Consensus 477 --kpv~Cp-Cg~~~-~-------------R~~L~~H~~thC-p~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C- 537 (567)
T PLN03086 477 --EPLQCP-CGVVL-E-------------KEQMVQHQASTC-PLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC- 537 (567)
T ss_pred --CCccCC-CCCCc-c-------------hhHHHhhhhccC-CCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-
Confidence 789999 99765 4 789999998888 6899999999999952 34788897774
Q ss_pred CCCCCCcccccccCCC
Q psy11761 166 KQSCLPFISRLFGFDD 181 (198)
Q Consensus 166 ~~~~~~~~~~~~~~~~ 181 (198)
|.++ +.|..|+...
T Consensus 538 G~rt--~~C~~Cgk~V 551 (567)
T PLN03086 538 GSRT--APCDSCGRSV 551 (567)
T ss_pred CCcc--eEccccCCee
Confidence 7774 5668887543
No 14
>KOG3993|consensus
Probab=98.74 E-value=3.4e-09 Score=84.22 Aligned_cols=113 Identities=19% Similarity=0.423 Sum_probs=79.8
Q ss_pred ceecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCC
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPT 122 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~ 122 (198)
-|.|+.|...|...-.|..|.-.......|+|++|++.|+..++|..|.++|.+...-.- ....+.+....
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~--------a~~~P~k~~~~- 337 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAK--------AGSPPPKQAVE- 337 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhh--------cCCCChhhhhh-
Confidence 589999999999999999999988888899999999999999999999999986542110 00001000000
Q ss_pred cCccccccccc-c-cccCCCCeeCCcchhhhcChhHHHhhhhhhCC
Q psy11761 123 YTKSNLAQHSC-M-NSHFPKPYQCDRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 123 ~~~~~l~~H~~-~-~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
...+.+-.- . ....+.-|.|..|+|.|.+..-|++|+.+|+.
T Consensus 338 --~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 338 --TRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred --hhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 000000000 0 00124589999999999999999999988863
No 15
>PHA00733 hypothetical protein
Probab=98.67 E-value=5.8e-09 Score=71.89 Aligned_cols=78 Identities=21% Similarity=0.330 Sum_probs=60.4
Q ss_pred ceecCccccccCChhH------HhhcccCCCCCCCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCC
Q psy11761 43 VHKCEYCHKVFDQQSS------LLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPT 116 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~------l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~ 116 (198)
++.|.+|...|..... |..|+. +++.+||.|+.|++.|.....|..|++.+ ..+|.|..|++.|..
T Consensus 40 ~~~~~~~~~~~~~~~~l~~~~~l~~~~~-~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~----- 111 (128)
T PHA00733 40 RLIRAVVKTLIYNPQLLDESSYLYKLLT-SKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRN----- 111 (128)
T ss_pred hHHHHHHhhhccChhhhcchHHHHhhcc-cCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCC-----
Confidence 3456666665555443 344443 34588999999999999999999999876 357999999999998
Q ss_pred cccCCCcCcccccccccccc
Q psy11761 117 STHTPTYTKSNLAQHSCMNS 136 (198)
Q Consensus 117 ~~~~~~~~~~~l~~H~~~~~ 136 (198)
...|..|++..+
T Consensus 112 --------~~sL~~H~~~~h 123 (128)
T PHA00733 112 --------TDSTLDHVCKKH 123 (128)
T ss_pred --------HHHHHHHHHHhc
Confidence 888999987766
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.64 E-value=1.6e-08 Score=58.11 Aligned_cols=39 Identities=21% Similarity=0.526 Sum_probs=29.8
Q ss_pred CccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhc
Q psy11761 71 PYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVN 111 (198)
Q Consensus 71 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~ 111 (198)
.|.|+.||+.|.....|..|+++|+ +++.|..|++.|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~ 43 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLR 43 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecc
Confidence 4677778888877777778877777 57777778777765
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.51 E-value=3.8e-08 Score=56.62 Aligned_cols=46 Identities=13% Similarity=0.275 Sum_probs=40.4
Q ss_pred CCceecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHH
Q psy11761 41 AGVHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLN 88 (198)
Q Consensus 41 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~ 88 (198)
+..|.|+.||+.|.....|..|++.|+ ++++|..|++.|.....|.
T Consensus 3 ~~~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 3 LLGYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 446899999999999999999999999 7999999999998765543
No 18
>PHA00616 hypothetical protein
Probab=98.50 E-value=6.8e-08 Score=52.89 Aligned_cols=32 Identities=38% Similarity=0.664 Sum_probs=29.4
Q ss_pred CeeCCcchhhhcChhHHHhhhhhhCCCCCCCc
Q psy11761 141 PYQCDRCSQFFGDRMNLISHHCHKHKQSCLPF 172 (198)
Q Consensus 141 ~~~C~~C~k~f~~~~~L~~H~~~~~~~~~~~~ 172 (198)
||+|+.||+.|..+++|.+|++.|||++++..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 68999999999999999999999999986653
No 19
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.46 E-value=6.3e-08 Score=47.58 Aligned_cols=25 Identities=48% Similarity=0.970 Sum_probs=21.8
Q ss_pred hHHHhhhhcCCCCcccCCcCchhhh
Q psy11761 86 NLNTHQLIHSGIRPFKCTTCDKSFV 110 (198)
Q Consensus 86 ~l~~H~~~h~~~k~~~C~~C~~~f~ 110 (198)
+|..|+++|++++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4778999999999999999998885
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=98.46 E-value=3.2e-08 Score=48.65 Aligned_cols=23 Identities=22% Similarity=0.544 Sum_probs=21.3
Q ss_pred hhhhhhhCCCCccccCcccchhh
Q psy11761 14 QTLLCIHGNDNAYKCHQCQRLIF 36 (198)
Q Consensus 14 ~~h~~~h~~~~~~~C~~C~~~f~ 36 (198)
+.||++|+|++||.|+.|++.|.
T Consensus 3 ~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 3 RRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHhhhcCCCCCCCCCCCcCeeC
Confidence 49999999999999999999885
No 21
>PHA00616 hypothetical protein
Probab=98.09 E-value=1.4e-06 Score=47.77 Aligned_cols=34 Identities=18% Similarity=0.302 Sum_probs=24.4
Q ss_pred CccCccchhcccCchhHHHhhhhcCCCCcccCCc
Q psy11761 71 PYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTT 104 (198)
Q Consensus 71 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~ 104 (198)
||+|+.||+.|....++..|++.|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5677777777777777777777777777776654
No 22
>KOG3993|consensus
Probab=98.07 E-value=1.4e-06 Score=69.73 Aligned_cols=70 Identities=30% Similarity=0.533 Sum_probs=55.6
Q ss_pred cccCcccchhhcccCCC----------ceecCccccccCChhHHhhcccCCCC--------C------------------
Q psy11761 26 YKCHQCQRLIFLSANAG----------VHKCEYCHKVFDQQSSLLSHNCPQMK--------P------------------ 69 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~----------~~~C~~C~~~f~~~~~l~~H~~~h~~--------~------------------ 69 (198)
|.|..|-..|.....|. .|+|++|++.|....+|..|++=|.. .
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 78888887776544443 58999999999999999999776631 1
Q ss_pred -------CCccCccchhcccCchhHHHhhhhcC
Q psy11761 70 -------RPYKCDTCEKSFTNSQNLNTHQLIHS 95 (198)
Q Consensus 70 -------~~~~C~~C~~~f~~~~~l~~H~~~h~ 95 (198)
.-|.|..|++.|...+-|..|+.+|.
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 12889999999999999999988764
No 23
>PHA00732 hypothetical protein
Probab=98.03 E-value=4e-06 Score=52.67 Aligned_cols=50 Identities=28% Similarity=0.422 Sum_probs=39.2
Q ss_pred ceecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcCCC
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGI 97 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~ 97 (198)
||.|..|++.|.....|..|++.++. ++.|+.|++.|. .+..|.+++.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~~CgKsF~---~l~~H~~~~~~~ 50 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCPVCNKSYR---RLNQHFYSQYDI 50 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccCCCCCEeC---ChhhhhcccCCc
Confidence 57899999999999999999875332 358999999987 477788777654
No 24
>PHA00732 hypothetical protein
Probab=98.01 E-value=1.5e-06 Score=54.54 Aligned_cols=47 Identities=28% Similarity=0.480 Sum_probs=36.4
Q ss_pred cccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhcChhHHHhhhhhh
Q psy11761 99 PFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHCHK 164 (198)
Q Consensus 99 ~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~ 164 (198)
||.|..|++.|.+ .++|..|++.++. ++.|+.|++.|. .|..|..++
T Consensus 1 py~C~~Cgk~F~s-------------~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVT-------------LFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCC-------------HHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 5789999999988 8889999885431 358999999997 467776544
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.96 E-value=3.5e-06 Score=49.10 Aligned_cols=52 Identities=33% Similarity=0.547 Sum_probs=38.8
Q ss_pred cccCCcCchhhhcccCCCcccCCCcCcccccccccccccCC-CCeeCCcchhhhcChhHHHhhhhhhCC
Q psy11761 99 PFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFP-KPYQCDRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 99 ~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~-~~~~C~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
.|.|+.|++.|. ...|..|....+..+ +.+.|++|...++ .+|..|+..+|+
T Consensus 2 ~f~CP~C~~~~~--------------~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKGFS--------------ESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCccC--------------HHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 478999999554 678888987765443 5688999998754 388888887663
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.92 E-value=4.8e-06 Score=39.47 Aligned_cols=23 Identities=30% Similarity=0.677 Sum_probs=21.3
Q ss_pred eeCCcchhhhcChhHHHhhhhhh
Q psy11761 142 YQCDRCSQFFGDRMNLISHHCHK 164 (198)
Q Consensus 142 ~~C~~C~k~f~~~~~L~~H~~~~ 164 (198)
|+|+.|++.|.+++.|..|++.|
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 68999999999999999999874
No 27
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.81 E-value=1.4e-05 Score=38.06 Aligned_cols=24 Identities=29% Similarity=0.641 Sum_probs=20.5
Q ss_pred eeCCcchhhhcChhHHHhhhhhhC
Q psy11761 142 YQCDRCSQFFGDRMNLISHHCHKH 165 (198)
Q Consensus 142 ~~C~~C~k~f~~~~~L~~H~~~~~ 165 (198)
|.|++|++.|.+...|..|+.++|
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 689999999999999999998875
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.70 E-value=1.9e-05 Score=38.96 Aligned_cols=26 Identities=27% Similarity=0.662 Sum_probs=23.7
Q ss_pred CeeCCcchhhhcChhHHHhhhhhhCC
Q psy11761 141 PYQCDRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 141 ~~~C~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
+|+|+.|++.|.+...|..|++.|++
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 68999999999999999999988763
No 29
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.42 E-value=5.9e-05 Score=58.54 Aligned_cols=53 Identities=28% Similarity=0.632 Sum_probs=40.7
Q ss_pred CCcccCCc--CchhhhcccCCCcccCCCcCcccccccccccc------------------cCCCCeeCCcchhhhcChhH
Q psy11761 97 IRPFKCTT--CDKSFVNQINPTSTHTPTYTKSNLAQHSCMNS------------------HFPKPYQCDRCSQFFGDRMN 156 (198)
Q Consensus 97 ~k~~~C~~--C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~------------------~~~~~~~C~~C~k~f~~~~~ 156 (198)
+|||.|++ |.+.+.+ ..+|+-|+.--+ ...|||.|++|+|.|.....
T Consensus 347 ~KpykCpV~gC~K~Ykn-------------qnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNG 413 (423)
T COG5189 347 GKPYKCPVEGCNKKYKN-------------QNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNG 413 (423)
T ss_pred CceecCCCCCchhhhcc-------------ccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCcc
Confidence 69999987 9999998 555555553221 02589999999999999988
Q ss_pred HHhhhh
Q psy11761 157 LISHHC 162 (198)
Q Consensus 157 L~~H~~ 162 (198)
|..|..
T Consensus 414 LKYHr~ 419 (423)
T COG5189 414 LKYHRK 419 (423)
T ss_pred ceeccc
Confidence 888853
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.29 E-value=0.00018 Score=47.00 Aligned_cols=73 Identities=23% Similarity=0.419 Sum_probs=21.4
Q ss_pred cCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhc
Q psy11761 73 KCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFG 152 (198)
Q Consensus 73 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~ 152 (198)
.|..|+..|.+...+..|+...++... +.. ..+.. ...+..+.... ....+.|..|++.|.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~---~~~-~~l~~-------------~~~~~~~~~~~--~~~~~~C~~C~~~f~ 61 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI---PDQ-KYLVD-------------PNRLLNYLRKK--VKESFRCPYCNKTFR 61 (100)
T ss_dssp -------------------------------------------------------------------SSEEBSSSS-EES
T ss_pred Ccccccccccccccccccccccccccc---ccc-ccccc-------------ccccccccccc--cCCCCCCCccCCCCc
Confidence 377788888877778888765554321 111 11112 33333333322 234799999999999
Q ss_pred ChhHHHhhhhhh
Q psy11761 153 DRMNLISHHCHK 164 (198)
Q Consensus 153 ~~~~L~~H~~~~ 164 (198)
+...|..|+..+
T Consensus 62 s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 62 SREALQEHMRSK 73 (100)
T ss_dssp SHHHHHHHHHHT
T ss_pred CHHHHHHHHcCc
Confidence 999999999865
No 31
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.27 E-value=0.0003 Score=39.53 Aligned_cols=40 Identities=20% Similarity=0.279 Sum_probs=26.6
Q ss_pred ccccccccCCCCeeCCcchhhhcChhHHHhhhhhhCCCCC
Q psy11761 130 QHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHCHKHKQSC 169 (198)
Q Consensus 130 ~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~~~~~ 169 (198)
.+.+.+...+.|..|++|+..+.+.-+|.+|+...|+.+|
T Consensus 13 ~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 13 KKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp ---CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3444444457899999999999999999999999998886
No 32
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.16 E-value=0.00038 Score=40.41 Aligned_cols=42 Identities=17% Similarity=0.392 Sum_probs=34.6
Q ss_pred CeeCCcchhhhcChhHHHhhhhhhCCCCCCCcccccccCCCcc
Q psy11761 141 PYQCDRCSQFFGDRMNLISHHCHKHKQSCLPFISRLFGFDDGD 183 (198)
Q Consensus 141 ~~~C~~C~k~f~~~~~L~~H~~~~~~~~~~~~~~~~~~~~~~~ 183 (198)
.|.|++|++.| +...|..|....|...+..+.|++|....++
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~ 43 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCEDEHRSESKNVVCPICSSRVTD 43 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHhHCcCCCCCccCCCchhhhhh
Confidence 58999999955 5669999999888777778999999976554
No 33
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.04 E-value=0.0002 Score=33.71 Aligned_cols=21 Identities=43% Similarity=0.762 Sum_probs=11.1
Q ss_pred cCccchhcccCchhHHHhhhh
Q psy11761 73 KCDTCEKSFTNSQNLNTHQLI 93 (198)
Q Consensus 73 ~C~~C~~~f~~~~~l~~H~~~ 93 (198)
.|+.|++.|.....|..|++.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHhH
Confidence 455555555555555555543
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.90 E-value=0.00066 Score=32.48 Aligned_cols=24 Identities=25% Similarity=0.632 Sum_probs=21.4
Q ss_pred eeCCcchhhhcChhHHHhhhhhhC
Q psy11761 142 YQCDRCSQFFGDRMNLISHHCHKH 165 (198)
Q Consensus 142 ~~C~~C~k~f~~~~~L~~H~~~~~ 165 (198)
|+|+.|++.|.+...|..|+..|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998653
No 35
>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=96.82 E-value=0.00061 Score=33.37 Aligned_cols=24 Identities=29% Similarity=0.592 Sum_probs=13.2
Q ss_pred eecCccccccCChhHHhhcccCCC
Q psy11761 44 HKCEYCHKVFDQQSSLLSHNCPQM 67 (198)
Q Consensus 44 ~~C~~C~~~f~~~~~l~~H~~~h~ 67 (198)
|.|..|++.|.....|..|++.|.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 455555555555555555555443
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.62 E-value=0.00046 Score=45.06 Aligned_cols=77 Identities=21% Similarity=0.374 Sum_probs=22.1
Q ss_pred ecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCCcC
Q psy11761 45 KCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPTYT 124 (198)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~ 124 (198)
+|..|+..|.....|..|+...++...- ....+.....+..+.+.... ..+.|..|++.|.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~-~~~~C~~C~~~f~s------------- 62 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVK-ESFRCPYCNKTFRS------------- 62 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESS-------------
T ss_pred Cccccccccccccccccccccccccccc----cccccccccccccccccccC-CCCCCCccCCCCcC-------------
Confidence 4889999999999999998776653211 11111222233333332222 26899999999988
Q ss_pred cccccccccccccCC
Q psy11761 125 KSNLAQHSCMNSHFP 139 (198)
Q Consensus 125 ~~~l~~H~~~~~~~~ 139 (198)
...|..|++.+.+..
T Consensus 63 ~~~l~~Hm~~~~H~~ 77 (100)
T PF12756_consen 63 REALQEHMRSKHHKK 77 (100)
T ss_dssp HHHHHHHHHHTTTTC
T ss_pred HHHHHHHHcCccCCC
Confidence 888999998765433
No 37
>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=96.57 E-value=0.001 Score=31.23 Aligned_cols=23 Identities=35% Similarity=0.787 Sum_probs=11.5
Q ss_pred ccCccchhcccCchhHHHhhhhc
Q psy11761 72 YKCDTCEKSFTNSQNLNTHQLIH 94 (198)
Q Consensus 72 ~~C~~C~~~f~~~~~l~~H~~~h 94 (198)
|.|+.|+..|.+...|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 34555555555555555555543
No 38
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.53 E-value=0.0011 Score=51.62 Aligned_cols=25 Identities=36% Similarity=0.946 Sum_probs=20.0
Q ss_pred CCCCccCccchhcccCchhHHHhhh
Q psy11761 68 KPRPYKCDTCEKSFTNSQNLNTHQL 92 (198)
Q Consensus 68 ~~~~~~C~~C~~~f~~~~~l~~H~~ 92 (198)
..+||+|+.|++++.+...|.-|+.
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCCceeccccchhhccCccceeccc
Confidence 3589999999999988877766643
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.40 E-value=0.0019 Score=30.65 Aligned_cols=24 Identities=33% Similarity=0.595 Sum_probs=19.3
Q ss_pred eeCCcchhhhcChhHHHhhhhhhCC
Q psy11761 142 YQCDRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 142 ~~C~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
|+|+.|+.... ...|..|+..+|+
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 68999999988 8899999998764
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.23 E-value=0.0024 Score=30.52 Aligned_cols=23 Identities=30% Similarity=0.609 Sum_probs=20.5
Q ss_pred eeCCcchhhhcChhHHHhhhhhh
Q psy11761 142 YQCDRCSQFFGDRMNLISHHCHK 164 (198)
Q Consensus 142 ~~C~~C~k~f~~~~~L~~H~~~~ 164 (198)
|.|++|++.|.+...|..|++.+
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 67999999999999999998643
No 41
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.87 E-value=0.004 Score=30.47 Aligned_cols=22 Identities=27% Similarity=0.730 Sum_probs=20.2
Q ss_pred eeCCcchhhhcChhHHHhhhhh
Q psy11761 142 YQCDRCSQFFGDRMNLISHHCH 163 (198)
Q Consensus 142 ~~C~~C~k~f~~~~~L~~H~~~ 163 (198)
|.|+.|++.|.+...|..|+..
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 7899999999999999999864
No 42
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.83 E-value=0.0079 Score=33.88 Aligned_cols=33 Identities=27% Similarity=0.478 Sum_probs=20.7
Q ss_pred CCCCCccCccchhcccCchhHHHhhhhcCCCCc
Q psy11761 67 MKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRP 99 (198)
Q Consensus 67 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~ 99 (198)
..+.|-.|++|+..++...+|.+|+...++.||
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 346677888888888888888888877776665
No 43
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.45 E-value=0.011 Score=27.97 Aligned_cols=23 Identities=35% Similarity=0.797 Sum_probs=14.6
Q ss_pred ccCccchhcccCchhHHHhhhhc
Q psy11761 72 YKCDTCEKSFTNSQNLNTHQLIH 94 (198)
Q Consensus 72 ~~C~~C~~~f~~~~~l~~H~~~h 94 (198)
|.|+.|++.|.....+..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 35666666666666666666644
No 44
>PRK04860 hypothetical protein; Provisional
Probab=95.24 E-value=0.0095 Score=42.66 Aligned_cols=38 Identities=24% Similarity=0.753 Sum_probs=31.6
Q ss_pred CCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhc
Q psy11761 70 RPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVN 111 (198)
Q Consensus 70 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~ 111 (198)
-+|.|. |+. ....+..|.+++.++++|.|..|+..|..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 368997 886 55668899999999999999999988764
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.61 E-value=0.012 Score=27.99 Aligned_cols=22 Identities=36% Similarity=0.792 Sum_probs=13.3
Q ss_pred ccCccchhcccCchhHHHhhhh
Q psy11761 72 YKCDTCEKSFTNSQNLNTHQLI 93 (198)
Q Consensus 72 ~~C~~C~~~f~~~~~l~~H~~~ 93 (198)
|.|.+|+..|.+...+..|++.
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 3466666666666666666554
No 46
>PRK04860 hypothetical protein; Provisional
Probab=94.48 E-value=0.013 Score=41.96 Aligned_cols=38 Identities=21% Similarity=0.531 Sum_probs=33.2
Q ss_pred ceecCccccccCChhHHhhcccCCCCCCCccCccchhcccCc
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNS 84 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 84 (198)
+|.|. |+. ....+.+|.+++.++++|.|..|+..|...
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 68998 987 567789999999999999999999988654
No 47
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=94.25 E-value=0.046 Score=31.86 Aligned_cols=50 Identities=24% Similarity=0.441 Sum_probs=31.6
Q ss_pred CccccCcccchhhcccCCCceecCccccc-cCChhHHhhcccCCCCCCCccCccchh
Q psy11761 24 NAYKCHQCQRLIFLSANAGVHKCEYCHKV-FDQQSSLLSHNCPQMKPRPYKCDTCEK 79 (198)
Q Consensus 24 ~~~~C~~C~~~f~~~~~~~~~~C~~C~~~-f~~~~~l~~H~~~h~~~~~~~C~~C~~ 79 (198)
.+..|..||...........|.|+.||+. ..+-..-+ ....+|.|+.||.
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CR------k~~~~Y~CP~CGF 56 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCR------KQSNPYTCPKCGF 56 (59)
T ss_pred cCccccCCCCcccCCCccCEeeCCCCCCeeEeechhHH------hcCCceECCCCCC
Confidence 45678888887766666678889999876 33222111 1135677777764
No 48
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.18 E-value=0.056 Score=44.34 Aligned_cols=62 Identities=29% Similarity=0.535 Sum_probs=52.9
Q ss_pred ceecCccccccCChhHHhhccc--CCCCC--CCccCc--cchhcccCchhHHHhhhhcCCCCcccCCc
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNC--PQMKP--RPYKCD--TCEKSFTNSQNLNTHQLIHSGIRPFKCTT 104 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~k~~~C~~ 104 (198)
++.|..|...|.....+..|.. .|.++ +++.|+ .|++.|.....+..|...|.+..++.+..
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 5778889999999999999988 78888 899999 79999999888889999888877766644
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.05 E-value=0.034 Score=26.66 Aligned_cols=20 Identities=25% Similarity=0.464 Sum_probs=16.8
Q ss_pred eeCCcchhhhcChhHHHhhhh
Q psy11761 142 YQCDRCSQFFGDRMNLISHHC 162 (198)
Q Consensus 142 ~~C~~C~k~f~~~~~L~~H~~ 162 (198)
..|+.||+.| ..+.|.+|..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4799999999 6668999975
No 50
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=94.00 E-value=0.042 Score=31.98 Aligned_cols=50 Identities=24% Similarity=0.424 Sum_probs=32.4
Q ss_pred ccccCcccchhhcccCCCceecCccccccCChhHHhhcccCCCCCCCccCccchh
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEK 79 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 79 (198)
+-.|..||...........|.|+.||+..-....-- .....+|.|+.||.
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~C-----Rk~g~~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKC-----RKLGNPYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhH-----HHcCCceECCCcCc
Confidence 457888998876667777889999986533322211 11235788888764
No 51
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=93.94 E-value=0.021 Score=27.81 Aligned_cols=21 Identities=33% Similarity=0.857 Sum_probs=11.3
Q ss_pred ccCccchhcccCchhHHHhhh
Q psy11761 72 YKCDTCEKSFTNSQNLNTHQL 92 (198)
Q Consensus 72 ~~C~~C~~~f~~~~~l~~H~~ 92 (198)
|.|..|++.|.+...+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 345555555555555555544
No 52
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.77 E-value=0.022 Score=26.81 Aligned_cols=23 Identities=39% Similarity=0.681 Sum_probs=13.5
Q ss_pred ccCccchhcccCchhHHHhhhhcC
Q psy11761 72 YKCDTCEKSFTNSQNLNTHQLIHS 95 (198)
Q Consensus 72 ~~C~~C~~~f~~~~~l~~H~~~h~ 95 (198)
|.|+.|+.... ...|..|++.+.
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 45777776666 666777766543
No 53
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.50 E-value=0.046 Score=30.40 Aligned_cols=29 Identities=31% Similarity=0.695 Sum_probs=21.4
Q ss_pred ccccCcccchhhcccCCCceecCcccccc
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKVF 53 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~f 53 (198)
.|.|+.||..|.-........|+.||..+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeE
Confidence 57888888877665555578888887654
No 54
>KOG2231|consensus
Probab=93.33 E-value=0.066 Score=46.54 Aligned_cols=120 Identities=23% Similarity=0.396 Sum_probs=60.1
Q ss_pred cccCcccchhhcccCCCceecCccccccCChhHHhhcccCCCCCCCccCccch---hcc------cCchhHHHhhhhcCC
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCE---KSF------TNSQNLNTHQLIHSG 96 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~---~~f------~~~~~l~~H~~~h~~ 96 (198)
+.|..|++.+... .....|..| ..|.....|..|+...|. -+.|..|- +.| -....|..|++....
T Consensus 100 ~~C~~C~~~~~~~--~~~~~~~~c-~~~~s~~~Lk~H~~~~H~--~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~ 174 (669)
T KOG2231|consen 100 HSCHICDRRFRAL--YNKKECLHC-TEFKSVENLKNHMRDQHK--LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDP 174 (669)
T ss_pred hhcCccccchhhh--cccCCCccc-cchhHHHHHHHHHHHhhh--hhccccccccceeeeeeeehehHHHHHHHHhcCCC
Confidence 4577777765321 112346666 666677788888755442 33343332 122 223556666654322
Q ss_pred -CC----cccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeC---CcchhhhcChhHHHhhhhhhC
Q psy11761 97 -IR----PFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQC---DRCSQFFGDRMNLISHHCHKH 165 (198)
Q Consensus 97 -~k----~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C---~~C~k~f~~~~~L~~H~~~~~ 165 (198)
++ --.|..|...|.. ...|.+|++..+. --.-| +.++.-|.....|..|.+..|
T Consensus 175 d~~s~rGhp~C~~C~~~fld-------------~~el~rH~~~~h~--~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 175 DDESCRGHPLCKFCHERFLD-------------DDELYRHLRFDHE--FCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ccccccCCccchhhhhhhcc-------------HHHHHHhhcccee--heeecCcccccchhcccchHHHHHhhhcC
Confidence 11 1366677777766 5556666654441 11112 112344444555555555444
No 55
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.25 E-value=0.047 Score=31.28 Aligned_cols=29 Identities=28% Similarity=0.484 Sum_probs=25.8
Q ss_pred CCCCeeCCcchhhhcChhHHHhhhhhhCC
Q psy11761 138 FPKPYQCDRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 138 ~~~~~~C~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
|+.-+.|+.||..|....++.+|....|+
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 67788999999999999999999987765
No 56
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.03 E-value=0.072 Score=27.46 Aligned_cols=23 Identities=22% Similarity=0.509 Sum_probs=20.4
Q ss_pred CCeeCCcchhhhcChhHHHhhhh
Q psy11761 140 KPYQCDRCSQFFGDRMNLISHHC 162 (198)
Q Consensus 140 ~~~~C~~C~k~f~~~~~L~~H~~ 162 (198)
.+|.|+.|++.|.....+..|+.
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHC
Confidence 36889999999999999999975
No 57
>KOG2893|consensus
Probab=91.89 E-value=0.055 Score=40.79 Aligned_cols=44 Identities=30% Similarity=0.736 Sum_probs=35.4
Q ss_pred ecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhh
Q psy11761 45 KCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQL 92 (198)
Q Consensus 45 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 92 (198)
+|..|+..|....-|+.|++. +-|+|-+|.+.+-+-..|..|..
T Consensus 12 wcwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcm 55 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCM 55 (341)
T ss_pred eeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehh
Confidence 588899999999888888875 44889999888777777777743
No 58
>KOG2893|consensus
Probab=91.80 E-value=0.03 Score=42.14 Aligned_cols=48 Identities=27% Similarity=0.477 Sum_probs=38.2
Q ss_pred cCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhcChhHHHhhhhhhCC
Q psy11761 101 KCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 101 ~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
=|..|.+.|.. ..-|.+|++ .+-|+|.+|.|..-+-..|..|....|+
T Consensus 12 wcwycnrefdd-------------ekiliqhqk-----akhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDD-------------EKILIQHQK-----AKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccch-------------hhhhhhhhh-----hccceeeeehhhhccCCCceeehhhhhh
Confidence 38899999998 888888884 4678999998877666688888665554
No 59
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.74 E-value=0.12 Score=42.40 Aligned_cols=75 Identities=23% Similarity=0.239 Sum_probs=62.2
Q ss_pred CcccCCcCchhhhcccCCCcccCCCcCccccccccc--ccccCC--CCeeCC--cchhhhcChhHHHhhhhhhCCCCCCC
Q psy11761 98 RPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSC--MNSHFP--KPYQCD--RCSQFFGDRMNLISHHCHKHKQSCLP 171 (198)
Q Consensus 98 k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~--~~~~~~--~~~~C~--~C~k~f~~~~~L~~H~~~~~~~~~~~ 171 (198)
.++.|..|...|.. ...+.+|.+ .|. ++ +++.|+ .|++.|.+...+..|..+|.+..+..
T Consensus 288 ~~~~~~~~~~~~s~-------------~~~l~~~~~~~~h~-~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 288 LPIKSKQCNISFSR-------------SSPLTRHLRSVNHS-GESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred cCCCCccccCCccc-------------cccccccccccccc-cccCCceeeeccCCCccccccccccCCcccccCCCccc
Confidence 46788889988888 888999999 566 78 999999 79999999999999999999888777
Q ss_pred cccccccCCCcccch
Q psy11761 172 FISRLFGFDDGDKVA 186 (198)
Q Consensus 172 ~~~~~~~~~~~~~~~ 186 (198)
+.-..+.........
T Consensus 354 ~~~~~~~~~~~~~~~ 368 (467)
T COG5048 354 EKLLNSSSKFSPLLN 368 (467)
T ss_pred cccccCccccccccC
Confidence 777766666555444
No 60
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=91.18 E-value=0.13 Score=32.50 Aligned_cols=33 Identities=24% Similarity=0.490 Sum_probs=27.0
Q ss_pred CccccCcccchhhcccCCCceecCccccccCCh
Q psy11761 24 NAYKCHQCQRLIFLSANAGVHKCEYCHKVFDQQ 56 (198)
Q Consensus 24 ~~~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~ 56 (198)
..|.||.|++.--.......|.|.-|+..|.-.
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCeeccc
Confidence 368999999986667777799999999988553
No 61
>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=91.09 E-value=0.16 Score=24.02 Aligned_cols=21 Identities=29% Similarity=0.466 Sum_probs=9.4
Q ss_pred cccchhhcccCCCceecCccc
Q psy11761 30 QCQRLIFLSANAGVHKCEYCH 50 (198)
Q Consensus 30 ~C~~~f~~~~~~~~~~C~~C~ 50 (198)
.|+...........|.|+.||
T Consensus 3 sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 3 SCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred cCCCcccCcccCceEeCCCCC
Confidence 344443333334455555554
No 62
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=90.93 E-value=0.13 Score=26.43 Aligned_cols=24 Identities=21% Similarity=0.458 Sum_probs=13.1
Q ss_pred cccCcccchhhcccCCCceecCcccc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
|.|..||..+... ..++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~--~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE--EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC--cCCCcCcCCCC
Confidence 4566666655332 24566666654
No 63
>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=90.77 E-value=0.19 Score=24.30 Aligned_cols=24 Identities=29% Similarity=0.574 Sum_probs=14.0
Q ss_pred ccCcccchhhcccCCCceecCccccccC
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHKVFD 54 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~~f~ 54 (198)
.||.|+....... -.|+.||..|.
T Consensus 2 ~CP~C~~~V~~~~----~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESA----KFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhc----CcCCCCCCCCc
Confidence 3677776653332 34777777664
No 64
>KOG1146|consensus
Probab=90.43 E-value=0.18 Score=46.84 Aligned_cols=97 Identities=21% Similarity=0.285 Sum_probs=58.2
Q ss_pred cccccCChhHHhhccc-CCCCCCCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCCcCccc
Q psy11761 49 CHKVFDQQSSLLSHNC-PQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSN 127 (198)
Q Consensus 49 C~~~f~~~~~l~~H~~-~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~ 127 (198)
|+..+.....+..|.. .+...+.+.|+.|+..+.....|..|+|+.+.+-.- ..|. .+.. ...
T Consensus 442 ~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~--~~c~-~gq~-------------~~~ 505 (1406)
T KOG1146|consen 442 AEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS--AYCK-AGQN-------------HPR 505 (1406)
T ss_pred hhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch--hHhH-hccc-------------ccc
Confidence 4444444444444422 344457789999999999888999998875543211 2221 1111 001
Q ss_pred ccccccccccCCCCeeCCcchhhhcChhHHHhhhh
Q psy11761 128 LAQHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHC 162 (198)
Q Consensus 128 l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~ 162 (198)
+.+-..... +.++|.|..|...++...+|..|+.
T Consensus 506 ~arg~~~~~-~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 506 LARGEVYRC-PGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ccccccccC-CCCcccceeeeeeeecchHHHHHHH
Confidence 111111111 4689999999999999999999975
No 65
>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=90.15 E-value=0.18 Score=33.59 Aligned_cols=30 Identities=23% Similarity=0.624 Sum_probs=24.6
Q ss_pred ccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhcCh
Q psy11761 100 FKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGDR 154 (198)
Q Consensus 100 ~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~ 154 (198)
..|+.||..|.. . +..|..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYD-------------L------------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD-------------L------------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc-------------C------------CCCCccCCCCCCccCcc
Confidence 699999999976 2 35788999999998655
No 66
>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=89.92 E-value=0.16 Score=26.25 Aligned_cols=12 Identities=17% Similarity=0.484 Sum_probs=9.5
Q ss_pred cccCCcCchhhh
Q psy11761 99 PFKCTTCDKSFV 110 (198)
Q Consensus 99 ~~~C~~C~~~f~ 110 (198)
.|+|..||..+.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 478999997764
No 67
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=89.12 E-value=0.18 Score=38.01 Aligned_cols=15 Identities=13% Similarity=0.348 Sum_probs=11.4
Q ss_pred CccccCcccchhhcc
Q psy11761 24 NAYKCHQCQRLIFLS 38 (198)
Q Consensus 24 ~~~~C~~C~~~f~~~ 38 (198)
+.+.||+|++.|...
T Consensus 4 k~~~CPvC~~~F~~~ 18 (214)
T PF09986_consen 4 KKITCPVCGKEFKTK 18 (214)
T ss_pred CceECCCCCCeeeee
Confidence 457788888888764
No 68
>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=89.02 E-value=0.27 Score=32.82 Aligned_cols=30 Identities=17% Similarity=0.408 Sum_probs=22.3
Q ss_pred cccCcccchhhcccCCCceecCccccccCCh
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKVFDQQ 56 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~ 56 (198)
-.|+.||+.|---.. .|..|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCccCcc
Confidence 358888888866554 678888888887665
No 69
>PF14369 zf-RING_3: zinc-finger
Probab=88.85 E-value=0.26 Score=25.71 Aligned_cols=30 Identities=33% Similarity=0.817 Sum_probs=16.9
Q ss_pred ccccCcccchhhcccCCCce-ecCccccccC
Q psy11761 25 AYKCHQCQRLIFLSANAGVH-KCEYCHKVFD 54 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~-~C~~C~~~f~ 54 (198)
.|.|..|.+.+........- .|+.|+.+|.
T Consensus 2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFv 32 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGFV 32 (35)
T ss_pred CEeCccCCCEeEeCcCCCCCcCCcCCCCcEe
Confidence 46777777666543222222 4777776663
No 70
>KOG4173|consensus
Probab=88.51 E-value=0.11 Score=38.27 Aligned_cols=81 Identities=22% Similarity=0.420 Sum_probs=54.8
Q ss_pred CCccCcc--chhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCCcCccccccccccccc---------C
Q psy11761 70 RPYKCDT--CEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSH---------F 138 (198)
Q Consensus 70 ~~~~C~~--C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~---------~ 138 (198)
..+.|++ |-..|.+.-.+..|..+-++. .|.+|.+.|++ ..-|..|+...+. |
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt-------------~hLLd~HI~E~HDs~Fqa~veRG 141 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPT-------------GHLLDAHILEWHDSLFQALVERG 141 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCc-------------hhhhhHHHHHHHHHHHHHHHHcC
Confidence 3466766 666777766677776655543 78888888887 5555556543331 3
Q ss_pred CCCeeCC--cchhhhcChhHHHhhhhhhCC
Q psy11761 139 PKPYQCD--RCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 139 ~~~~~C~--~C~k~f~~~~~L~~H~~~~~~ 166 (198)
...|+|- .|+..|.+...-..|+...|.
T Consensus 142 ~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 142 QDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred ccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 5568884 499999888888888876653
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=88.11 E-value=0.31 Score=26.86 Aligned_cols=27 Identities=26% Similarity=0.559 Sum_probs=16.8
Q ss_pred ccccCcccchhhcccCCCceecCccccc
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
.|.|..||..|... ...+..|+.||..
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCce
Confidence 36677777766554 3446677777654
No 72
>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=87.95 E-value=0.18 Score=32.25 Aligned_cols=31 Identities=29% Similarity=0.684 Sum_probs=25.1
Q ss_pred ccccCcccchhhcccCCCceecCccccccCC
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKVFDQ 55 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~ 55 (198)
.|.|+.||+.--.......|.|..|+..|.-
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEEE-
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEEeC
Confidence 7999999998777777778999999988743
No 73
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=87.79 E-value=0.25 Score=27.82 Aligned_cols=29 Identities=31% Similarity=0.708 Sum_probs=21.4
Q ss_pred CccccCcccchhhcccCCCceecCccccc
Q psy11761 24 NAYKCHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 24 ~~~~C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
..|.|-.||+.|..........|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 45888888888865666667788888764
No 74
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.30 E-value=0.54 Score=37.61 Aligned_cols=85 Identities=27% Similarity=0.461 Sum_probs=51.3
Q ss_pred ccCcc--chhcccCchhHHHhhhhcCCCCcccCCcCc---hhhhcccCCCcccCCCcCccccccccccccc--CCC-Cee
Q psy11761 72 YKCDT--CEKSFTNSQNLNTHQLIHSGIRPFKCTTCD---KSFVNQINPTSTHTPTYTKSNLAQHSCMNSH--FPK-PYQ 143 (198)
Q Consensus 72 ~~C~~--C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~---~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~--~~~-~~~ 143 (198)
|.|+. |.........|..|.+..++. +.|.+|- +.|..+..+ ...+.|..|...-.. |-+ --.
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~l-------F~~~~Lr~H~~~G~~e~GFKGHP~ 222 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRL-------FRSSTLRDHKNGGLEEEGFKGHPL 222 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceee-------eecccccccccCCccccCcCCCch
Confidence 67765 555555566788898877764 5777663 344432211 013344444432211 111 236
Q ss_pred CCcchhhhcChhHHHhhhhhhC
Q psy11761 144 CDRCSQFFGDRMNLISHHCHKH 165 (198)
Q Consensus 144 C~~C~k~f~~~~~L~~H~~~~~ 165 (198)
|.+|..-|-....|..|++..|
T Consensus 223 C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred hhhccceecChHHHHHHHHhhh
Confidence 9999999999999999998766
No 75
>KOG2231|consensus
Probab=85.94 E-value=0.51 Score=41.27 Aligned_cols=82 Identities=27% Similarity=0.446 Sum_probs=49.8
Q ss_pred CccchhcccCchhHHHhhhhcCCCCcccCCcCc---hhhhcccCCCcccCCCcCcccccccccccccCCC---C-eeCCc
Q psy11761 74 CDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCD---KSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPK---P-YQCDR 146 (198)
Q Consensus 74 C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~---~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~---~-~~C~~ 146 (198)
|..| ..|.....|..|+...++ .+.|..|- +.|..+..+ .....|..|+....++++ . -.|..
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H~--~~~c~lC~~~~kif~~e~k~-------Yt~~el~~h~~~gd~d~~s~rGhp~C~~ 187 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQHK--LHLCSLCLQNLKIFINERKL-------YTRAELNLHLMFGDPDDESCRGHPLCKF 187 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhhh--hhccccccccceeeeeeeeh-------ehHHHHHHHHhcCCCccccccCCccchh
Confidence 3344 344466788899865442 24554442 223222111 115677777776554322 2 47999
Q ss_pred chhhhcChhHHHhhhhhhC
Q psy11761 147 CSQFFGDRMNLISHHCHKH 165 (198)
Q Consensus 147 C~k~f~~~~~L~~H~~~~~ 165 (198)
|...|-....|.+|++..|
T Consensus 188 C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 188 CHERFLDDDELYRHLRFDH 206 (669)
T ss_pred hhhhhccHHHHHHhhccce
Confidence 9999999999999998775
No 76
>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=85.92 E-value=0.56 Score=23.90 Aligned_cols=25 Identities=24% Similarity=0.604 Sum_probs=12.8
Q ss_pred cccCcccchhhcccCCCceecCcccc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
|.|..||..+..+ ...+-+|+.||.
T Consensus 1 Y~C~~Cg~~~~~~-~~~~irC~~CG~ 25 (32)
T PF03604_consen 1 YICGECGAEVELK-PGDPIRCPECGH 25 (32)
T ss_dssp EBESSSSSSE-BS-TSSTSSBSSSS-
T ss_pred CCCCcCCCeeEcC-CCCcEECCcCCC
Confidence 4566666666532 233556666654
No 77
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.51 E-value=0.48 Score=35.73 Aligned_cols=14 Identities=29% Similarity=0.847 Sum_probs=12.0
Q ss_pred CcccCCcCchhhhc
Q psy11761 98 RPFKCTTCDKSFVN 111 (198)
Q Consensus 98 k~~~C~~C~~~f~~ 111 (198)
+...||+|++.|..
T Consensus 4 k~~~CPvC~~~F~~ 17 (214)
T PF09986_consen 4 KKITCPVCGKEFKT 17 (214)
T ss_pred CceECCCCCCeeee
Confidence 56799999999987
No 78
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.47 E-value=1.8 Score=29.02 Aligned_cols=102 Identities=16% Similarity=0.281 Sum_probs=59.1
Q ss_pred cccCcccchhhcccCCCceecCccccccCChhHHhhcccCCC--CCCCccCccchhcccCchhHHHhhhhcCCCCcccCC
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKVFDQQSSLLSHNCPQM--KPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCT 103 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~--~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~ 103 (198)
|.||.|+... =..|-.|+.|+...-....|++-. |+ ..++|. ... +. .....-.|-
T Consensus 2 Y~CPrC~skv----C~LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~---------ev~-~~------~~~~~~~C~ 59 (112)
T TIGR00622 2 YFCPQCRAKV----CELPVECPICGLTLILSTHLARSY--HHLFPLKAFQ---------EIP-LE------EYNGSRFCF 59 (112)
T ss_pred ccCCCCCCCc----cCCCCcCCcCCCEEeccchHHHhh--hccCCCcccc---------ccc-cc------ccCCCCccc
Confidence 7788887543 123677999998887777776432 33 122221 000 00 011113588
Q ss_pred cCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhcChhHHHhhhhhhC
Q psy11761 104 TCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHCHKH 165 (198)
Q Consensus 104 ~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~ 165 (198)
.|...|+. ......-. .. ....|+|+.|...|--.-+.-.|-.+|.
T Consensus 60 ~C~~~f~~-------------~~~~~~~~--~~-~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 60 GCQGPFPK-------------PPVSPFDE--LK-DSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred CcCCCCCC-------------cccccccc--cc-cccceeCCCCCCccccccchhhhhhccC
Confidence 89888875 21100000 11 3468999999999988888888876663
No 79
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=85.43 E-value=1.2 Score=29.61 Aligned_cols=27 Identities=19% Similarity=0.496 Sum_probs=24.5
Q ss_pred CCeeC----CcchhhhcChhHHHhhhhhhCC
Q psy11761 140 KPYQC----DRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 140 ~~~~C----~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
..|.| ..|+....+...+..|...+||
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 56899 9999999999999999998875
No 80
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=85.06 E-value=0.47 Score=34.15 Aligned_cols=25 Identities=20% Similarity=0.545 Sum_probs=20.6
Q ss_pred CcccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchh
Q psy11761 98 RPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQ 149 (198)
Q Consensus 98 k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k 149 (198)
+-|+|++||..+. |+-|-+||+||.
T Consensus 133 ~~~vC~vCGy~~~---------------------------ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYTHE---------------------------GEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCccc---------------------------CCCCCcCCCCCC
Confidence 3699999998864 577889999994
No 81
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=85.01 E-value=0.42 Score=30.59 Aligned_cols=33 Identities=21% Similarity=0.535 Sum_probs=26.1
Q ss_pred CccccCcccchhhcccCCCceecCccccccCCh
Q psy11761 24 NAYKCHQCQRLIFLSANAGVHKCEYCHKVFDQQ 56 (198)
Q Consensus 24 ~~~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~ 56 (198)
..|.|+.|++.--.......|.|..|+..|.-.
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred CCccCCCCCCCceeeeeeEEEEcCCCCCEEeCC
Confidence 379999999865556666799999999987553
No 82
>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=84.25 E-value=0.42 Score=30.65 Aligned_cols=32 Identities=22% Similarity=0.577 Sum_probs=26.0
Q ss_pred ccccCcccchhhcccCCCceecCccccccCCh
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKVFDQQ 56 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~ 56 (198)
.|.|+.|++.--.......|.|..|+..|.-.
T Consensus 35 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred CccCCCCCCCceEEEeeEEEEcCCCCCEEeCC
Confidence 79999999876666667799999999987553
No 83
>PF14353 CpXC: CpXC protein
Probab=84.17 E-value=0.33 Score=33.35 Aligned_cols=40 Identities=20% Similarity=0.368 Sum_probs=25.5
Q ss_pred ccCcccchhhcccC-------------------CCceecCccccccCChhHHhhcccCC
Q psy11761 27 KCHQCQRLIFLSAN-------------------AGVHKCEYCHKVFDQQSSLLSHNCPQ 66 (198)
Q Consensus 27 ~C~~C~~~f~~~~~-------------------~~~~~C~~C~~~f~~~~~l~~H~~~h 66 (198)
.||.|+..|....- +-.+.|+.||..|.-...+..|...+
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCCC
Confidence 68888877653211 11567888888877766666665443
No 84
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.15 E-value=1.2 Score=29.73 Aligned_cols=71 Identities=18% Similarity=0.368 Sum_probs=43.2
Q ss_pred CCccccCcccchhhcccCCC----------ce------------ecCccccccCChhHHhhcccCCCCCCCccCccchhc
Q psy11761 23 DNAYKCHQCQRLIFLSANAG----------VH------------KCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKS 80 (198)
Q Consensus 23 ~~~~~C~~C~~~f~~~~~~~----------~~------------~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 80 (198)
+.|..|+.||-..-....|. +| .|.-|...|........ ..-.....|.|+.|...
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~ 90 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNV 90 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCc
Confidence 46788888885543333322 22 37778887765431110 00223457889999999
Q ss_pred ccCchhHHHhhhhcC
Q psy11761 81 FTNSQNLNTHQLIHS 95 (198)
Q Consensus 81 f~~~~~l~~H~~~h~ 95 (198)
|-..-++..|...|.
T Consensus 91 FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 91 FCVDCDVFVHESLHC 105 (112)
T ss_pred cccccchhhhhhccC
Confidence 988888888865554
No 85
>KOG1146|consensus
Probab=83.96 E-value=0.5 Score=44.13 Aligned_cols=100 Identities=13% Similarity=0.119 Sum_probs=55.3
Q ss_pred eecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCCc
Q psy11761 44 HKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPTY 123 (198)
Q Consensus 44 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~ 123 (198)
+.|..|...+...-.+. ++- ....|.|..|...|.....+..|.+ .|.+.+..
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~---~~~~~~~~~~~~~~~~~~~l~~~~~-----------k~~~~~~~------------ 1313 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLD---VTHRYLCRQCKMAFDGEAPLTAHQR-----------KFCFAGRG------------ 1313 (1406)
T ss_pred chhhhccccccCcccee-ecc---cchhHHHHHHHhhhcchhHHHHHHH-----------HHHhccCc------------
Confidence 45555555554444333 221 1235666666666666665555551 12222222
Q ss_pred CcccccccccccccCCCCeeCCcchhhhcChhHHHhhhhhhCCCCCCCcc
Q psy11761 124 TKSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHCHKHKQSCLPFI 173 (198)
Q Consensus 124 ~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~~~~~~~~~~~~ 173 (198)
.....-+...+. .-+.| |..|...|.....|..||+..+++.-.++.
T Consensus 1314 -~~~~~~~~l~~~-d~~~~-c~~c~~~~~~~~alqihm~~~~~~~kt~~~ 1360 (1406)
T KOG1146|consen 1314 -SGGSMPPPLRVP-DCTYH-CLACEVLLSGREALQIHMRSSAHRRKTAPP 1360 (1406)
T ss_pred -cccCCCCcccCc-ccccc-chHHHhhcchhHHHHHHHHHhhhcccCCCC
Confidence 222333443333 44566 999999999999999999855444333444
No 86
>KOG2186|consensus
Probab=83.87 E-value=0.43 Score=36.42 Aligned_cols=47 Identities=21% Similarity=0.460 Sum_probs=39.5
Q ss_pred cccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhcChhHHHhhhh
Q psy11761 99 PFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNLISHHC 162 (198)
Q Consensus 99 ~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~~H~~ 162 (198)
-|.|..||.... +..+.+|+...+ + .-|-|-.|++.|.. .++.-|..
T Consensus 3 ~FtCnvCgEsvK--------------Kp~vekH~srCr-n-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVK--------------KPQVEKHMSRCR-N-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhcc--------------ccchHHHHHhcc-C-CeeEEeeccccccc-chhhhhhh
Confidence 378999999987 788899999887 3 78899999999987 57777754
No 87
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=83.28 E-value=0.55 Score=25.04 Aligned_cols=26 Identities=19% Similarity=0.603 Sum_probs=12.6
Q ss_pred cccCcccchhhcccC---CCceecCcccc
Q psy11761 26 YKCHQCQRLIFLSAN---AGVHKCEYCHK 51 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~---~~~~~C~~C~~ 51 (198)
|.|+.||..|..... ...-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 556666665543221 22344666654
No 88
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=82.02 E-value=0.55 Score=30.06 Aligned_cols=32 Identities=22% Similarity=0.489 Sum_probs=26.1
Q ss_pred ccccCcccchhhcccCCCceecCccccccCCh
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKVFDQQ 56 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~ 56 (198)
.|.|+.|++.--.......|.|..|+..|.-.
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECRKCGAKFAGG 67 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcCCCCCEEeCC
Confidence 79999999876666777799999999987543
No 89
>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=82.01 E-value=0.59 Score=25.37 Aligned_cols=11 Identities=27% Similarity=0.893 Sum_probs=5.6
Q ss_pred cccCcccchhh
Q psy11761 26 YKCHQCQRLIF 36 (198)
Q Consensus 26 ~~C~~C~~~f~ 36 (198)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 45555554443
No 90
>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=81.60 E-value=0.84 Score=31.12 Aligned_cols=33 Identities=15% Similarity=0.190 Sum_probs=25.6
Q ss_pred ccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhcChhHH
Q psy11761 100 FKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNL 157 (198)
Q Consensus 100 ~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L 157 (198)
..|+.||+.|.. . +..|..|+.||..|.-...+
T Consensus 10 r~Cp~cg~kFYD-------------L------------nk~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 10 RICPNTGSKFYD-------------L------------NRRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred ccCCCcCccccc-------------c------------CCCCccCCCcCCccCcchhh
Confidence 699999999875 2 45789999999998655333
No 91
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=78.53 E-value=1.1 Score=32.23 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=14.5
Q ss_pred ccccCcccchhhcccCCCceecCcccc
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
.+.|+.||..+.. ..|.+||+||.
T Consensus 134 ~~vC~vCGy~~~g---e~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTHEG---EAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcccC---CCCCcCCCCCC
Confidence 4667777666544 33666777663
No 92
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=77.00 E-value=0.66 Score=26.68 Aligned_cols=32 Identities=16% Similarity=0.347 Sum_probs=25.9
Q ss_pred hhcCCCCcccCCcCchhhhcccCCCcccCCCcCcccccccccccc
Q psy11761 92 LIHSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNS 136 (198)
Q Consensus 92 ~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~ 136 (198)
.+-.|+.-+.|+-|+..|.. ..++.+|+...+
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~-------------~K~Y~RHVNKaH 41 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRR-------------RKDYIRHVNKAH 41 (65)
T ss_pred eccCCceeeeCCchhHHHHH-------------hHHHHHHhhHHh
Confidence 34567888999999999998 888888886555
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=76.27 E-value=1.7 Score=29.62 Aligned_cols=30 Identities=10% Similarity=0.125 Sum_probs=21.2
Q ss_pred cccCcccchhhcccCCCceecCccccccCCh
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKVFDQQ 56 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~ 56 (198)
..|+.||+.|-.-.. .|-.|+.||..|...
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCccCcc
Confidence 468888888765443 577888888877555
No 94
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=76.02 E-value=1.5 Score=39.17 Aligned_cols=45 Identities=24% Similarity=0.679 Sum_probs=29.6
Q ss_pred ccCcccchhhcccCCCceecCccccccCC---hhHHhhcccCCCCCCCccCccchhc
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHKVFDQ---QSSLLSHNCPQMKPRPYKCDTCEKS 80 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~~f~~---~~~l~~H~~~h~~~~~~~C~~C~~~ 80 (198)
.|..||. ..+|+.|...+.. ...|..|.--+....|..|+.|+..
T Consensus 437 ~C~~Cg~---------v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGY---------IAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ecccCCC---------cccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 3888887 4568888765432 2355666666666777888888754
No 95
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=75.94 E-value=1.2 Score=23.37 Aligned_cols=27 Identities=26% Similarity=0.659 Sum_probs=14.1
Q ss_pred ccCcccchhhcccC-----CCceecCcccccc
Q psy11761 27 KCHQCQRLIFLSAN-----AGVHKCEYCHKVF 53 (198)
Q Consensus 27 ~C~~C~~~f~~~~~-----~~~~~C~~C~~~f 53 (198)
.||.|+..|..... ....+|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 56666666644332 1234566666554
No 96
>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=75.11 E-value=0.91 Score=23.84 Aligned_cols=10 Identities=20% Similarity=0.703 Sum_probs=5.1
Q ss_pred ccCcccchhh
Q psy11761 27 KCHQCQRLIF 36 (198)
Q Consensus 27 ~C~~C~~~f~ 36 (198)
.|+.|+..|.
T Consensus 4 ~CP~C~~~~~ 13 (38)
T TIGR02098 4 QCPNCKTSFR 13 (38)
T ss_pred ECCCCCCEEE
Confidence 4555555443
No 97
>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=75.03 E-value=0.98 Score=32.34 Aligned_cols=10 Identities=20% Similarity=0.793 Sum_probs=4.9
Q ss_pred CccCccchhc
Q psy11761 71 PYKCDTCEKS 80 (198)
Q Consensus 71 ~~~C~~C~~~ 80 (198)
.|.|+.||..
T Consensus 128 ~F~Cp~Cg~~ 137 (158)
T TIGR00373 128 NFTCPRCGAM 137 (158)
T ss_pred CCcCCCCCCE
Confidence 4555555543
No 98
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.65 E-value=1 Score=31.79 Aligned_cols=36 Identities=17% Similarity=0.432 Sum_probs=18.9
Q ss_pred ceecCccccccCChhHHhhcccCCCCCCCccCccchhccc
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFT 82 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 82 (198)
.|.|+.|+..|.....+.. . .. ...|.|+.||....
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~-~--d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQL-L--DM-DGTFTCPRCGEELE 134 (147)
T ss_pred EEECcCCCCEeeHHHHHHh-c--CC-CCcEECCCCCCEEE
Confidence 4666777666655433221 0 11 23377777776553
No 99
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=74.50 E-value=1.4 Score=25.66 Aligned_cols=49 Identities=22% Similarity=0.518 Sum_probs=27.1
Q ss_pred CCCcccCCc--CchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCc----chhhhcChhHHHhh
Q psy11761 96 GIRPFKCTT--CDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDR----CSQFFGDRMNLISH 160 (198)
Q Consensus 96 ~~k~~~C~~--C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~----C~k~f~~~~~L~~H 160 (198)
+..+..|+. |...+. +..|..|....- ..++..|+. |+..+... .|..|
T Consensus 6 ~~~~v~C~~~cc~~~i~--------------r~~l~~H~~~~C-~~~~v~C~~~~~GC~~~~~~~-~l~~H 60 (60)
T PF02176_consen 6 PFRPVPCPNGCCNEMIP--------------RKELDDHLENEC-PKRPVPCPYSPYGCKERVPRE-DLEEH 60 (60)
T ss_dssp TTSEEE-TT--S-BEEE--------------CCCHHHHHHTTS-TTSEEE-SS----S--EEEHH-HHHHC
T ss_pred CCCEeeCCCCCccccee--------------HHHHHHHHHccC-CCCcEECCCCCCCCCCccchh-HHhCC
Confidence 445667776 555555 567788887443 356778888 88776543 44443
No 100
>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=74.47 E-value=1.6 Score=24.34 Aligned_cols=11 Identities=27% Similarity=0.712 Sum_probs=5.5
Q ss_pred cccCcccchhh
Q psy11761 26 YKCHQCQRLIF 36 (198)
Q Consensus 26 ~~C~~C~~~f~ 36 (198)
|.|..|+..+.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 44555555443
No 101
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=73.96 E-value=1.6 Score=20.29 Aligned_cols=20 Identities=30% Similarity=0.592 Sum_probs=10.6
Q ss_pred cCcccchhhcccCCCceecCcccc
Q psy11761 28 CHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 28 C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
|+.||......... |+.||.
T Consensus 2 Cp~CG~~~~~~~~f----C~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDAKF----CPNCGT 21 (23)
T ss_pred CcccCCCCCCcCcc----hhhhCC
Confidence 66666655433322 666654
No 102
>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=73.66 E-value=2.1 Score=24.69 Aligned_cols=28 Identities=21% Similarity=0.548 Sum_probs=15.5
Q ss_pred cccCcccchhhcccCC--CceecCcccccc
Q psy11761 26 YKCHQCQRLIFLSANA--GVHKCEYCHKVF 53 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~--~~~~C~~C~~~f 53 (198)
+.||.||..+.-.... ....|+.||..+
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 5677777665443222 134677776654
No 103
>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=73.51 E-value=1.5 Score=24.77 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=5.4
Q ss_pred eecCccccccC
Q psy11761 44 HKCEYCHKVFD 54 (198)
Q Consensus 44 ~~C~~C~~~f~ 54 (198)
|+|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 44555555444
No 104
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=73.44 E-value=2.2 Score=23.96 Aligned_cols=28 Identities=14% Similarity=0.379 Sum_probs=15.4
Q ss_pred cCcccchhhcccCC--CceecCccccccCC
Q psy11761 28 CHQCQRLIFLSANA--GVHKCEYCHKVFDQ 55 (198)
Q Consensus 28 C~~C~~~f~~~~~~--~~~~C~~C~~~f~~ 55 (198)
|+.||......... ..+.|+.|+..+..
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCeEEC
Confidence 66676655443322 25667777765544
No 105
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=73.19 E-value=1.3 Score=31.57 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=11.2
Q ss_pred eecCccccccCChhHH
Q psy11761 44 HKCEYCHKVFDQQSSL 59 (198)
Q Consensus 44 ~~C~~C~~~f~~~~~l 59 (198)
++|+.||..|.....+
T Consensus 29 ~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 29 RECLACGKRFTTFERV 44 (154)
T ss_pred eeccccCCcceEeEec
Confidence 6788888877765443
No 106
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=72.90 E-value=1.6 Score=38.51 Aligned_cols=77 Identities=21% Similarity=0.460 Sum_probs=55.9
Q ss_pred cccCcccchhhcccCCC---ce-ecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcCCCCccc
Q psy11761 26 YKCHQCQRLIFLSANAG---VH-KCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFK 101 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~---~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~ 101 (198)
-.|+.|=+.+....+.. || .|..||-.|.-...|-.-+.-.+...--.|+.|.+.+.+..+ +|.|. .|..
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~n----RRfHA--Qp~a 175 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLN----RRFHA--QPIA 175 (750)
T ss_pred hhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccc----ccccc--cccc
Confidence 45888888877766655 44 699999999888777666555554455579999998877654 34454 4679
Q ss_pred CCcCchh
Q psy11761 102 CTTCDKS 108 (198)
Q Consensus 102 C~~C~~~ 108 (198)
|+.||-.
T Consensus 176 Cp~CGP~ 182 (750)
T COG0068 176 CPKCGPH 182 (750)
T ss_pred CcccCCC
Confidence 9999964
No 107
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=72.82 E-value=1.3 Score=32.41 Aligned_cols=31 Identities=19% Similarity=0.580 Sum_probs=16.3
Q ss_pred ceecCccccccCChhHHhhcccCCCCCCCccCccchhccc
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFT 82 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 82 (198)
-|.|+.|+..|.....+. ..|.|+.||....
T Consensus 117 ~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred EEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 355666665555444331 2566666665543
No 108
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=72.31 E-value=2.2 Score=27.26 Aligned_cols=27 Identities=15% Similarity=0.375 Sum_probs=14.9
Q ss_pred ccccCcccchhhcccCCCceecCcccc
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
|-.|..||..|....--.|..|+.|..
T Consensus 58 Pa~CkkCGfef~~~~ik~pSRCP~CKS 84 (97)
T COG3357 58 PARCKKCGFEFRDDKIKKPSRCPKCKS 84 (97)
T ss_pred ChhhcccCccccccccCCcccCCcchh
Confidence 455666666665533333566666643
No 109
>PHA00626 hypothetical protein
Probab=72.24 E-value=2.8 Score=24.17 Aligned_cols=13 Identities=23% Similarity=0.511 Sum_probs=6.3
Q ss_pred CCccCccchhccc
Q psy11761 70 RPYKCDTCEKSFT 82 (198)
Q Consensus 70 ~~~~C~~C~~~f~ 82 (198)
..|.|+.|++.|+
T Consensus 22 nrYkCkdCGY~ft 34 (59)
T PHA00626 22 DDYVCCDCGYNDS 34 (59)
T ss_pred cceEcCCCCCeec
Confidence 3455555554444
No 110
>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=71.52 E-value=1.4 Score=23.10 Aligned_cols=16 Identities=25% Similarity=0.407 Sum_probs=9.9
Q ss_pred CCCeeCCcchhhhcCh
Q psy11761 139 PKPYQCDRCSQFFGDR 154 (198)
Q Consensus 139 ~~~~~C~~C~k~f~~~ 154 (198)
...-.|+.||-.+.++
T Consensus 19 ~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 19 KVEGVCDNCGGELVQR 34 (36)
T ss_dssp SSTTBCTTTTEBEBEE
T ss_pred CCCCccCCCCCeeEeC
Confidence 4455788887655443
No 111
>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=71.39 E-value=3.2 Score=22.51 Aligned_cols=27 Identities=26% Similarity=0.330 Sum_probs=17.5
Q ss_pred CCCCeeCCcchhhhcCh----hHHHhhhhhh
Q psy11761 138 FPKPYQCDRCSQFFGDR----MNLISHHCHK 164 (198)
Q Consensus 138 ~~~~~~C~~C~k~f~~~----~~L~~H~~~~ 164 (198)
+.....|..|++.+... +.|..|+...
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~ 43 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKK 43 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhh
Confidence 45678999999999774 6899998543
No 112
>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=71.28 E-value=2.7 Score=23.79 Aligned_cols=11 Identities=27% Similarity=0.772 Sum_probs=5.4
Q ss_pred cccCcccchhh
Q psy11761 26 YKCHQCQRLIF 36 (198)
Q Consensus 26 ~~C~~C~~~f~ 36 (198)
|.|..||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 44555555443
No 113
>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=70.93 E-value=3 Score=20.00 Aligned_cols=19 Identities=26% Similarity=0.273 Sum_probs=15.2
Q ss_pred eCCcchhhhcChhHHHhhhh
Q psy11761 143 QCDRCSQFFGDRMNLISHHC 162 (198)
Q Consensus 143 ~C~~C~k~f~~~~~L~~H~~ 162 (198)
.|++|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 699999998 5567888864
No 114
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=70.43 E-value=4.1 Score=27.00 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=11.4
Q ss_pred ceecCccccccCChhHHhhccc
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNC 64 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~ 64 (198)
...|..|+.+... +++..|++
T Consensus 11 vlIC~~C~~av~~-~~v~~HL~ 31 (109)
T PF12013_consen 11 VLICRQCQYAVQP-SEVESHLR 31 (109)
T ss_pred EEEeCCCCcccCc-hHHHHHHH
Confidence 3456666655544 45555555
No 115
>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=70.21 E-value=2.5 Score=30.21 Aligned_cols=32 Identities=16% Similarity=0.066 Sum_probs=26.2
Q ss_pred CCCCeeCCcchhhhcChhHHHhhhhhhCCCCCCCcccccccCC
Q psy11761 138 FPKPYQCDRCSQFFGDRMNLISHHCHKHKQSCLPFISRLFGFD 180 (198)
Q Consensus 138 ~~~~~~C~~C~k~f~~~~~L~~H~~~~~~~~~~~~~~~~~~~~ 180 (198)
....|.|+.|+..|+....+. +-|.|+.||..
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~-----------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME-----------LNFTCPRCGAM 137 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH-----------cCCcCCCCCCE
Confidence 356799999999998877763 48999999975
No 116
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=68.57 E-value=1.8 Score=29.74 Aligned_cols=27 Identities=19% Similarity=0.470 Sum_probs=17.2
Q ss_pred ccccCcccchhhcccCCCceecCcccc
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
|++|-.||+.|...+...---|+.||.
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGG 27 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCC
Confidence 567777777776655443445777754
No 117
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=68.15 E-value=2.1 Score=22.32 Aligned_cols=11 Identities=27% Similarity=0.634 Sum_probs=5.6
Q ss_pred ccCcccchhhc
Q psy11761 27 KCHQCQRLIFL 37 (198)
Q Consensus 27 ~C~~C~~~f~~ 37 (198)
.|+.|+..|.-
T Consensus 4 ~Cp~C~~~y~i 14 (36)
T PF13717_consen 4 TCPNCQAKYEI 14 (36)
T ss_pred ECCCCCCEEeC
Confidence 45555555543
No 118
>PF12773 DZR: Double zinc ribbon
Probab=67.45 E-value=5.3 Score=22.22 Aligned_cols=9 Identities=22% Similarity=0.685 Sum_probs=4.9
Q ss_pred cCccccccC
Q psy11761 46 CEYCHKVFD 54 (198)
Q Consensus 46 C~~C~~~f~ 54 (198)
|+.||..+.
T Consensus 15 C~~CG~~l~ 23 (50)
T PF12773_consen 15 CPHCGTPLP 23 (50)
T ss_pred ChhhcCChh
Confidence 566655544
No 119
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=66.98 E-value=3.1 Score=30.41 Aligned_cols=32 Identities=16% Similarity=0.086 Sum_probs=25.7
Q ss_pred CCCeeCCcchhhhcChhHHHhhhhhhCCCCCCCcccccccCCC
Q psy11761 139 PKPYQCDRCSQFFGDRMNLISHHCHKHKQSCLPFISRLFGFDD 181 (198)
Q Consensus 139 ~~~~~C~~C~k~f~~~~~L~~H~~~~~~~~~~~~~~~~~~~~~ 181 (198)
...|.|+.|+..|+....+. +.|.|+.||...
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~-----------~~F~Cp~Cg~~L 146 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME-----------YGFRCPQCGEML 146 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh-----------cCCcCCCCCCCC
Confidence 46799999999998776652 489999999764
No 120
>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=66.93 E-value=3.3 Score=31.93 Aligned_cols=26 Identities=19% Similarity=0.476 Sum_probs=15.9
Q ss_pred CCCccCccchhcccCchhHHHhhhhc
Q psy11761 69 PRPYKCDTCEKSFTNSQNLNTHQLIH 94 (198)
Q Consensus 69 ~~~~~C~~C~~~f~~~~~l~~H~~~h 94 (198)
.+++.|+.|+........|..-.++|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 45667777776666655555555544
No 121
>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=66.34 E-value=4 Score=24.49 Aligned_cols=29 Identities=21% Similarity=0.438 Sum_probs=17.1
Q ss_pred ccCcccchhhcccCCCceecCccccccCC
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHKVFDQ 55 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~~f~~ 55 (198)
.|+.||...........|.|+.||..+..
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCcccccccccccceEEcCCCCCEECc
Confidence 36666665555444446677777665544
No 122
>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=65.77 E-value=3.9 Score=22.14 Aligned_cols=28 Identities=25% Similarity=0.559 Sum_probs=15.4
Q ss_pred cccCcccchh-hcccCCCceecCcccccc
Q psy11761 26 YKCHQCQRLI-FLSANAGVHKCEYCHKVF 53 (198)
Q Consensus 26 ~~C~~C~~~f-~~~~~~~~~~C~~C~~~f 53 (198)
|.||.|+... ........+.|..||...
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 4677777643 122333456777777654
No 123
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=64.85 E-value=2.8 Score=33.70 Aligned_cols=78 Identities=22% Similarity=0.336 Sum_probs=44.0
Q ss_pred cCccchhcccCchhHHHhhhhcCCCCcccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCc--c--h
Q psy11761 73 KCDTCEKSFTNSQNLNTHQLIHSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDR--C--S 148 (198)
Q Consensus 73 ~C~~C~~~f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~--C--~ 148 (198)
.|..|...|-+...|..|++..+. .|-+|+++-+- ..+.......|.+|.+. .-|.|.+ | |
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE----~ChICD~v~p~------~~QYFK~Y~~Le~HF~~-----~hy~ct~qtc~~~ 286 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHE----ACHICDMVGPI------RYQYFKSYEDLEAHFRN-----AHYCCTFQTCRVG 286 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhh----hhhhhhccCcc------chhhhhCHHHHHHHhhc-----CceEEEEEEEecC
Confidence 577777777777778888776552 34444443211 11112225666666642 3456654 3 2
Q ss_pred --hhhcChhHHHhhhhhhC
Q psy11761 149 --QFFGDRMNLISHHCHKH 165 (198)
Q Consensus 149 --k~f~~~~~L~~H~~~~~ 165 (198)
..|.....|..|+..-|
T Consensus 287 k~~vf~~~~el~~h~~~~h 305 (493)
T COG5236 287 KCYVFPYHTELLEHLTRFH 305 (493)
T ss_pred cEEEeccHHHHHHHHHHHh
Confidence 35666777888876554
No 124
>KOG0402|consensus
Probab=64.24 E-value=2.9 Score=26.21 Aligned_cols=31 Identities=29% Similarity=0.670 Sum_probs=26.1
Q ss_pred ccccCcccchhhcccCCCceecCccccccCC
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKVFDQ 55 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~ 55 (198)
-|.|+.||+.--.......|.|..|.+.+.-
T Consensus 36 ky~CsfCGK~~vKR~AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 36 KYTCSFCGKKTVKRKAVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhhcchhhhhhhceeEEecCCccceecc
Confidence 6899999998777788889999999887644
No 125
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=63.70 E-value=4.2 Score=19.41 Aligned_cols=23 Identities=26% Similarity=0.431 Sum_probs=11.9
Q ss_pred cccCcccchhhcccCCCceecCccccc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
..|+.||....... --|+.||..
T Consensus 3 ~~Cp~Cg~~~~~~~----~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPDA----KFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCccc----ccChhhCCC
Confidence 35777777432222 236666653
No 126
>PRK04023 DNA polymerase II large subunit; Validated
Probab=63.43 E-value=7.2 Score=36.02 Aligned_cols=22 Identities=23% Similarity=0.644 Sum_probs=14.8
Q ss_pred ccccCcccchhhcccCCCceecCccccc
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
...|+.||... ..+.|+.||..
T Consensus 626 ~RfCpsCG~~t------~~frCP~CG~~ 647 (1121)
T PRK04023 626 RRKCPSCGKET------FYRRCPFCGTH 647 (1121)
T ss_pred CccCCCCCCcC------CcccCCCCCCC
Confidence 35688888763 23678888775
No 127
>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=62.76 E-value=3.9 Score=21.10 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=11.3
Q ss_pred ccCcccchhhcccCCCceecCccc
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCH 50 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~ 50 (198)
.|..|++.|..+--+..|.+.+|.
T Consensus 5 ~C~eC~~~f~dSyL~~~F~~~VCD 28 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLNNFDLPVCD 28 (34)
T ss_dssp E-TTT--EES-SSCCCCTS-S--T
T ss_pred hHhHhCCHHHHHHHHHhCCccccc
Confidence 577777777776666666655554
No 128
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=62.64 E-value=5.7 Score=22.25 Aligned_cols=24 Identities=21% Similarity=0.396 Sum_probs=19.1
Q ss_pred CCeeCCcchhhhcCh-----hHHHhhhhh
Q psy11761 140 KPYQCDRCSQFFGDR-----MNLISHHCH 163 (198)
Q Consensus 140 ~~~~C~~C~k~f~~~-----~~L~~H~~~ 163 (198)
....|..|++.+... +.|.+|+..
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 346899999999765 589999884
No 129
>KOG2907|consensus
Probab=60.78 E-value=2.9 Score=27.84 Aligned_cols=29 Identities=17% Similarity=0.384 Sum_probs=19.7
Q ss_pred cccCcccchhhcccCCCceecCccccccC
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKVFD 54 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~f~ 54 (198)
.=|+.||......+......|..|...+.
T Consensus 8 ~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~ 36 (116)
T KOG2907|consen 8 DFCSDCGSLLEEPSAQSTVLCIRCKIEYP 36 (116)
T ss_pred chhhhhhhhcccccccCceEeccccccCC
Confidence 34777887776666666666777776554
No 130
>COG1773 Rubredoxin [Energy production and conversion]
Probab=60.56 E-value=4.9 Score=23.20 Aligned_cols=11 Identities=18% Similarity=0.664 Sum_probs=6.0
Q ss_pred cccCcccchhh
Q psy11761 26 YKCHQCQRLIF 36 (198)
Q Consensus 26 ~~C~~C~~~f~ 36 (198)
|.|..||..|.
T Consensus 4 ~~C~~CG~vYd 14 (55)
T COG1773 4 WRCSVCGYVYD 14 (55)
T ss_pred eEecCCceEec
Confidence 45555555553
No 131
>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=60.52 E-value=7.7 Score=21.30 Aligned_cols=27 Identities=22% Similarity=0.661 Sum_probs=16.6
Q ss_pred ccccCcccch-hhcccCCCceecCcccc
Q psy11761 25 AYKCHQCQRL-IFLSANAGVHKCEYCHK 51 (198)
Q Consensus 25 ~~~C~~C~~~-f~~~~~~~~~~C~~C~~ 51 (198)
.+.||.||.. .........|+|..|+.
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 3679998864 22222345788888764
No 132
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=59.98 E-value=7.4 Score=20.77 Aligned_cols=33 Identities=15% Similarity=0.421 Sum_probs=16.3
Q ss_pred cCcccchhhcc--cCCCceecCccccccCChhHHh
Q psy11761 28 CHQCQRLIFLS--ANAGVHKCEYCHKVFDQQSSLL 60 (198)
Q Consensus 28 C~~C~~~f~~~--~~~~~~~C~~C~~~f~~~~~l~ 60 (198)
||.|+...... ..+..+.|+.|+..+-...+|.
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGGIWFDAGELE 36 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCeEEccHHHHH
Confidence 55665533221 2223456666666655555543
No 133
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=59.23 E-value=8.4 Score=36.49 Aligned_cols=35 Identities=20% Similarity=0.601 Sum_probs=21.9
Q ss_pred cccCcccchhhcccCCCceecCccccccCChhHHhhcccCCCCCCCccCccchhcc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSF 81 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 81 (198)
+.|+.||..... ..|+.||... ...|.|+.|+...
T Consensus 668 rkCPkCG~~t~~------~fCP~CGs~t---------------e~vy~CPsCGaev 702 (1337)
T PRK14714 668 RRCPSCGTETYE------NRCPDCGTHT---------------EPVYVCPDCGAEV 702 (1337)
T ss_pred EECCCCCCcccc------ccCcccCCcC---------------CCceeCccCCCcc
Confidence 678888874321 2677777653 2246777777643
No 134
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=58.50 E-value=2.6 Score=31.72 Aligned_cols=31 Identities=19% Similarity=0.416 Sum_probs=23.6
Q ss_pred CCCCeeCCcchhhhcChhHHHhhhhhhCCCC
Q psy11761 138 FPKPYQCDRCSQFFGDRMNLISHHCHKHKQS 168 (198)
Q Consensus 138 ~~~~~~C~~C~k~f~~~~~L~~H~~~~~~~~ 168 (198)
.+..|.|+.|+|.|....-+.+|+...|.++
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 3567999999999999989999998887654
No 135
>KOG4173|consensus
Probab=58.38 E-value=2.8 Score=31.10 Aligned_cols=65 Identities=25% Similarity=0.587 Sum_probs=46.1
Q ss_pred eecCc--cccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhc----------CCCCcccCCc--Cchhh
Q psy11761 44 HKCEY--CHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIH----------SGIRPFKCTT--CDKSF 109 (198)
Q Consensus 44 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h----------~~~k~~~C~~--C~~~f 109 (198)
+.|++ |.+.|........|..+.++. .|..|.+.|.+...|..|+... .|.-.|.|.+ |+..|
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KF 156 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKF 156 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhh
Confidence 45655 566777777677776665543 6888999999888888887532 3455688854 88888
Q ss_pred hc
Q psy11761 110 VN 111 (198)
Q Consensus 110 ~~ 111 (198)
.+
T Consensus 157 kT 158 (253)
T KOG4173|consen 157 KT 158 (253)
T ss_pred hh
Confidence 87
No 136
>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=58.35 E-value=3.8 Score=28.91 Aligned_cols=36 Identities=17% Similarity=0.401 Sum_probs=20.2
Q ss_pred hhhhCCCCc----cccCcccchhhcccCCCceecCccccc
Q psy11761 17 LCIHGNDNA----YKCHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 17 ~~~h~~~~~----~~C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
-..++|+.+ |.|..||....-......-.|+.|+..
T Consensus 100 g~Y~sGE~~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 100 GVYHSGEVVGPGTLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred CCeecCcEecCceEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 355667654 667777765433333334457777553
No 137
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=57.95 E-value=11 Score=30.08 Aligned_cols=26 Identities=23% Similarity=0.547 Sum_probs=22.2
Q ss_pred CCCeeCCcchhhhcChhHHHhhhhhh
Q psy11761 139 PKPYQCDRCSQFFGDRMNLISHHCHK 164 (198)
Q Consensus 139 ~~~~~C~~C~k~f~~~~~L~~H~~~~ 164 (198)
...|.|+.|...|-...+.-.|-.+|
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHHHHh
Confidence 46899999999999888888887766
No 138
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=57.22 E-value=3.1 Score=27.20 Aligned_cols=26 Identities=15% Similarity=0.448 Sum_probs=12.3
Q ss_pred ccccCcccchhhcccCCCceecCccc
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCH 50 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~ 50 (198)
|+.|-.||..|...+....--|+.||
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG 27 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCG 27 (112)
T ss_pred CceecccccccccccHHHHccCcccc
Confidence 45555555555543333333455554
No 139
>KOG2186|consensus
Probab=56.68 E-value=4.8 Score=30.90 Aligned_cols=46 Identities=17% Similarity=0.428 Sum_probs=25.0
Q ss_pred eecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhh
Q psy11761 44 HKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQL 92 (198)
Q Consensus 44 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 92 (198)
|.|..||....... +..|+..-++ ..|.|..|+..|.. .++..|..
T Consensus 4 FtCnvCgEsvKKp~-vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQ-VEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccccc-hHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 45666666554433 4446555554 55666666666665 44444543
No 140
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.53 E-value=7.1 Score=33.53 Aligned_cols=44 Identities=25% Similarity=0.675 Sum_probs=26.4
Q ss_pred ccCcccchhhcccCCCceecCccccccC---ChhHHhhcccCCCCCCCccCccchh
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHKVFD---QQSSLLSHNCPQMKPRPYKCDTCEK 79 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~~f~---~~~~l~~H~~~h~~~~~~~C~~C~~ 79 (198)
.|..||. ...|+.|+.... ....|..|.--+....|..|+.|+.
T Consensus 215 ~C~~Cg~---------~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 215 LCRSCGY---------ILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred EhhhCcC---------ccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCC
Confidence 4667776 345777765432 1234555555555566778888875
No 141
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=56.27 E-value=8.7 Score=21.69 Aligned_cols=26 Identities=15% Similarity=0.341 Sum_probs=13.2
Q ss_pred ccCcccchhhcccCCCceecCcccccc
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHKVF 53 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~~f 53 (198)
-||.||..|.. .....+.|..|+..+
T Consensus 22 fCP~Cg~~~m~-~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSGFMA-EHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcchhe-ccCCcEECCCcCCEE
Confidence 36666654222 222456666666543
No 142
>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=55.94 E-value=7.1 Score=27.04 Aligned_cols=26 Identities=27% Similarity=0.430 Sum_probs=16.9
Q ss_pred CCCeeCCcchhhhcChhHHHhhhhhhCCC
Q psy11761 139 PKPYQCDRCSQFFGDRMNLISHHCHKHKQ 167 (198)
Q Consensus 139 ~~~~~C~~C~k~f~~~~~L~~H~~~~~~~ 167 (198)
+....|-+||+.|.. |.+|+..|||-
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S
T ss_pred cCeeEEccCCcccch---HHHHHHHccCC
Confidence 456789999999954 59999999874
No 143
>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=55.64 E-value=6.8 Score=19.58 Aligned_cols=24 Identities=21% Similarity=0.497 Sum_probs=8.6
Q ss_pred ccCcccchhhcccCCCceecCcccc
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
+|+.|+..+.- ..-..+.|+.|+.
T Consensus 4 ~Cp~C~se~~y-~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY-EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E-E-SSSEEETTTTE
T ss_pred CCCCCCCccee-ccCCEEeCCcccc
Confidence 46666655433 2233566666654
No 144
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.49 E-value=9.6 Score=25.31 Aligned_cols=33 Identities=12% Similarity=0.035 Sum_probs=23.8
Q ss_pred ccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhhhcChhHHH
Q psy11761 100 FKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQFFGDRMNLI 158 (198)
Q Consensus 100 ~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~f~~~~~L~ 158 (198)
-.|+.|++.|.. . +..|..|+.||++|. ++.|.
T Consensus 10 ridPetg~KFYD-------------L------------NrdPiVsPytG~s~P-~s~fe 42 (129)
T COG4530 10 RIDPETGKKFYD-------------L------------NRDPIVSPYTGKSYP-RSYFE 42 (129)
T ss_pred ccCccccchhhc-------------c------------CCCccccCcccccch-HHHHH
Confidence 478888888865 1 357899999999994 33443
No 145
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=54.77 E-value=7.8 Score=32.24 Aligned_cols=30 Identities=13% Similarity=0.349 Sum_probs=23.3
Q ss_pred ccCcccchhhcccCCCceecCccccccCChh
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHKVFDQQS 57 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~~ 57 (198)
.|+.||...++...- .|+|+-|+..+....
T Consensus 352 ~Cp~Cg~~m~S~G~~-g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSAGRN-GFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhcCCC-CcccccccccCCccc
Confidence 688888888776666 888888888776654
No 146
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=52.89 E-value=9.9 Score=34.17 Aligned_cols=23 Identities=30% Similarity=0.576 Sum_probs=12.2
Q ss_pred cccccccccccCCCCeeCCcchhh
Q psy11761 127 NLAQHSCMNSHFPKPYQCDRCSQF 150 (198)
Q Consensus 127 ~l~~H~~~~~~~~~~~~C~~C~k~ 150 (198)
.|..|..-+. ...|..|+.||..
T Consensus 462 ~L~CH~Cg~~-~~~p~~Cp~Cgs~ 484 (730)
T COG1198 462 QLRCHYCGYQ-EPIPQSCPECGSE 484 (730)
T ss_pred eeEeCCCCCC-CCCCCCCCCCCCC
Confidence 3444444443 3456677777644
No 147
>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=51.96 E-value=4.1 Score=27.36 Aligned_cols=24 Identities=17% Similarity=0.461 Sum_probs=10.5
Q ss_pred cccCcccchhhcccCCCceecCcccc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
..|..||..|...... +.|+.|+.
T Consensus 71 ~~C~~Cg~~~~~~~~~--~~CP~Cgs 94 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFD--FSCPRCGS 94 (113)
T ss_dssp EEETTTS-EEECHHCC--HH-SSSSS
T ss_pred EECCCCCCEEecCCCC--CCCcCCcC
Confidence 4455555555433322 44555554
No 148
>KOG1280|consensus
Probab=51.11 E-value=12 Score=30.20 Aligned_cols=43 Identities=16% Similarity=0.316 Sum_probs=35.6
Q ss_pred CCCeeCCcchhhhcChhHHHhhhhhhCCCCCCCcccccccCCC
Q psy11761 139 PKPYQCDRCSQFFGDRMNLISHHCHKHKQSCLPFISRLFGFDD 181 (198)
Q Consensus 139 ~~~~~C~~C~k~f~~~~~L~~H~~~~~~~~~~~~~~~~~~~~~ 181 (198)
...|.|+.|+++=-+...|..|....|-+-++-.+|++|+...
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~ 119 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANP 119 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCc
Confidence 4589999999988788899999988887777888888887543
No 149
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=50.80 E-value=13 Score=19.78 Aligned_cols=13 Identities=31% Similarity=0.641 Sum_probs=7.0
Q ss_pred ceecCccccccCC
Q psy11761 43 VHKCEYCHKVFDQ 55 (198)
Q Consensus 43 ~~~C~~C~~~f~~ 55 (198)
++.|..|+..|-.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 5555555555533
No 150
>PRK00420 hypothetical protein; Validated
Probab=50.50 E-value=11 Score=25.28 Aligned_cols=30 Identities=23% Similarity=0.385 Sum_probs=19.8
Q ss_pred ccccCcccchhhcccCCCceecCccccccCC
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKVFDQ 55 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~ 55 (198)
.-.||.||..+..- ..+...|+.||....-
T Consensus 23 ~~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCGLPLFEL-KDGEVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCCCcceec-CCCceECCCCCCeeee
Confidence 35688888766552 3336778888885543
No 151
>PRK05580 primosome assembly protein PriA; Validated
Probab=50.09 E-value=10 Score=33.93 Aligned_cols=46 Identities=28% Similarity=0.691 Sum_probs=28.0
Q ss_pred cccCcccchhhcccCCCceecCccccccC---ChhHHhhcccCCCCCCCccCccchhc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKVFD---QQSSLLSHNCPQMKPRPYKCDTCEKS 80 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~f~---~~~~l~~H~~~h~~~~~~~C~~C~~~ 80 (198)
..|..||. ...|+.|+..+. ....|..|.--+....+..|+.|+..
T Consensus 382 ~~C~~Cg~---------~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 382 LLCRDCGW---------VAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred eEhhhCcC---------ccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 34667776 345777766542 22345556666666667788888654
No 152
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=49.95 E-value=10 Score=22.69 Aligned_cols=28 Identities=25% Similarity=0.527 Sum_probs=10.5
Q ss_pred cccCcccchhhcccCCCceecCccccccCC
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKVFDQ 55 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~ 55 (198)
-.|..|++.|.. -...+.|..||..|-.
T Consensus 10 ~~C~~C~~~F~~--~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 10 SNCMICGKKFSL--FRRRHHCRNCGRVVCS 37 (69)
T ss_dssp SB-TTT--B-BS--SS-EEE-TTT--EEEC
T ss_pred CcCcCcCCcCCC--ceeeEccCCCCCEECC
Confidence 346667766622 2345666666665543
No 153
>KOG4167|consensus
Probab=49.71 E-value=5.2 Score=35.46 Aligned_cols=27 Identities=15% Similarity=0.306 Sum_probs=24.1
Q ss_pred CCCeeCCcchhhhcChhHHHhhhhhhC
Q psy11761 139 PKPYQCDRCSQFFGDRMNLISHHCHKH 165 (198)
Q Consensus 139 ~~~~~C~~C~k~f~~~~~L~~H~~~~~ 165 (198)
..-|-|..|+|.|-...++..||++|.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 346899999999999999999999985
No 154
>KOG4124|consensus
Probab=48.39 E-value=8.3 Score=31.15 Aligned_cols=23 Identities=35% Similarity=0.756 Sum_probs=18.3
Q ss_pred CCCeeCCcchhhhcChhHHHhhh
Q psy11761 139 PKPYQCDRCSQFFGDRMNLISHH 161 (198)
Q Consensus 139 ~~~~~C~~C~k~f~~~~~L~~H~ 161 (198)
.|+|.|++|.+.+.....|..|.
T Consensus 396 nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 396 NKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred cCcccChhhhhhhccCCCCCcee
Confidence 58999999999998776665554
No 155
>PRK12496 hypothetical protein; Provisional
Probab=47.95 E-value=10 Score=27.25 Aligned_cols=13 Identities=23% Similarity=0.618 Sum_probs=10.7
Q ss_pred cccCCcCchhhhc
Q psy11761 99 PFKCTTCDKSFVN 111 (198)
Q Consensus 99 ~~~C~~C~~~f~~ 111 (198)
.+.|..|++.|..
T Consensus 127 ~~~C~gC~~~~~~ 139 (164)
T PRK12496 127 RKVCKGCKKKYPE 139 (164)
T ss_pred eEECCCCCccccC
Confidence 4789999999964
No 156
>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=47.86 E-value=10 Score=21.56 Aligned_cols=20 Identities=25% Similarity=0.698 Sum_probs=6.4
Q ss_pred CccCccchhcccCchhHHHh
Q psy11761 71 PYKCDTCEKSFTNSQNLNTH 90 (198)
Q Consensus 71 ~~~C~~C~~~f~~~~~l~~H 90 (198)
.|.|+.|...|-..-++..|
T Consensus 21 ~y~C~~C~~~FC~dCD~fiH 40 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIH 40 (51)
T ss_dssp EE--TTTT--B-HHHHHTTT
T ss_pred eEECCCCCCccccCcChhhh
Confidence 34444444444444333333
No 157
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.62 E-value=7.3 Score=29.59 Aligned_cols=17 Identities=12% Similarity=0.335 Sum_probs=13.1
Q ss_pred CCccccCcccchhhccc
Q psy11761 23 DNAYKCHQCQRLIFLSA 39 (198)
Q Consensus 23 ~~~~~C~~C~~~f~~~~ 39 (198)
++-+.||+|+..|....
T Consensus 17 kk~ieCPvC~tkFkkee 33 (267)
T COG1655 17 KKTIECPVCNTKFKKEE 33 (267)
T ss_pred hceeccCcccchhhhhh
Confidence 35678999999987654
No 158
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.19 E-value=9.7 Score=33.92 Aligned_cols=44 Identities=16% Similarity=0.562 Sum_probs=23.5
Q ss_pred ccCcccchhhcccCCCceecCccccccCC---hhHHhhcccCCCCCCCccCccchhc
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHKVFDQ---QSSLLSHNCPQMKPRPYKCDTCEKS 80 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~~f~~---~~~l~~H~~~h~~~~~~~C~~C~~~ 80 (198)
.|..||. ...|+.|+..+.. ...|..|.--+.. .++.|+.|+..
T Consensus 385 ~C~~Cg~---------~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRT---------PARCRHCTGPLGLPSAGGTPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred EhhhCcC---------eeECCCCCCceeEecCCCeeECCCCcCCC-cCccCCCCcCC
Confidence 4777776 4567777654432 1234444444433 46667777653
No 159
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=47.19 E-value=17 Score=29.05 Aligned_cols=14 Identities=29% Similarity=0.605 Sum_probs=8.0
Q ss_pred CCCCCCccCccchh
Q psy11761 66 QMKPRPYKCDTCEK 79 (198)
Q Consensus 66 h~~~~~~~C~~C~~ 79 (198)
..|.+-..|..|+.
T Consensus 207 ~~G~RyL~CslC~t 220 (309)
T PRK03564 207 TQGLRYLHCNLCES 220 (309)
T ss_pred CCCceEEEcCCCCC
Confidence 34555666666653
No 160
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.71 E-value=12 Score=25.95 Aligned_cols=13 Identities=31% Similarity=0.685 Sum_probs=7.5
Q ss_pred ceecCccccccCC
Q psy11761 43 VHKCEYCHKVFDQ 55 (198)
Q Consensus 43 ~~~C~~C~~~f~~ 55 (198)
.+.|..||..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 4566666655543
No 161
>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=46.51 E-value=9.8 Score=20.60 Aligned_cols=16 Identities=25% Similarity=0.414 Sum_probs=13.5
Q ss_pred eCCcchhhhcChhHHH
Q psy11761 143 QCDRCSQFFGDRMNLI 158 (198)
Q Consensus 143 ~C~~C~k~f~~~~~L~ 158 (198)
.|..||+.|+.+..+.
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 7999999999886654
No 162
>KOG2785|consensus
Probab=46.46 E-value=8.3 Score=31.47 Aligned_cols=54 Identities=22% Similarity=0.339 Sum_probs=42.2
Q ss_pred CcccCCcCchhhhcccCCCcccCCCcCcccccccccccccC----------------------CCCeeCCcch---hhhc
Q psy11761 98 RPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHF----------------------PKPYQCDRCS---QFFG 152 (198)
Q Consensus 98 k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~----------------------~~~~~C~~C~---k~f~ 152 (198)
.|-.|..|++.+.+ ...-..|+..+|+. ...+.|-.|+ +.|.
T Consensus 165 ~Pt~CLfC~~~~k~-------------~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~ 231 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKS-------------LEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFS 231 (390)
T ss_pred CCcceeecCCCccc-------------HHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCccc
Confidence 34688999999887 66667788877732 2458899999 9999
Q ss_pred ChhHHHhhhhhh
Q psy11761 153 DRMNLISHHCHK 164 (198)
Q Consensus 153 ~~~~L~~H~~~~ 164 (198)
+....+.||...
T Consensus 232 sleavr~HM~~K 243 (390)
T KOG2785|consen 232 SLEAVRAHMRDK 243 (390)
T ss_pred ccHHHHHHHhhc
Confidence 999999999643
No 163
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=45.94 E-value=11 Score=19.37 Aligned_cols=25 Identities=20% Similarity=0.406 Sum_probs=9.4
Q ss_pred cCcccchhhcc----cCCCceecCccccc
Q psy11761 28 CHQCQRLIFLS----ANAGVHKCEYCHKV 52 (198)
Q Consensus 28 C~~C~~~f~~~----~~~~~~~C~~C~~~ 52 (198)
|+.||...... .+...+.|+.|+..
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred cccccChhhhhcCCCCCccceECCCCCCE
Confidence 55666544332 22224566666543
No 164
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=45.72 E-value=16 Score=28.04 Aligned_cols=11 Identities=36% Similarity=1.120 Sum_probs=5.3
Q ss_pred ccCCcCchhhh
Q psy11761 100 FKCTTCDKSFV 110 (198)
Q Consensus 100 ~~C~~C~~~f~ 110 (198)
|.|+.|+..|.
T Consensus 156 f~C~~C~h~F~ 166 (278)
T PF15135_consen 156 FHCPKCRHNFR 166 (278)
T ss_pred eecccccccch
Confidence 44545544443
No 165
>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=45.68 E-value=8.2 Score=24.27 Aligned_cols=32 Identities=22% Similarity=0.608 Sum_probs=13.5
Q ss_pred CccccCcccch------hhcccCCCceecCccccccCC
Q psy11761 24 NAYKCHQCQRL------IFLSANAGVHKCEYCHKVFDQ 55 (198)
Q Consensus 24 ~~~~C~~C~~~------f~~~~~~~~~~C~~C~~~f~~ 55 (198)
+.|.||.|+.. +..+.....-.|..|+..|..
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQT 58 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEE
Confidence 45888888832 222333445678888776644
No 166
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=45.34 E-value=14 Score=20.76 Aligned_cols=25 Identities=20% Similarity=0.602 Sum_probs=13.6
Q ss_pred cCcccchhhcccCCCceecCccccc
Q psy11761 28 CHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 28 C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
||.||-...-......|.|.-||..
T Consensus 22 CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 22 CPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred CCCCCCcchhhhcCceeEeccccce
Confidence 6667753333344446666666653
No 167
>KOG2482|consensus
Probab=43.16 E-value=17 Score=29.43 Aligned_cols=24 Identities=29% Similarity=0.564 Sum_probs=21.9
Q ss_pred CeeCCcchhhhcChhHHHhhhhhh
Q psy11761 141 PYQCDRCSQFFGDRMNLISHHCHK 164 (198)
Q Consensus 141 ~~~C~~C~k~f~~~~~L~~H~~~~ 164 (198)
.+.|-.|.+.|..+..|+.||+..
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhc
Confidence 578999999999999999999855
No 168
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=43.09 E-value=13 Score=21.35 Aligned_cols=12 Identities=42% Similarity=1.010 Sum_probs=9.6
Q ss_pred ccCCcCchhhhc
Q psy11761 100 FKCTTCDKSFVN 111 (198)
Q Consensus 100 ~~C~~C~~~f~~ 111 (198)
-.|+.||+.|..
T Consensus 6 ~~C~~Cg~~~~~ 17 (54)
T PF14446_consen 6 CKCPVCGKKFKD 17 (54)
T ss_pred ccChhhCCcccC
Confidence 478999998864
No 169
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=42.85 E-value=20 Score=31.85 Aligned_cols=23 Identities=26% Similarity=0.428 Sum_probs=13.6
Q ss_pred ccCcccchhhcccCCCceecCcccccc
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHKVF 53 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~~f 53 (198)
.|+.||........ -|+.||..+
T Consensus 3 ~Cp~Cg~~n~~~ak----FC~~CG~~l 25 (645)
T PRK14559 3 ICPQCQFENPNNNR----FCQKCGTSL 25 (645)
T ss_pred cCCCCCCcCCCCCc----cccccCCCC
Confidence 57888775433222 377777655
No 170
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=41.57 E-value=14 Score=24.81 Aligned_cols=10 Identities=20% Similarity=0.800 Sum_probs=4.6
Q ss_pred cccCcccchh
Q psy11761 26 YKCHQCQRLI 35 (198)
Q Consensus 26 ~~C~~C~~~f 35 (198)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 3444555444
No 171
>KOG2593|consensus
Probab=40.76 E-value=18 Score=30.09 Aligned_cols=40 Identities=15% Similarity=0.573 Sum_probs=25.2
Q ss_pred cCCCCcccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhh
Q psy11761 94 HSGIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQF 150 (198)
Q Consensus 94 h~~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~ 150 (198)
.+....|.|+.|.+.|.. ...+.. ..- ....|.|..|+-.
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~-------------Lea~~L---~~~-~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTS-------------LEALQL---LDN-ETGEFHCENCGGE 162 (436)
T ss_pred ccccccccCCccccchhh-------------hHHHHh---hcc-cCceEEEecCCCc
Confidence 345667999999999876 333221 111 2467889888743
No 172
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=40.13 E-value=12 Score=25.91 Aligned_cols=27 Identities=15% Similarity=0.048 Sum_probs=22.1
Q ss_pred CCeeCCcchhhhcChhHHHhhhhhhCCCCC
Q psy11761 140 KPYQCDRCSQFFGDRMNLISHHCHKHKQSC 169 (198)
Q Consensus 140 ~~~~C~~C~k~f~~~~~L~~H~~~~~~~~~ 169 (198)
.-..|-.+|+.| .+|.+|+.+|++.-|
T Consensus 75 D~IicLEDGkkf---KSLKRHL~t~~gmTP 101 (148)
T COG4957 75 DYIICLEDGKKF---KSLKRHLTTHYGLTP 101 (148)
T ss_pred CeEEEeccCcch---HHHHHHHhcccCCCH
Confidence 457899999999 478999999987544
No 173
>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=39.82 E-value=14 Score=24.86 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=4.7
Q ss_pred eecCcccccc
Q psy11761 44 HKCEYCHKVF 53 (198)
Q Consensus 44 ~~C~~C~~~f 53 (198)
..|..|+..|
T Consensus 71 ~~C~~Cg~~~ 80 (115)
T TIGR00100 71 CECEDCSEEV 80 (115)
T ss_pred EEcccCCCEE
Confidence 3455555443
No 174
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=39.58 E-value=12 Score=22.59 Aligned_cols=27 Identities=30% Similarity=0.896 Sum_probs=17.0
Q ss_pred ccccCcccchhhcccCCCceecCcccccc
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKVF 53 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~f 53 (198)
.|.| .||+..-.....+..+| .||...
T Consensus 3 ifrC-~Cgr~lya~e~~kTkkC-~CG~~l 29 (68)
T PF09082_consen 3 IFRC-DCGRYLYAKEGAKTKKC-VCGKTL 29 (68)
T ss_dssp EEEE-TTS--EEEETT-SEEEE-TTTEEE
T ss_pred EEEe-cCCCEEEecCCcceeEe-cCCCee
Confidence 3667 58877766677777788 787764
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=38.75 E-value=20 Score=23.76 Aligned_cols=29 Identities=14% Similarity=0.390 Sum_probs=17.4
Q ss_pred ccCcccchhhcccCCCceecCccccccCCh
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHKVFDQQ 56 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~ 56 (198)
.||.|+..+.-... ..|.|++|+..+...
T Consensus 4 ~CP~C~seytY~dg-~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHDG-TQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEecC-CeeECcccccccccc
Confidence 57777766543322 247777777766543
No 176
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=38.42 E-value=21 Score=18.56 Aligned_cols=27 Identities=19% Similarity=0.552 Sum_probs=16.4
Q ss_pred CccccCcccchhhcccCCCceecCcccc
Q psy11761 24 NAYKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 24 ~~~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
...+|++|+.. .-.....-+-|..||-
T Consensus 7 ~~~~C~~C~~~-~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 7 PNEPCPVCGSR-WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CCCcCCCCCCe-EeEccCCEEEhhhCce
Confidence 34568888876 3334445566766654
No 177
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=38.23 E-value=12 Score=24.41 Aligned_cols=30 Identities=23% Similarity=0.629 Sum_probs=15.6
Q ss_pred ccccCcccchhhc------ccCCCceecCccccccC
Q psy11761 25 AYKCHQCQRLIFL------SANAGVHKCEYCHKVFD 54 (198)
Q Consensus 25 ~~~C~~C~~~f~~------~~~~~~~~C~~C~~~f~ 54 (198)
.|.||.||..-.. ..+.....|..||..|.
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 4677777754222 22223445666666553
No 178
>KOG1842|consensus
Probab=38.21 E-value=20 Score=30.09 Aligned_cols=28 Identities=18% Similarity=0.236 Sum_probs=24.8
Q ss_pred CCeeCCcchhhhcChhHHHhhhhhhCCC
Q psy11761 140 KPYQCDRCSQFFGDRMNLISHHCHKHKQ 167 (198)
Q Consensus 140 ~~~~C~~C~k~f~~~~~L~~H~~~~~~~ 167 (198)
..|.|++|.+.|.+.+.|..|...-|++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~ 41 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFE 41 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhccc
Confidence 5799999999999999999999876653
No 179
>KOG0978|consensus
Probab=37.89 E-value=13 Score=33.13 Aligned_cols=12 Identities=33% Similarity=0.935 Sum_probs=7.3
Q ss_pred cCccchhcccCc
Q psy11761 73 KCDTCEKSFTNS 84 (198)
Q Consensus 73 ~C~~C~~~f~~~ 84 (198)
+||.|+.+|...
T Consensus 680 KCP~Cn~aFgan 691 (698)
T KOG0978|consen 680 KCPKCNAAFGAN 691 (698)
T ss_pred CCCCCCCCCCcc
Confidence 566666666544
No 180
>PRK10220 hypothetical protein; Provisional
Probab=37.57 E-value=24 Score=23.50 Aligned_cols=29 Identities=21% Similarity=0.582 Sum_probs=17.8
Q ss_pred ccCcccchhhcccCCCceecCccccccCCh
Q psy11761 27 KCHQCQRLIFLSANAGVHKCEYCHKVFDQQ 56 (198)
Q Consensus 27 ~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~ 56 (198)
.||.|+..+.-... ..|.|++|+..+...
T Consensus 5 ~CP~C~seytY~d~-~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYEDN-GMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcCC-CeEECCcccCcCCcc
Confidence 57777766543222 247788887766554
No 181
>KOG2636|consensus
Probab=37.48 E-value=20 Score=30.03 Aligned_cols=25 Identities=20% Similarity=0.514 Sum_probs=21.8
Q ss_pred CCCCeeCCcch-hhhcChhHHHhhhh
Q psy11761 138 FPKPYQCDRCS-QFFGDRMNLISHHC 162 (198)
Q Consensus 138 ~~~~~~C~~C~-k~f~~~~~L~~H~~ 162 (198)
-...|.|++|| +++..+..+.+|..
T Consensus 398 L~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 398 LDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred CCcccceeeccCccccCcHHHHHHhH
Confidence 45789999999 99999999999974
No 182
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=37.22 E-value=24 Score=19.64 Aligned_cols=29 Identities=21% Similarity=0.559 Sum_probs=17.3
Q ss_pred CCccccCcccchhhcccCCCceecCccccc
Q psy11761 23 DNAYKCHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 23 ~~~~~C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
..|..|..|++.... .....+.|..|+..
T Consensus 9 ~~~~~C~~C~~~i~g-~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWG-LGKQGYRCSWCGLV 37 (53)
T ss_dssp SSTEB-TTSSSBECS-SSSCEEEETTTT-E
T ss_pred CCCCCCcccCcccCC-CCCCeEEECCCCCh
Confidence 346678888877633 44446777777654
No 183
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=36.82 E-value=12 Score=22.96 Aligned_cols=7 Identities=43% Similarity=1.151 Sum_probs=3.5
Q ss_pred ccCcccc
Q psy11761 27 KCHQCQR 33 (198)
Q Consensus 27 ~C~~C~~ 33 (198)
.||.||.
T Consensus 3 ~CP~Cg~ 9 (72)
T PRK09678 3 HCPLCQH 9 (72)
T ss_pred cCCCCCC
Confidence 4555554
No 184
>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=36.26 E-value=22 Score=20.11 Aligned_cols=25 Identities=28% Similarity=0.754 Sum_probs=11.8
Q ss_pred cCcccchhhcccCCCceecCccccccC
Q psy11761 28 CHQCQRLIFLSANAGVHKCEYCHKVFD 54 (198)
Q Consensus 28 C~~C~~~f~~~~~~~~~~C~~C~~~f~ 54 (198)
|..|++.|.. ....+.|..||..|-
T Consensus 5 C~~C~~~F~~--~~rk~~Cr~Cg~~~C 29 (57)
T cd00065 5 CMGCGKPFTL--TRRRHHCRNCGRIFC 29 (57)
T ss_pred CcccCccccC--CccccccCcCcCCcC
Confidence 4555555543 222445555555543
No 185
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=35.44 E-value=16 Score=21.66 Aligned_cols=26 Identities=23% Similarity=0.444 Sum_probs=12.0
Q ss_pred cccCcccchhhcccCCCceecCcccc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
..|..|+......-....++|..|+.
T Consensus 31 IlCNDC~~~s~v~fH~lg~KC~~C~S 56 (61)
T PF14599_consen 31 ILCNDCNAKSEVPFHFLGHKCSHCGS 56 (61)
T ss_dssp EEESSS--EEEEE--TT----TTTS-
T ss_pred EECCCCCCccceeeeHhhhcCCCCCC
Confidence 34888888766666666778888864
No 186
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=34.39 E-value=26 Score=23.49 Aligned_cols=31 Identities=16% Similarity=0.434 Sum_probs=19.6
Q ss_pred CCccccCcccchhhcccCCCceecCccccccCC
Q psy11761 23 DNAYKCHQCQRLIFLSANAGVHKCEYCHKVFDQ 55 (198)
Q Consensus 23 ~~~~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~ 55 (198)
.....||.|++..+--.. ...|-.|++...-
T Consensus 67 av~V~CP~C~K~TKmLGr--~D~CM~C~~pLTL 97 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLGR--VDACMHCKEPLTL 97 (114)
T ss_pred ceeeECCCCCChHhhhch--hhccCcCCCcCcc
Confidence 355778888887644332 3478888775443
No 187
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=34.25 E-value=21 Score=24.02 Aligned_cols=10 Identities=30% Similarity=0.890 Sum_probs=4.4
Q ss_pred cccCcccchh
Q psy11761 26 YKCHQCQRLI 35 (198)
Q Consensus 26 ~~C~~C~~~f 35 (198)
..|..||..|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 3444444433
No 188
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=33.73 E-value=29 Score=19.95 Aligned_cols=30 Identities=20% Similarity=0.429 Sum_probs=14.8
Q ss_pred ccCc--ccchhhcccCCCc--eecCccccccCCh
Q psy11761 27 KCHQ--CQRLIFLSANAGV--HKCEYCHKVFDQQ 56 (198)
Q Consensus 27 ~C~~--C~~~f~~~~~~~~--~~C~~C~~~f~~~ 56 (198)
.|+. |+..+........ ..|+.|+..|=..
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~ 53 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFK 53 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEECSS
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCccc
Confidence 6765 7777666555444 6777777766544
No 189
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=33.43 E-value=19 Score=19.15 Aligned_cols=12 Identities=25% Similarity=0.811 Sum_probs=9.3
Q ss_pred CeeCCcchhhhc
Q psy11761 141 PYQCDRCSQFFG 152 (198)
Q Consensus 141 ~~~C~~C~k~f~ 152 (198)
-|.|..|+..+.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 588999987664
No 190
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=33.08 E-value=36 Score=17.87 Aligned_cols=26 Identities=19% Similarity=0.369 Sum_probs=14.9
Q ss_pred cccCcccc--h--hhcccCCCceecCcccc
Q psy11761 26 YKCHQCQR--L--IFLSANAGVHKCEYCHK 51 (198)
Q Consensus 26 ~~C~~C~~--~--f~~~~~~~~~~C~~C~~ 51 (198)
-+||.|+. . |..+.....|.|..|+.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 35788874 2 33333334677877754
No 191
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=32.91 E-value=31 Score=17.53 Aligned_cols=28 Identities=21% Similarity=0.567 Sum_probs=13.4
Q ss_pred cccCcccchhhcccCCCceecCcccccc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKVF 53 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~f 53 (198)
..|..|+..-.-.+....+.|..|+..|
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 3455555433222333345666666554
No 192
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.85 E-value=14 Score=20.58 Aligned_cols=17 Identities=24% Similarity=0.374 Sum_probs=13.6
Q ss_pred eeCCcchhhhcChhHHH
Q psy11761 142 YQCDRCSQFFGDRMNLI 158 (198)
Q Consensus 142 ~~C~~C~k~f~~~~~L~ 158 (198)
-.|++|++.|+.+..+.
T Consensus 13 KICpvCqRPFsWRkKW~ 29 (54)
T COG4338 13 KICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhhcCchHHHHHHH
Confidence 37999999998876554
No 193
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=32.81 E-value=29 Score=18.81 Aligned_cols=10 Identities=20% Similarity=0.571 Sum_probs=5.3
Q ss_pred ccCcccchhh
Q psy11761 27 KCHQCQRLIF 36 (198)
Q Consensus 27 ~C~~C~~~f~ 36 (198)
.|+.||..+.
T Consensus 4 ~C~~Cg~~l~ 13 (47)
T PF13005_consen 4 ACPDCGGELK 13 (47)
T ss_pred cCCCCCceee
Confidence 4555665443
No 194
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=32.79 E-value=8.3 Score=27.75 Aligned_cols=32 Identities=28% Similarity=0.600 Sum_probs=25.8
Q ss_pred ccccCcccchhhcccCCCceecCccccccCCh
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHKVFDQQ 56 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~~f~~~ 56 (198)
.-.|+.|++.|..-...+.+-|..|.+.|...
T Consensus 74 ~l~C~~C~~Tfk~f~~~g~fGCaeCY~tf~~~ 105 (176)
T COG3880 74 LLGCHNCGMTFKEFIQSGLFGCAECYKTFESQ 105 (176)
T ss_pred HhcCccccccHHHHHHhcccchHHHHHHHHHH
Confidence 45689999998887777788899998888664
No 195
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.37 E-value=20 Score=24.18 Aligned_cols=12 Identities=25% Similarity=0.855 Sum_probs=9.5
Q ss_pred ccCCcCchhhhc
Q psy11761 100 FKCTTCDKSFVN 111 (198)
Q Consensus 100 ~~C~~C~~~f~~ 111 (198)
+.|..||..|..
T Consensus 72 ~~C~~Cg~~~~~ 83 (117)
T PRK00564 72 LECKDCSHVFKP 83 (117)
T ss_pred EEhhhCCCcccc
Confidence 789999977764
No 196
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=32.10 E-value=16 Score=32.81 Aligned_cols=78 Identities=17% Similarity=0.422 Sum_probs=51.1
Q ss_pred cccCcccchhhcccCCC---ce-ecCccccccCChhHHhhcccCCCCCCCccCccchhcccCchhHHHhhhhcCCCCccc
Q psy11761 26 YKCHQCQRLIFLSANAG---VH-KCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTNSQNLNTHQLIHSGIRPFK 101 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~---~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~~~ 101 (198)
-.|+.|=+.+....+.+ || .|..||-.|.-...|-.-...-....--.|+.|.+.+.+..+ .+.|. .+-.
T Consensus 69 a~C~~Cl~E~~dp~~Rry~YpF~nCt~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p~~----rr~h~--~~~~ 142 (711)
T TIGR00143 69 ATCSDCLEEMLDKNDRRYLYPFISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLD----RRFHA--QPIA 142 (711)
T ss_pred hhHHHHHHHhcCCCcccccCCcccccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCCcc----ccCCC--CCcc
Confidence 56888888887766655 44 599999988776665544432233344579999877765533 34444 3568
Q ss_pred CCcCchhh
Q psy11761 102 CTTCDKSF 109 (198)
Q Consensus 102 C~~C~~~f 109 (198)
|+.||-..
T Consensus 143 C~~Cgp~l 150 (711)
T TIGR00143 143 CPRCGPQL 150 (711)
T ss_pred CCCCCcEE
Confidence 99998553
No 197
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=32.08 E-value=27 Score=24.21 Aligned_cols=11 Identities=36% Similarity=0.920 Sum_probs=6.1
Q ss_pred cCCcCchhhhc
Q psy11761 101 KCTTCDKSFVN 111 (198)
Q Consensus 101 ~C~~C~~~f~~ 111 (198)
+||.|..+|.+
T Consensus 123 vCPvCkTSFKs 133 (140)
T PF05290_consen 123 VCPVCKTSFKS 133 (140)
T ss_pred CCCcccccccc
Confidence 55555555544
No 198
>KOG3408|consensus
Probab=32.03 E-value=34 Score=23.26 Aligned_cols=28 Identities=25% Similarity=0.427 Sum_probs=24.3
Q ss_pred cCCCCeeCCcchhhhcChhHHHhhhhhh
Q psy11761 137 HFPKPYQCDRCSQFFGDRMNLISHHCHK 164 (198)
Q Consensus 137 ~~~~~~~C~~C~k~f~~~~~L~~H~~~~ 164 (198)
+|...|-|-.|.+-|.+...|..|.++.
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhcc
Confidence 3667899999999999999999998644
No 199
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=31.90 E-value=11 Score=19.90 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=8.7
Q ss_pred CeeCCcchhhh
Q psy11761 141 PYQCDRCSQFF 151 (198)
Q Consensus 141 ~~~C~~C~k~f 151 (198)
-|.|..|++.|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 57898898765
No 200
>KOG2593|consensus
Probab=31.79 E-value=19 Score=30.02 Aligned_cols=31 Identities=26% Similarity=0.524 Sum_probs=18.2
Q ss_pred CCccccCcccchhhcccCC-------CceecCcccccc
Q psy11761 23 DNAYKCHQCQRLIFLSANA-------GVHKCEYCHKVF 53 (198)
Q Consensus 23 ~~~~~C~~C~~~f~~~~~~-------~~~~C~~C~~~f 53 (198)
...|.||.|.+.|..-..+ ..|.|..|+...
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred cccccCCccccchhhhHHHHhhcccCceEEEecCCCch
Confidence 3457777777776543222 256777776543
No 201
>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=31.24 E-value=29 Score=17.03 Aligned_cols=22 Identities=27% Similarity=0.537 Sum_probs=11.2
Q ss_pred cccCcccchhhcccCCCceecCccc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCH 50 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~ 50 (198)
|+|..|++...... .|.|..|.
T Consensus 1 ~~C~~C~~~~~~~~---~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY---FYHCSECC 22 (30)
T ss_pred CCCCCCCCCcCCCE---eEEeCCCC
Confidence 34566665443322 56666655
No 202
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=31.19 E-value=21 Score=25.27 Aligned_cols=36 Identities=19% Similarity=0.739 Sum_probs=24.5
Q ss_pred CCCcccCCcCchhhhcccCCCcccCCCcCcccccccccccccCCCCeeCCcchhh
Q psy11761 96 GIRPFKCTTCDKSFVNQINPTSTHTPTYTKSNLAQHSCMNSHFPKPYQCDRCSQF 150 (198)
Q Consensus 96 ~~k~~~C~~C~~~f~~~~~~~~~~~~~~~~~~l~~H~~~~~~~~~~~~C~~C~k~ 150 (198)
..-+|.|. |+..|.+ ..+|..... |+ .|.|..|+-.
T Consensus 114 ~~~~Y~C~-C~q~~l~----------------~RRhn~~~~-g~-~YrC~~C~gk 149 (156)
T COG3091 114 TTYPYRCQ-CQQHYLR----------------IRRHNTVRR-GE-VYRCGKCGGK 149 (156)
T ss_pred cceeEEee-cCCccch----------------hhhcccccc-cc-eEEeccCCce
Confidence 34579999 9988765 234554444 45 8999999754
No 203
>KOG2785|consensus
Probab=31.06 E-value=33 Score=28.14 Aligned_cols=51 Identities=18% Similarity=0.338 Sum_probs=42.6
Q ss_pred ceecCccccccCChhHHhhcccCCCCC-----------------------CCccCccch---hcccCchhHHHhhhh
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKP-----------------------RPYKCDTCE---KSFTNSQNLNTHQLI 93 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~ 93 (198)
|=-|-.|+..+.....-..||..+|+- ..+.|..|+ +.|.+......||..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 456889999999998899999998872 337888888 899999999999874
No 204
>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=30.20 E-value=27 Score=24.48 Aligned_cols=31 Identities=26% Similarity=0.790 Sum_probs=15.4
Q ss_pred ceecCccccccCChhHHhhcccCCCCCCCccCccchhcc
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSF 81 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 81 (198)
.|.|..|+..+.. +.+. ....|.|..|+..+
T Consensus 123 ~~~C~~C~~~~~r------~~~~--~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRRS--KRKRYRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeee------eccc--chhhEECCCCCCEE
Confidence 4566666655422 2222 22336666666544
No 205
>KOG4167|consensus
Probab=29.49 E-value=12 Score=33.25 Aligned_cols=26 Identities=27% Similarity=0.531 Sum_probs=23.3
Q ss_pred CccCccchhcccCchhHHHhhhhcCC
Q psy11761 71 PYKCDTCEKSFTNSQNLNTHQLIHSG 96 (198)
Q Consensus 71 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 96 (198)
-|.|.+|++.|.-..++..||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 38999999999999999999999863
No 206
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=29.38 E-value=31 Score=18.48 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=11.3
Q ss_pred cccCcccch-----hhcccCCCceecCccc
Q psy11761 26 YKCHQCQRL-----IFLSANAGVHKCEYCH 50 (198)
Q Consensus 26 ~~C~~C~~~-----f~~~~~~~~~~C~~C~ 50 (198)
-+||.|+-. |..+.....|.|..|+
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQCG 33 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTTT
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCCC
Confidence 368888842 4444444578888883
No 207
>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=28.31 E-value=19 Score=19.44 Aligned_cols=15 Identities=27% Similarity=0.866 Sum_probs=10.0
Q ss_pred CCeeCCcchhhhcCh
Q psy11761 140 KPYQCDRCSQFFGDR 154 (198)
Q Consensus 140 ~~~~C~~C~k~f~~~ 154 (198)
-++.|+.|++.|-..
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 589999999999654
No 208
>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 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=28.28 E-value=37 Score=17.98 Aligned_cols=14 Identities=21% Similarity=0.351 Sum_probs=9.1
Q ss_pred CCCCeeCCcchhhh
Q psy11761 138 FPKPYQCDRCSQFF 151 (198)
Q Consensus 138 ~~~~~~C~~C~k~f 151 (198)
+.+.+.|.+|+...
T Consensus 21 ~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 21 GGKTWICNFCGTKN 34 (40)
T ss_dssp TTTEEEETTT--EE
T ss_pred CCCEEECcCCCCcC
Confidence 45789999998653
No 210
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=28.24 E-value=31 Score=29.26 Aligned_cols=25 Identities=24% Similarity=0.485 Sum_probs=19.0
Q ss_pred CccccCcccchhhcccCCCceecCccccc
Q psy11761 24 NAYKCHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 24 ~~~~C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
..|.|..||...... .++|+.|+..
T Consensus 6 ~~y~C~~Cg~~~~~~----~g~Cp~C~~w 30 (454)
T TIGR00416 6 SKFVCQHCGADSPKW----QGKCPACHAW 30 (454)
T ss_pred CeEECCcCCCCCccc----cEECcCCCCc
Confidence 369999999865443 4789999774
No 211
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=27.98 E-value=18 Score=28.60 Aligned_cols=10 Identities=20% Similarity=0.421 Sum_probs=4.7
Q ss_pred ccCCcCchhh
Q psy11761 100 FKCTTCDKSF 109 (198)
Q Consensus 100 ~~C~~C~~~f 109 (198)
-.|++||..-
T Consensus 173 g~CPvCGs~P 182 (290)
T PF04216_consen 173 GYCPVCGSPP 182 (290)
T ss_dssp SS-TTT---E
T ss_pred CcCCCCCCcC
Confidence 4899999663
No 212
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=27.96 E-value=37 Score=16.86 Aligned_cols=24 Identities=17% Similarity=0.480 Sum_probs=8.1
Q ss_pred cCcccchhhcccCCCceecCcccc
Q psy11761 28 CHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 28 C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
|+.||...........-.|+.|+.
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSSS-
T ss_pred cCcCCccccCCCCcCEeECCCCcC
Confidence 445554433333333345555543
No 213
>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=27.83 E-value=22 Score=20.18 Aligned_cols=12 Identities=17% Similarity=0.584 Sum_probs=6.7
Q ss_pred eCCcchhhhcCh
Q psy11761 143 QCDRCSQFFGDR 154 (198)
Q Consensus 143 ~C~~C~k~f~~~ 154 (198)
.||+|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 999999999753
No 214
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=27.76 E-value=38 Score=22.07 Aligned_cols=26 Identities=27% Similarity=0.593 Sum_probs=18.4
Q ss_pred cCcccchhhcccCCCceecCccccccCC
Q psy11761 28 CHQCQRLIFLSANAGVHKCEYCHKVFDQ 55 (198)
Q Consensus 28 C~~C~~~f~~~~~~~~~~C~~C~~~f~~ 55 (198)
|+.||..+.... ..+.|+.|+..+..
T Consensus 3 C~~Cg~~l~~~~--~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 3 CPKCGSLMTPKN--GVYVCPSCGYEKEK 28 (104)
T ss_pred CcccCcccccCC--CeEECcCCCCcccc
Confidence 788888775443 36889889876554
No 215
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=27.74 E-value=32 Score=16.72 Aligned_cols=19 Identities=16% Similarity=0.426 Sum_probs=7.7
Q ss_pred cCcccchhhcccCCCceec
Q psy11761 28 CHQCQRLIFLSANAGVHKC 46 (198)
Q Consensus 28 C~~C~~~f~~~~~~~~~~C 46 (198)
||.||...........+.|
T Consensus 2 CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 2 CPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp -TTT--BEEE-CCTTCEEE
T ss_pred cCCCCCEeEcCCCCEeEEC
Confidence 6667665554444444444
No 216
>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=27.19 E-value=20 Score=17.57 Aligned_cols=11 Identities=45% Similarity=1.144 Sum_probs=8.8
Q ss_pred ccCCcCchhhh
Q psy11761 100 FKCTTCDKSFV 110 (198)
Q Consensus 100 ~~C~~C~~~f~ 110 (198)
|.|-.|++.|.
T Consensus 1 ~sCiDC~~~F~ 11 (28)
T PF08790_consen 1 FSCIDCSKDFD 11 (28)
T ss_dssp EEETTTTEEEE
T ss_pred CeeecCCCCcC
Confidence 46888999995
No 217
>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=26.87 E-value=26 Score=18.67 Aligned_cols=8 Identities=25% Similarity=0.708 Sum_probs=3.5
Q ss_pred ecCccccc
Q psy11761 45 KCEYCHKV 52 (198)
Q Consensus 45 ~C~~C~~~ 52 (198)
.|+.||+.
T Consensus 34 ~C~~CGE~ 41 (46)
T TIGR03831 34 VCPQCGEE 41 (46)
T ss_pred ccccCCCE
Confidence 34444443
No 218
>PRK11823 DNA repair protein RadA; Provisional
Probab=26.76 E-value=38 Score=28.64 Aligned_cols=26 Identities=23% Similarity=0.494 Sum_probs=19.3
Q ss_pred CCccccCcccchhhcccCCCceecCccccc
Q psy11761 23 DNAYKCHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 23 ~~~~~C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
...|.|..||...... .++|+.|+..
T Consensus 5 ~~~y~C~~Cg~~~~~~----~g~Cp~C~~w 30 (446)
T PRK11823 5 KTAYVCQECGAESPKW----LGRCPECGAW 30 (446)
T ss_pred CCeEECCcCCCCCccc----CeeCcCCCCc
Confidence 3469999999865443 4789999774
No 219
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=26.62 E-value=42 Score=18.08 Aligned_cols=9 Identities=22% Similarity=0.807 Sum_probs=5.1
Q ss_pred ccccCcccc
Q psy11761 25 AYKCHQCQR 33 (198)
Q Consensus 25 ~~~C~~C~~ 33 (198)
|..|+.||.
T Consensus 2 ~~~Cp~Cg~ 10 (47)
T PF14690_consen 2 PPRCPHCGS 10 (47)
T ss_pred CccCCCcCC
Confidence 445666663
No 220
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=26.57 E-value=23 Score=18.25 Aligned_cols=9 Identities=22% Similarity=0.438 Sum_probs=4.3
Q ss_pred ecCcccccc
Q psy11761 45 KCEYCHKVF 53 (198)
Q Consensus 45 ~C~~C~~~f 53 (198)
.|..|+..+
T Consensus 22 ~C~~C~Y~~ 30 (35)
T PF02150_consen 22 ACRTCGYEE 30 (35)
T ss_dssp EESSSS-EE
T ss_pred CCCCCCCcc
Confidence 466665543
No 221
>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=26.46 E-value=36 Score=16.59 Aligned_cols=8 Identities=25% Similarity=0.895 Sum_probs=2.9
Q ss_pred ceecCccc
Q psy11761 43 VHKCEYCH 50 (198)
Q Consensus 43 ~~~C~~C~ 50 (198)
.|.|.+|+
T Consensus 15 ~Y~C~~Cd 22 (30)
T PF07649_consen 15 FYRCSECD 22 (30)
T ss_dssp EEE-TTT-
T ss_pred eEECccCC
Confidence 44555553
No 222
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=26.15 E-value=38 Score=27.59 Aligned_cols=25 Identities=16% Similarity=0.424 Sum_probs=21.0
Q ss_pred CCCCeeCCcch-hhhcChhHHHhhhh
Q psy11761 138 FPKPYQCDRCS-QFFGDRMNLISHHC 162 (198)
Q Consensus 138 ~~~~~~C~~C~-k~f~~~~~L~~H~~ 162 (198)
-.+.|.|++|| +.+..+..+.+|..
T Consensus 371 Ld~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 371 LDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred CCcceeeeecccccccchHHHHhhhh
Confidence 46789999999 88888888888863
No 223
>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=25.65 E-value=26 Score=18.75 Aligned_cols=11 Identities=18% Similarity=0.413 Sum_probs=7.2
Q ss_pred ccccCcccchh
Q psy11761 25 AYKCHQCQRLI 35 (198)
Q Consensus 25 ~~~C~~C~~~f 35 (198)
+-.|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 56677777654
No 224
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=25.23 E-value=44 Score=23.33 Aligned_cols=32 Identities=16% Similarity=0.475 Sum_probs=19.5
Q ss_pred ceecCccccccCChhHHhhcccCCCCCCCccCccchhcc
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSF 81 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 81 (198)
.|.|..|+..+.. +. .+.....|.|..|+..+
T Consensus 112 ~y~C~~C~~~~~~------~r-r~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLR------VR-RSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCce------Ec-cccCcceEEcCCCCCEE
Confidence 6788888876532 21 12222568888887665
No 225
>KOG0782|consensus
Probab=25.03 E-value=22 Score=30.94 Aligned_cols=47 Identities=15% Similarity=0.359 Sum_probs=32.6
Q ss_pred cceeeeechhhhhhhCCCCccccCcccchhhcccCCC-----ceecCccccccCChh
Q psy11761 6 PNLVLFSQQTLLCIHGNDNAYKCHQCQRLIFLSANAG-----VHKCEYCHKVFDQQS 57 (198)
Q Consensus 6 ~~l~~~~~~~h~~~h~~~~~~~C~~C~~~f~~~~~~~-----~~~C~~C~~~f~~~~ 57 (198)
+.|+ .|-=+|-.-.-.+|..||+.|.++..+. ...|.+|.+.|-.+-
T Consensus 239 ~~fv-----rHHWVHrrRqeGkC~~CgKgFQQKf~FhsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 239 SGFV-----RHHWVHRRRQEGKCNTCGKGFQQKFFFHSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccch-----HHhHhhHhhhccccchhhhhhhhheeeccccEEEEEehHHHHHhhcch
Confidence 4566 6766666555668999999987764432 457888888776553
No 226
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=24.89 E-value=30 Score=30.92 Aligned_cols=46 Identities=17% Similarity=0.517 Sum_probs=31.5
Q ss_pred cCcccchhhcccCC---------Cce-ecCccccccCChhHHhhcccCCCCCCCccCccchh
Q psy11761 28 CHQCQRLIFLSANA---------GVH-KCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEK 79 (198)
Q Consensus 28 C~~C~~~f~~~~~~---------~~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 79 (198)
|..||-.|.-...+ ..| .|+.|.+.+..... ++-|. .|..|+.||=
T Consensus 126 CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~n----RRfHA--Qp~aCp~CGP 181 (750)
T COG0068 126 CTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLN----RRFHA--QPIACPKCGP 181 (750)
T ss_pred cCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccc----ccccc--ccccCcccCC
Confidence 99999988764433 123 59999888877665 23333 5778999984
No 227
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=24.66 E-value=41 Score=23.24 Aligned_cols=26 Identities=23% Similarity=0.487 Sum_probs=16.9
Q ss_pred cccCcccchhhcccCCCceecCcccccc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKVF 53 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~f 53 (198)
+.|+.||..... .-+.--|+.|+..+
T Consensus 29 ~hCp~Cg~PLF~--KdG~v~CPvC~~~~ 54 (131)
T COG1645 29 KHCPKCGTPLFR--KDGEVFCPVCGYRE 54 (131)
T ss_pred hhCcccCCccee--eCCeEECCCCCceE
Confidence 678888876555 23345688888533
No 228
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.53 E-value=34 Score=23.34 Aligned_cols=12 Identities=17% Similarity=0.069 Sum_probs=6.7
Q ss_pred ceecCccccccCC
Q psy11761 43 VHKCEYCHKVFDQ 55 (198)
Q Consensus 43 ~~~C~~C~~~f~~ 55 (198)
...| .|+..|..
T Consensus 70 ~~~C-~Cg~~~~~ 81 (124)
T PRK00762 70 EIEC-ECGYEGVV 81 (124)
T ss_pred eEEe-eCcCcccc
Confidence 3466 66655543
No 229
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=24.39 E-value=33 Score=25.50 Aligned_cols=10 Identities=20% Similarity=0.571 Sum_probs=5.5
Q ss_pred ccCcccchhh
Q psy11761 27 KCHQCQRLIF 36 (198)
Q Consensus 27 ~C~~C~~~f~ 36 (198)
.||.||..+.
T Consensus 16 ~CPvCg~~l~ 25 (201)
T COG1779 16 DCPVCGGTLK 25 (201)
T ss_pred cCCcccceee
Confidence 4666665443
No 230
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.35 E-value=48 Score=22.82 Aligned_cols=17 Identities=24% Similarity=0.563 Sum_probs=13.8
Q ss_pred CCCCeeCCcchhhhcCh
Q psy11761 138 FPKPYQCDRCSQFFGDR 154 (198)
Q Consensus 138 ~~~~~~C~~C~k~f~~~ 154 (198)
+...|.|..|++.|...
T Consensus 50 ~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 50 GHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cccccccCCcCcceeee
Confidence 35679999999999754
No 231
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=24.08 E-value=43 Score=27.62 Aligned_cols=23 Identities=26% Similarity=0.569 Sum_probs=16.7
Q ss_pred cccCcccchhhcccCCCceecCccccc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
|.|..||...... .++|+.|+..
T Consensus 1 ~~c~~cg~~~~~~----~g~cp~c~~w 23 (372)
T cd01121 1 YVCSECGYVSPKW----LGKCPECGEW 23 (372)
T ss_pred CCCCCCCCCCCCc----cEECcCCCCc
Confidence 6799999865433 3689999774
No 232
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.72 E-value=28 Score=21.52 Aligned_cols=12 Identities=33% Similarity=0.952 Sum_probs=9.6
Q ss_pred ccCCcCchhhhc
Q psy11761 100 FKCTTCDKSFVN 111 (198)
Q Consensus 100 ~~C~~C~~~f~~ 111 (198)
|+|..|+..|.-
T Consensus 13 Y~c~~cg~~~dv 24 (82)
T COG2331 13 YECTECGNRFDV 24 (82)
T ss_pred EeecccchHHHH
Confidence 789999988753
No 233
>PRK11827 hypothetical protein; Provisional
Probab=23.67 E-value=61 Score=19.10 Aligned_cols=11 Identities=18% Similarity=0.335 Sum_probs=4.8
Q ss_pred eecCccccccC
Q psy11761 44 HKCEYCHKVFD 54 (198)
Q Consensus 44 ~~C~~C~~~f~ 54 (198)
..|..|+..|.
T Consensus 27 Lic~~~~laYP 37 (60)
T PRK11827 27 LICKLDNLAFP 37 (60)
T ss_pred EECCccCeecc
Confidence 34444444443
No 234
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=23.54 E-value=73 Score=18.50 Aligned_cols=22 Identities=18% Similarity=0.464 Sum_probs=14.8
Q ss_pred ccccCcccchhhcccCCCceecCcccc
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
...|+.||.. .+....|..||.
T Consensus 27 l~~C~~CG~~-----~~~H~vC~~CG~ 48 (57)
T PRK12286 27 LVECPNCGEP-----KLPHRVCPSCGY 48 (57)
T ss_pred ceECCCCCCc-----cCCeEECCCCCc
Confidence 4678888874 233567888874
No 235
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=23.19 E-value=47 Score=28.39 Aligned_cols=14 Identities=21% Similarity=0.726 Sum_probs=9.2
Q ss_pred ceecCccccccCCh
Q psy11761 43 VHKCEYCHKVFDQQ 56 (198)
Q Consensus 43 ~~~C~~C~~~f~~~ 56 (198)
.|.|..|+..+...
T Consensus 425 ~~~c~~c~~~yd~~ 438 (479)
T PRK05452 425 RMQCSVCQWIYDPA 438 (479)
T ss_pred eEEECCCCeEECCC
Confidence 57777777666554
No 236
>PF12907 zf-met2: Zinc-binding
Probab=23.02 E-value=67 Score=17.22 Aligned_cols=27 Identities=30% Similarity=0.491 Sum_probs=19.5
Q ss_pred eeCCcchhhhc---ChhHHHhhhhhhCCCC
Q psy11761 142 YQCDRCSQFFG---DRMNLISHHCHKHKQS 168 (198)
Q Consensus 142 ~~C~~C~k~f~---~~~~L~~H~~~~~~~~ 168 (198)
+.|.+|-..|. ....|..|....|...
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 57999997774 4567999987555443
No 237
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.00 E-value=23 Score=25.24 Aligned_cols=18 Identities=22% Similarity=0.591 Sum_probs=13.7
Q ss_pred CCCCccCccchhcccCch
Q psy11761 68 KPRPYKCDTCEKSFTNSQ 85 (198)
Q Consensus 68 ~~~~~~C~~C~~~f~~~~ 85 (198)
-+.|.-|..||+.|++..
T Consensus 65 ~~~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 65 YEAPSYCHNCGKPYPWTE 82 (158)
T ss_pred CCCChhHHhCCCCCchHH
Confidence 357888999998887753
No 238
>KOG1280|consensus
Probab=22.91 E-value=70 Score=26.03 Aligned_cols=38 Identities=21% Similarity=0.474 Sum_probs=26.5
Q ss_pred CCCccCccchhcccCchhHHHhhhhcCCCCc--ccCCcCc
Q psy11761 69 PRPYKCDTCEKSFTNSQNLNTHQLIHSGIRP--FKCTTCD 106 (198)
Q Consensus 69 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~k~--~~C~~C~ 106 (198)
+..|.|+.|+..-.+...|..|....+.+-. ..|++|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 4468899998887778888888776554433 3556664
No 239
>PRK11032 hypothetical protein; Provisional
Probab=22.89 E-value=40 Score=24.21 Aligned_cols=37 Identities=14% Similarity=0.324 Sum_probs=18.5
Q ss_pred hhhhhCCCCc----cccCcccchhhcccCCCceecCccccc
Q psy11761 16 LLCIHGNDNA----YKCHQCQRLIFLSANAGVHKCEYCHKV 52 (198)
Q Consensus 16 h~~~h~~~~~----~~C~~C~~~f~~~~~~~~~~C~~C~~~ 52 (198)
|-..|+|+.. ..|..||....-...-..-.|+.|+..
T Consensus 111 ~g~Y~sGEvvg~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 111 HGVYHSGEVVGLGNLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred cCeeecceeeecceEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 3345666643 557777754333222223356666543
No 240
>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=22.85 E-value=30 Score=22.56 Aligned_cols=12 Identities=17% Similarity=0.656 Sum_probs=5.8
Q ss_pred ccccCcccchhh
Q psy11761 25 AYKCHQCQRLIF 36 (198)
Q Consensus 25 ~~~C~~C~~~f~ 36 (198)
|+.|+.||..|+
T Consensus 79 ~~rC~eCG~~fk 90 (97)
T cd00924 79 PKRCPECGHVFK 90 (97)
T ss_pred ceeCCCCCcEEE
Confidence 455555554443
No 241
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.67 E-value=29 Score=25.38 Aligned_cols=31 Identities=19% Similarity=0.398 Sum_probs=14.7
Q ss_pred CCCccccCcccchhhccc-CCCceecCccccc
Q psy11761 22 NDNAYKCHQCQRLIFLSA-NAGVHKCEYCHKV 52 (198)
Q Consensus 22 ~~~~~~C~~C~~~f~~~~-~~~~~~C~~C~~~ 52 (198)
....|.|+.|...+.-.. ....|.|+.||..
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~ 141 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAMELGFTCPKCGED 141 (176)
T ss_pred cCCceeCCCCCCcccHHHHHHhCCCCCCCCch
Confidence 334566666554433211 1123566666654
No 242
>KOG4118|consensus
Probab=22.56 E-value=54 Score=19.62 Aligned_cols=31 Identities=26% Similarity=0.427 Sum_probs=25.7
Q ss_pred CeeCCcchhhhcChhHHHhhhhhhCCCCCCC
Q psy11761 141 PYQCDRCSQFFGDRMNLISHHCHKHKQSCLP 171 (198)
Q Consensus 141 ~~~C~~C~k~f~~~~~L~~H~~~~~~~~~~~ 171 (198)
-|+|.+|--.......+..|....|...|+|
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~kHpk~~~P 68 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFENKHPKEPLP 68 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhhcCCCCCCC
Confidence 4789999988888889999998888777665
No 243
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=22.42 E-value=61 Score=27.60 Aligned_cols=27 Identities=33% Similarity=0.641 Sum_probs=23.3
Q ss_pred CCeeCCcchhhhcChhHHHhhhhhhCC
Q psy11761 140 KPYQCDRCSQFFGDRMNLISHHCHKHK 166 (198)
Q Consensus 140 ~~~~C~~C~k~f~~~~~L~~H~~~~~~ 166 (198)
+-+.|+.|.+.|.....+..|+..-|-
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~ 82 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHP 82 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhh
Confidence 467999999999999999999985553
No 244
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=22.15 E-value=57 Score=20.34 Aligned_cols=9 Identities=33% Similarity=0.884 Sum_probs=5.5
Q ss_pred cccCcccch
Q psy11761 26 YKCHQCQRL 34 (198)
Q Consensus 26 ~~C~~C~~~ 34 (198)
|+||-||..
T Consensus 2 ~~CPCCg~~ 10 (78)
T PF14206_consen 2 YPCPCCGYY 10 (78)
T ss_pred ccCCCCCcE
Confidence 456666654
No 245
>PRK04351 hypothetical protein; Provisional
Probab=21.93 E-value=54 Score=23.21 Aligned_cols=33 Identities=15% Similarity=0.633 Sum_probs=22.3
Q ss_pred ceecCccccccCChhHHhhcccCCCCCCCccCccchhcccC
Q psy11761 43 VHKCEYCHKVFDQQSSLLSHNCPQMKPRPYKCDTCEKSFTN 83 (198)
Q Consensus 43 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 83 (198)
.|.|..|+..+.... . ++...|.|..|+..+..
T Consensus 112 ~Y~C~~Cg~~~~r~R-------r-~n~~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLRKR-------R-INTKRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeeeee-------e-cCCCcEEeCCCCcEeee
Confidence 588988987654321 1 23577999999877654
No 246
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=21.91 E-value=62 Score=17.20 Aligned_cols=25 Identities=28% Similarity=0.663 Sum_probs=12.3
Q ss_pred ccccCcccchhhcccCCCceecCcccc
Q psy11761 25 AYKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 25 ~~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
+..|..|++.+.... ..++|..|+.
T Consensus 11 ~~~C~~C~~~i~~~~--~~~~C~~C~~ 35 (49)
T smart00109 11 PTKCCVCRKSIWGSF--QGLRCSWCKV 35 (49)
T ss_pred CCCccccccccCcCC--CCcCCCCCCc
Confidence 445666665543322 2455555543
No 247
>PRK08402 replication factor A; Reviewed
Probab=21.84 E-value=52 Score=27.00 Aligned_cols=26 Identities=15% Similarity=0.363 Sum_probs=18.9
Q ss_pred cccCcccchhhcccCCCceecCcccc
Q psy11761 26 YKCHQCQRLIFLSANAGVHKCEYCHK 51 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~~~~C~~C~~ 51 (198)
..||.|++.+........|.|..|+.
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGE 238 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCC
Confidence 45888888776545556788888875
No 248
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=21.52 E-value=81 Score=16.80 Aligned_cols=24 Identities=13% Similarity=0.296 Sum_probs=17.3
Q ss_pred CeeCCcchhhhcC--hhHHHhhhhhh
Q psy11761 141 PYQCDRCSQFFGD--RMNLISHHCHK 164 (198)
Q Consensus 141 ~~~C~~C~k~f~~--~~~L~~H~~~~ 164 (198)
...|+.||-.|.. ...-..|.+.|
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHH
Confidence 4689999988875 44566676655
No 249
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.04 E-value=48 Score=19.57 Aligned_cols=38 Identities=24% Similarity=0.652 Sum_probs=20.8
Q ss_pred cCccchhc-ccCchhHHHhhhhcCCCCcccCCcCchhhh
Q psy11761 73 KCDTCEKS-FTNSQNLNTHQLIHSGIRPFKCTTCDKSFV 110 (198)
Q Consensus 73 ~C~~C~~~-f~~~~~l~~H~~~h~~~k~~~C~~C~~~f~ 110 (198)
.|.+|++. +-....+..-.....+...|.|+.|.....
T Consensus 4 kCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva 42 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVA 42 (68)
T ss_pred eEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhc
Confidence 45555542 223344444455566667777777765543
No 250
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=20.99 E-value=66 Score=18.25 Aligned_cols=27 Identities=22% Similarity=0.646 Sum_probs=15.6
Q ss_pred cccCcccchhhcccCCC--ceecCccccc
Q psy11761 26 YKCHQCQRLIFLSANAG--VHKCEYCHKV 52 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~~~--~~~C~~C~~~ 52 (198)
+.|..|++......... ..+|+-|+..
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCcc
Confidence 56777777655532222 4567777653
No 251
>PRK05978 hypothetical protein; Provisional
Probab=20.91 E-value=58 Score=23.06 Aligned_cols=9 Identities=33% Similarity=0.936 Sum_probs=4.1
Q ss_pred ecCcccccc
Q psy11761 45 KCEYCHKVF 53 (198)
Q Consensus 45 ~C~~C~~~f 53 (198)
.|+.||..|
T Consensus 54 ~C~~CG~~~ 62 (148)
T PRK05978 54 HCAACGEDF 62 (148)
T ss_pred CccccCCcc
Confidence 344454443
No 252
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.78 E-value=55 Score=18.63 Aligned_cols=14 Identities=29% Similarity=0.634 Sum_probs=7.5
Q ss_pred hCCCCccccCcccc
Q psy11761 20 HGNDNAYKCHQCQR 33 (198)
Q Consensus 20 h~~~~~~~C~~C~~ 33 (198)
..++....|+.||+
T Consensus 41 ~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 41 RKGDEIVFCPNCGR 54 (56)
T ss_pred HcCCCeEECcCCCc
Confidence 34445556666654
No 253
>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=20.70 E-value=72 Score=21.04 Aligned_cols=11 Identities=27% Similarity=0.902 Sum_probs=7.2
Q ss_pred CcccCCcCchh
Q psy11761 98 RPFKCTTCDKS 108 (198)
Q Consensus 98 k~~~C~~C~~~ 108 (198)
||-.|+.||..
T Consensus 1 ~p~~CpYCg~~ 11 (102)
T PF11672_consen 1 KPIICPYCGGP 11 (102)
T ss_pred CCcccCCCCCe
Confidence 45678888744
No 254
>KOG3214|consensus
Probab=20.61 E-value=73 Score=20.86 Aligned_cols=18 Identities=17% Similarity=0.340 Sum_probs=13.9
Q ss_pred CCCCeeCCcchhhhcChh
Q psy11761 138 FPKPYQCDRCSQFFGDRM 155 (198)
Q Consensus 138 ~~~~~~C~~C~k~f~~~~ 155 (198)
......|.+|+.+|.+.-
T Consensus 44 ~iG~~sC~iC~esFqt~i 61 (109)
T KOG3214|consen 44 NIGKASCRICEESFQTTI 61 (109)
T ss_pred Ccceeeeeehhhhhccch
Confidence 345678999999998753
No 255
>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=20.41 E-value=34 Score=25.47 Aligned_cols=24 Identities=25% Similarity=0.544 Sum_probs=0.0
Q ss_pred CCCeeCCcch-hhhcChhHHHhhhh
Q psy11761 139 PKPYQCDRCS-QFFGDRMNLISHHC 162 (198)
Q Consensus 139 ~~~~~C~~C~-k~f~~~~~L~~H~~ 162 (198)
...|.|++|| .+|..+..+.+|..
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp -------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcC
Confidence 5789999997 56666778888863
No 256
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.39 E-value=61 Score=27.94 Aligned_cols=10 Identities=20% Similarity=0.551 Sum_probs=6.7
Q ss_pred ceecCccccc
Q psy11761 43 VHKCEYCHKV 52 (198)
Q Consensus 43 ~~~C~~C~~~ 52 (198)
+..|+.|+..
T Consensus 253 ~~~Cp~C~s~ 262 (505)
T TIGR00595 253 PKTCPQCGSE 262 (505)
T ss_pred CCCCCCCCCC
Confidence 5677777653
No 257
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=20.23 E-value=46 Score=25.64 Aligned_cols=31 Identities=13% Similarity=0.381 Sum_probs=11.4
Q ss_pred cccCcccch----hhcccCCCceecCccccccCCh
Q psy11761 26 YKCHQCQRL----IFLSANAGVHKCEYCHKVFDQQ 56 (198)
Q Consensus 26 ~~C~~C~~~----f~~~~~~~~~~C~~C~~~f~~~ 56 (198)
+-||.||.. |..-....-|.|..|++.|.-+
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELK 66 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELK 66 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT--EEEEE
T ss_pred CcCCCCCChhHhhccCCCccceeECCCCchHHhhh
Confidence 458999975 4444444568899998877544
No 258
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=20.19 E-value=48 Score=23.89 Aligned_cols=12 Identities=25% Similarity=0.332 Sum_probs=7.3
Q ss_pred ceecCccccccC
Q psy11761 43 VHKCEYCHKVFD 54 (198)
Q Consensus 43 ~~~C~~C~~~f~ 54 (198)
.+.|+.||....
T Consensus 28 sf~C~~CGyr~~ 39 (163)
T TIGR00340 28 TYICEKCGYRST 39 (163)
T ss_pred EEECCCCCCchh
Confidence 356777766543
No 259
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=20.16 E-value=34 Score=24.15 Aligned_cols=30 Identities=20% Similarity=0.552 Sum_probs=16.1
Q ss_pred cccCcccchhhcccC-CC------ceecCccccccCC
Q psy11761 26 YKCHQCQRLIFLSAN-AG------VHKCEYCHKVFDQ 55 (198)
Q Consensus 26 ~~C~~C~~~f~~~~~-~~------~~~C~~C~~~f~~ 55 (198)
..||.||..-....+ ++ .|.|..|.+-|..
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf~~ 142 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEPFEY 142 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcHhh
Confidence 567777754333221 11 4667777666643
No 260
>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=20.13 E-value=60 Score=16.10 Aligned_cols=7 Identities=43% Similarity=1.478 Sum_probs=2.7
Q ss_pred ccCccch
Q psy11761 72 YKCDTCE 78 (198)
Q Consensus 72 ~~C~~C~ 78 (198)
|.|..|+
T Consensus 28 f~C~~C~ 34 (39)
T smart00132 28 FKCSKCG 34 (39)
T ss_pred CCCcccC
Confidence 3344333
No 261
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=20.04 E-value=46 Score=19.31 Aligned_cols=36 Identities=22% Similarity=0.539 Sum_probs=17.2
Q ss_pred cCccchhcccCch-hHHHhhhhcCCCCcccCCcCchh
Q psy11761 73 KCDTCEKSFTNSQ-NLNTHQLIHSGIRPFKCTTCDKS 108 (198)
Q Consensus 73 ~C~~C~~~f~~~~-~l~~H~~~h~~~k~~~C~~C~~~ 108 (198)
.|..|++...-.. ++..-.....+...|.|+.|...
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~R 40 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKER 40 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHH
Confidence 3555665544321 12222223345566777777644
No 262
>KOG3507|consensus
Probab=20.02 E-value=60 Score=19.01 Aligned_cols=9 Identities=33% Similarity=0.781 Sum_probs=4.6
Q ss_pred ceecCcccc
Q psy11761 43 VHKCEYCHK 51 (198)
Q Consensus 43 ~~~C~~C~~ 51 (198)
+..|.+||.
T Consensus 37 ~irCReCG~ 45 (62)
T KOG3507|consen 37 VIRCRECGY 45 (62)
T ss_pred cEehhhcch
Confidence 445555544
Done!