Query psy14694
Match_columns 102
No_of_seqs 113 out of 1848
Neff 11.4
Searched_HMMs 46136
Date Fri Aug 16 18:15:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14694.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14694hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 1.7E-32 3.8E-37 156.2 4.0 92 2-102 162-253 (279)
2 KOG2462|consensus 99.9 5.3E-28 1.1E-32 138.0 3.5 95 2-102 131-225 (279)
3 KOG3576|consensus 99.8 2.2E-21 4.7E-26 107.2 -0.4 92 2-100 118-220 (267)
4 KOG3623|consensus 99.8 2E-20 4.3E-25 118.8 -0.0 70 33-102 891-960 (1007)
5 KOG3623|consensus 99.7 6.1E-19 1.3E-23 112.2 1.0 78 1-85 894-971 (1007)
6 KOG3576|consensus 99.6 1.6E-17 3.4E-22 92.1 -0.8 70 33-102 114-183 (267)
7 KOG3608|consensus 99.5 7.7E-15 1.7E-19 87.4 2.5 91 1-101 237-330 (467)
8 PLN03086 PRLI-interacting fact 99.5 1.1E-13 2.4E-18 87.6 6.0 88 2-102 454-551 (567)
9 KOG1074|consensus 99.4 9.2E-14 2E-18 90.1 2.0 67 35-101 604-677 (958)
10 KOG3608|consensus 99.4 8.3E-14 1.8E-18 83.1 0.3 67 34-102 235-302 (467)
11 PHA02768 hypothetical protein; 99.3 5.1E-13 1.1E-17 59.9 1.7 44 36-81 5-48 (55)
12 PF13465 zf-H2C2_2: Zinc-finge 99.3 5.2E-13 1.1E-17 51.8 0.5 24 79-102 1-24 (26)
13 PHA00733 hypothetical protein 99.3 3.3E-12 7.2E-17 67.6 3.7 54 33-88 70-123 (128)
14 PHA02768 hypothetical protein; 99.3 1.3E-12 2.8E-17 58.6 1.7 37 64-102 5-41 (55)
15 KOG1074|consensus 99.3 1.6E-12 3.4E-17 84.5 2.7 83 1-90 605-694 (958)
16 PHA00733 hypothetical protein 99.2 4.9E-12 1.1E-16 67.0 2.0 68 33-102 37-109 (128)
17 PF13465 zf-H2C2_2: Zinc-finge 99.1 5E-11 1.1E-15 46.2 1.5 25 51-75 1-25 (26)
18 PLN03086 PRLI-interacting fact 99.0 1.5E-09 3.2E-14 69.4 6.4 93 3-102 409-514 (567)
19 PHA00616 hypothetical protein 99.0 1.1E-10 2.4E-15 50.1 0.6 34 64-97 1-34 (44)
20 KOG3993|consensus 98.7 1.1E-09 2.3E-14 67.2 -0.8 81 2-89 268-381 (500)
21 PHA00732 hypothetical protein 98.7 8.7E-09 1.9E-13 50.2 2.2 47 36-88 1-48 (79)
22 PHA00616 hypothetical protein 98.6 3.7E-08 8.1E-13 42.3 1.9 33 1-40 1-33 (44)
23 PHA00732 hypothetical protein 98.5 1.2E-07 2.6E-12 46.2 2.9 47 1-60 1-48 (79)
24 PF00096 zf-C2H2: Zinc finger, 98.2 2.9E-07 6.3E-12 34.3 0.3 23 65-87 1-23 (23)
25 PF05605 zf-Di19: Drought indu 98.2 6.6E-06 1.4E-10 37.3 4.5 49 2-58 3-51 (54)
26 KOG3993|consensus 98.1 2.7E-07 5.8E-12 57.0 -1.6 51 37-87 268-318 (500)
27 PF00096 zf-C2H2: Zinc finger, 98.1 2.9E-06 6.3E-11 31.5 1.7 22 2-24 1-22 (23)
28 PF13912 zf-C2H2_6: C2H2-type 98.1 1.4E-06 3.1E-11 33.7 0.8 25 64-88 1-25 (27)
29 PRK04860 hypothetical protein; 98.1 1.9E-06 4.1E-11 47.4 1.5 35 64-102 119-153 (160)
30 PF05605 zf-Di19: Drought indu 98.0 9.5E-06 2.1E-10 36.7 2.9 50 36-88 2-53 (54)
31 PF13912 zf-C2H2_6: C2H2-type 98.0 4.2E-06 9.2E-11 32.3 1.3 25 1-26 1-25 (27)
32 PF13894 zf-C2H2_4: C2H2-type 97.9 4.2E-06 9.1E-11 31.2 0.9 23 65-87 1-23 (24)
33 PF12756 zf-C2H2_2: C2H2 type 97.8 1.3E-05 2.8E-10 40.5 1.4 73 3-87 1-73 (100)
34 PF13894 zf-C2H2_4: C2H2-type 97.7 3.8E-05 8.1E-10 28.4 2.1 23 2-25 1-23 (24)
35 PF09237 GAGA: GAGA factor; I 97.7 2.5E-05 5.4E-10 34.4 1.4 32 61-92 21-52 (54)
36 COG5189 SFP1 Putative transcri 97.7 2.6E-05 5.6E-10 47.0 1.7 40 62-101 347-407 (423)
37 smart00355 ZnF_C2H2 zinc finge 97.6 4.1E-05 8.8E-10 28.8 1.6 24 65-88 1-24 (26)
38 PRK04860 hypothetical protein; 97.5 9.2E-05 2E-09 40.9 2.4 39 36-78 119-157 (160)
39 smart00355 ZnF_C2H2 zinc finge 97.3 0.00035 7.6E-09 26.1 2.4 23 2-25 1-23 (26)
40 PF09237 GAGA: GAGA factor; I 97.1 0.00031 6.6E-09 31.1 1.3 32 33-64 21-52 (54)
41 COG5189 SFP1 Putative transcri 97.1 0.00038 8.3E-09 42.2 1.9 53 33-85 346-419 (423)
42 PF12171 zf-C2H2_jaz: Zinc-fin 97.0 0.00044 9.5E-09 26.6 1.3 22 65-86 2-23 (27)
43 PF12874 zf-met: Zinc-finger o 97.0 0.0002 4.4E-09 26.9 0.3 22 65-86 1-22 (25)
44 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00023 5E-09 26.5 0.3 23 65-88 1-23 (24)
45 cd00350 rubredoxin_like Rubred 96.7 0.001 2.3E-08 26.9 1.3 9 91-99 16-24 (33)
46 PF12874 zf-met: Zinc-finger o 96.7 0.0012 2.7E-08 24.7 1.4 23 2-25 1-23 (25)
47 COG5048 FOG: Zn-finger [Genera 96.6 0.0016 3.5E-08 40.7 2.0 62 35-96 288-355 (467)
48 PF12756 zf-C2H2_2: C2H2 type 96.1 0.0016 3.4E-08 32.8 0.0 59 38-102 1-60 (100)
49 COG2888 Predicted Zn-ribbon RN 95.9 0.0049 1.1E-07 28.2 1.2 32 64-100 27-58 (61)
50 PF13913 zf-C2HC_2: zinc-finge 95.8 0.0061 1.3E-07 23.0 1.2 21 65-86 3-23 (25)
51 PF09986 DUF2225: Uncharacteri 95.5 0.0067 1.4E-07 35.3 1.2 10 93-102 49-58 (214)
52 smart00451 ZnF_U1 U1-like zinc 95.5 0.014 3E-07 23.6 1.8 23 1-24 3-25 (35)
53 KOG2893|consensus 95.3 0.0071 1.5E-07 35.6 0.8 42 42-87 16-58 (341)
54 cd00729 rubredoxin_SM Rubredox 95.2 0.013 2.8E-07 23.8 1.2 8 92-99 18-25 (34)
55 TIGR00622 ssl1 transcription f 94.8 0.12 2.6E-06 27.0 4.3 26 63-88 80-105 (112)
56 PRK14890 putative Zn-ribbon RN 94.8 0.019 4.1E-07 26.3 1.2 32 64-100 25-56 (59)
57 COG1592 Rubrerythrin [Energy p 94.6 0.021 4.6E-07 31.9 1.4 23 64-99 134-156 (166)
58 PF09723 Zn-ribbon_8: Zinc rib 94.6 0.015 3.2E-07 24.8 0.6 29 65-100 6-34 (42)
59 PRK00464 nrdR transcriptional 94.3 0.022 4.7E-07 31.5 1.0 12 65-76 29-40 (154)
60 PF13719 zinc_ribbon_5: zinc-r 94.3 0.035 7.6E-07 23.0 1.4 11 64-74 25-35 (37)
61 TIGR02098 MJ0042_CXXC MJ0042 f 94.2 0.029 6.4E-07 23.2 1.1 10 92-101 25-34 (38)
62 smart00834 CxxC_CXXC_SSSS Puta 94.2 0.019 4.2E-07 24.0 0.5 11 65-75 6-16 (41)
63 TIGR02605 CxxC_CxxC_SSSS putat 94.1 0.02 4.3E-07 25.5 0.5 11 37-47 6-16 (52)
64 KOG2186|consensus 93.5 0.035 7.6E-07 32.9 0.9 49 36-87 3-51 (276)
65 PF13717 zinc_ribbon_4: zinc-r 93.4 0.068 1.5E-06 22.0 1.5 9 92-100 25-33 (36)
66 PHA00626 hypothetical protein 93.4 0.041 8.9E-07 24.9 0.9 15 63-77 22-36 (59)
67 PRK00398 rpoP DNA-directed RNA 93.1 0.034 7.3E-07 24.1 0.4 12 36-47 3-14 (46)
68 COG5048 FOG: Zn-finger [Genera 92.9 0.035 7.6E-07 34.8 0.4 61 1-68 289-355 (467)
69 PF07754 DUF1610: Domain of un 92.7 0.044 9.6E-07 20.5 0.3 9 92-100 16-24 (24)
70 COG3357 Predicted transcriptio 92.6 0.082 1.8E-06 26.4 1.3 27 63-99 57-83 (97)
71 smart00659 RPOLCX RNA polymera 92.6 0.089 1.9E-06 22.7 1.3 26 37-73 3-28 (44)
72 TIGR00373 conserved hypothetic 92.2 0.12 2.6E-06 28.7 1.9 19 34-52 107-125 (158)
73 PF13240 zinc_ribbon_2: zinc-r 91.8 0.11 2.5E-06 19.1 1.0 7 95-101 16-22 (23)
74 smart00531 TFIIE Transcription 91.7 0.18 3.9E-06 27.6 2.1 34 63-100 98-131 (147)
75 PRK06266 transcription initiat 91.1 0.18 3.8E-06 28.6 1.8 13 65-77 118-130 (178)
76 PF14353 CpXC: CpXC protein 91.0 0.094 2E-06 27.9 0.6 10 38-47 3-12 (128)
77 KOG2186|consensus 90.8 0.16 3.5E-06 30.3 1.4 46 2-57 4-49 (276)
78 KOG2893|consensus 90.6 0.1 2.2E-06 30.9 0.5 41 4-55 13-53 (341)
79 COG1996 RPC10 DNA-directed RNA 90.1 0.14 3.1E-06 22.6 0.7 12 35-46 5-16 (49)
80 PF13451 zf-trcl: Probable zin 89.7 0.13 2.9E-06 22.7 0.4 15 63-77 3-17 (49)
81 PF09538 FYDLN_acid: Protein o 89.6 0.35 7.6E-06 25.2 2.0 17 33-49 23-39 (108)
82 COG1997 RPL43A Ribosomal prote 88.4 0.35 7.7E-06 24.0 1.4 33 35-77 34-66 (89)
83 PRK03824 hypA hydrogenase nick 87.5 0.32 7E-06 26.3 1.0 12 65-76 71-82 (135)
84 COG4049 Uncharacterized protei 87.5 0.17 3.7E-06 22.9 -0.0 26 33-58 14-39 (65)
85 KOG1146|consensus 87.4 0.28 6E-06 35.8 0.9 24 63-86 517-540 (1406)
86 PF05443 ROS_MUCR: ROS/MUCR tr 84.9 0.48 1E-05 25.6 0.9 27 63-92 71-97 (132)
87 PF10571 UPF0547: Uncharacteri 84.4 0.48 1E-05 18.0 0.6 9 94-102 16-24 (26)
88 KOG1146|consensus 84.3 0.37 8.1E-06 35.2 0.4 27 60-86 461-487 (1406)
89 PF03604 DNA_RNApol_7kD: DNA d 84.2 0.9 2E-05 18.2 1.3 7 65-71 18-24 (32)
90 PF12760 Zn_Tnp_IS1595: Transp 83.7 0.61 1.3E-05 20.2 0.8 11 90-100 35-45 (46)
91 smart00614 ZnF_BED BED zinc fi 83.6 0.84 1.8E-05 20.1 1.3 21 65-85 19-44 (50)
92 COG1773 Rubredoxin [Energy pro 83.0 0.98 2.1E-05 20.5 1.3 13 36-48 3-15 (55)
93 PF02892 zf-BED: BED zinc fing 82.8 0.65 1.4E-05 19.7 0.7 24 62-85 14-41 (45)
94 PF08274 PhnA_Zn_Ribbon: PhnA 82.8 0.51 1.1E-05 18.6 0.3 8 92-99 19-26 (30)
95 COG5236 Uncharacterized conser 82.3 1.3 2.8E-05 28.0 2.1 51 46-97 198-252 (493)
96 TIGR02300 FYDLN_acid conserved 81.9 1.4 3.1E-05 23.6 1.9 17 33-49 23-39 (129)
97 PF01780 Ribosomal_L37ae: Ribo 81.6 0.31 6.7E-06 24.5 -0.6 32 35-76 34-65 (90)
98 COG3091 SprT Zn-dependent meta 81.3 0.75 1.6E-05 25.4 0.7 33 63-100 116-148 (156)
99 TIGR00100 hypA hydrogenase nic 81.1 0.81 1.8E-05 24.1 0.8 12 65-76 71-82 (115)
100 PRK09678 DNA-binding transcrip 80.8 0.71 1.5E-05 22.2 0.5 41 37-79 2-44 (72)
101 smart00440 ZnF_C2C2 C2C2 Zinc 80.5 0.82 1.8E-05 19.2 0.6 9 65-73 29-37 (40)
102 PF11789 zf-Nse: Zinc-finger o 80.4 0.64 1.4E-05 21.2 0.3 33 62-98 22-54 (57)
103 COG0068 HypF Hydrogenase matur 80.0 0.39 8.4E-06 33.0 -0.7 56 38-100 125-181 (750)
104 PRK12380 hydrogenase nickel in 79.8 0.99 2.1E-05 23.7 0.9 12 65-76 71-82 (113)
105 PF09845 DUF2072: Zn-ribbon co 79.0 1.2 2.6E-05 24.0 1.1 15 64-78 1-15 (131)
106 PF14311 DUF4379: Domain of un 78.9 1.6 3.5E-05 19.6 1.3 15 65-79 29-43 (55)
107 COG1198 PriA Primosomal protei 78.7 1.3 2.8E-05 30.8 1.3 22 79-100 462-483 (730)
108 PRK03564 formate dehydrogenase 78.4 1.7 3.7E-05 27.1 1.7 10 90-99 250-259 (309)
109 PRK03681 hypA hydrogenase nick 76.0 1.2 2.7E-05 23.3 0.6 11 65-75 71-81 (114)
110 PRK00564 hypA hydrogenase nick 75.6 1.5 3.2E-05 23.2 0.8 12 65-76 72-83 (117)
111 smart00734 ZnF_Rad18 Rad18-lik 75.2 2.4 5.1E-05 16.0 1.1 19 66-85 3-21 (26)
112 PF04810 zf-Sec23_Sec24: Sec23 75.0 1.6 3.5E-05 18.3 0.7 9 63-71 23-31 (40)
113 PF03811 Zn_Tnp_IS1: InsA N-te 74.8 1.8 3.8E-05 17.8 0.8 31 65-99 6-36 (36)
114 PF01428 zf-AN1: AN1-like Zinc 74.8 0.68 1.5E-05 19.7 -0.5 11 92-102 13-23 (43)
115 PF12907 zf-met2: Zinc-binding 74.2 0.51 1.1E-05 20.0 -0.9 26 65-90 2-31 (40)
116 TIGR01206 lysW lysine biosynth 73.9 2 4.4E-05 19.4 0.9 9 38-46 4-12 (54)
117 PF07282 OrfB_Zn_ribbon: Putat 73.8 1.9 4.1E-05 20.2 0.9 14 62-75 44-57 (69)
118 smart00154 ZnF_AN1 AN1-like Zi 73.6 1.6 3.4E-05 18.3 0.5 11 92-102 12-22 (39)
119 TIGR01562 FdhE formate dehydro 73.5 3.6 7.9E-05 25.6 2.2 10 90-99 250-259 (305)
120 COG5432 RAD18 RING-finger-cont 73.4 1.5 3.2E-05 27.1 0.5 26 70-101 43-68 (391)
121 PF12013 DUF3505: Protein of u 73.1 2.2 4.8E-05 22.0 1.1 26 64-89 80-109 (109)
122 KOG3408|consensus 72.4 1.5 3.4E-05 23.3 0.4 26 61-86 54-79 (129)
123 PF02176 zf-TRAF: TRAF-type zi 72.4 2.1 4.6E-05 19.3 0.9 41 35-75 8-53 (60)
124 PF15269 zf-C2H2_7: Zinc-finge 72.2 2.1 4.5E-05 18.5 0.7 21 65-85 21-41 (54)
125 PF14787 zf-CCHC_5: GAG-polypr 72.1 1.9 4E-05 17.8 0.5 9 94-102 4-12 (36)
126 PF01155 HypA: Hydrogenase exp 71.7 1.3 2.7E-05 23.3 -0.0 13 65-77 71-83 (113)
127 smart00132 LIM Zinc-binding do 71.6 2.6 5.6E-05 16.7 1.0 8 93-100 28-35 (39)
128 COG1675 TFA1 Transcription ini 71.2 5.4 0.00012 22.8 2.4 7 65-71 133-139 (176)
129 KOG0978|consensus 70.4 1.7 3.7E-05 30.0 0.4 16 87-102 673-688 (698)
130 PRK14714 DNA polymerase II lar 70.2 7.8 0.00017 29.0 3.4 12 64-75 692-703 (1337)
131 COG3677 Transposase and inacti 70.2 2.2 4.8E-05 23.0 0.7 15 88-102 49-63 (129)
132 PF01096 TFIIS_C: Transcriptio 69.8 0.63 1.4E-05 19.4 -1.1 9 93-101 29-37 (39)
133 PF04959 ARS2: Arsenite-resist 69.5 0.79 1.7E-05 26.9 -1.1 27 64-90 77-103 (214)
134 PTZ00255 60S ribosomal protein 69.5 2.1 4.5E-05 21.6 0.5 34 34-77 34-67 (90)
135 COG1571 Predicted DNA-binding 68.7 3.7 8.1E-05 26.7 1.6 14 64-77 367-380 (421)
136 PF04423 Rad50_zn_hook: Rad50 68.4 1.3 2.8E-05 19.8 -0.3 9 94-102 22-30 (54)
137 COG3364 Zn-ribbon containing p 67.9 3.5 7.6E-05 21.3 1.1 12 36-47 2-13 (112)
138 cd00065 FYVE FYVE domain; Zinc 66.7 5.3 0.00011 17.7 1.5 28 38-77 4-31 (57)
139 PF07295 DUF1451: Protein of u 66.5 3.2 6.9E-05 22.9 0.9 8 65-72 113-120 (146)
140 PF02891 zf-MIZ: MIZ/SP-RING z 66.5 1.2 2.5E-05 19.8 -0.7 8 93-100 42-49 (50)
141 PF11672 DUF3268: Protein of u 65.4 5.3 0.00011 20.7 1.5 7 65-71 32-38 (102)
142 PF13878 zf-C2H2_3: zinc-finge 65.1 10 0.00022 15.9 2.4 23 3-25 15-38 (41)
143 PF15135 UPF0515: Uncharacteri 64.9 9.8 0.00021 23.1 2.7 57 33-102 109-165 (278)
144 PF13824 zf-Mss51: Zinc-finger 64.1 4.3 9.2E-05 18.5 0.9 13 89-101 11-23 (55)
145 PF10263 SprT-like: SprT-like 63.1 2.5 5.5E-05 23.1 0.1 30 64-101 123-152 (157)
146 PF13453 zf-TFIIB: Transcripti 63.1 3.4 7.5E-05 17.3 0.5 19 63-81 18-36 (41)
147 COG1655 Uncharacterized protei 62.9 2.6 5.6E-05 25.2 0.1 26 33-58 16-41 (267)
148 PRK00762 hypA hydrogenase nick 62.1 4.2 9.1E-05 21.7 0.8 10 65-75 71-80 (124)
149 PF08209 Sgf11: Sgf11 (transcr 61.0 2.3 5E-05 17.1 -0.2 10 92-101 4-13 (33)
150 PF07975 C1_4: TFIIH C1-like d 60.9 4.3 9.3E-05 18.2 0.6 25 63-87 20-44 (51)
151 TIGR03831 YgiT_finger YgiT-typ 60.8 3.2 7E-05 17.4 0.2 13 89-101 29-41 (46)
152 PLN02294 cytochrome c oxidase 60.6 3.8 8.1E-05 23.3 0.5 17 85-102 135-151 (174)
153 PRK04023 DNA polymerase II lar 60.6 10 0.00022 27.8 2.5 9 92-100 663-671 (1121)
154 PF14205 Cys_rich_KTR: Cystein 60.5 4.9 0.00011 18.2 0.7 9 64-72 28-36 (55)
155 PF08790 zf-LYAR: LYAR-type C2 60.1 3.6 7.9E-05 15.9 0.3 9 66-74 2-10 (28)
156 PRK05978 hypothetical protein; 60.0 6.1 0.00013 21.9 1.2 10 66-75 54-63 (148)
157 PF14634 zf-RING_5: zinc-RING 59.6 9.8 0.00021 16.0 1.6 11 90-100 34-44 (44)
158 PF02591 DUF164: Putative zinc 59.6 5.2 0.00011 18.0 0.8 10 90-99 44-53 (56)
159 PF01927 Mut7-C: Mut7-C RNAse 59.5 5.3 0.00011 21.9 0.9 13 90-102 122-134 (147)
160 smart00064 FYVE Protein presen 57.8 8.2 0.00018 17.9 1.3 28 37-76 11-38 (68)
161 smart00661 RPOL9 RNA polymeras 57.5 9.8 0.00021 16.5 1.5 14 64-77 20-33 (52)
162 COG4957 Predicted transcriptio 57.4 5 0.00011 21.9 0.6 25 65-92 77-101 (148)
163 PF14446 Prok-RING_1: Prokaryo 57.3 7.7 0.00017 17.6 1.1 11 63-73 20-30 (54)
164 COG4896 Uncharacterized protei 56.9 4.7 0.0001 18.7 0.4 51 38-92 4-55 (68)
165 KOG2907|consensus 56.9 7.6 0.00017 20.5 1.2 36 65-102 75-112 (116)
166 PRK01343 zinc-binding protein; 56.6 8 0.00017 17.8 1.1 9 65-73 10-18 (57)
167 PF01363 FYVE: FYVE zinc finge 56.3 5.3 0.00012 18.6 0.6 28 36-75 9-36 (69)
168 smart00731 SprT SprT homologue 55.9 6.8 0.00015 21.4 1.0 31 64-101 112-142 (146)
169 COG1327 Predicted transcriptio 55.8 6.5 0.00014 21.9 0.9 13 64-76 28-40 (156)
170 COG4888 Uncharacterized Zn rib 55.6 2.3 5.1E-05 21.8 -0.8 38 34-75 20-57 (104)
171 KOG2593|consensus 55.4 12 0.00026 24.6 2.1 38 33-73 125-162 (436)
172 PF06397 Desulfoferrod_N: Desu 55.1 4.5 9.8E-05 16.7 0.2 10 91-100 5-14 (36)
173 TIGR00244 transcriptional regu 55.1 6.6 0.00014 21.8 0.8 14 64-77 28-41 (147)
174 KOG4173|consensus 54.6 1.5 3.3E-05 25.6 -1.7 19 3-22 108-126 (253)
175 PRK00432 30S ribosomal protein 54.4 8.3 0.00018 17.1 1.0 9 64-72 37-45 (50)
176 PF10013 DUF2256: Uncharacteri 54.2 5.9 0.00013 16.9 0.4 8 95-102 11-18 (42)
177 KOG4167|consensus 54.1 3.3 7.1E-05 29.0 -0.5 24 2-26 793-816 (907)
178 PHA02998 RNA polymerase subuni 53.8 5.8 0.00013 22.7 0.5 12 65-76 172-183 (195)
179 cd00924 Cyt_c_Oxidase_Vb Cytoc 53.7 5.5 0.00012 20.4 0.4 18 84-102 72-89 (97)
180 TIGR00595 priA primosomal prot 53.6 9.1 0.0002 25.6 1.4 21 80-100 241-261 (505)
181 COG1885 Uncharacterized protei 53.1 6.5 0.00014 20.4 0.6 9 93-101 50-58 (115)
182 COG0675 Transposase and inacti 52.2 7.7 0.00017 23.9 0.9 12 63-74 321-332 (364)
183 PRK05580 primosome assembly pr 52.1 11 0.00023 26.3 1.6 21 80-100 409-429 (679)
184 KOG3214|consensus 51.5 4.9 0.00011 20.6 0.0 13 65-77 48-60 (109)
185 PF09416 UPF1_Zn_bind: RNA hel 50.5 19 0.00041 20.2 2.1 43 3-45 16-69 (152)
186 PF14369 zf-RING_3: zinc-finge 50.2 6.3 0.00014 16.0 0.2 9 94-102 23-31 (35)
187 COG5216 Uncharacterized conser 49.6 12 0.00025 17.3 1.0 26 42-72 27-52 (67)
188 PRK14873 primosome assembly pr 49.5 8.6 0.00019 26.8 0.9 10 91-100 421-430 (665)
189 PRK08222 hydrogenase 4 subunit 49.4 9.5 0.00021 21.8 0.9 38 63-100 113-162 (181)
190 PF13248 zf-ribbon_3: zinc-rib 49.4 6.6 0.00014 14.6 0.2 6 95-100 19-24 (26)
191 PF09963 DUF2197: Uncharacteri 48.3 6.8 0.00015 17.9 0.2 36 37-72 3-39 (56)
192 COG1326 Uncharacterized archae 48.3 16 0.00034 21.4 1.6 36 35-76 5-42 (201)
193 PF00412 LIM: LIM domain; Int 47.7 7.9 0.00017 17.1 0.4 15 64-78 26-40 (58)
194 PRK14892 putative transcriptio 47.2 11 0.00024 19.4 0.9 11 65-75 43-53 (99)
195 PRK12387 formate hydrogenlyase 47.2 5.3 0.00012 22.7 -0.3 18 63-80 113-130 (180)
196 PF15616 TerY-C: TerY-C metal 47.1 9.8 0.00021 20.7 0.7 14 88-101 101-114 (131)
197 PF10276 zf-CHCC: Zinc-finger 47.0 5.2 0.00011 16.9 -0.3 11 92-102 29-39 (40)
198 KOG1729|consensus 46.9 12 0.00026 23.3 1.1 53 35-98 167-220 (288)
199 KOG2482|consensus 45.9 22 0.00048 22.8 2.1 29 2-31 196-224 (423)
200 PF10083 DUF2321: Uncharacteri 45.8 13 0.00029 20.8 1.1 16 63-78 67-82 (158)
201 KOG0782|consensus 45.5 7.7 0.00017 26.6 0.2 24 79-102 240-263 (1004)
202 PTZ00448 hypothetical protein; 45.1 21 0.00047 23.0 2.0 23 2-25 315-337 (373)
203 PF09297 zf-NADH-PPase: NADH p 45.1 12 0.00026 14.6 0.7 12 89-100 18-29 (32)
204 PF05129 Elf1: Transcription e 44.9 4.3 9.4E-05 20.0 -0.8 39 34-76 20-58 (81)
205 PF08792 A2L_zn_ribbon: A2L zi 44.8 7.9 0.00017 15.5 0.1 9 93-101 22-30 (33)
206 KOG2785|consensus 44.2 39 0.00085 22.0 3.0 23 3-26 168-190 (390)
207 PRK05452 anaerobic nitric oxid 44.1 16 0.00034 24.4 1.4 16 62-77 423-438 (479)
208 KOG0717|consensus 43.8 11 0.00023 25.2 0.6 22 65-86 293-314 (508)
209 KOG1409|consensus 43.5 4.8 0.0001 25.6 -0.9 37 65-102 283-319 (404)
210 PF00301 Rubredoxin: Rubredoxi 43.5 9.9 0.00022 16.6 0.3 9 92-100 34-42 (47)
211 PF00130 C1_1: Phorbol esters/ 43.4 24 0.00053 15.3 1.6 8 64-71 28-35 (53)
212 KOG3002|consensus 43.3 34 0.00073 21.5 2.6 61 34-98 78-142 (299)
213 PRK04351 hypothetical protein; 43.2 12 0.00027 20.7 0.7 29 64-100 112-140 (149)
214 PRK14559 putative protein seri 42.8 32 0.00068 24.1 2.7 8 3-10 3-10 (645)
215 smart00109 C1 Protein kinase C 42.7 24 0.00053 14.7 1.6 7 65-71 28-34 (49)
216 PRK07591 threonine synthase; V 42.6 17 0.00036 23.8 1.3 27 36-75 18-44 (421)
217 PF15227 zf-C3HC4_4: zinc fing 42.5 21 0.00045 15.0 1.3 27 70-98 16-42 (42)
218 cd00730 rubredoxin Rubredoxin; 42.0 11 0.00024 16.7 0.4 9 92-100 34-42 (50)
219 COG2331 Uncharacterized protei 41.8 8.1 0.00018 18.9 -0.1 10 2-11 13-22 (82)
220 PRK12496 hypothetical protein; 41.3 24 0.00052 19.9 1.7 12 37-48 128-139 (164)
221 PF14803 Nudix_N_2: Nudix N-te 40.8 12 0.00025 15.2 0.3 7 93-99 23-29 (34)
222 KOG2923|consensus 40.8 34 0.00075 16.1 1.9 25 42-71 27-51 (67)
223 cd00974 DSRD Desulforedoxin (D 40.7 11 0.00025 14.9 0.3 9 92-100 4-12 (34)
224 KOG2231|consensus 40.6 49 0.0011 23.4 3.2 19 39-57 185-203 (669)
225 PF01286 XPA_N: XPA protein N- 40.3 8.1 0.00018 15.7 -0.2 14 65-78 4-17 (34)
226 PF07649 C1_3: C1-like domain; 39.2 11 0.00024 14.4 0.1 10 91-100 14-23 (30)
227 TIGR00319 desulf_FeS4 desulfof 39.1 12 0.00027 14.8 0.3 9 92-100 7-15 (34)
228 PTZ00043 cytochrome c oxidase 38.6 14 0.0003 22.2 0.5 15 88-102 177-191 (268)
229 smart00647 IBR In Between Ring 37.9 20 0.00043 16.1 0.9 17 61-77 37-53 (64)
230 PF01215 COX5B: Cytochrome c o 37.6 9.4 0.0002 20.9 -0.2 18 84-102 105-122 (136)
231 PRK08270 anaerobic ribonucleos 37.5 23 0.0005 24.8 1.5 9 92-100 639-647 (656)
232 KOG2636|consensus 37.5 24 0.00052 23.5 1.4 27 57-83 394-421 (497)
233 PHA02942 putative transposase; 37.4 22 0.00048 23.0 1.3 11 90-100 340-350 (383)
234 PRK10220 hypothetical protein; 36.9 44 0.00096 17.6 2.1 18 33-50 17-34 (111)
235 PF10071 DUF2310: Zn-ribbon-co 36.8 23 0.0005 21.7 1.2 28 65-99 221-248 (258)
236 cd04476 RPA1_DBD_C RPA1_DBD_C: 36.4 18 0.00039 20.1 0.8 12 63-74 50-61 (166)
237 PF04438 zf-HIT: HIT zinc fing 36.3 9.1 0.0002 14.9 -0.3 9 92-100 13-21 (30)
238 PF14149 YhfH: YhfH-like prote 36.1 5.6 0.00012 16.5 -1.0 7 94-100 15-21 (37)
239 COG4306 Uncharacterized protei 35.9 39 0.00084 18.3 1.8 16 62-77 66-81 (160)
240 TIGR00627 tfb4 transcription f 35.5 33 0.00071 21.3 1.7 25 64-102 255-279 (279)
241 PF05741 zf-nanos: Nanos RNA b 35.3 15 0.00032 16.8 0.2 9 91-99 32-40 (55)
242 PF09082 DUF1922: Domain of un 35.2 13 0.00029 17.7 0.1 14 60-74 16-29 (68)
243 TIGR00686 phnA alkylphosphonat 34.8 36 0.00077 17.9 1.6 17 34-50 17-33 (109)
244 PF11023 DUF2614: Protein of u 34.7 17 0.00037 19.2 0.4 12 89-100 66-77 (114)
245 PF04032 Rpr2: RNAse P Rpr2/Rp 34.5 16 0.00035 17.7 0.3 37 63-99 45-84 (85)
246 TIGR00280 L37a ribosomal prote 34.4 13 0.00029 18.8 0.0 10 92-101 53-62 (91)
247 COG4530 Uncharacterized protei 34.1 20 0.00044 18.9 0.6 11 92-102 26-36 (129)
248 COG4391 Uncharacterized protei 33.6 16 0.00035 17.0 0.2 8 93-100 49-56 (62)
249 PRK11032 hypothetical protein; 33.6 24 0.00051 20.0 0.9 7 65-71 125-131 (160)
250 PF04780 DUF629: Protein of un 33.6 41 0.0009 22.6 2.1 24 2-26 58-81 (466)
251 CHL00174 accD acetyl-CoA carbo 33.5 25 0.00055 22.0 1.1 13 35-47 56-68 (296)
252 KOG2461|consensus 33.4 70 0.0015 21.1 3.0 57 44-100 339-395 (396)
253 PF02146 SIR2: Sir2 family; I 33.3 25 0.00054 19.8 1.0 12 65-76 106-117 (178)
254 KOG3507|consensus 33.1 24 0.00053 16.3 0.7 13 63-75 36-48 (62)
255 PRK03976 rpl37ae 50S ribosomal 32.6 15 0.00032 18.6 0.0 10 92-101 54-63 (90)
256 PF07503 zf-HYPF: HypF finger; 32.5 3.4 7.3E-05 16.9 -1.9 7 66-72 23-29 (35)
257 PF05876 Terminase_GpA: Phage 32.0 31 0.00068 23.6 1.4 8 93-100 230-237 (557)
258 PF00628 PHD: PHD-finger; Int 31.8 31 0.00068 14.7 1.0 38 62-99 12-49 (51)
259 PF14952 zf-tcix: Putative tre 31.5 20 0.00042 15.5 0.3 6 94-99 13-18 (44)
260 cd01675 RNR_III Class III ribo 31.5 37 0.0008 23.3 1.7 9 92-100 532-540 (555)
261 PLN03238 probable histone acet 31.5 39 0.00084 21.1 1.6 26 62-87 46-71 (290)
262 COG1631 RPL42A Ribosomal prote 31.3 17 0.00038 18.4 0.1 10 92-101 68-77 (94)
263 PF04216 FdhE: Protein involve 30.9 6.9 0.00015 24.0 -1.6 12 88-99 234-245 (290)
264 TIGR00515 accD acetyl-CoA carb 30.7 29 0.00064 21.6 1.0 11 37-47 46-56 (285)
265 COG5112 UFD2 U1-like Zn-finger 30.3 12 0.00027 19.5 -0.5 24 63-86 54-77 (126)
266 KOG0696|consensus 30.1 23 0.00051 23.7 0.6 36 64-99 92-128 (683)
267 TIGR02487 NrdD anaerobic ribon 30.1 37 0.00081 23.4 1.5 8 93-100 539-546 (579)
268 TIGR00310 ZPR1_znf ZPR1 zinc f 29.7 19 0.00042 20.9 0.2 13 64-76 30-42 (192)
269 cd01410 SIRT7 SIRT7: Eukaryoti 29.5 68 0.0015 18.8 2.4 12 64-75 95-106 (206)
270 PF04606 Ogr_Delta: Ogr/Delta- 29.2 12 0.00026 16.2 -0.6 11 65-75 26-38 (47)
271 PF12230 PRP21_like_P: Pre-mRN 29.1 18 0.0004 21.4 0.0 30 63-93 167-196 (229)
272 PRK14704 anaerobic ribonucleos 29.0 38 0.00083 23.6 1.4 7 93-99 573-579 (618)
273 cd01413 SIR2_Af2 SIR2_Af2: Arc 28.6 57 0.0012 19.3 2.0 15 63-77 112-126 (222)
274 KOG4602|consensus 28.5 30 0.00065 21.3 0.8 38 63-100 232-276 (318)
275 PF10609 ParA: ParA/MinD ATPas 28.5 21 0.00046 17.6 0.2 8 93-100 66-73 (81)
276 COG1439 Predicted nucleic acid 28.4 30 0.00064 19.9 0.7 11 65-75 140-150 (177)
277 PF10058 DUF2296: Predicted in 28.2 24 0.00051 15.9 0.3 8 92-99 44-51 (54)
278 PRK00481 NAD-dependent deacety 28.2 55 0.0012 19.6 1.9 15 63-77 121-135 (242)
279 COG5533 UBP5 Ubiquitin C-termi 28.0 27 0.00059 22.2 0.6 13 88-100 280-292 (415)
280 PF06220 zf-U1: U1 zinc finger 27.7 47 0.001 13.7 1.1 11 2-12 4-14 (38)
281 KOG2071|consensus 27.6 41 0.0009 23.2 1.4 26 62-87 416-441 (579)
282 COG4338 Uncharacterized protei 27.4 22 0.00047 15.7 0.1 7 95-101 15-21 (54)
283 PF12677 DUF3797: Domain of un 27.2 26 0.00056 15.5 0.3 6 94-99 15-20 (49)
284 PF03966 Trm112p: Trm112p-like 27.0 20 0.00044 16.8 -0.0 16 87-102 48-63 (68)
285 PRK05654 acetyl-CoA carboxylas 26.8 35 0.00075 21.3 0.9 11 37-47 47-57 (292)
286 TIGR02159 PA_CoA_Oxy4 phenylac 26.8 14 0.0003 20.5 -0.7 35 65-102 106-140 (146)
287 PF10537 WAC_Acf1_DNA_bd: ATP- 26.3 1.1E+02 0.0023 15.9 2.8 36 2-45 4-39 (102)
288 PF00935 Ribosomal_L44: Riboso 26.2 24 0.00051 17.3 0.1 10 92-101 53-62 (77)
289 PRK07111 anaerobic ribonucleos 25.5 48 0.001 23.7 1.4 7 93-99 694-700 (735)
290 PF06524 NOA36: NOA36 protein; 25.4 30 0.00064 21.4 0.4 11 63-73 208-218 (314)
291 TIGR00143 hypF [NiFe] hydrogen 25.2 12 0.00025 26.4 -1.4 55 38-99 92-147 (711)
292 KOG4118|consensus 24.9 33 0.00071 16.3 0.4 23 64-86 38-60 (74)
293 PF10367 Vps39_2: Vacuolar sor 24.5 34 0.00074 17.2 0.5 7 95-101 81-87 (109)
294 PF05495 zf-CHY: CHY zinc fing 24.4 8.3 0.00018 18.4 -1.7 30 64-101 41-70 (71)
295 TIGR02827 RNR_anaer_Bdell anae 24.2 54 0.0012 22.8 1.5 8 92-99 546-553 (586)
296 PF02748 PyrI_C: Aspartate car 23.6 25 0.00055 15.7 -0.1 13 88-100 31-43 (52)
297 PF02318 FYVE_2: FYVE-type zin 23.4 31 0.00068 18.2 0.3 49 36-100 54-102 (118)
298 COG1594 RPB9 DNA-directed RNA 23.4 33 0.00072 18.1 0.3 9 93-101 101-109 (113)
299 PRK06921 hypothetical protein; 23.1 43 0.00092 20.5 0.8 11 90-100 30-40 (266)
300 PF11931 DUF3449: Domain of un 23.0 28 0.0006 20.4 0.0 25 59-83 96-121 (196)
301 COG0846 SIR2 NAD-dependent pro 23.0 52 0.0011 20.1 1.1 34 63-100 121-154 (250)
302 PRK12722 transcriptional activ 22.9 71 0.0015 18.7 1.6 28 64-99 134-161 (187)
303 PF02150 RNA_POL_M_15KD: RNA p 22.8 26 0.00056 14.1 -0.1 7 66-72 22-28 (35)
304 COG2995 PqiA Uncharacterized p 22.6 63 0.0014 21.3 1.4 33 36-76 18-50 (418)
305 KOG4727|consensus 22.4 37 0.00079 19.5 0.4 21 64-84 75-95 (193)
306 smart00249 PHD PHD zinc finger 22.3 47 0.001 13.3 0.7 12 90-101 12-23 (47)
307 TIGR03830 CxxCG_CxxCG_HTH puta 22.3 1E+02 0.0022 16.0 2.1 19 2-21 32-50 (127)
308 PF06170 DUF983: Protein of un 22.1 42 0.00091 16.8 0.5 10 3-12 10-19 (86)
309 TIGR03829 YokU_near_AblA uncha 21.9 83 0.0018 16.0 1.5 16 2-18 36-51 (89)
310 COG1579 Zn-ribbon protein, pos 21.8 67 0.0014 19.6 1.4 11 89-99 218-228 (239)
311 PRK03922 hypothetical protein; 21.8 42 0.00091 17.7 0.5 7 95-101 52-58 (113)
312 PRK08271 anaerobic ribonucleos 21.5 72 0.0016 22.4 1.6 8 92-99 580-587 (623)
313 PF08271 TF_Zn_Ribbon: TFIIB z 21.5 41 0.00088 14.1 0.4 8 65-72 20-27 (43)
314 KOG1280|consensus 21.3 95 0.0021 20.2 2.0 23 64-86 79-101 (381)
315 cd02335 ZZ_ADA2 Zinc finger, Z 21.3 94 0.002 13.4 1.9 8 35-42 14-21 (49)
316 PRK02935 hypothetical protein; 21.3 44 0.00095 17.5 0.5 13 88-100 66-78 (110)
317 PTZ00303 phosphatidylinositol 21.2 75 0.0016 23.3 1.7 32 37-75 461-492 (1374)
318 PF01485 IBR: IBR domain; Int 21.1 38 0.00083 15.1 0.3 9 93-101 41-49 (64)
319 PRK07218 replication factor A; 21.0 61 0.0013 21.5 1.2 10 65-74 298-307 (423)
320 PLN00104 MYST -like histone ac 21.0 52 0.0011 22.0 0.9 26 62-87 196-221 (450)
321 PRK12860 transcriptional activ 20.9 80 0.0017 18.5 1.5 29 63-99 133-161 (189)
322 PF09855 DUF2082: Nucleic-acid 20.8 52 0.0011 15.5 0.7 9 65-73 1-9 (64)
323 PTZ00064 histone acetyltransfe 20.6 61 0.0013 22.2 1.1 26 62-87 278-303 (552)
324 PF13696 zf-CCHC_2: Zinc knuck 20.5 42 0.00092 13.4 0.3 8 93-100 9-16 (32)
325 PRK05767 rpl44e 50S ribosomal 20.5 36 0.00078 17.4 0.1 9 93-101 68-76 (92)
326 PF14690 zf-ISL3: zinc-finger 20.4 54 0.0012 13.7 0.7 6 3-8 4-9 (47)
327 PRK08579 anaerobic ribonucleos 20.3 76 0.0016 22.3 1.6 8 92-99 582-589 (625)
328 KOG1088|consensus 20.2 54 0.0012 17.6 0.7 22 58-79 92-113 (124)
329 KOG1008|consensus 20.1 39 0.00084 23.9 0.2 38 65-102 737-776 (783)
No 1
>KOG2462|consensus
Probab=99.97 E-value=1.7e-32 Score=156.21 Aligned_cols=92 Identities=18% Similarity=0.361 Sum_probs=86.3
Q ss_pred ccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhh
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLM 81 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~ 81 (102)
+.|+.|++.|. +-..|..|+++|+ -++.|.+||+.|..++-|+.|+|+|+|||||.|..|+++|.+.+||+
T Consensus 162 ~~C~~C~K~Yv-SmpALkMHirTH~--------l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLR 232 (279)
T KOG2462|consen 162 FSCKYCGKVYV-SMPALKMHIRTHT--------LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLR 232 (279)
T ss_pred ccCCCCCceee-ehHHHhhHhhccC--------CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHH
Confidence 56888888888 8888888888864 67899999999999999999999999999999999999999999999
Q ss_pred hhhhhcCCCCccccccccccC
Q psy14694 82 SHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 82 ~h~~~~~~~~~~~C~~c~~~~ 102 (102)
.|+++|.+.|.|+|+.|+|+|
T Consensus 233 AHmQTHS~~K~~qC~~C~KsF 253 (279)
T KOG2462|consen 233 AHMQTHSDVKKHQCPRCGKSF 253 (279)
T ss_pred HHHHhhcCCccccCcchhhHH
Confidence 999999999999999999998
No 2
>KOG2462|consensus
Probab=99.94 E-value=5.3e-28 Score=138.03 Aligned_cols=95 Identities=19% Similarity=0.322 Sum_probs=88.5
Q ss_pred ccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhh
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLM 81 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~ 81 (102)
|+|..|++.+. ...+|..|..+|.... ..+-+.|..|++.+....+|.+|+++|+ .+++|.+||+.|.++=.|+
T Consensus 131 ~~c~eCgk~ys-T~snLsrHkQ~H~~~~---s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQ 204 (279)
T KOG2462|consen 131 YKCPECGKSYS-TSSNLSRHKQTHRSLD---SKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQ 204 (279)
T ss_pred eeccccccccc-cccccchhhccccccc---ccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhh
Confidence 68999999999 8899999999987444 4677899999999999999999999997 6899999999999999999
Q ss_pred hhhhhcCCCCccccccccccC
Q psy14694 82 SHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 82 ~h~~~~~~~~~~~C~~c~~~~ 102 (102)
.|+|+|||||||.|+.|+|+|
T Consensus 205 GHiRTHTGEKPF~C~hC~kAF 225 (279)
T KOG2462|consen 205 GHIRTHTGEKPFSCPHCGKAF 225 (279)
T ss_pred cccccccCCCCccCCcccchh
Confidence 999999999999999999998
No 3
>KOG3576|consensus
Probab=99.81 E-value=2.2e-21 Score=107.23 Aligned_cols=92 Identities=26% Similarity=0.417 Sum_probs=83.6
Q ss_pred ccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhh
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLM 81 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~ 81 (102)
|.|..|++.|. ....|.+|++.|. ..+.+-|..||+.|.....|.+|.++|+|.+||+|..|+++|.+.-.|.
T Consensus 118 ftCrvCgK~F~-lQRmlnrh~kch~------~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsle 190 (267)
T KOG3576|consen 118 FTCRVCGKKFG-LQRMLNRHLKCHS------DVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLE 190 (267)
T ss_pred eeeehhhhhhh-HHHHHHHHhhhcc------HHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHH
Confidence 67999999998 8889999999988 8888999999999999999999999999999999999999999999999
Q ss_pred hhhhh-c----------CCCCccccccccc
Q psy14694 82 SHPLV-Q----------ISDEQLRFKKIRI 100 (102)
Q Consensus 82 ~h~~~-~----------~~~~~~~C~~c~~ 100 (102)
.|.+- | ..++.|.|.+||.
T Consensus 191 shl~kvhgv~~~yaykerr~kl~vcedcg~ 220 (267)
T KOG3576|consen 191 SHLKKVHGVQHQYAYKERRAKLYVCEDCGY 220 (267)
T ss_pred HHHHHHcCchHHHHHHHhhhheeeecccCC
Confidence 99554 5 3467789999985
No 4
>KOG3623|consensus
Probab=99.78 E-value=2e-20 Score=118.78 Aligned_cols=70 Identities=21% Similarity=0.466 Sum_probs=65.6
Q ss_pred CCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 33 SRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
.+.+|.|+.|.+.|...+.|.+|...|+|.+||+|.+|.++|..+-.|..|.|.|.|||||.|++|+|.|
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRF 960 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRF 960 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhc
Confidence 5677999999999999999999999999999999999999999999999999999999999999999987
No 5
>KOG3623|consensus
Probab=99.73 E-value=6.1e-19 Score=112.20 Aligned_cols=78 Identities=21% Similarity=0.499 Sum_probs=73.3
Q ss_pred CccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhh
Q psy14694 1 ILKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANL 80 (102)
Q Consensus 1 ~~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l 80 (102)
+|.|+.|+|+|. ..+.|.+|.-.|+ |.+||+|.+|.+.|.....|..|.|.|.|||||+|.+|++.|+....+
T Consensus 894 myaCDqCDK~Fq-KqSSLaRHKYEHs------GqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSY 966 (1007)
T KOG3623|consen 894 MYACDQCDKAFQ-KQSSLARHKYEHS------GQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSY 966 (1007)
T ss_pred cchHHHHHHHHH-hhHHHHHhhhhhc------CCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccch
Confidence 588999999998 8888999999988 999999999999999999999999999999999999999999999888
Q ss_pred hhhhh
Q psy14694 81 MSHPL 85 (102)
Q Consensus 81 ~~h~~ 85 (102)
.+|+-
T Consensus 967 SQHMN 971 (1007)
T KOG3623|consen 967 SQHMN 971 (1007)
T ss_pred Hhhhc
Confidence 88864
No 6
>KOG3576|consensus
Probab=99.64 E-value=1.6e-17 Score=92.14 Aligned_cols=70 Identities=16% Similarity=0.304 Sum_probs=66.6
Q ss_pred CCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 33 SRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
+...+.|..|++.|....-|.+|+.-|...+.+-|..||+.|.+.-.|++|.|+|+|.+||+|..|+|+|
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaf 183 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAF 183 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHH
Confidence 4566899999999999999999999999999999999999999999999999999999999999999997
No 7
>KOG3608|consensus
Probab=99.51 E-value=7.7e-15 Score=87.40 Aligned_cols=91 Identities=21% Similarity=0.469 Sum_probs=66.3
Q ss_pred CccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhhh-hcCCCCccCCCCCCccCCchh
Q psy14694 1 ILKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRA-HIGDRPYKCFVCPYRSNQRAN 79 (102)
Q Consensus 1 ~~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~-h~~~~~~~c~~c~~~f~~~~~ 79 (102)
||.|..|.+.|. ....|..|+..|- .-|+|+.|.......+.|..|++. |...|||+|..|++.+...+.
T Consensus 237 ~fqC~~C~KrFa-TeklL~~Hv~rHv--------n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esd 307 (467)
T KOG3608|consen 237 SFQCAQCFKRFA-TEKLLKSHVVRHV--------NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESD 307 (467)
T ss_pred chHHHHHHHHHh-HHHHHHHHHHHhh--------hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHH
Confidence 466777777777 6667777776653 457777777777777888888775 677788888888888888888
Q ss_pred hhhhhhhcCCCCcccccc--cccc
Q psy14694 80 LMSHPLVQISDEQLRFKK--IRIA 101 (102)
Q Consensus 80 l~~h~~~~~~~~~~~C~~--c~~~ 101 (102)
|.+|..+|. +-.|+|+. |..+
T Consensus 308 L~kH~~~HS-~~~y~C~h~~C~~s 330 (467)
T KOG3608|consen 308 LAKHVQVHS-KTVYQCEHPDCHYS 330 (467)
T ss_pred HHHHHHhcc-ccceecCCCCCcHH
Confidence 888877777 55777765 6554
No 8
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.48 E-value=1.1e-13 Score=87.64 Aligned_cols=88 Identities=15% Similarity=0.241 Sum_probs=74.4
Q ss_pred ccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCC-----
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQ----- 76 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~----- 76 (102)
+.|+.|++.|. ...|..|+++++ +++.|+ |++.+ ....|..|+.+|.+++++.|..|++.+..
T Consensus 454 ~~C~~Cgk~f~--~s~LekH~~~~H--------kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~ 521 (567)
T PLN03086 454 VHCEKCGQAFQ--QGEMEKHMKVFH--------EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAM 521 (567)
T ss_pred ccCCCCCCccc--hHHHHHHHHhcC--------CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCcccc
Confidence 57999999995 467889988863 678898 99755 56899999999999999999999999852
Q ss_pred -----chhhhhhhhhcCCCCccccccccccC
Q psy14694 77 -----RANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 77 -----~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
.+.|..|..++ |.+++.|+.||+.|
T Consensus 522 d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~V 551 (567)
T PLN03086 522 DVRDRLRGMSEHESIC-GSRTAPCDSCGRSV 551 (567)
T ss_pred chhhhhhhHHHHHHhc-CCcceEccccCCee
Confidence 35799999986 99999999999865
No 9
>KOG1074|consensus
Probab=99.40 E-value=9.2e-14 Score=90.05 Aligned_cols=67 Identities=22% Similarity=0.481 Sum_probs=52.2
Q ss_pred CceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhcCCCCc----cccc---ccccc
Q psy14694 35 KKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQISDEQ----LRFK---KIRIA 101 (102)
Q Consensus 35 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~----~~C~---~c~~~ 101 (102)
.+-+|.+|.+..+-.++|++|.++|+||+||+|.+||++|..+.+|+.|+.+|....+ ++|| +|-+-
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~k 677 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKK 677 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccc
Confidence 3457888888888888888888888888888888888888888888888888876655 5577 66543
No 10
>KOG3608|consensus
Probab=99.37 E-value=8.3e-14 Score=83.09 Aligned_cols=67 Identities=18% Similarity=0.419 Sum_probs=49.4
Q ss_pred CCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhh-cCCCCccccccccccC
Q psy14694 34 RKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLV-QISDEQLRFKKIRIAV 102 (102)
Q Consensus 34 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~-~~~~~~~~C~~c~~~~ 102 (102)
..+|.|..|.+.|.....|..|++.|. .-|+|+.|+.+...++.|.+|++. |..++||+|+.|++.|
T Consensus 235 ~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c 302 (467)
T KOG3608|consen 235 TNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRC 302 (467)
T ss_pred CCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhh
Confidence 344555555555555555555555543 347888899999999999999988 9999999999998764
No 11
>PHA02768 hypothetical protein; Provisional
Probab=99.34 E-value=5.1e-13 Score=59.88 Aligned_cols=44 Identities=23% Similarity=0.325 Sum_probs=35.6
Q ss_pred ceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhh
Q psy14694 36 KYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLM 81 (102)
Q Consensus 36 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~ 81 (102)
.|.|+.||+.|...++|..|+++|+ ++++|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 3678888888888888888888887 6788888888888777664
No 12
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.30 E-value=5.2e-13 Score=51.82 Aligned_cols=24 Identities=13% Similarity=0.116 Sum_probs=19.6
Q ss_pred hhhhhhhhcCCCCccccccccccC
Q psy14694 79 NLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 79 ~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
+|..|+++|+|++||.|+.|+++|
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEE
T ss_pred CHHHHhhhcCCCCCCCCCCCcCee
Confidence 467888888888888888888876
No 13
>PHA00733 hypothetical protein
Probab=99.30 E-value=3.3e-12 Score=67.60 Aligned_cols=54 Identities=20% Similarity=0.360 Sum_probs=34.3
Q ss_pred CCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhcC
Q psy14694 33 SRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQI 88 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 88 (102)
++++|.|..|++.|.....|..|++.+ +.++.|..|++.|.....|..|+...+
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 456666666666666666666666654 345666666666666666666665533
No 14
>PHA02768 hypothetical protein; Provisional
Probab=99.29 E-value=1.3e-12 Score=58.58 Aligned_cols=37 Identities=16% Similarity=0.340 Sum_probs=27.3
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
.|.|++||+.|+..++|..|+++|+ ++|+|..|+++|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f 41 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRIS 41 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCccccee
Confidence 4677777777777777777777777 577777777765
No 15
>KOG1074|consensus
Probab=99.29 E-value=1.6e-12 Score=84.51 Aligned_cols=83 Identities=17% Similarity=0.442 Sum_probs=74.6
Q ss_pred CccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhhhhcCCC----CccCC---CCCCc
Q psy14694 1 ILKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRAHIGDR----PYKCF---VCPYR 73 (102)
Q Consensus 1 ~~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~----~~~c~---~c~~~ 73 (102)
|..|..|-+..+ -...|+.|.++|+ ||+||.|.+|++.|....+|..|+.+|...- .+.|+ +|-+.
T Consensus 605 PNqCiiC~rVlS-C~saLqmHyrtHt------GERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~k 677 (958)
T KOG1074|consen 605 PNQCIICLRVLS-CPSALQMHYRTHT------GERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKK 677 (958)
T ss_pred ccceeeeeeccc-chhhhhhhhhccc------CcCccccccccchhccccchhhcccccccCccccccccCCchhhhccc
Confidence 457888999998 9999999999999 9999999999999999999999999886543 37888 89999
Q ss_pred cCCchhhhhhhhhcCCC
Q psy14694 74 SNQRANLMSHPLVQISD 90 (102)
Q Consensus 74 f~~~~~l~~h~~~~~~~ 90 (102)
|.....|++|++.|.+.
T Consensus 678 ftn~V~lpQhIriH~~~ 694 (958)
T KOG1074|consen 678 FTNAVTLPQHIRIHLGG 694 (958)
T ss_pred ccccccccceEEeecCC
Confidence 99999999999999844
No 16
>PHA00733 hypothetical protein
Probab=99.22 E-value=4.9e-12 Score=66.97 Aligned_cols=68 Identities=10% Similarity=0.070 Sum_probs=55.0
Q ss_pred CCCceeCCCCCCCCCCcchHHHH--hh---hhcCCCCccCCCCCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 33 SRKKYDCFMCPYRTPYSGTMRRH--IR---AHIGDRPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~~~l~~h--~~---~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
..+++.|.+|...+.....|..+ +. .+.+++||.|..|++.|.....|..|++.+ +.+|.|+.|+++|
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F 109 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEF 109 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCcc
Confidence 56788899988877776666555 11 234578999999999999999999999976 4579999999987
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.09 E-value=5e-11 Score=46.18 Aligned_cols=25 Identities=44% Similarity=0.996 Sum_probs=21.7
Q ss_pred hHHHHhhhhcCCCCccCCCCCCccC
Q psy14694 51 TMRRHIRAHIGDRPYKCFVCPYRSN 75 (102)
Q Consensus 51 ~l~~h~~~h~~~~~~~c~~c~~~f~ 75 (102)
+|..|+++|+|++||.|..|++.|.
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 4778999999999999999998886
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.01 E-value=1.5e-09 Score=69.40 Aligned_cols=93 Identities=18% Similarity=0.378 Sum_probs=69.6
Q ss_pred cCCccccccccCHHHHHHHHhhhcc-------------ccccCCCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCC
Q psy14694 3 KCTHCKVDLNLDTEIILQHYKLCSE-------------GARQSSRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFV 69 (102)
Q Consensus 3 ~c~~c~~~f~~~~~~l~~h~~~~~~-------------~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~ 69 (102)
.|+.|.+... ...|..|.....- ......++.+.|..|++.|. ...|..|+.++. +++.|+
T Consensus 409 ~C~NC~~~i~--l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp- 482 (567)
T PLN03086 409 ECRNCKHYIP--SRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP- 482 (567)
T ss_pred ECCCCCCccc--hhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-
Confidence 4778877764 4556666543310 01112346678999999886 578999999874 889999
Q ss_pred CCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 70 CPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 70 c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
|++.+ ....|..|+.+|.+++++.|+.|++.|
T Consensus 483 Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 483 CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 99765 568999999999999999999999864
No 19
>PHA00616 hypothetical protein
Probab=98.99 E-value=1.1e-10 Score=50.07 Aligned_cols=34 Identities=18% Similarity=0.392 Sum_probs=27.3
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCcccccc
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKK 97 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~ 97 (102)
||+|..||+.|...+.|..|++.|+|++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5788888888888888888888888888887753
No 20
>KOG3993|consensus
Probab=98.74 E-value=1.1e-09 Score=67.17 Aligned_cols=81 Identities=23% Similarity=0.387 Sum_probs=61.2
Q ss_pred ccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhhhhc--------C------------
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRAHI--------G------------ 61 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~--------~------------ 61 (102)
|.|..|...|. +.-.|-+|.-..= ....|.|++|++.|+-..+|..|+|.|. +
T Consensus 268 yiCqLCK~kYe-D~F~LAQHrC~RI------V~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ra 340 (500)
T KOG3993|consen 268 YICQLCKEKYE-DAFALAQHRCPRI------VHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRA 340 (500)
T ss_pred HHHHHHHHhhh-hHHHHhhccCCee------EEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhh
Confidence 56777888887 7777777753211 2345889999999999999999988772 1
Q ss_pred -------------CCCccCCCCCCccCCchhhhhhhhhcCC
Q psy14694 62 -------------DRPYKCFVCPYRSNQRANLMSHPLVQIS 89 (102)
Q Consensus 62 -------------~~~~~c~~c~~~f~~~~~l~~h~~~~~~ 89 (102)
+..|.|..|++.|.+...|+.|+.+|..
T Consensus 341 e~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 341 EVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred hhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 1247899999999999999999888653
No 21
>PHA00732 hypothetical protein
Probab=98.72 E-value=8.7e-09 Score=50.17 Aligned_cols=47 Identities=28% Similarity=0.458 Sum_probs=37.1
Q ss_pred ceeCCCCCCCCCCcchHHHHhhh-hcCCCCccCCCCCCccCCchhhhhhhhhcC
Q psy14694 36 KYDCFMCPYRTPYSGTMRRHIRA-HIGDRPYKCFVCPYRSNQRANLMSHPLVQI 88 (102)
Q Consensus 36 ~~~c~~c~~~~~~~~~l~~h~~~-h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~ 88 (102)
+|.|..|++.|.....|..|++. |.+ +.|..|++.|.. +..|.+++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~---l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRR---LNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCC---hhhhhcccC
Confidence 47799999999999999999874 653 579999999983 667776543
No 22
>PHA00616 hypothetical protein
Probab=98.59 E-value=3.7e-08 Score=42.29 Aligned_cols=33 Identities=12% Similarity=0.293 Sum_probs=19.3
Q ss_pred CccCCccccccccCHHHHHHHHhhhccccccCCCCceeCC
Q psy14694 1 ILKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCF 40 (102)
Q Consensus 1 ~~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~ 40 (102)
||.|..||+.|. ....|..|++.++ +++++.++
T Consensus 1 pYqC~~CG~~F~-~~s~l~~H~r~~h------g~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFR-KKKEVIEHLLSVH------KQNKLTLE 33 (44)
T ss_pred CCccchhhHHHh-hHHHHHHHHHHhc------CCCcccee
Confidence 456666666665 5556666666555 55555543
No 23
>PHA00732 hypothetical protein
Probab=98.52 E-value=1.2e-07 Score=46.21 Aligned_cols=47 Identities=17% Similarity=0.345 Sum_probs=37.9
Q ss_pred CccCCccccccccCHHHHHHHHhh-hccccccCCCCceeCCCCCCCCCCcchHHHHhhhhc
Q psy14694 1 ILKCTHCKVDLNLDTEIILQHYKL-CSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRAHI 60 (102)
Q Consensus 1 ~~~c~~c~~~f~~~~~~l~~h~~~-~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~ 60 (102)
||.|+.|++.|. ....|..|++. |. + +.|..|++.|. .+..|.....
T Consensus 1 py~C~~Cgk~F~-s~s~Lk~H~r~~H~------~---~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTV-TLFALKQHARRNHT------L---TKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccC-CHHHHHHHhhcccC------C---CccCCCCCEeC---ChhhhhcccC
Confidence 799999999998 99999999885 43 2 47999999997 4777776443
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.22 E-value=2.9e-07 Score=34.33 Aligned_cols=23 Identities=30% Similarity=0.555 Sum_probs=17.2
Q ss_pred ccCCCCCCccCCchhhhhhhhhc
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQ 87 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~ 87 (102)
|.|..|++.|.....|..|++.|
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 46777888888888888877653
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=98.20 E-value=6.6e-06 Score=37.27 Aligned_cols=49 Identities=20% Similarity=0.487 Sum_probs=26.2
Q ss_pred ccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhhh
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRA 58 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~ 58 (102)
|.|+.|++.| +...|..|....+ ....+.+.|++|...+. .+|..|+..
T Consensus 3 f~CP~C~~~~--~~~~L~~H~~~~H----~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYCGKGF--SESSLVEHCEDEH----RSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred cCCCCCCCcc--CHHHHHHHHHhHC----cCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 5677777743 4556666665543 11234566666665332 355555544
No 26
>KOG3993|consensus
Probab=98.09 E-value=2.7e-07 Score=57.00 Aligned_cols=51 Identities=25% Similarity=0.351 Sum_probs=42.9
Q ss_pred eeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhc
Q psy14694 37 YDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQ 87 (102)
Q Consensus 37 ~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 87 (102)
|.|.-|...|.....|.+|.-.-..-.-|+|.+|+|.|+-+.||-.|.|=|
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhccc
Confidence 778888888999999999986433334599999999999999999998876
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.08 E-value=2.9e-06 Score=31.53 Aligned_cols=22 Identities=18% Similarity=0.474 Sum_probs=16.3
Q ss_pred ccCCccccccccCHHHHHHHHhh
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKL 24 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~ 24 (102)
|.|+.|++.|. ....|..|++.
T Consensus 1 y~C~~C~~~f~-~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFS-SKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEES-SHHHHHHHHHH
T ss_pred CCCCCCCCccC-CHHHHHHHHhH
Confidence 56777888887 77777777765
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=98.07 E-value=1.4e-06 Score=33.72 Aligned_cols=25 Identities=20% Similarity=0.378 Sum_probs=19.8
Q ss_pred CccCCCCCCccCCchhhhhhhhhcC
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQI 88 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~ 88 (102)
||.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5778888888888888888887764
No 29
>PRK04860 hypothetical protein; Provisional
Probab=98.07 E-value=1.9e-06 Score=47.44 Aligned_cols=35 Identities=20% Similarity=0.455 Sum_probs=29.7
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
+|.|. |+. ....+..|.++|+++++|.|..|+..|
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 58897 886 666788999999999999999998765
No 30
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.00 E-value=9.5e-06 Score=36.74 Aligned_cols=50 Identities=22% Similarity=0.419 Sum_probs=38.2
Q ss_pred ceeCCCCCCCCCCcchHHHHhhh-hcCC-CCccCCCCCCccCCchhhhhhhhhcC
Q psy14694 36 KYDCFMCPYRTPYSGTMRRHIRA-HIGD-RPYKCFVCPYRSNQRANLMSHPLVQI 88 (102)
Q Consensus 36 ~~~c~~c~~~~~~~~~l~~h~~~-h~~~-~~~~c~~c~~~f~~~~~l~~h~~~~~ 88 (102)
.|.|+.|++ ......|..|... |..+ +.+.|++|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 478999999 4556889999765 6554 5699999987654 48888987754
No 31
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.97 E-value=4.2e-06 Score=32.34 Aligned_cols=25 Identities=12% Similarity=0.379 Sum_probs=19.8
Q ss_pred CccCCccccccccCHHHHHHHHhhhc
Q psy14694 1 ILKCTHCKVDLNLDTEIILQHYKLCS 26 (102)
Q Consensus 1 ~~~c~~c~~~f~~~~~~l~~h~~~~~ 26 (102)
||.|..|++.|. +...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~-~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFS-SLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEES-SHHHHHHHHCTTT
T ss_pred CCCCCccCCccC-ChhHHHHHhHHhc
Confidence 678888888887 8888888877654
No 32
>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=97.93 E-value=4.2e-06 Score=31.17 Aligned_cols=23 Identities=17% Similarity=0.472 Sum_probs=16.1
Q ss_pred ccCCCCCCccCCchhhhhhhhhc
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQ 87 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~ 87 (102)
|.|..|++.|.....|..|++.+
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 56778888888888888887764
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.77 E-value=1.3e-05 Score=40.49 Aligned_cols=73 Identities=16% Similarity=0.269 Sum_probs=21.1
Q ss_pred cCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhh
Q psy14694 3 KCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMS 82 (102)
Q Consensus 3 ~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~ 82 (102)
.|..|+..|. +...+..|+...+ +-..- ....+.....+..+.+... ...+.|..|++.|.....|..
T Consensus 1 ~C~~C~~~f~-~~~~l~~H~~~~H------~~~~~----~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~ 68 (100)
T PF12756_consen 1 QCLFCDESFS-SVDDLLQHMKKKH------GFDIP----DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQE 68 (100)
T ss_dssp ------------------------------------------------------------SSEEBSSSS-EESSHHHHHH
T ss_pred Cccccccccc-ccccccccccccc------ccccc----ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHH
Confidence 4889999998 8888889986544 22110 0111222333333333222 236899999999999999999
Q ss_pred hhhhc
Q psy14694 83 HPLVQ 87 (102)
Q Consensus 83 h~~~~ 87 (102)
|++.+
T Consensus 69 Hm~~~ 73 (100)
T PF12756_consen 69 HMRSK 73 (100)
T ss_dssp HHHHT
T ss_pred HHcCc
Confidence 99874
No 34
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.72 E-value=3.8e-05 Score=28.45 Aligned_cols=23 Identities=17% Similarity=0.460 Sum_probs=15.2
Q ss_pred ccCCccccccccCHHHHHHHHhhh
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLC 25 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~ 25 (102)
|.|+.|+..|. +...|..|+..+
T Consensus 1 ~~C~~C~~~~~-~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFR-SKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EES-SHHHHHHHHHHH
T ss_pred CCCcCCCCcCC-cHHHHHHHHHhh
Confidence 56777777777 777777777654
No 35
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.68 E-value=2.5e-05 Score=34.44 Aligned_cols=32 Identities=22% Similarity=0.365 Sum_probs=19.9
Q ss_pred CCCCccCCCCCCccCCchhhhhhhhhcCCCCc
Q psy14694 61 GDRPYKCFVCPYRSNQRANLMSHPLVQISDEQ 92 (102)
Q Consensus 61 ~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 92 (102)
.+.|..|++|+..+.+..+|.+|+...++.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 35677888888888888888888877776665
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.66 E-value=2.6e-05 Score=47.05 Aligned_cols=40 Identities=28% Similarity=0.473 Sum_probs=27.6
Q ss_pred CCCccCCC--CCCccCCchhhhhhhhh-c------------------CCCCcccccccccc
Q psy14694 62 DRPYKCFV--CPYRSNQRANLMSHPLV-Q------------------ISDEQLRFKKIRIA 101 (102)
Q Consensus 62 ~~~~~c~~--c~~~f~~~~~l~~h~~~-~------------------~~~~~~~C~~c~~~ 101 (102)
+|||+|++ |++.+.....|+.|+.- | ..+|||.|++|+|.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KR 407 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKR 407 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchh
Confidence 46777755 66666666666666543 2 35699999999985
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.63 E-value=4.1e-05 Score=28.80 Aligned_cols=24 Identities=21% Similarity=0.390 Sum_probs=16.3
Q ss_pred ccCCCCCCccCCchhhhhhhhhcC
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQI 88 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~~ 88 (102)
++|..|+++|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 456777777777777777766543
No 38
>PRK04860 hypothetical protein; Provisional
Probab=97.51 E-value=9.2e-05 Score=40.89 Aligned_cols=39 Identities=31% Similarity=0.525 Sum_probs=33.3
Q ss_pred ceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCch
Q psy14694 36 KYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRA 78 (102)
Q Consensus 36 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~ 78 (102)
+|.|. |+. ....+..|.++++|+++|.|..|+..|....
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 58897 876 5678899999999999999999999887543
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.31 E-value=0.00035 Score=26.07 Aligned_cols=23 Identities=13% Similarity=0.459 Sum_probs=14.9
Q ss_pred ccCCccccccccCHHHHHHHHhhh
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLC 25 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~ 25 (102)
|.|..|++.|. ....+..|++.|
T Consensus 1 ~~C~~C~~~f~-~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFK-SKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhC-CHHHHHHHHHHh
Confidence 45667777776 666666666644
No 40
>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=97.11 E-value=0.00031 Score=31.08 Aligned_cols=32 Identities=25% Similarity=0.421 Sum_probs=23.2
Q ss_pred CCCceeCCCCCCCCCCcchHHHHhhhhcCCCC
Q psy14694 33 SRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRP 64 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~ 64 (102)
.+.|..|++|+..+.++.+|.+|+.+..+.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 67889999999999999999999988777665
No 41
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.07 E-value=0.00038 Score=42.22 Aligned_cols=53 Identities=28% Similarity=0.572 Sum_probs=42.2
Q ss_pred CCCceeCCC--CCCCCCCcchHHHHhhh-h------------------cCCCCccCCCCCCccCCchhhhhhhh
Q psy14694 33 SRKKYDCFM--CPYRTPYSGTMRRHIRA-H------------------IGDRPYKCFVCPYRSNQRANLMSHPL 85 (102)
Q Consensus 33 ~~~~~~c~~--c~~~~~~~~~l~~h~~~-h------------------~~~~~~~c~~c~~~f~~~~~l~~h~~ 85 (102)
++++|.|++ |.+.+.....|..|+.. | ...|||.|.+|++.+..-..|+.|..
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 458899976 88899998899888652 2 23489999999999998888877754
No 42
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.03 E-value=0.00044 Score=26.58 Aligned_cols=22 Identities=18% Similarity=0.295 Sum_probs=18.8
Q ss_pred ccCCCCCCccCCchhhhhhhhh
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLV 86 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~ 86 (102)
|.|..|++.|.....+..|++.
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 5788999999999999888775
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.01 E-value=0.0002 Score=26.91 Aligned_cols=22 Identities=18% Similarity=0.360 Sum_probs=16.6
Q ss_pred ccCCCCCCccCCchhhhhhhhh
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLV 86 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~ 86 (102)
|.|..|++.|.....+..|++.
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 4577788888888888777765
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.97 E-value=0.00023 Score=26.54 Aligned_cols=23 Identities=35% Similarity=0.684 Sum_probs=14.6
Q ss_pred ccCCCCCCccCCchhhhhhhhhcC
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQI 88 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~~ 88 (102)
|+|..|+.... ...|..|++.++
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 46777777776 777777776643
No 45
>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=96.72 E-value=0.001 Score=26.89 Aligned_cols=9 Identities=0% Similarity=-0.296 Sum_probs=5.2
Q ss_pred Ccccccccc
Q psy14694 91 EQLRFKKIR 99 (102)
Q Consensus 91 ~~~~C~~c~ 99 (102)
.++.||.||
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 455666665
No 46
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.70 E-value=0.0012 Score=24.67 Aligned_cols=23 Identities=17% Similarity=0.433 Sum_probs=16.1
Q ss_pred ccCCccccccccCHHHHHHHHhhh
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLC 25 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~ 25 (102)
|.|..|++.|. +...+..|++.+
T Consensus 1 ~~C~~C~~~f~-s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFS-SENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEES-SHHHHHHHHTTH
T ss_pred CCCCCCCCCcC-CHHHHHHHHCcC
Confidence 45777777777 777777776543
No 47
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.56 E-value=0.0016 Score=40.72 Aligned_cols=62 Identities=24% Similarity=0.415 Sum_probs=54.4
Q ss_pred CceeCCCCCCCCCCcchHHHHhh--hhcCC--CCccCC--CCCCccCCchhhhhhhhhcCCCCccccc
Q psy14694 35 KKYDCFMCPYRTPYSGTMRRHIR--AHIGD--RPYKCF--VCPYRSNQRANLMSHPLVQISDEQLRFK 96 (102)
Q Consensus 35 ~~~~c~~c~~~~~~~~~l~~h~~--~h~~~--~~~~c~--~c~~~f~~~~~l~~h~~~~~~~~~~~C~ 96 (102)
....+..|...+.....+..|.+ .|.++ +++.|. .|++.|.+...+..|...|++..+..+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 35778888899999999999999 89999 999999 7999999999999999999988877664
No 48
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.08 E-value=0.0016 Score=32.77 Aligned_cols=59 Identities=14% Similarity=0.223 Sum_probs=9.1
Q ss_pred eCCCCCCCCCCcchHHHHhhhhcCC-CCccCCCCCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 38 DCFMCPYRTPYSGTMRRHIRAHIGD-RPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 38 ~c~~c~~~~~~~~~l~~h~~~h~~~-~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
+|..|+..|.....|..|+....+. .+ . ...+.....+..+.+... ...+.|..|++.|
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-~----~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f 60 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-D----QKYLVDPNRLLNYLRKKV-KESFRCPYCNKTF 60 (100)
T ss_dssp ------------------------------------------------------SSEEBSSSS-EE
T ss_pred Cccccccccccccccccccccccccccc-c----cccccccccccccccccc-CCCCCCCccCCCC
Confidence 4788999999999999999753332 22 1 111223333334444322 2379999999875
No 49
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=95.90 E-value=0.0049 Score=28.16 Aligned_cols=32 Identities=16% Similarity=0.175 Sum_probs=20.9
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCccccccccc
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
.|.|+.||........ +--.-..+|.||+||+
T Consensus 27 ~F~CPnCGe~~I~Rc~-----~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCA-----KCRKLGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhh-----hHHHcCCceECCCcCc
Confidence 4788889866554432 2222345899999986
No 50
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.85 E-value=0.0061 Score=23.00 Aligned_cols=21 Identities=19% Similarity=0.406 Sum_probs=13.7
Q ss_pred ccCCCCCCccCCchhhhhhhhh
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLV 86 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~ 86 (102)
..|..|++.| .+..|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3677788888 34556677654
No 51
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=95.54 E-value=0.0067 Score=35.26 Aligned_cols=10 Identities=10% Similarity=-0.124 Sum_probs=7.1
Q ss_pred cccccccccC
Q psy14694 93 LRFKKIRIAV 102 (102)
Q Consensus 93 ~~C~~c~~~~ 102 (102)
..||.||.+|
T Consensus 49 ~vCP~CgyA~ 58 (214)
T PF09986_consen 49 WVCPHCGYAA 58 (214)
T ss_pred EECCCCCCcc
Confidence 4588888765
No 52
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=95.53 E-value=0.014 Score=23.55 Aligned_cols=23 Identities=26% Similarity=0.411 Sum_probs=15.8
Q ss_pred CccCCccccccccCHHHHHHHHhh
Q psy14694 1 ILKCTHCKVDLNLDTEIILQHYKL 24 (102)
Q Consensus 1 ~~~c~~c~~~f~~~~~~l~~h~~~ 24 (102)
+|.|+.|++.|. +...+..|+..
T Consensus 3 ~~~C~~C~~~~~-~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFT-DEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccC-CHHHHHHHHCh
Confidence 366777777776 66677766654
No 53
>KOG2893|consensus
Probab=95.33 E-value=0.0071 Score=35.55 Aligned_cols=42 Identities=19% Similarity=0.381 Sum_probs=23.1
Q ss_pred CCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhh-hhhc
Q psy14694 42 CPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSH-PLVQ 87 (102)
Q Consensus 42 c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h-~~~~ 87 (102)
|.+.|.....|.+|+. .|-|+|.+|.+.+...-.|..| +++|
T Consensus 16 cnrefddekiliqhqk----akhfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 16 CNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred cccccchhhhhhhhhh----hccceeeeehhhhccCCCceeehhhhh
Confidence 5556666666666655 3446666666544444444444 4444
No 54
>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=95.21 E-value=0.013 Score=23.84 Aligned_cols=8 Identities=0% Similarity=-0.242 Sum_probs=4.3
Q ss_pred cccccccc
Q psy14694 92 QLRFKKIR 99 (102)
Q Consensus 92 ~~~C~~c~ 99 (102)
|..||.||
T Consensus 18 p~~CP~Cg 25 (34)
T cd00729 18 PEKCPICG 25 (34)
T ss_pred CCcCcCCC
Confidence 44555555
No 55
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.82 E-value=0.12 Score=27.02 Aligned_cols=26 Identities=19% Similarity=0.385 Sum_probs=16.7
Q ss_pred CCccCCCCCCccCCchhhhhhhhhcC
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLVQI 88 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~~~ 88 (102)
..|.|..|...|-..-++..|...|.
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cceeCCCCCCccccccchhhhhhccC
Confidence 35777777777776666666655444
No 56
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=94.78 E-value=0.019 Score=26.31 Aligned_cols=32 Identities=13% Similarity=0.114 Sum_probs=19.5
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCccccccccc
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
.|.|+.||......- .+--.-..+|.||+||+
T Consensus 25 ~F~CPnCG~~~I~RC-----~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRC-----EKCRKQSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeec-----hhHHhcCCceECCCCCC
Confidence 478888886633322 12222245899999986
No 57
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=94.63 E-value=0.021 Score=31.86 Aligned_cols=23 Identities=17% Similarity=0.294 Sum_probs=17.6
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCcccccccc
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIR 99 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~ 99 (102)
.|.|.+||.+ +.|+.|-.||.||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 5888888743 4557788898887
No 58
>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=94.60 E-value=0.015 Score=24.82 Aligned_cols=29 Identities=14% Similarity=0.277 Sum_probs=14.1
Q ss_pred ccCCCCCCccCCchhhhhhhhhcCCCCccccccccc
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
|.|..||..|..... ... ..+-.||.||.
T Consensus 6 y~C~~Cg~~fe~~~~------~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS------ISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEE------cCC-CCCCcCCCCCC
Confidence 556666655553321 111 34555666654
No 59
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.29 E-value=0.022 Score=31.48 Aligned_cols=12 Identities=25% Similarity=0.645 Sum_probs=8.6
Q ss_pred ccCCCCCCccCC
Q psy14694 65 YKCFVCPYRSNQ 76 (102)
Q Consensus 65 ~~c~~c~~~f~~ 76 (102)
++|+.||++|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 677777777754
No 60
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.26 E-value=0.035 Score=22.98 Aligned_cols=11 Identities=18% Similarity=0.301 Sum_probs=5.0
Q ss_pred CccCCCCCCcc
Q psy14694 64 PYKCFVCPYRS 74 (102)
Q Consensus 64 ~~~c~~c~~~f 74 (102)
..+|..|+..|
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 34455554443
No 61
>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=94.19 E-value=0.029 Score=23.19 Aligned_cols=10 Identities=20% Similarity=0.172 Sum_probs=5.0
Q ss_pred cccccccccc
Q psy14694 92 QLRFKKIRIA 101 (102)
Q Consensus 92 ~~~C~~c~~~ 101 (102)
...|+.|+..
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 3445555543
No 62
>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=94.18 E-value=0.019 Score=24.05 Aligned_cols=11 Identities=27% Similarity=0.630 Sum_probs=5.6
Q ss_pred ccCCCCCCccC
Q psy14694 65 YKCFVCPYRSN 75 (102)
Q Consensus 65 ~~c~~c~~~f~ 75 (102)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 45555555444
No 63
>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=94.15 E-value=0.02 Score=25.48 Aligned_cols=11 Identities=36% Similarity=0.781 Sum_probs=6.9
Q ss_pred eeCCCCCCCCC
Q psy14694 37 YDCFMCPYRTP 47 (102)
Q Consensus 37 ~~c~~c~~~~~ 47 (102)
|.|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 56666666554
No 64
>KOG2186|consensus
Probab=93.53 E-value=0.035 Score=32.94 Aligned_cols=49 Identities=12% Similarity=0.304 Sum_probs=35.8
Q ss_pred ceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhc
Q psy14694 36 KYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQ 87 (102)
Q Consensus 36 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~ 87 (102)
.|+|..||....- ..+..|+..-.+ ..|.|..|++.|.+ ..+..|..--
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCI 51 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCI 51 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhhhc
Confidence 4789999887654 456678876555 66899999999988 5566776543
No 65
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=93.42 E-value=0.068 Score=21.98 Aligned_cols=9 Identities=22% Similarity=0.231 Sum_probs=4.1
Q ss_pred ccccccccc
Q psy14694 92 QLRFKKIRI 100 (102)
Q Consensus 92 ~~~C~~c~~ 100 (102)
..+|+.|+.
T Consensus 25 ~v~C~~C~~ 33 (36)
T PF13717_consen 25 KVRCSKCGH 33 (36)
T ss_pred EEECCCCCC
Confidence 344444443
No 66
>PHA00626 hypothetical protein
Probab=93.42 E-value=0.041 Score=24.88 Aligned_cols=15 Identities=27% Similarity=0.744 Sum_probs=10.4
Q ss_pred CCccCCCCCCccCCc
Q psy14694 63 RPYKCFVCPYRSNQR 77 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~ 77 (102)
..|+|..||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 457888888777643
No 67
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.12 E-value=0.034 Score=24.14 Aligned_cols=12 Identities=25% Similarity=0.694 Sum_probs=6.5
Q ss_pred ceeCCCCCCCCC
Q psy14694 36 KYDCFMCPYRTP 47 (102)
Q Consensus 36 ~~~c~~c~~~~~ 47 (102)
.|.|..||..+.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 355666665443
No 68
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.92 E-value=0.035 Score=34.81 Aligned_cols=61 Identities=21% Similarity=0.416 Sum_probs=49.9
Q ss_pred CccCCccccccccCHHHHHHHHh--hhccccccCCC--CceeCC--CCCCCCCCcchHHHHhhhhcCCCCccCC
Q psy14694 1 ILKCTHCKVDLNLDTEIILQHYK--LCSEGARQSSR--KKYDCF--MCPYRTPYSGTMRRHIRAHIGDRPYKCF 68 (102)
Q Consensus 1 ~~~c~~c~~~f~~~~~~l~~h~~--~~~~~~~~~~~--~~~~c~--~c~~~~~~~~~l~~h~~~h~~~~~~~c~ 68 (102)
++.|..|...|. ....+..|.+ .|. ++ +++.|+ .|++.|.....+..|...|.+..+..+.
T Consensus 289 ~~~~~~~~~~~s-~~~~l~~~~~~~~h~------~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 289 PIKSKQCNISFS-RSSPLTRHLRSVNHS------GESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred CCCCccccCCcc-ccccccccccccccc------cccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 356778888887 7888888888 566 88 899999 7999999999999999988877765553
No 69
>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=92.65 E-value=0.044 Score=20.46 Aligned_cols=9 Identities=0% Similarity=-0.027 Sum_probs=6.1
Q ss_pred ccccccccc
Q psy14694 92 QLRFKKIRI 100 (102)
Q Consensus 92 ~~~C~~c~~ 100 (102)
.|.||.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 577777764
No 70
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=92.60 E-value=0.082 Score=26.41 Aligned_cols=27 Identities=22% Similarity=0.450 Sum_probs=16.2
Q ss_pred CCccCCCCCCccCCchhhhhhhhhcCCCCcccccccc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIR 99 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~ 99 (102)
+|-.|..||+.|.+. ...+|-.||.|.
T Consensus 57 ~Pa~CkkCGfef~~~----------~ik~pSRCP~CK 83 (97)
T COG3357 57 RPARCKKCGFEFRDD----------KIKKPSRCPKCK 83 (97)
T ss_pred cChhhcccCcccccc----------ccCCcccCCcch
Confidence 466777777777652 113466677664
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=92.57 E-value=0.089 Score=22.72 Aligned_cols=26 Identities=27% Similarity=0.582 Sum_probs=14.7
Q ss_pred eeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCc
Q psy14694 37 YDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYR 73 (102)
Q Consensus 37 ~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~ 73 (102)
|.|..||..+... ...+..|++||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 5677776655432 1244677777643
No 72
>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=92.24 E-value=0.12 Score=28.70 Aligned_cols=19 Identities=16% Similarity=0.177 Sum_probs=8.6
Q ss_pred CCceeCCCCCCCCCCcchH
Q psy14694 34 RKKYDCFMCPYRTPYSGTM 52 (102)
Q Consensus 34 ~~~~~c~~c~~~~~~~~~l 52 (102)
...|.|+.|+..|+...++
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CCeEECCCCCcEeeHHHHH
Confidence 3444455555444444333
No 73
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=91.85 E-value=0.11 Score=19.07 Aligned_cols=7 Identities=0% Similarity=-0.140 Sum_probs=4.0
Q ss_pred ccccccc
Q psy14694 95 FKKIRIA 101 (102)
Q Consensus 95 C~~c~~~ 101 (102)
|+.||..
T Consensus 16 C~~CG~~ 22 (23)
T PF13240_consen 16 CPNCGTP 22 (23)
T ss_pred hhhhCCc
Confidence 6666654
No 74
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=91.74 E-value=0.18 Score=27.64 Aligned_cols=34 Identities=15% Similarity=0.155 Sum_probs=16.8
Q ss_pred CCccCCCCCCccCCchhhhhhhhhcCCCCccccccccc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
.-|.|+.|+..|.....+.. . .. +..|.||.||.
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~-~--d~-~~~f~Cp~Cg~ 131 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQL-L--DM-DGTFTCPRCGE 131 (147)
T ss_pred cEEECcCCCCEeeHHHHHHh-c--CC-CCcEECCCCCC
Confidence 34667777766664332211 0 11 22267777764
No 75
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=91.11 E-value=0.18 Score=28.64 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=6.2
Q ss_pred ccCCCCCCccCCc
Q psy14694 65 YKCFVCPYRSNQR 77 (102)
Q Consensus 65 ~~c~~c~~~f~~~ 77 (102)
|.|+.|+..|+..
T Consensus 118 Y~Cp~C~~rytf~ 130 (178)
T PRK06266 118 FFCPNCHIRFTFD 130 (178)
T ss_pred EECCCCCcEEeHH
Confidence 4455555444443
No 76
>PF14353 CpXC: CpXC protein
Probab=90.97 E-value=0.094 Score=27.93 Aligned_cols=10 Identities=20% Similarity=0.394 Sum_probs=5.4
Q ss_pred eCCCCCCCCC
Q psy14694 38 DCFMCPYRTP 47 (102)
Q Consensus 38 ~c~~c~~~~~ 47 (102)
+|+.|+..|.
T Consensus 3 tCP~C~~~~~ 12 (128)
T PF14353_consen 3 TCPHCGHEFE 12 (128)
T ss_pred CCCCCCCeeE
Confidence 4566665543
No 77
>KOG2186|consensus
Probab=90.75 E-value=0.16 Score=30.31 Aligned_cols=46 Identities=15% Similarity=0.464 Sum_probs=35.7
Q ss_pred ccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHHhh
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRHIR 57 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h~~ 57 (102)
|.|..||.... ...+..|+-..+ + ..|.|..|+..|.. ..+..|..
T Consensus 4 FtCnvCgEsvK--Kp~vekH~srCr------n-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVK--KPQVEKHMSRCR------N-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhcc--ccchHHHHHhcc------C-CeeEEeeccccccc-chhhhhhh
Confidence 67899998874 456677887776 5 67999999999988 66667754
No 78
>KOG2893|consensus
Probab=90.65 E-value=0.1 Score=30.92 Aligned_cols=41 Identities=27% Similarity=0.639 Sum_probs=28.5
Q ss_pred CCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCCCCCcchHHHH
Q psy14694 4 CTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYRTPYSGTMRRH 55 (102)
Q Consensus 4 c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~l~~h 55 (102)
|=.|++.|. +..-|++|++. +.|.|-+|.+...+-..|..|
T Consensus 13 cwycnrefd-dekiliqhqka----------khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFD-DEKILIQHQKA----------KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccc-hhhhhhhhhhh----------ccceeeeehhhhccCCCceee
Confidence 446888887 77777777654 457788888776666666555
No 79
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=90.13 E-value=0.14 Score=22.61 Aligned_cols=12 Identities=25% Similarity=0.669 Sum_probs=7.2
Q ss_pred CceeCCCCCCCC
Q psy14694 35 KKYDCFMCPYRT 46 (102)
Q Consensus 35 ~~~~c~~c~~~~ 46 (102)
..|.|..|++.+
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 346666666655
No 80
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=89.74 E-value=0.13 Score=22.72 Aligned_cols=15 Identities=13% Similarity=0.191 Sum_probs=8.2
Q ss_pred CCccCCCCCCccCCc
Q psy14694 63 RPYKCFVCPYRSNQR 77 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~ 77 (102)
+++.|..||..|...
T Consensus 3 k~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFT 17 (49)
T ss_pred eeEEcccCCCeEEEe
Confidence 445566666555443
No 81
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=89.60 E-value=0.35 Score=25.17 Aligned_cols=17 Identities=18% Similarity=0.336 Sum_probs=7.9
Q ss_pred CCCceeCCCCCCCCCCc
Q psy14694 33 SRKKYDCFMCPYRTPYS 49 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~ 49 (102)
++.|..|+.||..|...
T Consensus 23 nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 23 NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCCccCCCCCCccCcc
Confidence 33444555555544433
No 82
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=88.36 E-value=0.35 Score=24.04 Aligned_cols=33 Identities=21% Similarity=0.310 Sum_probs=19.4
Q ss_pred CceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCc
Q psy14694 35 KKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQR 77 (102)
Q Consensus 35 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~ 77 (102)
..+.|+.|++. .+.++ +...|+|..|+..|.-.
T Consensus 34 ~~~~Cp~C~~~--------~VkR~--a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRI--ATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCc--------ceeee--ccCeEEcCCCCCeeccc
Confidence 45677777654 11232 23467888888777644
No 83
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=87.48 E-value=0.32 Score=26.33 Aligned_cols=12 Identities=25% Similarity=0.395 Sum_probs=6.4
Q ss_pred ccCCCCCCccCC
Q psy14694 65 YKCFVCPYRSNQ 76 (102)
Q Consensus 65 ~~c~~c~~~f~~ 76 (102)
+.|..||..|..
T Consensus 71 ~~C~~CG~~~~~ 82 (135)
T PRK03824 71 LKCRNCGNEWSL 82 (135)
T ss_pred EECCCCCCEEec
Confidence 556666655543
No 84
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=87.48 E-value=0.17 Score=22.91 Aligned_cols=26 Identities=15% Similarity=0.220 Sum_probs=19.9
Q ss_pred CCCceeCCCCCCCCCCcchHHHHhhh
Q psy14694 33 SRKKYDCFMCPYRTPYSGTMRRHIRA 58 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~~~l~~h~~~ 58 (102)
|+..+.|+.|++.|........|...
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhH
Confidence 67778888888888877777777653
No 85
>KOG1146|consensus
Probab=87.37 E-value=0.28 Score=35.80 Aligned_cols=24 Identities=33% Similarity=0.731 Sum_probs=14.4
Q ss_pred CCccCCCCCCccCCchhhhhhhhh
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLV 86 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~ 86 (102)
++|.|..|..++....+|-+|+..
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHH
Confidence 456666666666666666666543
No 86
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=84.94 E-value=0.48 Score=25.62 Aligned_cols=27 Identities=15% Similarity=0.161 Sum_probs=16.7
Q ss_pred CCccCCCCCCccCCchhhhhhhhhcCCCCc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLVQISDEQ 92 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 92 (102)
.-..|-+||+.|.. |.+|++.|+|--|
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCH
Confidence 34679999999886 5899999877544
No 87
>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=84.40 E-value=0.48 Score=17.98 Aligned_cols=9 Identities=0% Similarity=-0.256 Sum_probs=4.5
Q ss_pred ccccccccC
Q psy14694 94 RFKKIRIAV 102 (102)
Q Consensus 94 ~C~~c~~~~ 102 (102)
.|+.||-.|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 355555544
No 88
>KOG1146|consensus
Probab=84.28 E-value=0.37 Score=35.21 Aligned_cols=27 Identities=19% Similarity=0.159 Sum_probs=16.6
Q ss_pred cCCCCccCCCCCCccCCchhhhhhhhh
Q psy14694 60 IGDRPYKCFVCPYRSNQRANLMSHPLV 86 (102)
Q Consensus 60 ~~~~~~~c~~c~~~f~~~~~l~~h~~~ 86 (102)
.-.+.++|++|+-.+.....|..|+|+
T Consensus 461 S~~kt~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 461 SFFKTLKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred cccccccCCccchhhhhHHHhhhcccc
Confidence 334556666666666666666666665
No 89
>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=84.24 E-value=0.9 Score=18.17 Aligned_cols=7 Identities=29% Similarity=0.842 Sum_probs=3.6
Q ss_pred ccCCCCC
Q psy14694 65 YKCFVCP 71 (102)
Q Consensus 65 ~~c~~c~ 71 (102)
..|.+||
T Consensus 18 irC~~CG 24 (32)
T PF03604_consen 18 IRCPECG 24 (32)
T ss_dssp SSBSSSS
T ss_pred EECCcCC
Confidence 4555555
No 90
>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=83.73 E-value=0.61 Score=20.17 Aligned_cols=11 Identities=27% Similarity=0.262 Sum_probs=6.6
Q ss_pred CCccccccccc
Q psy14694 90 DEQLRFKKIRI 100 (102)
Q Consensus 90 ~~~~~C~~c~~ 100 (102)
...|+|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 45566666653
No 91
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=83.65 E-value=0.84 Score=20.06 Aligned_cols=21 Identities=29% Similarity=0.433 Sum_probs=12.2
Q ss_pred ccCCCCCCccCCc-----hhhhhhhh
Q psy14694 65 YKCFVCPYRSNQR-----ANLMSHPL 85 (102)
Q Consensus 65 ~~c~~c~~~f~~~-----~~l~~h~~ 85 (102)
..|..|++.+... ++|.+|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 4566666655433 56666666
No 92
>COG1773 Rubredoxin [Energy production and conversion]
Probab=83.02 E-value=0.98 Score=20.51 Aligned_cols=13 Identities=23% Similarity=0.687 Sum_probs=6.7
Q ss_pred ceeCCCCCCCCCC
Q psy14694 36 KYDCFMCPYRTPY 48 (102)
Q Consensus 36 ~~~c~~c~~~~~~ 48 (102)
.+.|..||..|..
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 3555555555443
No 93
>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=82.85 E-value=0.65 Score=19.73 Aligned_cols=24 Identities=25% Similarity=0.314 Sum_probs=12.5
Q ss_pred CCCccCCCCCCccCC----chhhhhhhh
Q psy14694 62 DRPYKCFVCPYRSNQ----RANLMSHPL 85 (102)
Q Consensus 62 ~~~~~c~~c~~~f~~----~~~l~~h~~ 85 (102)
.....|..|++.+.. .++|..|++
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 344667777766554 366667763
No 94
>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=82.78 E-value=0.51 Score=18.61 Aligned_cols=8 Identities=13% Similarity=-0.076 Sum_probs=4.5
Q ss_pred cccccccc
Q psy14694 92 QLRFKKIR 99 (102)
Q Consensus 92 ~~~C~~c~ 99 (102)
.|.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 45566554
No 95
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=82.33 E-value=1.3 Score=28.00 Aligned_cols=51 Identities=18% Similarity=0.170 Sum_probs=32.2
Q ss_pred CCCcchHHHHhhhhc---CCCC-ccCCCCCCccCCchhhhhhhhhcCCCCcccccc
Q psy14694 46 TPYSGTMRRHIRAHI---GDRP-YKCFVCPYRSNQRANLMSHPLVQISDEQLRFKK 97 (102)
Q Consensus 46 ~~~~~~l~~h~~~h~---~~~~-~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~ 97 (102)
.+....|..|...-. |-+. -.|..|...|.....|..|.|..+ ++-|-|+.
T Consensus 198 lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~ 252 (493)
T COG5236 198 LFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRH-EACHICDM 252 (493)
T ss_pred eeecccccccccCCccccCcCCCchhhhccceecChHHHHHHHHhhh-hhhhhhhc
Confidence 444566666665422 2232 258888888999999999988755 44455544
No 96
>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=81.88 E-value=1.4 Score=23.60 Aligned_cols=17 Identities=12% Similarity=-0.039 Sum_probs=9.2
Q ss_pred CCCceeCCCCCCCCCCc
Q psy14694 33 SRKKYDCFMCPYRTPYS 49 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~ 49 (102)
++.|..|+.||..|...
T Consensus 23 nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 23 NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred CCCCccCCCcCCccCcc
Confidence 44555666666555443
No 97
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=81.65 E-value=0.31 Score=24.48 Aligned_cols=32 Identities=25% Similarity=0.506 Sum_probs=17.2
Q ss_pred CceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCC
Q psy14694 35 KKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQ 76 (102)
Q Consensus 35 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~ 76 (102)
..|.|+.|++.- + .+.-. -.|+|..|++.|.-
T Consensus 34 ~ky~Cp~Cgk~~-----v---kR~a~--GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTS-----V---KRVAT--GIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSE-----E---EEEET--TEEEETTTTEEEE-
T ss_pred CCCcCCCCCCce-----e---EEeee--EEeecCCCCCEEeC
Confidence 457777777642 1 12222 34778888776653
No 98
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=81.27 E-value=0.75 Score=25.44 Aligned_cols=33 Identities=24% Similarity=0.355 Sum_probs=24.3
Q ss_pred CCccCCCCCCccCCchhhhhhhhhcCCCCccccccccc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
-+|.|. |+..+.+. .+|-.+-.|+ .|.|..|+-
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCc
Confidence 468898 98776653 4566666777 899999974
No 99
>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=81.11 E-value=0.81 Score=24.06 Aligned_cols=12 Identities=17% Similarity=0.409 Sum_probs=7.5
Q ss_pred ccCCCCCCccCC
Q psy14694 65 YKCFVCPYRSNQ 76 (102)
Q Consensus 65 ~~c~~c~~~f~~ 76 (102)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 567777766554
No 100
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=80.83 E-value=0.71 Score=22.22 Aligned_cols=41 Identities=12% Similarity=0.220 Sum_probs=23.3
Q ss_pred eeCCCCCCCCCCcchHHHHhhhhcCCCCccCC--CCCCccCCchh
Q psy14694 37 YDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCF--VCPYRSNQRAN 79 (102)
Q Consensus 37 ~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~--~c~~~f~~~~~ 79 (102)
+.|+.|+..-.....-... ...-++.++|. +||.+|.....
T Consensus 2 m~CP~Cg~~a~irtSr~~s--~~~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYIT--DTTKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhcC--hhhheeeeecCCCCCCCEEEEEEE
Confidence 4678887654222221111 12345668897 89999876543
No 101
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=80.53 E-value=0.82 Score=19.22 Aligned_cols=9 Identities=44% Similarity=0.966 Sum_probs=4.5
Q ss_pred ccCCCCCCc
Q psy14694 65 YKCFVCPYR 73 (102)
Q Consensus 65 ~~c~~c~~~ 73 (102)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 455555543
No 102
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=80.45 E-value=0.64 Score=21.22 Aligned_cols=33 Identities=18% Similarity=0.110 Sum_probs=18.9
Q ss_pred CCCccCCCCCCccCCchhhhhhhhhcCCCCccccccc
Q psy14694 62 DRPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKI 98 (102)
Q Consensus 62 ~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c 98 (102)
+.|+....|+..|...+.+. ++ .......||+-
T Consensus 22 ~~PV~s~~C~H~fek~aI~~-~i---~~~~~~~CPv~ 54 (57)
T PF11789_consen 22 EDPVKSKKCGHTFEKEAILQ-YI---QRNGSKRCPVA 54 (57)
T ss_dssp SSEEEESSS--EEEHHHHHH-HC---TTTS-EE-SCC
T ss_pred hCCcCcCCCCCeecHHHHHH-HH---HhcCCCCCCCC
Confidence 35677778999998776543 33 34567788873
No 103
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=80.04 E-value=0.39 Score=32.95 Aligned_cols=56 Identities=16% Similarity=0.213 Sum_probs=36.8
Q ss_pred eCCCCCCCCCCcchHHHHhhhhcCCCCc-cCCCCCCccCCchhhhhhhhhcCCCCccccccccc
Q psy14694 38 DCFMCPYRTPYSGTMRRHIRAHIGDRPY-KCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 38 ~c~~c~~~~~~~~~l~~h~~~h~~~~~~-~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
.|..||=.|+...+|.- .|..+.-..| .|+.|.+.+..+.+..-|. +|..||.||-
T Consensus 125 ~CT~CGPRfTIi~alPY-DR~nTsM~~F~lC~~C~~EY~dP~nRRfHA------Qp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPY-DRENTSMADFPLCPFCDKEYKDPLNRRFHA------QPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCC-CcccCccccCcCCHHHHHHhcCcccccccc------ccccCcccCC
Confidence 46678888887777643 3333333333 4888988888886644333 3788999984
No 104
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=79.80 E-value=0.99 Score=23.68 Aligned_cols=12 Identities=17% Similarity=0.354 Sum_probs=7.5
Q ss_pred ccCCCCCCccCC
Q psy14694 65 YKCFVCPYRSNQ 76 (102)
Q Consensus 65 ~~c~~c~~~f~~ 76 (102)
..|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PRK12380 71 AWCWDCSQVVEI 82 (113)
T ss_pred EEcccCCCEEec
Confidence 567777755554
No 105
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=78.99 E-value=1.2 Score=24.00 Aligned_cols=15 Identities=20% Similarity=0.439 Sum_probs=10.9
Q ss_pred CccCCCCCCccCCch
Q psy14694 64 PYKCFVCPYRSNQRA 78 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~ 78 (102)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 567788888777665
No 106
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=78.86 E-value=1.6 Score=19.55 Aligned_cols=15 Identities=27% Similarity=0.498 Sum_probs=10.6
Q ss_pred ccCCCCCCccCCchh
Q psy14694 65 YKCFVCPYRSNQRAN 79 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~ 79 (102)
++|..|+..+.....
T Consensus 29 W~C~~Cgh~w~~~v~ 43 (55)
T PF14311_consen 29 WKCPKCGHEWKASVN 43 (55)
T ss_pred EECCCCCCeeEccHh
Confidence 788888877765543
No 107
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=78.68 E-value=1.3 Score=30.84 Aligned_cols=22 Identities=9% Similarity=-0.174 Sum_probs=14.4
Q ss_pred hhhhhhhhcCCCCccccccccc
Q psy14694 79 NLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 79 ~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
.|.-|.--+....|..||.||-
T Consensus 462 ~L~CH~Cg~~~~~p~~Cp~Cgs 483 (730)
T COG1198 462 QLRCHYCGYQEPIPQSCPECGS 483 (730)
T ss_pred eeEeCCCCCCCCCCCCCCCCCC
Confidence 3444444456677888888874
No 108
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=78.42 E-value=1.7 Score=27.06 Aligned_cols=10 Identities=0% Similarity=-0.276 Sum_probs=6.7
Q ss_pred CCcccccccc
Q psy14694 90 DEQLRFKKIR 99 (102)
Q Consensus 90 ~~~~~C~~c~ 99 (102)
.+...|..|+
T Consensus 250 ~r~e~C~~C~ 259 (309)
T PRK03564 250 VKAESCGDCG 259 (309)
T ss_pred eEeeeccccc
Confidence 4556777776
No 109
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=76.04 E-value=1.2 Score=23.34 Aligned_cols=11 Identities=18% Similarity=0.332 Sum_probs=6.7
Q ss_pred ccCCCCCCccC
Q psy14694 65 YKCFVCPYRSN 75 (102)
Q Consensus 65 ~~c~~c~~~f~ 75 (102)
..|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (114)
T PRK03681 71 CWCETCQQYVT 81 (114)
T ss_pred EEcccCCCeee
Confidence 56667765544
No 110
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=75.64 E-value=1.5 Score=23.19 Aligned_cols=12 Identities=17% Similarity=0.335 Sum_probs=6.7
Q ss_pred ccCCCCCCccCC
Q psy14694 65 YKCFVCPYRSNQ 76 (102)
Q Consensus 65 ~~c~~c~~~f~~ 76 (102)
..|..|+..|..
T Consensus 72 ~~C~~Cg~~~~~ 83 (117)
T PRK00564 72 LECKDCSHVFKP 83 (117)
T ss_pred EEhhhCCCcccc
Confidence 456666655543
No 111
>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=75.18 E-value=2.4 Score=15.97 Aligned_cols=19 Identities=26% Similarity=0.305 Sum_probs=11.9
Q ss_pred cCCCCCCccCCchhhhhhhh
Q psy14694 66 KCFVCPYRSNQRANLMSHPL 85 (102)
Q Consensus 66 ~c~~c~~~f~~~~~l~~h~~ 85 (102)
.|+.|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777776 4455666654
No 112
>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=75.03 E-value=1.6 Score=18.25 Aligned_cols=9 Identities=22% Similarity=0.859 Sum_probs=3.7
Q ss_pred CCccCCCCC
Q psy14694 63 RPYKCFVCP 71 (102)
Q Consensus 63 ~~~~c~~c~ 71 (102)
+.|.|..|+
T Consensus 23 ~~w~C~~C~ 31 (40)
T PF04810_consen 23 KTWICNFCG 31 (40)
T ss_dssp TEEEETTT-
T ss_pred CEEECcCCC
Confidence 344444444
No 113
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=74.82 E-value=1.8 Score=17.82 Aligned_cols=31 Identities=16% Similarity=0.273 Sum_probs=18.9
Q ss_pred ccCCCCCCccCCchhhhhhhhhcCCCCcccccccc
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIR 99 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~ 99 (102)
..|+.|+.+- .+..|=+...|..-|.|..|.
T Consensus 6 v~CP~C~s~~----~v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 6 VHCPRCQSTE----GVKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeCCCCCCCC----cceeCCCCCCCCEeEecCcCC
Confidence 3566665221 144566667777778888774
No 114
>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=74.80 E-value=0.68 Score=19.72 Aligned_cols=11 Identities=9% Similarity=0.138 Sum_probs=5.4
Q ss_pred ccccccccccC
Q psy14694 92 QLRFKKIRIAV 102 (102)
Q Consensus 92 ~~~C~~c~~~~ 102 (102)
|+.|+.|++.|
T Consensus 13 ~~~C~~C~~~F 23 (43)
T PF01428_consen 13 PFKCKHCGKSF 23 (43)
T ss_dssp HEE-TTTS-EE
T ss_pred CeECCCCCccc
Confidence 56666666554
No 115
>PF12907 zf-met2: Zinc-binding
Probab=74.18 E-value=0.51 Score=19.96 Aligned_cols=26 Identities=15% Similarity=0.249 Sum_probs=13.8
Q ss_pred ccCCCCCCccC---Cchhhhhhhhh-cCCC
Q psy14694 65 YKCFVCPYRSN---QRANLMSHPLV-QISD 90 (102)
Q Consensus 65 ~~c~~c~~~f~---~~~~l~~h~~~-~~~~ 90 (102)
++|.+|..+|. ....|..|... |..+
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 35666665443 33446667655 4443
No 116
>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=73.91 E-value=2 Score=19.42 Aligned_cols=9 Identities=22% Similarity=0.552 Sum_probs=4.5
Q ss_pred eCCCCCCCC
Q psy14694 38 DCFMCPYRT 46 (102)
Q Consensus 38 ~c~~c~~~~ 46 (102)
.|+.|+..+
T Consensus 4 ~CP~CG~~i 12 (54)
T TIGR01206 4 ECPDCGAEI 12 (54)
T ss_pred CCCCCCCEE
Confidence 455555543
No 117
>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=73.81 E-value=1.9 Score=20.19 Aligned_cols=14 Identities=21% Similarity=0.712 Sum_probs=9.2
Q ss_pred CCCccCCCCCCccC
Q psy14694 62 DRPYKCFVCPYRSN 75 (102)
Q Consensus 62 ~~~~~c~~c~~~f~ 75 (102)
.+.+.|+.||....
T Consensus 44 ~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 44 GRVFTCPNCGFEMD 57 (69)
T ss_pred cceEEcCCCCCEEC
Confidence 35577777776644
No 118
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=73.58 E-value=1.6 Score=18.27 Aligned_cols=11 Identities=0% Similarity=0.009 Sum_probs=5.5
Q ss_pred ccccccccccC
Q psy14694 92 QLRFKKIRIAV 102 (102)
Q Consensus 92 ~~~C~~c~~~~ 102 (102)
|+.|+.|+..|
T Consensus 12 ~f~C~~C~~~F 22 (39)
T smart00154 12 GFKCRHCGNLF 22 (39)
T ss_pred CeECCccCCcc
Confidence 45555555443
No 119
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=73.45 E-value=3.6 Score=25.62 Aligned_cols=10 Identities=0% Similarity=-0.190 Sum_probs=6.6
Q ss_pred CCcccccccc
Q psy14694 90 DEQLRFKKIR 99 (102)
Q Consensus 90 ~~~~~C~~c~ 99 (102)
.+...|..|+
T Consensus 250 ~r~e~C~~C~ 259 (305)
T TIGR01562 250 LKAETCDSCQ 259 (305)
T ss_pred eEEeeccccc
Confidence 3556677776
No 120
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=73.40 E-value=1.5 Score=27.06 Aligned_cols=26 Identities=8% Similarity=-0.020 Sum_probs=13.8
Q ss_pred CCCccCCchhhhhhhhhcCCCCcccccccccc
Q psy14694 70 CPYRSNQRANLMSHPLVQISDEQLRFKKIRIA 101 (102)
Q Consensus 70 c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~ 101 (102)
||.+|..- -+|.|.|+.|+ ||.|...
T Consensus 43 CgHtFCsl-----CIR~hL~~qp~-CP~Cr~~ 68 (391)
T COG5432 43 CGHTFCSL-----CIRRHLGTQPF-CPVCRED 68 (391)
T ss_pred cccchhHH-----HHHHHhcCCCC-Ccccccc
Confidence 55555432 23556666666 6666543
No 121
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=73.13 E-value=2.2 Score=22.02 Aligned_cols=26 Identities=19% Similarity=0.423 Sum_probs=22.4
Q ss_pred CccC----CCCCCccCCchhhhhhhhhcCC
Q psy14694 64 PYKC----FVCPYRSNQRANLMSHPLVQIS 89 (102)
Q Consensus 64 ~~~c----~~c~~~f~~~~~l~~h~~~~~~ 89 (102)
.|.| ..|+........+.+|.+.++|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4889 8899999999999999988664
No 122
>KOG3408|consensus
Probab=72.42 E-value=1.5 Score=23.27 Aligned_cols=26 Identities=19% Similarity=0.328 Sum_probs=21.7
Q ss_pred CCCCccCCCCCCccCCchhhhhhhhh
Q psy14694 61 GDRPYKCFVCPYRSNQRANLMSHPLV 86 (102)
Q Consensus 61 ~~~~~~c~~c~~~f~~~~~l~~h~~~ 86 (102)
|.--|.|..|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44458899999999999999988776
No 123
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=72.38 E-value=2.1 Score=19.26 Aligned_cols=41 Identities=20% Similarity=0.351 Sum_probs=18.2
Q ss_pred CceeCCC-CCCCCCCcchHHHHhhhhcCCCCccCCC----CCCccC
Q psy14694 35 KKYDCFM-CPYRTPYSGTMRRHIRAHIGDRPYKCFV----CPYRSN 75 (102)
Q Consensus 35 ~~~~c~~-c~~~~~~~~~l~~h~~~h~~~~~~~c~~----c~~~f~ 75 (102)
.+..|+. |+..-.....|..|....-..++..|.. |...+.
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 3455554 2222222456666666555555666666 655444
No 124
>PF15269 zf-C2H2_7: Zinc-finger
Probab=72.23 E-value=2.1 Score=18.53 Aligned_cols=21 Identities=43% Similarity=1.119 Sum_probs=13.1
Q ss_pred ccCCCCCCccCCchhhhhhhh
Q psy14694 65 YKCFVCPYRSNQRANLMSHPL 85 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~ 85 (102)
|+|-.|..+-...+.|.+|++
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 456666666666666666654
No 125
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=72.07 E-value=1.9 Score=17.76 Aligned_cols=9 Identities=0% Similarity=-0.164 Sum_probs=5.3
Q ss_pred ccccccccC
Q psy14694 94 RFKKIRIAV 102 (102)
Q Consensus 94 ~C~~c~~~~ 102 (102)
.|+.|+++|
T Consensus 4 ~CprC~kg~ 12 (36)
T PF14787_consen 4 LCPRCGKGF 12 (36)
T ss_dssp C-TTTSSSC
T ss_pred cCcccCCCc
Confidence 477777764
No 126
>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=71.74 E-value=1.3 Score=23.25 Aligned_cols=13 Identities=15% Similarity=0.299 Sum_probs=7.4
Q ss_pred ccCCCCCCccCCc
Q psy14694 65 YKCFVCPYRSNQR 77 (102)
Q Consensus 65 ~~c~~c~~~f~~~ 77 (102)
..|..|+..|...
T Consensus 71 ~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 71 ARCRDCGHEFEPD 83 (113)
T ss_dssp EEETTTS-EEECH
T ss_pred EECCCCCCEEecC
Confidence 5666777666543
No 127
>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=71.58 E-value=2.6 Score=16.73 Aligned_cols=8 Identities=13% Similarity=0.127 Sum_probs=3.7
Q ss_pred cccccccc
Q psy14694 93 LRFKKIRI 100 (102)
Q Consensus 93 ~~C~~c~~ 100 (102)
|.|..|++
T Consensus 28 f~C~~C~~ 35 (39)
T smart00132 28 FKCSKCGK 35 (39)
T ss_pred CCCcccCC
Confidence 44444444
No 128
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=71.20 E-value=5.4 Score=22.80 Aligned_cols=7 Identities=29% Similarity=1.004 Sum_probs=3.7
Q ss_pred ccCCCCC
Q psy14694 65 YKCFVCP 71 (102)
Q Consensus 65 ~~c~~c~ 71 (102)
|.|+.||
T Consensus 133 F~Cp~Cg 139 (176)
T COG1675 133 FTCPKCG 139 (176)
T ss_pred CCCCCCC
Confidence 4555555
No 129
>KOG0978|consensus
Probab=70.42 E-value=1.7 Score=30.02 Aligned_cols=16 Identities=19% Similarity=0.154 Sum_probs=10.1
Q ss_pred cCCCCccccccccccC
Q psy14694 87 QISDEQLRFKKIRIAV 102 (102)
Q Consensus 87 ~~~~~~~~C~~c~~~~ 102 (102)
-.+.+.-.||.|+.+|
T Consensus 673 r~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 673 RYETRQRKCPKCNAAF 688 (698)
T ss_pred HHHHhcCCCCCCCCCC
Confidence 3445556677777766
No 130
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=70.25 E-value=7.8 Score=29.02 Aligned_cols=12 Identities=25% Similarity=0.426 Sum_probs=7.9
Q ss_pred CccCCCCCCccC
Q psy14694 64 PYKCFVCPYRSN 75 (102)
Q Consensus 64 ~~~c~~c~~~f~ 75 (102)
++.|+.||....
T Consensus 692 vy~CPsCGaev~ 703 (1337)
T PRK14714 692 VYVCPDCGAEVP 703 (1337)
T ss_pred ceeCccCCCccC
Confidence 567888876543
No 131
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=70.16 E-value=2.2 Score=22.99 Aligned_cols=15 Identities=7% Similarity=0.082 Sum_probs=10.5
Q ss_pred CCCCccccccccccC
Q psy14694 88 ISDEQLRFKKIRIAV 102 (102)
Q Consensus 88 ~~~~~~~C~~c~~~~ 102 (102)
.|..-|.|+.|++.|
T Consensus 49 ~~~qRyrC~~C~~tf 63 (129)
T COG3677 49 RGHQRYKCKSCGSTF 63 (129)
T ss_pred ccccccccCCcCcce
Confidence 345668888888776
No 132
>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=69.82 E-value=0.63 Score=19.43 Aligned_cols=9 Identities=0% Similarity=-0.355 Sum_probs=5.5
Q ss_pred ccccccccc
Q psy14694 93 LRFKKIRIA 101 (102)
Q Consensus 93 ~~C~~c~~~ 101 (102)
|.|..||..
T Consensus 29 y~C~~C~~~ 37 (39)
T PF01096_consen 29 YVCCNCGHR 37 (39)
T ss_dssp EEESSSTEE
T ss_pred EEeCCCCCe
Confidence 666666643
No 133
>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=69.51 E-value=0.79 Score=26.90 Aligned_cols=27 Identities=11% Similarity=0.250 Sum_probs=18.0
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCC
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISD 90 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~ 90 (102)
-|.|..|+|.|.....+..|+...+.+
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred EECCCCCCcccCChHHHHHHHhhcCHH
Confidence 478888888888888888887764433
No 134
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=69.47 E-value=2.1 Score=21.59 Aligned_cols=34 Identities=21% Similarity=0.343 Sum_probs=20.3
Q ss_pred CCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCc
Q psy14694 34 RKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQR 77 (102)
Q Consensus 34 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~ 77 (102)
...|.|+.|++.-.. + .+..+|.|..|++.|.-.
T Consensus 34 ~a~y~CpfCgk~~vk--------R--~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 34 HAKYFCPFCGKHAVK--------R--QAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred hCCccCCCCCCCcee--------e--eeeEEEEcCCCCCEEeCC
Confidence 345788888753211 1 122468888888877543
No 135
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=68.74 E-value=3.7 Score=26.73 Aligned_cols=14 Identities=21% Similarity=0.674 Sum_probs=7.8
Q ss_pred CccCCCCCCccCCc
Q psy14694 64 PYKCFVCPYRSNQR 77 (102)
Q Consensus 64 ~~~c~~c~~~f~~~ 77 (102)
-|.|..|+..+...
T Consensus 367 g~rC~kCg~~~~~~ 380 (421)
T COG1571 367 GFRCKKCGTRARET 380 (421)
T ss_pred CcccccccccCCcc
Confidence 56666666555433
No 136
>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=68.43 E-value=1.3 Score=19.79 Aligned_cols=9 Identities=0% Similarity=-0.297 Sum_probs=3.5
Q ss_pred ccccccccC
Q psy14694 94 RFKKIRIAV 102 (102)
Q Consensus 94 ~C~~c~~~~ 102 (102)
.||.|++.|
T Consensus 22 ~CPlC~r~l 30 (54)
T PF04423_consen 22 CCPLCGRPL 30 (54)
T ss_dssp E-TTT--EE
T ss_pred cCCCCCCCC
Confidence 566666543
No 137
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=67.89 E-value=3.5 Score=21.28 Aligned_cols=12 Identities=17% Similarity=0.224 Sum_probs=6.5
Q ss_pred ceeCCCCCCCCC
Q psy14694 36 KYDCFMCPYRTP 47 (102)
Q Consensus 36 ~~~c~~c~~~~~ 47 (102)
+..|..||..|.
T Consensus 2 pH~CtrCG~vf~ 13 (112)
T COG3364 2 PHQCTRCGEVFD 13 (112)
T ss_pred Cceecccccccc
Confidence 345555665554
No 138
>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=66.65 E-value=5.3 Score=17.73 Aligned_cols=28 Identities=18% Similarity=0.308 Sum_probs=17.1
Q ss_pred eCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCc
Q psy14694 38 DCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQR 77 (102)
Q Consensus 38 ~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~ 77 (102)
.|..|++.|.. ..+.+.|..||+.|-..
T Consensus 4 ~C~~C~~~F~~------------~~rk~~Cr~Cg~~~C~~ 31 (57)
T cd00065 4 SCMGCGKPFTL------------TRRRHHCRNCGRIFCSK 31 (57)
T ss_pred cCcccCccccC------------CccccccCcCcCCcChH
Confidence 46667766653 13446777788776543
No 139
>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=66.54 E-value=3.2 Score=22.94 Aligned_cols=8 Identities=25% Similarity=0.476 Sum_probs=4.4
Q ss_pred ccCCCCCC
Q psy14694 65 YKCFVCPY 72 (102)
Q Consensus 65 ~~c~~c~~ 72 (102)
|.|..||.
T Consensus 113 l~C~~Cg~ 120 (146)
T PF07295_consen 113 LVCENCGH 120 (146)
T ss_pred EecccCCC
Confidence 55555553
No 140
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=66.50 E-value=1.2 Score=19.76 Aligned_cols=8 Identities=0% Similarity=-0.180 Sum_probs=3.2
Q ss_pred cccccccc
Q psy14694 93 LRFKKIRI 100 (102)
Q Consensus 93 ~~C~~c~~ 100 (102)
|.||.|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 77887765
No 141
>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=65.36 E-value=5.3 Score=20.69 Aligned_cols=7 Identities=43% Similarity=1.160 Sum_probs=3.8
Q ss_pred ccCCCCC
Q psy14694 65 YKCFVCP 71 (102)
Q Consensus 65 ~~c~~c~ 71 (102)
|.|..|+
T Consensus 32 y~C~~C~ 38 (102)
T PF11672_consen 32 YVCTPCD 38 (102)
T ss_pred EECCCCC
Confidence 5555554
No 142
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=65.08 E-value=10 Score=15.95 Aligned_cols=23 Identities=22% Similarity=0.229 Sum_probs=12.6
Q ss_pred cCCccccccc-cCHHHHHHHHhhh
Q psy14694 3 KCTHCKVDLN-LDTEIILQHYKLC 25 (102)
Q Consensus 3 ~c~~c~~~f~-~~~~~l~~h~~~~ 25 (102)
.|+.||..|. ...++...|.+-|
T Consensus 15 ~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 15 TCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCCCCEECCCCHHHHHHHHHHH
Confidence 5777887663 1333444555544
No 143
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=64.91 E-value=9.8 Score=23.10 Aligned_cols=57 Identities=14% Similarity=0.135 Sum_probs=29.2
Q ss_pred CCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 33 SRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
..+.|.|..|...+.. +.-.-...-.|..|.+.|..-- .....|---|.|+.|+..|
T Consensus 109 ~drqFaC~~Cd~~WwR--------rvp~rKeVSRCr~C~~rYDPVP-----~dkmwG~aef~C~~C~h~F 165 (278)
T PF15135_consen 109 VDRQFACSSCDHMWWR--------RVPQRKEVSRCRKCRKRYDPVP-----CDKMWGIAEFHCPKCRHNF 165 (278)
T ss_pred cceeeeccccchHHHh--------ccCcccccccccccccccCCCc-----cccccceeeeecccccccc
Confidence 3466788877544321 2212222345666665554321 1224555557777777655
No 144
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=64.13 E-value=4.3 Score=18.49 Aligned_cols=13 Identities=8% Similarity=0.105 Sum_probs=8.7
Q ss_pred CCCcccccccccc
Q psy14694 89 SDEQLRFKKIRIA 101 (102)
Q Consensus 89 ~~~~~~C~~c~~~ 101 (102)
+...|+|+.||..
T Consensus 11 ~~v~~~Cp~cGip 23 (55)
T PF13824_consen 11 AHVNFECPDCGIP 23 (55)
T ss_pred cccCCcCCCCCCc
Confidence 3456788888763
No 145
>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=63.13 E-value=2.5 Score=23.14 Aligned_cols=30 Identities=17% Similarity=0.311 Sum_probs=19.4
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCcccccccccc
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIA 101 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~ 101 (102)
.|.|..|+..+.. +.++ ....|.|..|+-.
T Consensus 123 ~~~C~~C~~~~~r------~~~~--~~~~~~C~~C~~~ 152 (157)
T PF10263_consen 123 VYRCPSCGREYKR------HRRS--KRKRYRCGRCGGP 152 (157)
T ss_pred EEEcCCCCCEeee------eccc--chhhEECCCCCCE
Confidence 4788889876643 3333 3334899999853
No 146
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=63.06 E-value=3.4 Score=17.25 Aligned_cols=19 Identities=16% Similarity=0.016 Sum_probs=12.9
Q ss_pred CCccCCCCCCccCCchhhh
Q psy14694 63 RPYKCFVCPYRSNQRANLM 81 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~ 81 (102)
....|..|+-.+.....|.
T Consensus 18 ~id~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 18 EIDVCPSCGGIWFDAGELE 36 (41)
T ss_pred EEEECCCCCeEEccHHHHH
Confidence 4467888887777666554
No 147
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.87 E-value=2.6 Score=25.16 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=15.1
Q ss_pred CCCceeCCCCCCCCCCcchHHHHhhh
Q psy14694 33 SRKKYDCFMCPYRTPYSGTMRRHIRA 58 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~~~l~~h~~~ 58 (102)
-++..+|++|+-.|.....+..-.++
T Consensus 16 ~kk~ieCPvC~tkFkkeev~tgsiRi 41 (267)
T COG1655 16 YKKTIECPVCNTKFKKEEVKTGSIRI 41 (267)
T ss_pred hhceeccCcccchhhhhheeccceeE
Confidence 35567777777766655444444443
No 148
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.05 E-value=4.2 Score=21.73 Aligned_cols=10 Identities=30% Similarity=0.879 Sum_probs=5.8
Q ss_pred ccCCCCCCccC
Q psy14694 65 YKCFVCPYRSN 75 (102)
Q Consensus 65 ~~c~~c~~~f~ 75 (102)
..| .|+..|.
T Consensus 71 ~~C-~Cg~~~~ 80 (124)
T PRK00762 71 IEC-ECGYEGV 80 (124)
T ss_pred EEe-eCcCccc
Confidence 456 6665554
No 149
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=60.97 E-value=2.3 Score=17.14 Aligned_cols=10 Identities=0% Similarity=-0.140 Sum_probs=5.1
Q ss_pred cccccccccc
Q psy14694 92 QLRFKKIRIA 101 (102)
Q Consensus 92 ~~~C~~c~~~ 101 (102)
.+.|+.|++.
T Consensus 4 ~~~C~nC~R~ 13 (33)
T PF08209_consen 4 YVECPNCGRP 13 (33)
T ss_dssp EEE-TTTSSE
T ss_pred eEECCCCcCC
Confidence 3566666653
No 150
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=60.90 E-value=4.3 Score=18.15 Aligned_cols=25 Identities=16% Similarity=0.404 Sum_probs=11.0
Q ss_pred CCccCCCCCCccCCchhhhhhhhhc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLVQ 87 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~~ 87 (102)
..|.|+.|...|-..-.+-.|...|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 3477777777776655555554433
No 151
>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=60.76 E-value=3.2 Score=17.43 Aligned_cols=13 Identities=8% Similarity=-0.135 Sum_probs=7.9
Q ss_pred CCCcccccccccc
Q psy14694 89 SDEQLRFKKIRIA 101 (102)
Q Consensus 89 ~~~~~~C~~c~~~ 101 (102)
+-..+.|+.||..
T Consensus 29 ~vp~~~C~~CGE~ 41 (46)
T TIGR03831 29 NVPALVCPQCGEE 41 (46)
T ss_pred CCCccccccCCCE
Confidence 3344667777764
No 152
>PLN02294 cytochrome c oxidase subunit Vb
Probab=60.62 E-value=3.8 Score=23.26 Aligned_cols=17 Identities=0% Similarity=-0.066 Sum_probs=11.9
Q ss_pred hhcCCCCccccccccccC
Q psy14694 85 LVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 85 ~~~~~~~~~~C~~c~~~~ 102 (102)
.++.| +|++|++||.-|
T Consensus 135 ~L~kG-kp~RCpeCG~~f 151 (174)
T PLN02294 135 WLEKG-KSFECPVCTQYF 151 (174)
T ss_pred EecCC-CceeCCCCCCEE
Confidence 34444 699999998644
No 153
>PRK04023 DNA polymerase II large subunit; Validated
Probab=60.58 E-value=10 Score=27.85 Aligned_cols=9 Identities=11% Similarity=-0.101 Sum_probs=6.0
Q ss_pred ccccccccc
Q psy14694 92 QLRFKKIRI 100 (102)
Q Consensus 92 ~~~C~~c~~ 100 (102)
++.|+.||.
T Consensus 663 ~y~CPKCG~ 671 (1121)
T PRK04023 663 EDECEKCGR 671 (1121)
T ss_pred CCcCCCCCC
Confidence 366777775
No 154
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=60.46 E-value=4.9 Score=18.22 Aligned_cols=9 Identities=33% Similarity=0.766 Sum_probs=4.5
Q ss_pred CccCCCCCC
Q psy14694 64 PYKCFVCPY 72 (102)
Q Consensus 64 ~~~c~~c~~ 72 (102)
|+-|+.|.+
T Consensus 28 PlyCpKCK~ 36 (55)
T PF14205_consen 28 PLYCPKCKQ 36 (55)
T ss_pred cccCCCCCc
Confidence 445555543
No 155
>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=60.09 E-value=3.6 Score=15.92 Aligned_cols=9 Identities=22% Similarity=0.608 Sum_probs=4.8
Q ss_pred cCCCCCCcc
Q psy14694 66 KCFVCPYRS 74 (102)
Q Consensus 66 ~c~~c~~~f 74 (102)
.|..|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 345555555
No 156
>PRK05978 hypothetical protein; Provisional
Probab=60.01 E-value=6.1 Score=21.93 Aligned_cols=10 Identities=20% Similarity=0.484 Sum_probs=5.0
Q ss_pred cCCCCCCccC
Q psy14694 66 KCFVCPYRSN 75 (102)
Q Consensus 66 ~c~~c~~~f~ 75 (102)
.|+.||..|.
T Consensus 54 ~C~~CG~~~~ 63 (148)
T PRK05978 54 HCAACGEDFT 63 (148)
T ss_pred CccccCCccc
Confidence 4555554443
No 157
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=59.65 E-value=9.8 Score=16.01 Aligned_cols=11 Identities=9% Similarity=0.123 Sum_probs=7.2
Q ss_pred CCccccccccc
Q psy14694 90 DEQLRFKKIRI 100 (102)
Q Consensus 90 ~~~~~C~~c~~ 100 (102)
.....||.|++
T Consensus 34 ~~~~~CP~C~k 44 (44)
T PF14634_consen 34 GKSVKCPICRK 44 (44)
T ss_pred CCCCCCcCCCC
Confidence 45667777764
No 158
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=59.60 E-value=5.2 Score=17.95 Aligned_cols=10 Identities=20% Similarity=0.079 Sum_probs=4.7
Q ss_pred CCcccccccc
Q psy14694 90 DEQLRFKKIR 99 (102)
Q Consensus 90 ~~~~~C~~c~ 99 (102)
+....||.||
T Consensus 44 ~~i~~Cp~Cg 53 (56)
T PF02591_consen 44 DEIVFCPNCG 53 (56)
T ss_pred CCeEECcCCC
Confidence 3444455554
No 159
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=59.50 E-value=5.3 Score=21.92 Aligned_cols=13 Identities=23% Similarity=0.031 Sum_probs=8.4
Q ss_pred CCccccccccccC
Q psy14694 90 DEQLRFKKIRIAV 102 (102)
Q Consensus 90 ~~~~~C~~c~~~~ 102 (102)
+.-|.|+.||+-|
T Consensus 122 ~~f~~C~~C~kiy 134 (147)
T PF01927_consen 122 DEFWRCPGCGKIY 134 (147)
T ss_pred CeEEECCCCCCEe
Confidence 3357788887743
No 160
>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 smart00661 RPOL9 RNA polymerase subunit 9.
Probab=57.54 E-value=9.8 Score=16.51 Aligned_cols=14 Identities=21% Similarity=0.596 Sum_probs=10.0
Q ss_pred CccCCCCCCccCCc
Q psy14694 64 PYKCFVCPYRSNQR 77 (102)
Q Consensus 64 ~~~c~~c~~~f~~~ 77 (102)
.+.|+.|+..+...
T Consensus 20 ~~vC~~Cg~~~~~~ 33 (52)
T smart00661 20 RFVCRKCGYEEPIE 33 (52)
T ss_pred EEECCcCCCeEECC
Confidence 57899898766543
No 162
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=57.44 E-value=5 Score=21.87 Aligned_cols=25 Identities=12% Similarity=0.058 Sum_probs=16.9
Q ss_pred ccCCCCCCccCCchhhhhhhhhcCCCCc
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQISDEQ 92 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 92 (102)
..|.++|+.|.. |++|+.+|.|--|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 457777777764 6777777766543
No 163
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=57.32 E-value=7.7 Score=17.59 Aligned_cols=11 Identities=18% Similarity=0.211 Sum_probs=6.1
Q ss_pred CCccCCCCCCc
Q psy14694 63 RPYKCFVCPYR 73 (102)
Q Consensus 63 ~~~~c~~c~~~ 73 (102)
....|+.|+..
T Consensus 20 DiVvCp~Cgap 30 (54)
T PF14446_consen 20 DIVVCPECGAP 30 (54)
T ss_pred CEEECCCCCCc
Confidence 34566666643
No 164
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.91 E-value=4.7 Score=18.74 Aligned_cols=51 Identities=18% Similarity=0.263 Sum_probs=24.0
Q ss_pred eCCCCCCC-CCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhcCCCCc
Q psy14694 38 DCFMCPYR-TPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQISDEQ 92 (102)
Q Consensus 38 ~c~~c~~~-~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~ 92 (102)
.|.+|.+. +-....+..-+......+.|.|++|......+ .-.|+.+|...
T Consensus 4 kCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva~k----t~~R~~~g~f~ 55 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVAIK----TISRVNSGHFN 55 (68)
T ss_pred eEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhchh----hHHHhccCCcc
Confidence 45566543 22223333222223334568899886544332 33455555443
No 165
>KOG2907|consensus
Probab=56.90 E-value=7.6 Score=20.46 Aligned_cols=36 Identities=14% Similarity=0.105 Sum_probs=18.6
Q ss_pred ccCCCCCCccCCchhhhhhhhhcCCCCc--cccccccccC
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQISDEQ--LRFKKIRIAV 102 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~--~~C~~c~~~~ 102 (102)
.+|+.||..=..-..+ .+|..-.... |.|+.|+..|
T Consensus 75 ~kCpkCghe~m~Y~T~--QlRSADEGQTVFYTC~kC~~k~ 112 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTL--QLRSADEGQTVFYTCPKCKYKF 112 (116)
T ss_pred ccCcccCCchhhhhhh--hcccccCCceEEEEcCccceee
Confidence 5788887432221121 2333333333 8888888654
No 166
>PRK01343 zinc-binding protein; Provisional
Probab=56.61 E-value=8 Score=17.76 Aligned_cols=9 Identities=22% Similarity=0.382 Sum_probs=4.9
Q ss_pred ccCCCCCCc
Q psy14694 65 YKCFVCPYR 73 (102)
Q Consensus 65 ~~c~~c~~~ 73 (102)
..|+.|++.
T Consensus 10 ~~CP~C~k~ 18 (57)
T PRK01343 10 RPCPECGKP 18 (57)
T ss_pred CcCCCCCCc
Confidence 456666643
No 167
>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=56.31 E-value=5.3 Score=18.60 Aligned_cols=28 Identities=18% Similarity=0.362 Sum_probs=11.2
Q ss_pred ceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccC
Q psy14694 36 KYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSN 75 (102)
Q Consensus 36 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~ 75 (102)
.-.|..|++.|.. ..+.+.|..||..|-
T Consensus 9 ~~~C~~C~~~F~~------------~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 9 ASNCMICGKKFSL------------FRRRHHCRNCGRVVC 36 (69)
T ss_dssp -SB-TTT--B-BS------------SS-EEE-TTT--EEE
T ss_pred CCcCcCcCCcCCC------------ceeeEccCCCCCEEC
Confidence 3467788887742 124456777777664
No 168
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=55.87 E-value=6.8 Score=21.41 Aligned_cols=31 Identities=23% Similarity=0.266 Sum_probs=19.3
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCcccccccccc
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIA 101 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~ 101 (102)
.|.|..|+..+.. +.+ +....-|.|..|+-.
T Consensus 112 ~y~C~~C~~~~~~------~rr-~~~~~~y~C~~C~g~ 142 (146)
T smart00731 112 PYRCTGCGQRYLR------VRR-SNNVSRYRCGKCGGK 142 (146)
T ss_pred EEECCCCCCCCce------Ecc-ccCcceEEcCCCCCE
Confidence 5888888866542 222 222256889888754
No 169
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=55.80 E-value=6.5 Score=21.91 Aligned_cols=13 Identities=23% Similarity=0.506 Sum_probs=9.5
Q ss_pred CccCCCCCCccCC
Q psy14694 64 PYKCFVCPYRSNQ 76 (102)
Q Consensus 64 ~~~c~~c~~~f~~ 76 (102)
.-.|..|+..|.+
T Consensus 28 RReC~~C~~RFTT 40 (156)
T COG1327 28 RRECLECGERFTT 40 (156)
T ss_pred hhcccccccccch
Confidence 3578888887764
No 170
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=55.60 E-value=2.3 Score=21.81 Aligned_cols=38 Identities=18% Similarity=0.301 Sum_probs=20.6
Q ss_pred CCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccC
Q psy14694 34 RKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSN 75 (102)
Q Consensus 34 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~ 75 (102)
++.|+|+.|+..-...-.+..- ...-...|..||..|.
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~----~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKT----VNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEec----CceeEEEcccCcceEE
Confidence 5668888887654433222111 1112356888887664
No 171
>KOG2593|consensus
Probab=55.36 E-value=12 Score=24.58 Aligned_cols=38 Identities=13% Similarity=0.241 Sum_probs=26.4
Q ss_pred CCCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCc
Q psy14694 33 SRKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYR 73 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~ 73 (102)
....|.|+.|.+.|+...++. -+....-.|.|..|+-.
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGGE 162 (436)
T ss_pred ccccccCCccccchhhhHHHH---hhcccCceEEEecCCCc
Confidence 567799999999988766653 23333445888888753
No 172
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=55.09 E-value=4.5 Score=16.66 Aligned_cols=10 Identities=10% Similarity=-0.004 Sum_probs=4.7
Q ss_pred Cccccccccc
Q psy14694 91 EQLRFKKIRI 100 (102)
Q Consensus 91 ~~~~C~~c~~ 100 (102)
+-|.|..||-
T Consensus 5 ~~YkC~~CGn 14 (36)
T PF06397_consen 5 EFYKCEHCGN 14 (36)
T ss_dssp EEEE-TTT--
T ss_pred cEEEccCCCC
Confidence 3477777763
No 173
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=55.06 E-value=6.6 Score=21.76 Aligned_cols=14 Identities=21% Similarity=0.406 Sum_probs=10.5
Q ss_pred CccCCCCCCccCCc
Q psy14694 64 PYKCFVCPYRSNQR 77 (102)
Q Consensus 64 ~~~c~~c~~~f~~~ 77 (102)
.-.|..|++.|++-
T Consensus 28 RReC~~C~~RFTTy 41 (147)
T TIGR00244 28 RRECLECHERFTTF 41 (147)
T ss_pred cccCCccCCcccee
Confidence 36788899888753
No 174
>KOG4173|consensus
Probab=54.56 E-value=1.5 Score=25.61 Aligned_cols=19 Identities=21% Similarity=0.571 Sum_probs=9.4
Q ss_pred cCCccccccccCHHHHHHHH
Q psy14694 3 KCTHCKVDLNLDTEIILQHY 22 (102)
Q Consensus 3 ~c~~c~~~f~~~~~~l~~h~ 22 (102)
.|..|.++|. +...|..|+
T Consensus 108 sCs~C~r~~P-t~hLLd~HI 126 (253)
T KOG4173|consen 108 SCSFCKRAFP-TGHLLDAHI 126 (253)
T ss_pred hhHHHHHhCC-chhhhhHHH
Confidence 3445555555 444444444
No 175
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=54.41 E-value=8.3 Score=17.09 Aligned_cols=9 Identities=33% Similarity=0.966 Sum_probs=4.3
Q ss_pred CccCCCCCC
Q psy14694 64 PYKCFVCPY 72 (102)
Q Consensus 64 ~~~c~~c~~ 72 (102)
.+.|..|+.
T Consensus 37 r~~C~~Cgy 45 (50)
T PRK00432 37 RWHCGKCGY 45 (50)
T ss_pred cEECCCcCC
Confidence 344555543
No 176
>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=54.22 E-value=5.9 Score=16.93 Aligned_cols=8 Identities=0% Similarity=-0.296 Sum_probs=4.2
Q ss_pred cccccccC
Q psy14694 95 FKKIRIAV 102 (102)
Q Consensus 95 C~~c~~~~ 102 (102)
|+.||+.|
T Consensus 11 C~~C~rpf 18 (42)
T PF10013_consen 11 CPVCGRPF 18 (42)
T ss_pred CcccCCcc
Confidence 55555544
No 177
>KOG4167|consensus
Probab=54.10 E-value=3.3 Score=28.96 Aligned_cols=24 Identities=17% Similarity=0.247 Sum_probs=19.4
Q ss_pred ccCCccccccccCHHHHHHHHhhhc
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCS 26 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~ 26 (102)
|.|.+|++.|- ....+..|+++|.
T Consensus 793 FpCreC~kvF~-KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFF-KIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHH-HHhhhhHHHHHHH
Confidence 78999999997 6666778888875
No 178
>PHA02998 RNA polymerase subunit; Provisional
Probab=53.83 E-value=5.8 Score=22.73 Aligned_cols=12 Identities=17% Similarity=0.279 Sum_probs=5.9
Q ss_pred ccCCCCCCccCC
Q psy14694 65 YKCFVCPYRSNQ 76 (102)
Q Consensus 65 ~~c~~c~~~f~~ 76 (102)
|.|..|++.|..
T Consensus 172 YkC~~CG~~wkp 183 (195)
T PHA02998 172 HACRDCKKHFKP 183 (195)
T ss_pred EEcCCCCCccCC
Confidence 445555554443
No 179
>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=53.74 E-value=5.5 Score=20.41 Aligned_cols=18 Identities=6% Similarity=-0.034 Sum_probs=12.6
Q ss_pred hhhcCCCCccccccccccC
Q psy14694 84 PLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 84 ~~~~~~~~~~~C~~c~~~~ 102 (102)
...+.| +++.|+.||.-|
T Consensus 72 ~~l~~g-~~~rC~eCG~~f 89 (97)
T cd00924 72 MWLEKG-KPKRCPECGHVF 89 (97)
T ss_pred EEEeCC-CceeCCCCCcEE
Confidence 445666 689999988643
No 180
>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=53.64 E-value=9.1 Score=25.63 Aligned_cols=21 Identities=10% Similarity=-0.197 Sum_probs=11.1
Q ss_pred hhhhhhhcCCCCccccccccc
Q psy14694 80 LMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 80 l~~h~~~~~~~~~~~C~~c~~ 100 (102)
|.-|.--+....|..||.||-
T Consensus 241 l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 241 LRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred EEcCCCcCcCCCCCCCCCCCC
Confidence 333433344455667777764
No 181
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=53.14 E-value=6.5 Score=20.38 Aligned_cols=9 Identities=11% Similarity=-0.152 Sum_probs=5.4
Q ss_pred ccccccccc
Q psy14694 93 LRFKKIRIA 101 (102)
Q Consensus 93 ~~C~~c~~~ 101 (102)
..||+||..
T Consensus 50 t~CP~Cg~~ 58 (115)
T COG1885 50 TSCPKCGEP 58 (115)
T ss_pred ccCCCCCCc
Confidence 456666654
No 182
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.21 E-value=7.7 Score=23.89 Aligned_cols=12 Identities=33% Similarity=0.811 Sum_probs=6.8
Q ss_pred CCccCCCCCCcc
Q psy14694 63 RPYKCFVCPYRS 74 (102)
Q Consensus 63 ~~~~c~~c~~~f 74 (102)
+.+.|+.||..+
T Consensus 321 r~~~C~~cg~~~ 332 (364)
T COG0675 321 RLFKCPRCGFVH 332 (364)
T ss_pred eeEECCCCCCee
Confidence 445666666543
No 183
>PRK05580 primosome assembly protein PriA; Validated
Probab=52.12 E-value=11 Score=26.34 Aligned_cols=21 Identities=10% Similarity=-0.176 Sum_probs=12.6
Q ss_pred hhhhhhhcCCCCccccccccc
Q psy14694 80 LMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 80 l~~h~~~~~~~~~~~C~~c~~ 100 (102)
|.-|.--+....|..|+.||.
T Consensus 409 l~Ch~Cg~~~~~~~~Cp~Cg~ 429 (679)
T PRK05580 409 LRCHHCGYQEPIPKACPECGS 429 (679)
T ss_pred EECCCCcCCCCCCCCCCCCcC
Confidence 344444445555777888864
No 184
>KOG3214|consensus
Probab=51.51 E-value=4.9 Score=20.65 Aligned_cols=13 Identities=15% Similarity=0.388 Sum_probs=8.7
Q ss_pred ccCCCCCCccCCc
Q psy14694 65 YKCFVCPYRSNQR 77 (102)
Q Consensus 65 ~~c~~c~~~f~~~ 77 (102)
..|.+|+..|...
T Consensus 48 ~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 48 ASCRICEESFQTT 60 (109)
T ss_pred eeeeehhhhhccc
Confidence 5677777777543
No 185
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=50.50 E-value=19 Score=20.15 Aligned_cols=43 Identities=21% Similarity=0.389 Sum_probs=17.7
Q ss_pred cCCcccccccc-----CHHHHHHHHhhhc--ccccc----CCCCceeCCCCCCC
Q psy14694 3 KCTHCKVDLNL-----DTEIILQHYKLCS--EGARQ----SSRKKYDCFMCPYR 45 (102)
Q Consensus 3 ~c~~c~~~f~~-----~~~~l~~h~~~~~--~~~~~----~~~~~~~c~~c~~~ 45 (102)
+|..|+++|.+ ..+++..|+.... +...| .++..++|-.||..
T Consensus 16 ~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~ 69 (152)
T PF09416_consen 16 KCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSR 69 (152)
T ss_dssp EETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT---
T ss_pred EcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCC
Confidence 57778888842 3345666654322 11222 24556778777753
No 186
>PF14369 zf-RING_3: zinc-finger
Probab=50.23 E-value=6.3 Score=16.01 Aligned_cols=9 Identities=0% Similarity=-0.134 Sum_probs=6.3
Q ss_pred ccccccccC
Q psy14694 94 RFKKIRIAV 102 (102)
Q Consensus 94 ~C~~c~~~~ 102 (102)
.||.|+-+|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 577777665
No 187
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=49.56 E-value=12 Score=17.30 Aligned_cols=26 Identities=23% Similarity=0.446 Sum_probs=15.7
Q ss_pred CCCCCCCcchHHHHhhhhcCCCCccCCCCCC
Q psy14694 42 CPYRTPYSGTMRRHIRAHIGDRPYKCFVCPY 72 (102)
Q Consensus 42 c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~ 72 (102)
||..|... |. -...|++...|+.|..
T Consensus 27 CGDRFeIs--Le---Dl~~GE~VArCPSCSL 52 (67)
T COG5216 27 CGDRFEIS--LE---DLRNGEVVARCPSCSL 52 (67)
T ss_pred CCCEeEEE--HH---HhhCCceEEEcCCceE
Confidence 66666542 32 2346777777877753
No 188
>PRK14873 primosome assembly protein PriA; Provisional
Probab=49.49 E-value=8.6 Score=26.77 Aligned_cols=10 Identities=10% Similarity=0.062 Sum_probs=7.1
Q ss_pred Cccccccccc
Q psy14694 91 EQLRFKKIRI 100 (102)
Q Consensus 91 ~~~~C~~c~~ 100 (102)
.|+.|+.||-
T Consensus 421 ~p~~Cp~Cgs 430 (665)
T PRK14873 421 PDWRCPRCGS 430 (665)
T ss_pred cCccCCCCcC
Confidence 4777888874
No 189
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=49.43 E-value=9.5 Score=21.80 Aligned_cols=38 Identities=8% Similarity=0.070 Sum_probs=23.4
Q ss_pred CCccCCCCCCccCCchhhhhhhhh--cCC----------CCccccccccc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLV--QIS----------DEQLRFKKIRI 100 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~--~~~----------~~~~~C~~c~~ 100 (102)
....|..||+.|.....+..=... +.+ +..+-|++|..
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~~~~~~l~~~~~~~~~~~~~~~~~~~Cp~Cr~ 162 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVALAAELLAQQQNAPQNREMLRAQASVCPECKQ 162 (181)
T ss_pred ccCcCcccCCccCcHhHHHHHHHHhhhccCcHhhHHHHHHHhccCHHHHh
Confidence 467899999999866544422211 221 12467999974
No 190
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.41 E-value=6.6 Score=14.61 Aligned_cols=6 Identities=0% Similarity=-0.191 Sum_probs=3.2
Q ss_pred cccccc
Q psy14694 95 FKKIRI 100 (102)
Q Consensus 95 C~~c~~ 100 (102)
|+.||.
T Consensus 19 C~~CG~ 24 (26)
T PF13248_consen 19 CPNCGA 24 (26)
T ss_pred ChhhCC
Confidence 555554
No 191
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=48.30 E-value=6.8 Score=17.91 Aligned_cols=36 Identities=17% Similarity=0.346 Sum_probs=17.3
Q ss_pred eeCCCCCCCCCCcchHHHHhhhh-cCCCCccCCCCCC
Q psy14694 37 YDCFMCPYRTPYSGTMRRHIRAH-IGDRPYKCFVCPY 72 (102)
Q Consensus 37 ~~c~~c~~~~~~~~~l~~h~~~h-~~~~~~~c~~c~~ 72 (102)
..|..|++..........-.+.- .....|.|..|..
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~ 39 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKE 39 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHH
Confidence 35666666544443333222221 2234477777753
No 192
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=48.26 E-value=16 Score=21.38 Aligned_cols=36 Identities=14% Similarity=0.170 Sum_probs=19.3
Q ss_pred CceeCCCCCCCCCCcchHHHHhhhhc--CCCCccCCCCCCccCC
Q psy14694 35 KKYDCFMCPYRTPYSGTMRRHIRAHI--GDRPYKCFVCPYRSNQ 76 (102)
Q Consensus 35 ~~~~c~~c~~~~~~~~~l~~h~~~h~--~~~~~~c~~c~~~f~~ 76 (102)
..+.|+.|+. .. ..|.-+-. .+-.+.|..||..+..
T Consensus 5 iy~~Cp~Cg~----ee--v~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 5 IYIECPSCGS----EE--VSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EEEECCCCCc----ch--hhHHHHHhcCCceEEEccCCCcEeec
Confidence 3467888871 11 12222222 2234789999877643
No 193
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=47.66 E-value=7.9 Score=17.08 Aligned_cols=15 Identities=27% Similarity=0.454 Sum_probs=10.5
Q ss_pred CccCCCCCCccCCch
Q psy14694 64 PYKCFVCPYRSNQRA 78 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~ 78 (102)
=+.|..|++.+....
T Consensus 26 Cf~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 26 CFKCSKCGKPLNDGD 40 (58)
T ss_dssp TSBETTTTCBTTTSS
T ss_pred ccccCCCCCccCCCe
Confidence 478888887776553
No 194
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=47.21 E-value=11 Score=19.38 Aligned_cols=11 Identities=18% Similarity=0.425 Sum_probs=7.3
Q ss_pred ccCCCCCCccC
Q psy14694 65 YKCFVCPYRSN 75 (102)
Q Consensus 65 ~~c~~c~~~f~ 75 (102)
..|..||..+.
T Consensus 43 ~~C~~CG~y~~ 53 (99)
T PRK14892 43 ITCGNCGLYTE 53 (99)
T ss_pred EECCCCCCccC
Confidence 56777776554
No 195
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=47.18 E-value=5.3 Score=22.67 Aligned_cols=18 Identities=17% Similarity=0.307 Sum_probs=13.7
Q ss_pred CCccCCCCCCccCCchhh
Q psy14694 63 RPYKCFVCPYRSNQRANL 80 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l 80 (102)
.++.|..||+.|.....+
T Consensus 113 ~~~~C~~CG~~f~~~~~i 130 (180)
T PRK12387 113 ALCNCRVCGRPFAVQKEI 130 (180)
T ss_pred CcccchhhCCccccHHHH
Confidence 467899999999765543
No 196
>PF15616 TerY-C: TerY-C metal binding domain
Probab=47.11 E-value=9.8 Score=20.69 Aligned_cols=14 Identities=0% Similarity=-0.187 Sum_probs=10.1
Q ss_pred CCCCcccccccccc
Q psy14694 88 ISDEQLRFKKIRIA 101 (102)
Q Consensus 88 ~~~~~~~C~~c~~~ 101 (102)
.++....||+|+..
T Consensus 101 ~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 101 DGEGEVTCPWCGNE 114 (131)
T ss_pred CCCCCEECCCCCCe
Confidence 44557889999864
No 197
>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=46.96 E-value=5.2 Score=16.89 Aligned_cols=11 Identities=0% Similarity=-0.248 Sum_probs=6.8
Q ss_pred ccccccccccC
Q psy14694 92 QLRFKKIRIAV 102 (102)
Q Consensus 92 ~~~C~~c~~~~ 102 (102)
+-.|+.||..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 56677776543
No 198
>KOG1729|consensus
Probab=46.89 E-value=12 Score=23.28 Aligned_cols=53 Identities=15% Similarity=0.208 Sum_probs=25.5
Q ss_pred CceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhcCCCCc-cccccc
Q psy14694 35 KKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQISDEQ-LRFKKI 98 (102)
Q Consensus 35 ~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~-~~C~~c 98 (102)
..-.|..|+...+. |. .|.| -|..||..|...-.-..........++ +.|+.|
T Consensus 167 ea~~C~~C~~~~Ft---l~--~RRH------HCR~CG~ivC~~Cs~n~~~l~~~~~k~~rvC~~C 220 (288)
T KOG1729|consen 167 EATECMVCGCTEFT---LS--ERRH------HCRNCGDIVCAPCSRNRFLLPNLSTKPIRVCDIC 220 (288)
T ss_pred cceecccCCCcccc---HH--HHHH------HHHhcchHhhhhhhcCcccccccCCCCceecHHH
Confidence 34567888875222 21 1222 266677666553332222222333444 477776
No 199
>KOG2482|consensus
Probab=45.90 E-value=22 Score=22.81 Aligned_cols=29 Identities=17% Similarity=0.371 Sum_probs=22.4
Q ss_pred ccCCccccccccCHHHHHHHHhhhcccccc
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCSEGARQ 31 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~ 31 (102)
+.|-.|.+.|+ +...|..||+.-.+.+.-
T Consensus 196 ~~CLyCekifr-dkntLkeHMrkK~Hrrin 224 (423)
T KOG2482|consen 196 LRCLYCEKIFR-DKNTLKEHMRKKRHRRIN 224 (423)
T ss_pred heeeeeccccC-CcHHHHHHHHhccCcccC
Confidence 46888999999 999999999875544433
No 200
>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=45.75 E-value=13 Score=20.82 Aligned_cols=16 Identities=19% Similarity=0.281 Sum_probs=10.4
Q ss_pred CCccCCCCCCccCCch
Q psy14694 63 RPYKCFVCPYRSNQRA 78 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~ 78 (102)
.|.-|..||+.|.+..
T Consensus 67 ~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 67 APSYCHNCGKPYPWTE 82 (158)
T ss_pred CChhHHhCCCCCchHH
Confidence 5666777777776653
No 201
>KOG0782|consensus
Probab=45.50 E-value=7.7 Score=26.62 Aligned_cols=24 Identities=8% Similarity=0.112 Sum_probs=11.8
Q ss_pred hhhhhhhhcCCCCccccccccccC
Q psy14694 79 NLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 79 ~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
.|.+|.=+|..-.--+|..|||+|
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgF 263 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGF 263 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhh
Confidence 444444444444444555555554
No 202
>PTZ00448 hypothetical protein; Provisional
Probab=45.08 E-value=21 Score=23.02 Aligned_cols=23 Identities=35% Similarity=0.716 Sum_probs=17.4
Q ss_pred ccCCccccccccCHHHHHHHHhhh
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLC 25 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~ 25 (102)
|.|..|+..|. +......|.++.
T Consensus 315 ~tC~~C~v~F~-~~~~qR~H~KSD 337 (373)
T PTZ00448 315 LLCRKCNIQLM-DHNAFKQHYRSE 337 (373)
T ss_pred ccccccccccC-CHHHHHHHhhhh
Confidence 66888888887 777777777763
No 203
>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=45.07 E-value=12 Score=14.61 Aligned_cols=12 Identities=8% Similarity=-0.194 Sum_probs=5.0
Q ss_pred CCCccccccccc
Q psy14694 89 SDEQLRFKKIRI 100 (102)
Q Consensus 89 ~~~~~~C~~c~~ 100 (102)
++..-.|+.|+.
T Consensus 18 ~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 18 GGWARRCPSCGH 29 (32)
T ss_dssp SSS-EEESSSS-
T ss_pred CcCEeECCCCcC
Confidence 344445555553
No 204
>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=44.89 E-value=4.3 Score=19.98 Aligned_cols=39 Identities=23% Similarity=0.365 Sum_probs=13.0
Q ss_pred CCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCC
Q psy14694 34 RKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQ 76 (102)
Q Consensus 34 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~ 76 (102)
++.|.|+.|+..-+..-.+. .-.+.-...|..|+..|..
T Consensus 20 ~~~F~CPfC~~~~sV~v~id----kk~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKID----KKEGIGILSCRVCGESFQT 58 (81)
T ss_dssp SS----TTT--SS-EEEEEE----TTTTEEEEEESSS--EEEE
T ss_pred CceEcCCcCCCCCeEEEEEE----ccCCEEEEEecCCCCeEEE
Confidence 45677777764322222221 0112223567777766643
No 205
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=44.84 E-value=7.9 Score=15.52 Aligned_cols=9 Identities=0% Similarity=-0.507 Sum_probs=4.4
Q ss_pred ccccccccc
Q psy14694 93 LRFKKIRIA 101 (102)
Q Consensus 93 ~~C~~c~~~ 101 (102)
+.|..||.+
T Consensus 22 ~~C~~Cg~~ 30 (33)
T PF08792_consen 22 EVCIFCGSS 30 (33)
T ss_pred EEcccCCcE
Confidence 345555544
No 206
>KOG2785|consensus
Probab=44.18 E-value=39 Score=22.01 Aligned_cols=23 Identities=22% Similarity=0.293 Sum_probs=15.6
Q ss_pred cCCccccccccCHHHHHHHHhhhc
Q psy14694 3 KCTHCKVDLNLDTEIILQHYKLCS 26 (102)
Q Consensus 3 ~c~~c~~~f~~~~~~l~~h~~~~~ 26 (102)
.|-.|++.+. +...-..|+..++
T Consensus 168 ~CLfC~~~~k-~~e~~~~HM~~~H 190 (390)
T KOG2785|consen 168 DCLFCDKKSK-SLEENLKHMFKEH 190 (390)
T ss_pred ceeecCCCcc-cHHHHHHHHhhcc
Confidence 4677888887 6665566776654
No 207
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=44.09 E-value=16 Score=24.37 Aligned_cols=16 Identities=19% Similarity=0.505 Sum_probs=10.8
Q ss_pred CCCccCCCCCCccCCc
Q psy14694 62 DRPYKCFVCPYRSNQR 77 (102)
Q Consensus 62 ~~~~~c~~c~~~f~~~ 77 (102)
...|+|..|+..+...
T Consensus 423 ~~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 423 GPRMQCSVCQWIYDPA 438 (479)
T ss_pred CCeEEECCCCeEECCC
Confidence 3457888888766543
No 208
>KOG0717|consensus
Probab=43.79 E-value=11 Score=25.15 Aligned_cols=22 Identities=23% Similarity=0.381 Sum_probs=19.3
Q ss_pred ccCCCCCCccCCchhhhhhhhh
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLV 86 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~ 86 (102)
+.|.+|.++|.....+.+|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999988765
No 209
>KOG1409|consensus
Probab=43.54 E-value=4.8 Score=25.63 Aligned_cols=37 Identities=19% Similarity=0.023 Sum_probs=22.1
Q ss_pred ccCCCCCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
..|.+|...|.+.. ...+.+.-.|-+.+-|++||+++
T Consensus 283 ~~cQ~c~qpffwn~-~~m~~~k~~glr~h~crkcg~av 319 (404)
T KOG1409|consen 283 DSCQKCNQPFFWNF-RQMWDRKQLGLRQHHCRKCGKAV 319 (404)
T ss_pred chhhhhCchHHHHH-HHHHhhhhhhhhhhhhhhhhhhc
Confidence 45666666665432 23455556667777777777654
No 210
>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=43.45 E-value=9.9 Score=16.63 Aligned_cols=9 Identities=0% Similarity=-0.285 Sum_probs=4.6
Q ss_pred ccccccccc
Q psy14694 92 QLRFKKIRI 100 (102)
Q Consensus 92 ~~~C~~c~~ 100 (102)
.|.||.|+-
T Consensus 34 ~w~CP~C~a 42 (47)
T PF00301_consen 34 DWVCPVCGA 42 (47)
T ss_dssp T-B-TTTSS
T ss_pred CCcCcCCCC
Confidence 377888764
No 211
>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=43.44 E-value=24 Score=15.28 Aligned_cols=8 Identities=38% Similarity=1.036 Sum_probs=3.9
Q ss_pred CccCCCCC
Q psy14694 64 PYKCFVCP 71 (102)
Q Consensus 64 ~~~c~~c~ 71 (102)
.+.|..|+
T Consensus 28 g~~C~~C~ 35 (53)
T PF00130_consen 28 GYRCSWCG 35 (53)
T ss_dssp EEEETTTT
T ss_pred eEEECCCC
Confidence 35555554
No 212
>KOG3002|consensus
Probab=43.27 E-value=34 Score=21.50 Aligned_cols=61 Identities=10% Similarity=-0.033 Sum_probs=34.5
Q ss_pred CCceeCCCCCCCCCCcchHHHHhhhhcCCCCccCC----CCCCccCCchhhhhhhhhcCCCCccccccc
Q psy14694 34 RKKYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCF----VCPYRSNQRANLMSHPLVQISDEQLRFKKI 98 (102)
Q Consensus 34 ~~~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~----~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c 98 (102)
+....|+.|...+.....+..-.- .......|+ -|.+.|.+... ..|.+.... .||.||.=
T Consensus 78 ~~~~~CP~Cr~~~g~~R~~amEkV--~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f-~~~~CP~p 142 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNIRCRAMEKV--AEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEF-RPCSCPVP 142 (299)
T ss_pred hhcccCCccccccccHHHHHHHHH--HHhceecccccccCCceeeccccc-ccccccccc-CCcCCCCC
Confidence 444556666665554333322211 222334444 37777877766 578887776 78888754
No 213
>PRK04351 hypothetical protein; Provisional
Probab=43.19 E-value=12 Score=20.72 Aligned_cols=29 Identities=21% Similarity=0.303 Sum_probs=18.9
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCccccccccc
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
.|.|..|+..+.+. +.+ ...-|.|..|+-
T Consensus 112 ~Y~C~~Cg~~~~r~-------Rr~-n~~~yrCg~C~g 140 (149)
T PRK04351 112 LYECQSCGQQYLRK-------RRI-NTKRYRCGKCRG 140 (149)
T ss_pred EEECCCCCCEeeee-------eec-CCCcEEeCCCCc
Confidence 38898898655432 222 246799999874
No 214
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=42.80 E-value=32 Score=24.14 Aligned_cols=8 Identities=25% Similarity=1.103 Sum_probs=4.4
Q ss_pred cCCccccc
Q psy14694 3 KCTHCKVD 10 (102)
Q Consensus 3 ~c~~c~~~ 10 (102)
.|+.|+..
T Consensus 3 ~Cp~Cg~~ 10 (645)
T PRK14559 3 ICPQCQFE 10 (645)
T ss_pred cCCCCCCc
Confidence 45666544
No 215
>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=42.68 E-value=24 Score=14.66 Aligned_cols=7 Identities=29% Similarity=0.937 Sum_probs=3.2
Q ss_pred ccCCCCC
Q psy14694 65 YKCFVCP 71 (102)
Q Consensus 65 ~~c~~c~ 71 (102)
+.|..|+
T Consensus 28 ~~C~~C~ 34 (49)
T smart00109 28 LRCSWCK 34 (49)
T ss_pred cCCCCCC
Confidence 4454443
No 216
>PRK07591 threonine synthase; Validated
Probab=42.58 E-value=17 Score=23.80 Aligned_cols=27 Identities=19% Similarity=0.260 Sum_probs=17.3
Q ss_pred ceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccC
Q psy14694 36 KYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSN 75 (102)
Q Consensus 36 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~ 75 (102)
.+.|..|++.+... .. +.|+.|+-.+.
T Consensus 18 ~l~C~~Cg~~~~~~------------~~-~~C~~cg~~l~ 44 (421)
T PRK07591 18 ALKCRECGAEYPLG------------PI-HVCEECFGPLE 44 (421)
T ss_pred EEEeCCCCCcCCCC------------CC-ccCCCCCCeEE
Confidence 47888888766421 22 78888875543
No 217
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=42.49 E-value=21 Score=14.96 Aligned_cols=27 Identities=7% Similarity=-0.079 Sum_probs=10.3
Q ss_pred CCCccCCchhhhhhhhhcCCCCccccccc
Q psy14694 70 CPYRSNQRANLMSHPLVQISDEQLRFKKI 98 (102)
Q Consensus 70 c~~~f~~~~~l~~h~~~~~~~~~~~C~~c 98 (102)
||.+|-..- |.+..+... ...+.||.|
T Consensus 16 CGH~FC~~C-l~~~~~~~~-~~~~~CP~C 42 (42)
T PF15227_consen 16 CGHSFCRSC-LERLWKEPS-GSGFSCPEC 42 (42)
T ss_dssp SSSEEEHHH-HHHHHCCSS-SST---SSS
T ss_pred CcCHHHHHH-HHHHHHccC-CcCCCCcCC
Confidence 566665443 223333222 223777766
No 218
>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=41.97 E-value=11 Score=16.72 Aligned_cols=9 Identities=0% Similarity=-0.285 Sum_probs=6.3
Q ss_pred ccccccccc
Q psy14694 92 QLRFKKIRI 100 (102)
Q Consensus 92 ~~~C~~c~~ 100 (102)
.|.||.|+-
T Consensus 34 ~w~CP~C~a 42 (50)
T cd00730 34 DWVCPVCGA 42 (50)
T ss_pred CCCCCCCCC
Confidence 477888874
No 219
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.83 E-value=8.1 Score=18.85 Aligned_cols=10 Identities=30% Similarity=0.849 Sum_probs=6.6
Q ss_pred ccCCcccccc
Q psy14694 2 LKCTHCKVDL 11 (102)
Q Consensus 2 ~~c~~c~~~f 11 (102)
|.|.+|+..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 5677777555
No 220
>PRK12496 hypothetical protein; Provisional
Probab=41.35 E-value=24 Score=19.91 Aligned_cols=12 Identities=25% Similarity=0.395 Sum_probs=9.2
Q ss_pred eeCCCCCCCCCC
Q psy14694 37 YDCFMCPYRTPY 48 (102)
Q Consensus 37 ~~c~~c~~~~~~ 48 (102)
+.|.-|++.|..
T Consensus 128 ~~C~gC~~~~~~ 139 (164)
T PRK12496 128 KVCKGCKKKYPE 139 (164)
T ss_pred EECCCCCccccC
Confidence 678888888865
No 221
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=40.79 E-value=12 Score=15.16 Aligned_cols=7 Identities=14% Similarity=-0.088 Sum_probs=3.2
Q ss_pred ccccccc
Q psy14694 93 LRFKKIR 99 (102)
Q Consensus 93 ~~C~~c~ 99 (102)
+.|+.||
T Consensus 23 ~vC~~Cg 29 (34)
T PF14803_consen 23 LVCPACG 29 (34)
T ss_dssp EEETTTT
T ss_pred eECCCCC
Confidence 3444444
No 222
>KOG2923|consensus
Probab=40.78 E-value=34 Score=16.11 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=13.7
Q ss_pred CCCCCCCcchHHHHhhhhcCCCCccCCCCC
Q psy14694 42 CPYRTPYSGTMRRHIRAHIGDRPYKCFVCP 71 (102)
Q Consensus 42 c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~ 71 (102)
||-.|..... -.-.|+....|+.|.
T Consensus 27 CGDrf~It~e-----dL~~ge~Va~CpsCS 51 (67)
T KOG2923|consen 27 CGDRFQITLE-----DLENGEDVARCPSCS 51 (67)
T ss_pred CCCeeeecHH-----HHhCCCeeecCCCce
Confidence 6666554322 233566666777665
No 223
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=40.75 E-value=11 Score=14.92 Aligned_cols=9 Identities=0% Similarity=-0.197 Sum_probs=5.9
Q ss_pred ccccccccc
Q psy14694 92 QLRFKKIRI 100 (102)
Q Consensus 92 ~~~C~~c~~ 100 (102)
-|+|..||.
T Consensus 4 ~ykC~~CGn 12 (34)
T cd00974 4 VYKCEICGN 12 (34)
T ss_pred EEEcCCCCc
Confidence 467777764
No 224
>KOG2231|consensus
Probab=40.60 E-value=49 Score=23.37 Aligned_cols=19 Identities=32% Similarity=0.607 Sum_probs=9.1
Q ss_pred CCCCCCCCCCcchHHHHhh
Q psy14694 39 CFMCPYRTPYSGTMRRHIR 57 (102)
Q Consensus 39 c~~c~~~~~~~~~l~~h~~ 57 (102)
|..|...|.....|..|++
T Consensus 185 C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLR 203 (669)
T ss_pred chhhhhhhccHHHHHHhhc
Confidence 4444444444444444444
No 225
>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=40.26 E-value=8.1 Score=15.70 Aligned_cols=14 Identities=21% Similarity=0.135 Sum_probs=7.1
Q ss_pred ccCCCCCCccCCch
Q psy14694 65 YKCFVCPYRSNQRA 78 (102)
Q Consensus 65 ~~c~~c~~~f~~~~ 78 (102)
-.|.+|++.|..+.
T Consensus 4 ~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 4 PKCDECGKPFMDSY 17 (34)
T ss_dssp EE-TTT--EES-SS
T ss_pred chHhHhCCHHHHHH
Confidence 36888888888754
No 226
>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=39.24 E-value=11 Score=14.43 Aligned_cols=10 Identities=10% Similarity=-0.067 Sum_probs=3.4
Q ss_pred Cccccccccc
Q psy14694 91 EQLRFKKIRI 100 (102)
Q Consensus 91 ~~~~C~~c~~ 100 (102)
..|.|..|+.
T Consensus 14 ~~Y~C~~Cdf 23 (30)
T PF07649_consen 14 WFYRCSECDF 23 (30)
T ss_dssp -EEE-TTT--
T ss_pred ceEECccCCC
Confidence 3455555554
No 227
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=39.07 E-value=12 Score=14.78 Aligned_cols=9 Identities=0% Similarity=-0.182 Sum_probs=6.0
Q ss_pred ccccccccc
Q psy14694 92 QLRFKKIRI 100 (102)
Q Consensus 92 ~~~C~~c~~ 100 (102)
-|+|..||.
T Consensus 7 ~ykC~~Cgn 15 (34)
T TIGR00319 7 VYKCEVCGN 15 (34)
T ss_pred EEEcCCCCc
Confidence 577777764
No 228
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=38.64 E-value=14 Score=22.17 Aligned_cols=15 Identities=7% Similarity=-0.166 Sum_probs=10.7
Q ss_pred CCCCccccccccccC
Q psy14694 88 ISDEQLRFKKIRIAV 102 (102)
Q Consensus 88 ~~~~~~~C~~c~~~~ 102 (102)
...++.+|+.||.-|
T Consensus 177 rEGkpqRCpECGqVF 191 (268)
T PTZ00043 177 REGFLYRCGECDQIF 191 (268)
T ss_pred cCCCCccCCCCCcEE
Confidence 345589999998644
No 229
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=37.92 E-value=20 Score=16.06 Aligned_cols=17 Identities=24% Similarity=0.395 Sum_probs=10.6
Q ss_pred CCCCccCCCCCCccCCc
Q psy14694 61 GDRPYKCFVCPYRSNQR 77 (102)
Q Consensus 61 ~~~~~~c~~c~~~f~~~ 77 (102)
+.....|+.|+..|-..
T Consensus 37 ~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 37 GCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CCCeeECCCCCCeECCC
Confidence 34456777777777543
No 230
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=37.61 E-value=9.4 Score=20.89 Aligned_cols=18 Identities=6% Similarity=-0.055 Sum_probs=12.4
Q ss_pred hhhcCCCCccccccccccC
Q psy14694 84 PLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 84 ~~~~~~~~~~~C~~c~~~~ 102 (102)
+.++.| ++.+|+.||.-|
T Consensus 105 ~~l~~g-~~~RCpeCG~~f 122 (136)
T PF01215_consen 105 FWLHKG-KPQRCPECGQVF 122 (136)
T ss_dssp EEEETT-SEEEETTTEEEE
T ss_pred EEEeCC-CccCCCCCCeEE
Confidence 344555 489999998644
No 231
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=37.53 E-value=23 Score=24.77 Aligned_cols=9 Identities=11% Similarity=-0.285 Sum_probs=7.5
Q ss_pred ccccccccc
Q psy14694 92 QLRFKKIRI 100 (102)
Q Consensus 92 ~~~C~~c~~ 100 (102)
-+.||.||.
T Consensus 639 ~~~CP~CG~ 647 (656)
T PRK08270 639 HEFCPKCGE 647 (656)
T ss_pred CCCCcCCcC
Confidence 588999985
No 232
>KOG2636|consensus
Probab=37.48 E-value=24 Score=23.47 Aligned_cols=27 Identities=30% Similarity=0.520 Sum_probs=21.6
Q ss_pred hhhcCCCCccCCCCC-CccCCchhhhhh
Q psy14694 57 RAHIGDRPYKCFVCP-YRSNQRANLMSH 83 (102)
Q Consensus 57 ~~h~~~~~~~c~~c~-~~f~~~~~l~~h 83 (102)
+.|--...|.|.+|| +++.-+..+.+|
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRH 421 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHH
Confidence 456667789999999 788888888877
No 233
>PHA02942 putative transposase; Provisional
Probab=37.43 E-value=22 Score=23.01 Aligned_cols=11 Identities=0% Similarity=-0.070 Sum_probs=7.2
Q ss_pred CCccccccccc
Q psy14694 90 DEQLRFKKIRI 100 (102)
Q Consensus 90 ~~~~~C~~c~~ 100 (102)
.+.|.|+.||.
T Consensus 340 ~r~f~C~~CG~ 350 (383)
T PHA02942 340 HRYFHCPSCGY 350 (383)
T ss_pred CCEEECCCCCC
Confidence 34677777774
No 234
>PRK10220 hypothetical protein; Provisional
Probab=36.90 E-value=44 Score=17.63 Aligned_cols=18 Identities=17% Similarity=0.207 Sum_probs=12.5
Q ss_pred CCCceeCCCCCCCCCCcc
Q psy14694 33 SRKKYDCFMCPYRTPYSG 50 (102)
Q Consensus 33 ~~~~~~c~~c~~~~~~~~ 50 (102)
....+.|++|+.-|....
T Consensus 17 d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 17 DNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCCeEECCcccCcCCccc
Confidence 344588888888776654
No 235
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=36.84 E-value=23 Score=21.69 Aligned_cols=28 Identities=18% Similarity=0.166 Sum_probs=14.3
Q ss_pred ccCCCCCCccCCchhhhhhhhhcCCCCcccccccc
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIR 99 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~ 99 (102)
-.|+.||....-...| ++-.-|+|+.|+
T Consensus 221 r~CP~Cg~~W~L~~pl-------h~iFdFKCD~CR 248 (258)
T PF10071_consen 221 RKCPSCGGDWRLKEPL-------HDIFDFKCDPCR 248 (258)
T ss_pred CCCCCCCCccccCCch-------hhceeccCCcce
Confidence 3566666544433322 334456666664
No 236
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=36.39 E-value=18 Score=20.12 Aligned_cols=12 Identities=25% Similarity=0.634 Sum_probs=7.5
Q ss_pred CCccCCCCCCcc
Q psy14694 63 RPYKCFVCPYRS 74 (102)
Q Consensus 63 ~~~~c~~c~~~f 74 (102)
..|.|..|+...
T Consensus 50 ~~~~C~~C~~~~ 61 (166)
T cd04476 50 GTYRCEKCNKSV 61 (166)
T ss_pred CcEECCCCCCcC
Confidence 446777776654
No 237
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=36.34 E-value=9.1 Score=14.94 Aligned_cols=9 Identities=11% Similarity=0.172 Sum_probs=3.4
Q ss_pred ccccccccc
Q psy14694 92 QLRFKKIRI 100 (102)
Q Consensus 92 ~~~C~~c~~ 100 (102)
.|.|+.|+.
T Consensus 13 kY~Cp~C~~ 21 (30)
T PF04438_consen 13 KYRCPRCGA 21 (30)
T ss_dssp SEE-TTT--
T ss_pred EEECCCcCC
Confidence 455665553
No 238
>PF14149 YhfH: YhfH-like protein
Probab=36.14 E-value=5.6 Score=16.50 Aligned_cols=7 Identities=0% Similarity=-0.045 Sum_probs=3.6
Q ss_pred ccccccc
Q psy14694 94 RFKKIRI 100 (102)
Q Consensus 94 ~C~~c~~ 100 (102)
.|..||+
T Consensus 15 ~C~~CG~ 21 (37)
T PF14149_consen 15 KCTECGK 21 (37)
T ss_pred ccHHHHH
Confidence 3555554
No 239
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.91 E-value=39 Score=18.33 Aligned_cols=16 Identities=25% Similarity=0.407 Sum_probs=10.5
Q ss_pred CCCccCCCCCCccCCc
Q psy14694 62 DRPYKCFVCPYRSNQR 77 (102)
Q Consensus 62 ~~~~~c~~c~~~f~~~ 77 (102)
+.|--|..||..|.+.
T Consensus 66 e~psfchncgs~fpwt 81 (160)
T COG4306 66 EPPSFCHNCGSRFPWT 81 (160)
T ss_pred CCcchhhcCCCCCCcH
Confidence 3455677777777764
No 240
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.49 E-value=33 Score=21.31 Aligned_cols=25 Identities=24% Similarity=0.223 Sum_probs=17.1
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
.|.|+.|.-.|.. .|-+|+.||-.|
T Consensus 255 GyvCs~Clsi~C~--------------~p~~C~~Cgt~f 279 (279)
T TIGR00627 255 GFVCSVCLSVLCQ--------------YTPICKTCKTAF 279 (279)
T ss_pred eEECCCccCCcCC--------------CCCCCCCCCCCC
Confidence 4888888765553 234799998766
No 241
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=35.33 E-value=15 Score=16.76 Aligned_cols=9 Identities=0% Similarity=-0.208 Sum_probs=2.9
Q ss_pred Ccccccccc
Q psy14694 91 EQLRFKKIR 99 (102)
Q Consensus 91 ~~~~C~~c~ 99 (102)
+.|.|+.||
T Consensus 32 r~y~Cp~Cg 40 (55)
T PF05741_consen 32 RKYVCPICG 40 (55)
T ss_dssp GG---TTT-
T ss_pred hcCcCCCCc
Confidence 446666665
No 242
>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=35.24 E-value=13 Score=17.72 Aligned_cols=14 Identities=36% Similarity=0.665 Sum_probs=7.2
Q ss_pred cCCCCccCCCCCCcc
Q psy14694 60 IGDRPYKCFVCPYRS 74 (102)
Q Consensus 60 ~~~~~~~c~~c~~~f 74 (102)
.+.+.-+| .||+..
T Consensus 16 e~~kTkkC-~CG~~l 29 (68)
T PF09082_consen 16 EGAKTKKC-VCGKTL 29 (68)
T ss_dssp TT-SEEEE-TTTEEE
T ss_pred CCcceeEe-cCCCee
Confidence 33455566 666554
No 243
>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=34.84 E-value=36 Score=17.93 Aligned_cols=17 Identities=18% Similarity=0.266 Sum_probs=11.8
Q ss_pred CCceeCCCCCCCCCCcc
Q psy14694 34 RKKYDCFMCPYRTPYSG 50 (102)
Q Consensus 34 ~~~~~c~~c~~~~~~~~ 50 (102)
...+.|++|+..|....
T Consensus 17 g~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 17 GTQLICPSCLYEWNENE 33 (109)
T ss_pred CCeeECccccccccccc
Confidence 34588888888776553
No 244
>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=34.69 E-value=17 Score=19.22 Aligned_cols=12 Identities=8% Similarity=-0.053 Sum_probs=7.2
Q ss_pred CCCccccccccc
Q psy14694 89 SDEQLRFKKIRI 100 (102)
Q Consensus 89 ~~~~~~C~~c~~ 100 (102)
...+.+||.|++
T Consensus 66 kav~V~CP~C~K 77 (114)
T PF11023_consen 66 KAVQVECPNCGK 77 (114)
T ss_pred cceeeECCCCCC
Confidence 334566777765
No 245
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=34.55 E-value=16 Score=17.71 Aligned_cols=37 Identities=8% Similarity=-0.130 Sum_probs=14.7
Q ss_pred CCccCCCCCCccCCchhhhhhhh---hcCCCCcccccccc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPL---VQISDEQLRFKKIR 99 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~---~~~~~~~~~C~~c~ 99 (102)
+..-|..|+-.+....+....++ ...+.-.+.|..||
T Consensus 45 kr~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~ 84 (85)
T PF04032_consen 45 KRTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCG 84 (85)
T ss_dssp CCTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTT
T ss_pred hcccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccC
Confidence 33456666665555444322222 12333346777776
No 246
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=34.40 E-value=13 Score=18.81 Aligned_cols=10 Identities=10% Similarity=-0.031 Sum_probs=5.6
Q ss_pred cccccccccc
Q psy14694 92 QLRFKKIRIA 101 (102)
Q Consensus 92 ~~~C~~c~~~ 101 (102)
.|.|..|++.
T Consensus 53 IW~C~~C~~~ 62 (91)
T TIGR00280 53 IWTCRKCGAK 62 (91)
T ss_pred EEEcCCCCCE
Confidence 4566666554
No 247
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.05 E-value=20 Score=18.88 Aligned_cols=11 Identities=0% Similarity=-0.257 Sum_probs=6.2
Q ss_pred ccccccccccC
Q psy14694 92 QLRFKKIRIAV 102 (102)
Q Consensus 92 ~~~C~~c~~~~ 102 (102)
|-.||+||++|
T Consensus 26 PiVsPytG~s~ 36 (129)
T COG4530 26 PIVSPYTGKSY 36 (129)
T ss_pred ccccCcccccc
Confidence 55566666554
No 248
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.64 E-value=16 Score=17.03 Aligned_cols=8 Identities=0% Similarity=-0.230 Sum_probs=4.1
Q ss_pred cccccccc
Q psy14694 93 LRFKKIRI 100 (102)
Q Consensus 93 ~~C~~c~~ 100 (102)
-.|+.|+.
T Consensus 49 v~CPYC~t 56 (62)
T COG4391 49 VVCPYCST 56 (62)
T ss_pred EecCcccc
Confidence 44555554
No 249
>PRK11032 hypothetical protein; Provisional
Probab=33.64 E-value=24 Score=19.97 Aligned_cols=7 Identities=29% Similarity=0.695 Sum_probs=3.9
Q ss_pred ccCCCCC
Q psy14694 65 YKCFVCP 71 (102)
Q Consensus 65 ~~c~~c~ 71 (102)
+.|..||
T Consensus 125 LvC~~Cg 131 (160)
T PRK11032 125 LVCEKCH 131 (160)
T ss_pred EEecCCC
Confidence 4555555
No 250
>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=33.59 E-value=41 Score=22.59 Aligned_cols=24 Identities=25% Similarity=0.488 Sum_probs=20.2
Q ss_pred ccCCccccccccCHHHHHHHHhhhc
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCS 26 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~ 26 (102)
+.|+.|.+.|. +...+..|+...+
T Consensus 58 WiCp~CskkF~-d~~~~~~H~~~eH 81 (466)
T PF04780_consen 58 WICPRCSKKFS-DAESCLSHMEQEH 81 (466)
T ss_pred eeCCcccceeC-CHHHHHHHHHHhh
Confidence 46889999999 9999999987654
No 251
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=33.46 E-value=25 Score=21.99 Aligned_cols=13 Identities=31% Similarity=0.503 Sum_probs=7.5
Q ss_pred CceeCCCCCCCCC
Q psy14694 35 KKYDCFMCPYRTP 47 (102)
Q Consensus 35 ~~~~c~~c~~~~~ 47 (102)
..+.|+.|+..|.
T Consensus 56 ~~~vcp~c~~h~r 68 (296)
T CHL00174 56 KMNICEQCGYHLK 68 (296)
T ss_pred cCCCCCCCCCCcC
Confidence 3456666666554
No 252
>KOG2461|consensus
Probab=33.41 E-value=70 Score=21.07 Aligned_cols=57 Identities=4% Similarity=-0.172 Sum_probs=26.9
Q ss_pred CCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhcCCCCccccccccc
Q psy14694 44 YRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 44 ~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
........+..+...+.++.+..+..+.........+...+.+++....+.+..|++
T Consensus 339 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 395 (396)
T KOG2461|consen 339 RTPAGQLIYTQSHSMEVAEPTDMAPNQIWKIYHTGVLGFLIITTDESECNNMSFVCK 395 (396)
T ss_pred cccccccchhhhhhcccCCCCcccccccccceeccccceeeeeccccccccccccCC
Confidence 333344444455555555544444333333333333444555566666665555543
No 253
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=33.29 E-value=25 Score=19.84 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=7.0
Q ss_pred ccCCCCCCccCC
Q psy14694 65 YKCFVCPYRSNQ 76 (102)
Q Consensus 65 ~~c~~c~~~f~~ 76 (102)
..|..|++.+..
T Consensus 106 ~~C~~C~~~~~~ 117 (178)
T PF02146_consen 106 LRCSKCGKEYDR 117 (178)
T ss_dssp EEETTTSBEEEG
T ss_pred eeecCCCccccc
Confidence 456666665543
No 254
>KOG3507|consensus
Probab=33.15 E-value=24 Score=16.30 Aligned_cols=13 Identities=31% Similarity=0.613 Sum_probs=8.5
Q ss_pred CCccCCCCCCccC
Q psy14694 63 RPYKCFVCPYRSN 75 (102)
Q Consensus 63 ~~~~c~~c~~~f~ 75 (102)
.+..|.+||....
T Consensus 36 D~irCReCG~RIl 48 (62)
T KOG3507|consen 36 DVIRCRECGYRIL 48 (62)
T ss_pred CcEehhhcchHHH
Confidence 4577888876544
No 255
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=32.55 E-value=15 Score=18.60 Aligned_cols=10 Identities=10% Similarity=-0.011 Sum_probs=5.7
Q ss_pred cccccccccc
Q psy14694 92 QLRFKKIRIA 101 (102)
Q Consensus 92 ~~~C~~c~~~ 101 (102)
.|.|..|++.
T Consensus 54 IW~C~~C~~~ 63 (90)
T PRK03976 54 IWECRKCGAK 63 (90)
T ss_pred EEEcCCCCCE
Confidence 4566666554
No 256
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=32.51 E-value=3.4 Score=16.87 Aligned_cols=7 Identities=29% Similarity=0.667 Sum_probs=2.5
Q ss_pred cCCCCCC
Q psy14694 66 KCFVCPY 72 (102)
Q Consensus 66 ~c~~c~~ 72 (102)
.|..||-
T Consensus 23 sC~~CGP 29 (35)
T PF07503_consen 23 SCTNCGP 29 (35)
T ss_dssp -BTTCC-
T ss_pred cCCCCCC
Confidence 4444543
No 257
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=32.04 E-value=31 Score=23.59 Aligned_cols=8 Identities=0% Similarity=-0.247 Sum_probs=5.1
Q ss_pred cccccccc
Q psy14694 93 LRFKKIRI 100 (102)
Q Consensus 93 ~~C~~c~~ 100 (102)
|.|+.||.
T Consensus 230 y~C~~Cg~ 237 (557)
T PF05876_consen 230 YVCPHCGC 237 (557)
T ss_pred EECCCCcC
Confidence 66666664
No 258
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=31.81 E-value=31 Score=14.73 Aligned_cols=38 Identities=13% Similarity=0.086 Sum_probs=18.1
Q ss_pred CCCccCCCCCCccCCchhhhhhhhhcCCCCcccccccc
Q psy14694 62 DRPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIR 99 (102)
Q Consensus 62 ~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~ 99 (102)
+....|..|+..|-..=.-......-.....|.|+.|.
T Consensus 12 ~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 12 GDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp SSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred CCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 44577888887654321111111111111278887774
No 259
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=31.53 E-value=20 Score=15.51 Aligned_cols=6 Identities=17% Similarity=0.135 Sum_probs=3.3
Q ss_pred cccccc
Q psy14694 94 RFKKIR 99 (102)
Q Consensus 94 ~C~~c~ 99 (102)
+||.||
T Consensus 13 kCp~CG 18 (44)
T PF14952_consen 13 KCPKCG 18 (44)
T ss_pred cCCcCc
Confidence 455555
No 260
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=31.53 E-value=37 Score=23.26 Aligned_cols=9 Identities=11% Similarity=0.062 Sum_probs=7.2
Q ss_pred ccccccccc
Q psy14694 92 QLRFKKIRI 100 (102)
Q Consensus 92 ~~~C~~c~~ 100 (102)
.++||.||.
T Consensus 532 ~~~CP~CGs 540 (555)
T cd01675 532 GFKCPKCGS 540 (555)
T ss_pred CCCCcCCCC
Confidence 488999984
No 261
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=31.52 E-value=39 Score=21.14 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=20.1
Q ss_pred CCCccCCCCCCccCCchhhhhhhhhc
Q psy14694 62 DRPYKCFVCPYRSNQRANLMSHPLVQ 87 (102)
Q Consensus 62 ~~~~~c~~c~~~f~~~~~l~~h~~~~ 87 (102)
...|.|..|-+-|.....+.+|+...
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C 71 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKC 71 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhC
Confidence 45688888888888888888887643
No 262
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=31.29 E-value=17 Score=18.40 Aligned_cols=10 Identities=30% Similarity=0.298 Sum_probs=7.3
Q ss_pred cccccccccc
Q psy14694 92 QLRFKKIRIA 101 (102)
Q Consensus 92 ~~~C~~c~~~ 101 (102)
-|+|.+||++
T Consensus 68 r~~Ct~Cgka 77 (94)
T COG1631 68 RLRCTECGKA 77 (94)
T ss_pred EEEehhhccc
Confidence 3778888875
No 263
>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=30.87 E-value=6.9 Score=24.04 Aligned_cols=12 Identities=0% Similarity=-0.324 Sum_probs=7.1
Q ss_pred CCCCcccccccc
Q psy14694 88 ISDEQLRFKKIR 99 (102)
Q Consensus 88 ~~~~~~~C~~c~ 99 (102)
.+.+.+.|..|+
T Consensus 234 ~~~rve~C~~C~ 245 (290)
T PF04216_consen 234 PAYRVEVCESCG 245 (290)
T ss_dssp -SEEEEEETTTT
T ss_pred CcEEEEECCccc
Confidence 345556677776
No 264
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=30.71 E-value=29 Score=21.56 Aligned_cols=11 Identities=18% Similarity=0.256 Sum_probs=5.8
Q ss_pred eeCCCCCCCCC
Q psy14694 37 YDCFMCPYRTP 47 (102)
Q Consensus 37 ~~c~~c~~~~~ 47 (102)
+.|+.|+..+.
T Consensus 46 ~vc~~c~~h~r 56 (285)
T TIGR00515 46 EVCPKCDHHMR 56 (285)
T ss_pred CCCCCCCCcCc
Confidence 45555555543
No 265
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=30.34 E-value=12 Score=19.48 Aligned_cols=24 Identities=21% Similarity=0.223 Sum_probs=17.3
Q ss_pred CCccCCCCCCccCCchhhhhhhhh
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLV 86 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~ 86 (102)
..+-|-+|.+-|.....|..|.+.
T Consensus 54 GqhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 54 GQHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred ceeeeehhHHHHHHHHHHHHHhcc
Confidence 346777888888888777777653
No 266
>KOG0696|consensus
Probab=30.13 E-value=23 Score=23.70 Aligned_cols=36 Identities=6% Similarity=0.003 Sum_probs=17.7
Q ss_pred CccCCCCCCccCCchhhhhh-hhhcCCCCcccccccc
Q psy14694 64 PYKCFVCPYRSNQRANLMSH-PLVQISDEQLRFKKIR 99 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h-~~~~~~~~~~~C~~c~ 99 (102)
.|.|+--++.+........| .++|+=.-|-=|+.||
T Consensus 92 tF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCG 128 (683)
T KOG0696|consen 92 TFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCG 128 (683)
T ss_pred EEECCCCCCCCCCCCcccccceeeeecCCCchhhhHH
Confidence 34555444545444444455 3335444444466665
No 267
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=30.12 E-value=37 Score=23.39 Aligned_cols=8 Identities=13% Similarity=-0.139 Sum_probs=6.3
Q ss_pred cccccccc
Q psy14694 93 LRFKKIRI 100 (102)
Q Consensus 93 ~~C~~c~~ 100 (102)
++||.||.
T Consensus 539 ~~CP~Cgs 546 (579)
T TIGR02487 539 DKCPKCGS 546 (579)
T ss_pred CcCcCCCC
Confidence 78888883
No 268
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=29.65 E-value=19 Score=20.91 Aligned_cols=13 Identities=46% Similarity=0.802 Sum_probs=8.7
Q ss_pred CccCCCCCCccCC
Q psy14694 64 PYKCFVCPYRSNQ 76 (102)
Q Consensus 64 ~~~c~~c~~~f~~ 76 (102)
.+.|..||...+.
T Consensus 30 sf~C~~CGyr~~e 42 (192)
T TIGR00310 30 STICEHCGYRSND 42 (192)
T ss_pred EEECCCCCCccce
Confidence 4778888865543
No 269
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=29.48 E-value=68 Score=18.79 Aligned_cols=12 Identities=17% Similarity=0.094 Sum_probs=6.9
Q ss_pred CccCCCCCCccC
Q psy14694 64 PYKCFVCPYRSN 75 (102)
Q Consensus 64 ~~~c~~c~~~f~ 75 (102)
...|..|+..+.
T Consensus 95 ~~~C~~C~~~~~ 106 (206)
T cd01410 95 IEVCKSCGPEYV 106 (206)
T ss_pred cccCCCCCCccc
Confidence 355666665544
No 270
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=29.16 E-value=12 Score=16.19 Aligned_cols=11 Identities=18% Similarity=0.322 Sum_probs=5.4
Q ss_pred ccCCC--CCCccC
Q psy14694 65 YKCFV--CPYRSN 75 (102)
Q Consensus 65 ~~c~~--c~~~f~ 75 (102)
++|.. ||.+|.
T Consensus 26 ~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 26 CQCTNPECGHTFV 38 (47)
T ss_pred EEECCCcCCCEEE
Confidence 44533 555554
No 271
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=29.15 E-value=18 Score=21.41 Aligned_cols=30 Identities=10% Similarity=0.129 Sum_probs=0.0
Q ss_pred CCccCCCCCCccCCchhhhhhhhhcCCCCcc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLVQISDEQL 93 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~ 93 (102)
....|+.||....- +.+..|+|+...+..|
T Consensus 167 ~~~~cPitGe~IP~-~e~~eHmRi~LlDP~w 196 (229)
T PF12230_consen 167 KMIICPITGEMIPA-DEMDEHMRIELLDPRW 196 (229)
T ss_dssp -------------------------------
T ss_pred cccccccccccccc-cccccccccccccccc
Confidence 33567777765553 3466677766655544
No 272
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.01 E-value=38 Score=23.60 Aligned_cols=7 Identities=0% Similarity=-0.282 Sum_probs=6.1
Q ss_pred ccccccc
Q psy14694 93 LRFKKIR 99 (102)
Q Consensus 93 ~~C~~c~ 99 (102)
+.||.||
T Consensus 573 ~~CP~CG 579 (618)
T PRK14704 573 NECPSCG 579 (618)
T ss_pred ccCcCCC
Confidence 8899998
No 273
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=28.62 E-value=57 Score=19.32 Aligned_cols=15 Identities=13% Similarity=0.368 Sum_probs=9.0
Q ss_pred CCccCCCCCCccCCc
Q psy14694 63 RPYKCFVCPYRSNQR 77 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~ 77 (102)
....|..|+..+...
T Consensus 112 ~~~~C~~C~~~~~~~ 126 (222)
T cd01413 112 QTAYCVNCGSKYDLE 126 (222)
T ss_pred CcceECCCCCCcchh
Confidence 345677777666543
No 274
>KOG4602|consensus
Probab=28.54 E-value=30 Score=21.26 Aligned_cols=38 Identities=21% Similarity=0.268 Sum_probs=19.6
Q ss_pred CCccCCCCCCccCCchhhhhhhhh-------cCCCCccccccccc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLV-------QISDEQLRFKKIRI 100 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~-------~~~~~~~~C~~c~~ 100 (102)
++..|..|...-.....+..|... .-.-+.|.|+.||-
T Consensus 232 r~l~CvFC~nN~E~~A~y~tH~lkd~dgRVLCPkLR~YVCPiCGA 276 (318)
T KOG4602|consen 232 RPLCCVFCFNNAEEFARYHTHPLKDKDGRVLCPKLRSYVCPICGA 276 (318)
T ss_pred CceeEEeecCCCchhhheecccccCCCCcEechhHhhhcCccccc
Confidence 345666665443333334444221 33445588888874
No 275
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=28.51 E-value=21 Score=17.65 Aligned_cols=8 Identities=0% Similarity=-0.230 Sum_probs=3.3
Q ss_pred cccccccc
Q psy14694 93 LRFKKIRI 100 (102)
Q Consensus 93 ~~C~~c~~ 100 (102)
|.|+.|++
T Consensus 66 ~~Cp~Cg~ 73 (81)
T PF10609_consen 66 FVCPHCGE 73 (81)
T ss_dssp EE-TTT--
T ss_pred cCCCCCCC
Confidence 66666664
No 276
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=28.40 E-value=30 Score=19.95 Aligned_cols=11 Identities=18% Similarity=0.419 Sum_probs=6.9
Q ss_pred ccCCCCCCccC
Q psy14694 65 YKCFVCPYRSN 75 (102)
Q Consensus 65 ~~c~~c~~~f~ 75 (102)
+.|.-|.+.|.
T Consensus 140 ~rC~GC~~~f~ 150 (177)
T COG1439 140 LRCHGCKRIFP 150 (177)
T ss_pred EEEecCceecC
Confidence 45666666665
No 277
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=28.16 E-value=24 Score=15.94 Aligned_cols=8 Identities=25% Similarity=0.077 Sum_probs=5.3
Q ss_pred cccccccc
Q psy14694 92 QLRFKKIR 99 (102)
Q Consensus 92 ~~~C~~c~ 99 (102)
.|.|+.||
T Consensus 44 ~y~C~~Cg 51 (54)
T PF10058_consen 44 QYRCPYCG 51 (54)
T ss_pred EEEcCCCC
Confidence 46677666
No 278
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=28.15 E-value=55 Score=19.59 Aligned_cols=15 Identities=13% Similarity=0.255 Sum_probs=9.8
Q ss_pred CCccCCCCCCccCCc
Q psy14694 63 RPYKCFVCPYRSNQR 77 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~ 77 (102)
....|..|++.+...
T Consensus 121 ~~~~C~~C~~~~~~~ 135 (242)
T PRK00481 121 LRARCTKCGQTYDLD 135 (242)
T ss_pred CceeeCCCCCCcChh
Confidence 446788887766544
No 279
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=27.98 E-value=27 Score=22.24 Aligned_cols=13 Identities=15% Similarity=0.054 Sum_probs=10.4
Q ss_pred CCCCccccccccc
Q psy14694 88 ISDEQLRFKKIRI 100 (102)
Q Consensus 88 ~~~~~~~C~~c~~ 100 (102)
.|.-.|.||+|++
T Consensus 280 ~g~d~W~CpkC~~ 292 (415)
T COG5533 280 EGKDAWRCPKCGR 292 (415)
T ss_pred cCcccccCchhcc
Confidence 4566799999986
No 280
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=27.73 E-value=47 Score=13.68 Aligned_cols=11 Identities=36% Similarity=0.664 Sum_probs=4.4
Q ss_pred ccCCccccccc
Q psy14694 2 LKCTHCKVDLN 12 (102)
Q Consensus 2 ~~c~~c~~~f~ 12 (102)
|-|+.|...+.
T Consensus 4 yyCdyC~~~~~ 14 (38)
T PF06220_consen 4 YYCDYCKKYLT 14 (38)
T ss_dssp -B-TTT--B-S
T ss_pred eecccccceec
Confidence 56888888873
No 281
>KOG2071|consensus
Probab=27.62 E-value=41 Score=23.21 Aligned_cols=26 Identities=23% Similarity=0.455 Sum_probs=20.5
Q ss_pred CCCccCCCCCCccCCchhhhhhhhhc
Q psy14694 62 DRPYKCFVCPYRSNQRANLMSHPLVQ 87 (102)
Q Consensus 62 ~~~~~c~~c~~~f~~~~~l~~h~~~~ 87 (102)
.+|.+|..||..|........|+..|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhh
Confidence 56789999999998877776666655
No 282
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.37 E-value=22 Score=15.72 Aligned_cols=7 Identities=0% Similarity=-0.225 Sum_probs=3.3
Q ss_pred ccccccc
Q psy14694 95 FKKIRIA 101 (102)
Q Consensus 95 C~~c~~~ 101 (102)
|++|++-
T Consensus 15 CpvCqRP 21 (54)
T COG4338 15 CPVCQRP 21 (54)
T ss_pred hhhhcCc
Confidence 4555443
No 283
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=27.19 E-value=26 Score=15.54 Aligned_cols=6 Identities=17% Similarity=0.135 Sum_probs=3.3
Q ss_pred cccccc
Q psy14694 94 RFKKIR 99 (102)
Q Consensus 94 ~C~~c~ 99 (102)
.||+||
T Consensus 15 ~Cp~CG 20 (49)
T PF12677_consen 15 KCPKCG 20 (49)
T ss_pred cCcccC
Confidence 356555
No 284
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=26.96 E-value=20 Score=16.75 Aligned_cols=16 Identities=13% Similarity=0.088 Sum_probs=9.2
Q ss_pred cCCCCccccccccccC
Q psy14694 87 QISDEQLRFKKIRIAV 102 (102)
Q Consensus 87 ~~~~~~~~C~~c~~~~ 102 (102)
+..+-...|+.||..|
T Consensus 48 ~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 48 EIVEGELICPECGREY 63 (68)
T ss_dssp ETTTTEEEETTTTEEE
T ss_pred cccCCEEEcCCCCCEE
Confidence 4445556677776643
No 285
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=26.80 E-value=35 Score=21.34 Aligned_cols=11 Identities=18% Similarity=0.268 Sum_probs=6.3
Q ss_pred eeCCCCCCCCC
Q psy14694 37 YDCFMCPYRTP 47 (102)
Q Consensus 37 ~~c~~c~~~~~ 47 (102)
+.|+.|+..+.
T Consensus 47 ~vc~~c~~h~r 57 (292)
T PRK05654 47 NVCPKCGHHMR 57 (292)
T ss_pred CCCCCCCCCee
Confidence 45666666554
No 286
>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=26.76 E-value=14 Score=20.46 Aligned_cols=35 Identities=9% Similarity=0.051 Sum_probs=17.4
Q ss_pred ccCCCCCCccCCchhhhhhhhhcCCCCccccccccccC
Q psy14694 65 YKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~~ 102 (102)
..|+.||.......+ ..-.-.-.-.|.|..|..-|
T Consensus 106 ~~cp~c~s~~t~~~s---~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 106 VQCPRCGSADTTITS---IFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CcCCCCCCCCcEeec---CCCChhhHHHhhhhhhCCcH
Confidence 577778754443211 11111223357777776644
No 287
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=26.34 E-value=1.1e+02 Score=15.92 Aligned_cols=36 Identities=14% Similarity=0.162 Sum_probs=24.6
Q ss_pred ccCCccccccccCHHHHHHHHhhhccccccCCCCceeCCCCCCC
Q psy14694 2 LKCTHCKVDLNLDTEIILQHYKLCSEGARQSSRKKYDCFMCPYR 45 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h~~~~~~~~~~~~~~~~~c~~c~~~ 45 (102)
|.|+.=|..|. +...+..-+... ..+-|.|...|+.
T Consensus 4 f~i~~T~EiF~-dYe~Y~~R~~~y-------~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 4 FYIPFTGEIFR-DYEEYLKRMILY-------NQRVWTCEITGKS 39 (102)
T ss_pred EEeCCCCcccC-CHHHHHHHHHHH-------hCCeeEEecCCCC
Confidence 45667788888 766665544444 5678899887763
No 288
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=26.20 E-value=24 Score=17.34 Aligned_cols=10 Identities=20% Similarity=0.155 Sum_probs=5.9
Q ss_pred cccccccccc
Q psy14694 92 QLRFKKIRIA 101 (102)
Q Consensus 92 ~~~C~~c~~~ 101 (102)
-|+|.+|+++
T Consensus 53 rl~C~~C~~~ 62 (77)
T PF00935_consen 53 RLECTECGKA 62 (77)
T ss_dssp EEEETTTS-E
T ss_pred EEEeCCCCcc
Confidence 3677777654
No 289
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.50 E-value=48 Score=23.70 Aligned_cols=7 Identities=14% Similarity=-0.073 Sum_probs=6.0
Q ss_pred ccccccc
Q psy14694 93 LRFKKIR 99 (102)
Q Consensus 93 ~~C~~c~ 99 (102)
+.||.||
T Consensus 694 ~~CP~CG 700 (735)
T PRK07111 694 DKCPKCG 700 (735)
T ss_pred ccCcCCC
Confidence 7888888
No 290
>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=25.44 E-value=30 Score=21.37 Aligned_cols=11 Identities=36% Similarity=1.002 Sum_probs=4.8
Q ss_pred CCccCCCCCCc
Q psy14694 63 RPYKCFVCPYR 73 (102)
Q Consensus 63 ~~~~c~~c~~~ 73 (102)
+++.|++|+..
T Consensus 208 k~~PCPKCg~e 218 (314)
T PF06524_consen 208 KPIPCPKCGYE 218 (314)
T ss_pred CCCCCCCCCCc
Confidence 34444444443
No 291
>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=25.25 E-value=12 Score=26.40 Aligned_cols=55 Identities=13% Similarity=0.150 Sum_probs=27.6
Q ss_pred eCCCCCCCCCCcchHHHHhhhhcCCCC-ccCCCCCCccCCchhhhhhhhhcCCCCcccccccc
Q psy14694 38 DCFMCPYRTPYSGTMRRHIRAHIGDRP-YKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIR 99 (102)
Q Consensus 38 ~c~~c~~~~~~~~~l~~h~~~h~~~~~-~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~ 99 (102)
.|..||=.|+....|.. .+..+.-.. -.|..|.+.+..+.+..-| -.+-.|+.||
T Consensus 92 nCt~CGPr~~i~~~lpy-dr~~t~m~~f~~C~~C~~ey~~p~~rr~h------~~~~~C~~Cg 147 (711)
T TIGR00143 92 SCTHCGPRFTIIEALPY-DRENTSMADFPLCPDCAKEYKDPLDRRFH------AQPIACPRCG 147 (711)
T ss_pred cccCCCCCeEEeecCCC-CCCCcCCCCCcCCHHHHHHhcCCccccCC------CCCccCCCCC
Confidence 46667766666555442 222222122 2466776666555432222 2355677776
No 292
>KOG4118|consensus
Probab=24.91 E-value=33 Score=16.27 Aligned_cols=23 Identities=22% Similarity=0.261 Sum_probs=15.6
Q ss_pred CccCCCCCCccCCchhhhhhhhh
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLV 86 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~ 86 (102)
.++|.+|.-....+..+..|...
T Consensus 38 ~~kCtVC~~~mpdpktfkqhfe~ 60 (74)
T KOG4118|consen 38 HHKCTVCMVQMPDPKTFKQHFEN 60 (74)
T ss_pred HhhhHhhHhhCCCCchHHHHHhh
Confidence 36777777777777666666555
No 293
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=24.50 E-value=34 Score=17.18 Aligned_cols=7 Identities=0% Similarity=-0.296 Sum_probs=4.2
Q ss_pred ccccccc
Q psy14694 95 FKKIRIA 101 (102)
Q Consensus 95 C~~c~~~ 101 (102)
|..|++.
T Consensus 81 C~vC~k~ 87 (109)
T PF10367_consen 81 CSVCGKP 87 (109)
T ss_pred ccCcCCc
Confidence 6666654
No 294
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=24.42 E-value=8.3 Score=18.39 Aligned_cols=30 Identities=7% Similarity=-0.025 Sum_probs=13.8
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCcccccccccc
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRIA 101 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~~ 101 (102)
...|..|+..+..... ..+ ..|.|+.|+-.
T Consensus 41 ~v~Cg~C~~~~~~~~~-------~c~-~~~~C~~C~~~ 70 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEY-------SCG-ADYFCPICGLY 70 (71)
T ss_dssp EEEETTT--EEES-SB-------TT---SEEETTTTEE
T ss_pred CeECCCCCCccChhhh-------hcC-CCccCcCcCCC
Confidence 4556666655554322 111 45777777654
No 295
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=24.20 E-value=54 Score=22.80 Aligned_cols=8 Identities=13% Similarity=-0.164 Sum_probs=5.4
Q ss_pred cccccccc
Q psy14694 92 QLRFKKIR 99 (102)
Q Consensus 92 ~~~C~~c~ 99 (102)
.+.||.||
T Consensus 546 ~~~CP~CG 553 (586)
T TIGR02827 546 LHRCPVCG 553 (586)
T ss_pred CCcCcCCC
Confidence 36677776
No 296
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=23.60 E-value=25 Score=15.70 Aligned_cols=13 Identities=15% Similarity=-0.010 Sum_probs=6.0
Q ss_pred CCCCccccccccc
Q psy14694 88 ISDEQLRFKKIRI 100 (102)
Q Consensus 88 ~~~~~~~C~~c~~ 100 (102)
.+...|+|..|++
T Consensus 31 ~~~~~~rC~YCe~ 43 (52)
T PF02748_consen 31 KEPIKLRCHYCER 43 (52)
T ss_dssp TTTCEEEETTT--
T ss_pred CCCCEEEeeCCCC
Confidence 3444566666654
No 297
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=23.44 E-value=31 Score=18.16 Aligned_cols=49 Identities=14% Similarity=0.198 Sum_probs=24.4
Q ss_pred ceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCCchhhhhhhhhcCCCCccccccccc
Q psy14694 36 KYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 36 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
...|..|+..|....+ ....|..|.+.+-..-... ..++..|.|..|.+
T Consensus 54 ~~~C~~C~~~fg~l~~-----------~~~~C~~C~~~VC~~C~~~-----~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFN-----------RGRVCVDCKHRVCKKCGVY-----SKKEPIWLCKVCQK 102 (118)
T ss_dssp CSB-TTTS-BCSCTST-----------TCEEETTTTEEEETTSEEE-----TSSSCCEEEHHHHH
T ss_pred CcchhhhCCcccccCC-----------CCCcCCcCCccccCccCCc-----CCCCCCEEChhhHH
Confidence 3478888776643221 2245555554443332111 44566788887754
No 298
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=23.42 E-value=33 Score=18.07 Aligned_cols=9 Identities=0% Similarity=0.050 Sum_probs=6.9
Q ss_pred ccccccccc
Q psy14694 93 LRFKKIRIA 101 (102)
Q Consensus 93 ~~C~~c~~~ 101 (102)
|+|..||..
T Consensus 101 y~C~~Cg~~ 109 (113)
T COG1594 101 YKCTRCGYR 109 (113)
T ss_pred EEecccCCE
Confidence 888888764
No 299
>PRK06921 hypothetical protein; Provisional
Probab=23.08 E-value=43 Score=20.46 Aligned_cols=11 Identities=18% Similarity=0.126 Sum_probs=7.0
Q ss_pred CCccccccccc
Q psy14694 90 DEQLRFKKIRI 100 (102)
Q Consensus 90 ~~~~~C~~c~~ 100 (102)
+..|.||.|+.
T Consensus 30 ~~~~~Cp~C~d 40 (266)
T PRK06921 30 AERYDCPKCKD 40 (266)
T ss_pred CCCCCCCCCCC
Confidence 34577777764
No 300
>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=23.03 E-value=28 Score=20.43 Aligned_cols=25 Identities=28% Similarity=0.437 Sum_probs=0.0
Q ss_pred hcCCCCccCCCCCC-ccCCchhhhhh
Q psy14694 59 HIGDRPYKCFVCPY-RSNQRANLMSH 83 (102)
Q Consensus 59 h~~~~~~~c~~c~~-~f~~~~~l~~h 83 (102)
|--.+.|.|.+||- .+.-+..+.+|
T Consensus 96 hGL~~ey~CEICGN~~Y~GrkaFekH 121 (196)
T PF11931_consen 96 HGLGVEYKCEICGNQSYKGRKAFEKH 121 (196)
T ss_dssp --------------------------
T ss_pred hCCCCeeeeEeCCCcceecHHHHHHh
Confidence 33346688888873 44555556655
No 301
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=22.98 E-value=52 Score=20.09 Aligned_cols=34 Identities=12% Similarity=0.131 Sum_probs=16.9
Q ss_pred CCccCCCCCCccCCchhhhhhhhhcCCCCccccccccc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIRI 100 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~~ 100 (102)
..+.|..|+..+...... .....++ +=.|++||.
T Consensus 121 ~~~~C~~C~~~~~~~~~~---~~~~~~~-~p~C~~Cg~ 154 (250)
T COG0846 121 KRVRCSKCGNQYYDEDVI---KFIEDGL-IPRCPKCGG 154 (250)
T ss_pred eeeEeCCCcCccchhhhh---hhcccCC-CCcCccCCC
Confidence 456777787666533211 1112222 334777764
No 302
>PRK12722 transcriptional activator FlhC; Provisional
Probab=22.89 E-value=71 Score=18.66 Aligned_cols=28 Identities=11% Similarity=-0.003 Sum_probs=16.6
Q ss_pred CccCCCCCCccCCchhhhhhhhhcCCCCcccccccc
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIR 99 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~ 99 (102)
...|..|+-.|.... +.....|.|+-|.
T Consensus 134 l~~C~~Cgg~fv~~~--------~e~~~~f~CplC~ 161 (187)
T PRK12722 134 LSSCNCCGGHFVTHA--------HDPVGSFVCGLCQ 161 (187)
T ss_pred eccCCCCCCCeeccc--------cccCCCCcCCCCC
Confidence 356788886666432 1223467777774
No 303
>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=22.79 E-value=26 Score=14.13 Aligned_cols=7 Identities=43% Similarity=1.217 Sum_probs=2.8
Q ss_pred cCCCCCC
Q psy14694 66 KCFVCPY 72 (102)
Q Consensus 66 ~c~~c~~ 72 (102)
.|..|+.
T Consensus 22 ~C~~C~Y 28 (35)
T PF02150_consen 22 ACRTCGY 28 (35)
T ss_dssp EESSSS-
T ss_pred CCCCCCC
Confidence 3444443
No 304
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=22.57 E-value=63 Score=21.34 Aligned_cols=33 Identities=15% Similarity=0.264 Sum_probs=17.6
Q ss_pred ceeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccCC
Q psy14694 36 KYDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSNQ 76 (102)
Q Consensus 36 ~~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~~ 76 (102)
-..|++|+..+.-+ .| ..++ .-.|+.|+....+
T Consensus 18 ~~~C~eCd~~~~~P-~l------~~~q-~A~CPRC~~~l~~ 50 (418)
T COG2995 18 LILCPECDMLVSLP-RL------DSGQ-SAYCPRCGHTLTR 50 (418)
T ss_pred eecCCCCCceeccc-cC------CCCC-cccCCCCCCcccc
Confidence 35677787765543 22 2222 2467777755443
No 305
>KOG4727|consensus
Probab=22.41 E-value=37 Score=19.52 Aligned_cols=21 Identities=29% Similarity=0.556 Sum_probs=17.5
Q ss_pred CccCCCCCCccCCchhhhhhh
Q psy14694 64 PYKCFVCPYRSNQRANLMSHP 84 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~ 84 (102)
.|-|.+|+-.+....++..|+
T Consensus 75 GyyCdVCdcvvKDSinflDHi 95 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHI 95 (193)
T ss_pred ceeeeecceeehhhHHHHHHh
Confidence 488999999998888877764
No 306
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=22.34 E-value=1e+02 Score=16.03 Aligned_cols=19 Identities=26% Similarity=0.434 Sum_probs=13.2
Q ss_pred ccCCccccccccCHHHHHHH
Q psy14694 2 LKCTHCKVDLNLDTEIILQH 21 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l~~h 21 (102)
+.|+.||..+- +.......
T Consensus 32 ~~C~~CGe~~~-~~e~~~~~ 50 (127)
T TIGR03830 32 WYCPACGEELL-DPEESKRN 50 (127)
T ss_pred eECCCCCCEEE-cHHHHHHH
Confidence 47899998886 66655433
No 308
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=22.06 E-value=42 Score=16.77 Aligned_cols=10 Identities=40% Similarity=1.268 Sum_probs=6.5
Q ss_pred cCCccccccc
Q psy14694 3 KCTHCKVDLN 12 (102)
Q Consensus 3 ~c~~c~~~f~ 12 (102)
.|+.||..|.
T Consensus 10 ~C~~CG~d~~ 19 (86)
T PF06170_consen 10 RCPHCGLDYS 19 (86)
T ss_pred cccccCCccc
Confidence 4677776664
No 309
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=21.91 E-value=83 Score=15.97 Aligned_cols=16 Identities=25% Similarity=0.924 Sum_probs=11.0
Q ss_pred ccCCccccccccCHHHH
Q psy14694 2 LKCTHCKVDLNLDTEII 18 (102)
Q Consensus 2 ~~c~~c~~~f~~~~~~l 18 (102)
..|++||..|. +..-+
T Consensus 36 ~~C~~CGe~y~-~dev~ 51 (89)
T TIGR03829 36 ISCSHCGMEYQ-DDTTV 51 (89)
T ss_pred ccccCCCcEee-cHHHH
Confidence 36888998886 54443
No 310
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=21.81 E-value=67 Score=19.56 Aligned_cols=11 Identities=18% Similarity=-0.013 Sum_probs=4.9
Q ss_pred CCCcccccccc
Q psy14694 89 SDEQLRFKKIR 99 (102)
Q Consensus 89 ~~~~~~C~~c~ 99 (102)
++..-.||.||
T Consensus 218 ~d~iv~CP~Cg 228 (239)
T COG1579 218 KDEIVFCPYCG 228 (239)
T ss_pred CCCCccCCccc
Confidence 33344455554
No 311
>PRK03922 hypothetical protein; Provisional
Probab=21.78 E-value=42 Score=17.72 Aligned_cols=7 Identities=14% Similarity=-0.126 Sum_probs=3.7
Q ss_pred ccccccc
Q psy14694 95 FKKIRIA 101 (102)
Q Consensus 95 C~~c~~~ 101 (102)
||.||.-
T Consensus 52 cP~cge~ 58 (113)
T PRK03922 52 CPKCGEP 58 (113)
T ss_pred CCCCCCc
Confidence 5555543
No 312
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.51 E-value=72 Score=22.43 Aligned_cols=8 Identities=13% Similarity=-0.164 Sum_probs=5.8
Q ss_pred cccccccc
Q psy14694 92 QLRFKKIR 99 (102)
Q Consensus 92 ~~~C~~c~ 99 (102)
-+.||.||
T Consensus 580 ~~~CP~CG 587 (623)
T PRK08271 580 GKRCPICG 587 (623)
T ss_pred CcCCcCCC
Confidence 36788887
No 313
>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=21.47 E-value=41 Score=14.05 Aligned_cols=8 Identities=25% Similarity=0.571 Sum_probs=3.3
Q ss_pred ccCCCCCC
Q psy14694 65 YKCFVCPY 72 (102)
Q Consensus 65 ~~c~~c~~ 72 (102)
+.|..||.
T Consensus 20 ~vC~~CG~ 27 (43)
T PF08271_consen 20 LVCPNCGL 27 (43)
T ss_dssp EEETTT-B
T ss_pred EECCCCCC
Confidence 34555543
No 314
>KOG1280|consensus
Probab=21.31 E-value=95 Score=20.16 Aligned_cols=23 Identities=17% Similarity=0.359 Sum_probs=10.5
Q ss_pred CccCCCCCCccCCchhhhhhhhh
Q psy14694 64 PYKCFVCPYRSNQRANLMSHPLV 86 (102)
Q Consensus 64 ~~~c~~c~~~f~~~~~l~~h~~~ 86 (102)
.|.|++|+..=.....|..|...
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s 101 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLS 101 (381)
T ss_pred cccCCcccccccchhHHHHHhhh
Confidence 34555555443334444445433
No 315
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=21.30 E-value=94 Score=13.45 Aligned_cols=8 Identities=25% Similarity=0.795 Sum_probs=4.2
Q ss_pred CceeCCCC
Q psy14694 35 KKYDCFMC 42 (102)
Q Consensus 35 ~~~~c~~c 42 (102)
..+.|.+|
T Consensus 14 ~r~~C~~C 21 (49)
T cd02335 14 IRIKCAEC 21 (49)
T ss_pred cEEECCCC
Confidence 44555555
No 316
>PRK02935 hypothetical protein; Provisional
Probab=21.30 E-value=44 Score=17.54 Aligned_cols=13 Identities=8% Similarity=-0.118 Sum_probs=7.1
Q ss_pred CCCCccccccccc
Q psy14694 88 ISDEQLRFKKIRI 100 (102)
Q Consensus 88 ~~~~~~~C~~c~~ 100 (102)
+...+..||.|+|
T Consensus 66 tkavqV~CP~C~K 78 (110)
T PRK02935 66 TKAVQVICPSCEK 78 (110)
T ss_pred ccceeeECCCCCc
Confidence 3334456666665
No 317
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=21.22 E-value=75 Score=23.32 Aligned_cols=32 Identities=22% Similarity=0.268 Sum_probs=17.5
Q ss_pred eeCCCCCCCCCCcchHHHHhhhhcCCCCccCCCCCCccC
Q psy14694 37 YDCFMCPYRTPYSGTMRRHIRAHIGDRPYKCFVCPYRSN 75 (102)
Q Consensus 37 ~~c~~c~~~~~~~~~l~~h~~~h~~~~~~~c~~c~~~f~ 75 (102)
-.|..|++.|....... +.+.+-|..||..|.
T Consensus 461 dtC~~C~kkFfSlsK~L-------~~RKHHCRkCGrVFC 492 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPL-------GTRAHHCRSCGIRLC 492 (1374)
T ss_pred CcccCcCCccccccccc-------ccccccccCCccccC
Confidence 35778888776542111 223445666666553
No 318
>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=21.08 E-value=38 Score=15.05 Aligned_cols=9 Identities=0% Similarity=-0.086 Sum_probs=4.2
Q ss_pred ccccccccc
Q psy14694 93 LRFKKIRIA 101 (102)
Q Consensus 93 ~~C~~c~~~ 101 (102)
..|+.|+..
T Consensus 41 ~~C~~C~~~ 49 (64)
T PF01485_consen 41 VTCPSCGTE 49 (64)
T ss_dssp CCTTSCCSE
T ss_pred eECCCCCCc
Confidence 445555443
No 319
>PRK07218 replication factor A; Provisional
Probab=21.02 E-value=61 Score=21.51 Aligned_cols=10 Identities=20% Similarity=0.338 Sum_probs=6.3
Q ss_pred ccCCCCCCcc
Q psy14694 65 YKCFVCPYRS 74 (102)
Q Consensus 65 ~~c~~c~~~f 74 (102)
..|+.|++..
T Consensus 298 ~rCP~C~r~v 307 (423)
T PRK07218 298 ERCPECGRVI 307 (423)
T ss_pred ecCcCccccc
Confidence 4577776554
No 320
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=21.01 E-value=52 Score=22.03 Aligned_cols=26 Identities=19% Similarity=0.277 Sum_probs=21.9
Q ss_pred CCCccCCCCCCccCCchhhhhhhhhc
Q psy14694 62 DRPYKCFVCPYRSNQRANLMSHPLVQ 87 (102)
Q Consensus 62 ~~~~~c~~c~~~f~~~~~l~~h~~~~ 87 (102)
...|.|..|-+-|.....|.+|+...
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~C 221 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKKC 221 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhcC
Confidence 45689999999999999999998754
No 321
>PRK12860 transcriptional activator FlhC; Provisional
Probab=20.86 E-value=80 Score=18.49 Aligned_cols=29 Identities=10% Similarity=0.088 Sum_probs=17.3
Q ss_pred CCccCCCCCCccCCchhhhhhhhhcCCCCcccccccc
Q psy14694 63 RPYKCFVCPYRSNQRANLMSHPLVQISDEQLRFKKIR 99 (102)
Q Consensus 63 ~~~~c~~c~~~f~~~~~l~~h~~~~~~~~~~~C~~c~ 99 (102)
....|..|+-.|.... +.....|.|+-|.
T Consensus 133 ~l~~C~~Cgg~fv~~~--------~e~~~~f~CplC~ 161 (189)
T PRK12860 133 QLARCCRCGGKFVTHA--------HDLRHNFVCGLCQ 161 (189)
T ss_pred eeccCCCCCCCeeccc--------cccCCCCcCCCCC
Confidence 3467888887666432 2333467787774
No 322
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=20.80 E-value=52 Score=15.48 Aligned_cols=9 Identities=44% Similarity=0.958 Sum_probs=6.2
Q ss_pred ccCCCCCCc
Q psy14694 65 YKCFVCPYR 73 (102)
Q Consensus 65 ~~c~~c~~~ 73 (102)
|.|++|+..
T Consensus 1 y~C~KCg~~ 9 (64)
T PF09855_consen 1 YKCPKCGNE 9 (64)
T ss_pred CCCCCCCCc
Confidence 578888743
No 323
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.58 E-value=61 Score=22.18 Aligned_cols=26 Identities=19% Similarity=0.050 Sum_probs=22.0
Q ss_pred CCCccCCCCCCccCCchhhhhhhhhc
Q psy14694 62 DRPYKCFVCPYRSNQRANLMSHPLVQ 87 (102)
Q Consensus 62 ~~~~~c~~c~~~f~~~~~l~~h~~~~ 87 (102)
...|.|..|-+-|.....|.+|+...
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~C 303 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSRC 303 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhcC
Confidence 45689999999999999999997754
No 324
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=20.52 E-value=42 Score=13.42 Aligned_cols=8 Identities=0% Similarity=-0.143 Sum_probs=4.6
Q ss_pred cccccccc
Q psy14694 93 LRFKKIRI 100 (102)
Q Consensus 93 ~~C~~c~~ 100 (102)
|.|..|++
T Consensus 9 Y~C~~C~~ 16 (32)
T PF13696_consen 9 YVCHRCGQ 16 (32)
T ss_pred CEeecCCC
Confidence 56666654
No 325
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=20.52 E-value=36 Score=17.35 Aligned_cols=9 Identities=22% Similarity=0.128 Sum_probs=6.8
Q ss_pred ccccccccc
Q psy14694 93 LRFKKIRIA 101 (102)
Q Consensus 93 ~~C~~c~~~ 101 (102)
|+|.+|+++
T Consensus 68 ~~C~~C~~~ 76 (92)
T PRK05767 68 YRCTECGKA 76 (92)
T ss_pred EEecccChh
Confidence 778888764
No 326
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=20.41 E-value=54 Score=13.69 Aligned_cols=6 Identities=50% Similarity=1.702 Sum_probs=2.7
Q ss_pred cCCccc
Q psy14694 3 KCTHCK 8 (102)
Q Consensus 3 ~c~~c~ 8 (102)
.|+.||
T Consensus 4 ~Cp~Cg 9 (47)
T PF14690_consen 4 RCPHCG 9 (47)
T ss_pred cCCCcC
Confidence 344444
No 327
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.25 E-value=76 Score=22.32 Aligned_cols=8 Identities=13% Similarity=0.040 Sum_probs=5.7
Q ss_pred cccccccc
Q psy14694 92 QLRFKKIR 99 (102)
Q Consensus 92 ~~~C~~c~ 99 (102)
-+.||.||
T Consensus 582 ~~~CP~CG 589 (625)
T PRK08579 582 YTRCPRCG 589 (625)
T ss_pred CCcCcCCC
Confidence 36788887
No 328
>KOG1088|consensus
Probab=20.23 E-value=54 Score=17.58 Aligned_cols=22 Identities=5% Similarity=-0.120 Sum_probs=16.0
Q ss_pred hhcCCCCccCCCCCCccCCchh
Q psy14694 58 AHIGDRPYKCFVCPYRSNQRAN 79 (102)
Q Consensus 58 ~h~~~~~~~c~~c~~~f~~~~~ 79 (102)
++..+...+|++||+.|.-...
T Consensus 92 ~~v~EG~l~CpetG~vfpI~~G 113 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFPISDG 113 (124)
T ss_pred hhhccceEecCCCCcEeecccC
Confidence 3455667899999999875443
No 329
>KOG1008|consensus
Probab=20.14 E-value=39 Score=23.85 Aligned_cols=38 Identities=11% Similarity=0.049 Sum_probs=21.4
Q ss_pred ccCCCCCCccCCchhhh--hhhhhcCCCCccccccccccC
Q psy14694 65 YKCFVCPYRSNQRANLM--SHPLVQISDEQLRFKKIRIAV 102 (102)
Q Consensus 65 ~~c~~c~~~f~~~~~l~--~h~~~~~~~~~~~C~~c~~~~ 102 (102)
.+|..|++....+..-. .-.++-.+...+.||.||++|
T Consensus 737 ~~c~~c~~~i~~~~~~~p~~~~~ts~~n~~~~cp~c~s~~ 776 (783)
T KOG1008|consen 737 IQCQNCKQNINTPRTSSPSSAVSTSAGNYKNGCPHCGSSF 776 (783)
T ss_pred ehhhhHHhhhccccCCCCCccccccccccccCCCCCCCCC
Confidence 35777765443221111 123345666677899998876
Done!