Query psy1778
Match_columns 66
No_of_seqs 112 out of 2420
Neff 11.8
Searched_HMMs 46136
Date Fri Aug 16 22:48:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1778.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1778hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 1.2E-19 2.6E-24 88.9 3.2 59 3-66 187-245 (279)
2 KOG2462|consensus 99.6 6.8E-16 1.5E-20 75.9 2.9 53 1-58 213-265 (279)
3 KOG3623|consensus 99.4 4.6E-14 1E-18 77.0 1.4 51 2-57 921-971 (1007)
4 KOG3623|consensus 99.3 3.3E-13 7.2E-18 73.8 1.7 59 3-66 894-952 (1007)
5 PHA02768 hypothetical protein; 99.2 7.9E-12 1.7E-16 48.7 2.5 43 4-53 6-48 (55)
6 KOG1074|consensus 99.2 2.8E-12 6E-17 70.9 0.1 56 3-63 353-408 (958)
7 KOG3576|consensus 99.2 9.3E-12 2E-16 59.8 0.9 54 3-61 145-198 (267)
8 PHA00733 hypothetical protein 99.1 4.2E-10 9.1E-15 51.1 4.6 53 2-61 72-124 (128)
9 KOG1074|consensus 99.1 6.4E-11 1.4E-15 65.8 2.2 56 4-64 880-935 (958)
10 KOG3576|consensus 98.9 1.1E-10 2.3E-15 56.3 -0.4 58 4-66 118-175 (267)
11 PF13465 zf-H2C2_2: Zinc-finge 98.9 2.2E-09 4.8E-14 36.2 2.2 26 20-48 1-26 (26)
12 PHA00616 hypothetical protein 98.9 1.9E-09 4.1E-14 40.4 1.9 34 3-39 1-34 (44)
13 PHA00616 hypothetical protein 98.7 1.1E-08 2.4E-13 38.3 1.6 30 35-66 2-31 (44)
14 KOG3608|consensus 98.7 4.1E-08 8.9E-13 50.9 3.8 55 2-60 291-345 (467)
15 PHA00732 hypothetical protein 98.6 1E-07 2.3E-12 40.0 2.8 44 3-57 1-45 (79)
16 KOG3993|consensus 98.4 1.7E-07 3.6E-12 49.6 1.7 53 4-61 296-381 (500)
17 KOG3608|consensus 98.3 1.3E-06 2.8E-11 45.6 3.9 52 4-60 264-316 (467)
18 PF00096 zf-C2H2: Zinc finger, 98.3 5.8E-07 1.3E-11 29.1 1.7 21 5-27 2-22 (23)
19 PHA02768 hypothetical protein; 98.2 1.3E-06 2.9E-11 34.2 1.8 24 35-60 6-29 (55)
20 COG5189 SFP1 Putative transcri 98.2 6.4E-07 1.4E-11 46.1 1.1 54 1-57 347-419 (423)
21 PF00096 zf-C2H2: Zinc finger, 98.1 2.9E-06 6.2E-11 27.4 1.5 23 35-59 1-23 (23)
22 PF05605 zf-Di19: Drought indu 98.1 3.5E-05 7.5E-10 30.1 4.7 51 3-61 2-54 (54)
23 PF13912 zf-C2H2_6: C2H2-type 97.9 4.7E-06 1E-10 28.0 1.1 22 4-27 2-23 (27)
24 PF13894 zf-C2H2_4: C2H2-type 97.9 1.1E-05 2.4E-10 26.0 1.7 18 10-27 5-22 (24)
25 PLN03086 PRLI-interacting fact 97.9 3.1E-05 6.8E-10 42.8 4.2 53 2-64 452-504 (567)
26 PF13894 zf-C2H2_4: C2H2-type 97.9 2E-05 4.3E-10 25.3 2.1 24 35-60 1-24 (24)
27 PF09237 GAGA: GAGA factor; I 97.9 2.6E-05 5.6E-10 30.1 2.5 33 30-65 21-53 (54)
28 PF13912 zf-C2H2_6: C2H2-type 97.9 5.5E-06 1.2E-10 27.8 0.6 25 35-61 2-26 (27)
29 PHA00733 hypothetical protein 97.8 1.1E-05 2.3E-10 36.9 1.1 53 2-59 39-96 (128)
30 smart00355 ZnF_C2H2 zinc finge 97.7 9.9E-05 2.1E-09 23.9 2.8 22 5-28 2-23 (26)
31 PF09237 GAGA: GAGA factor; I 97.7 6.7E-05 1.4E-09 29.0 2.2 30 2-33 23-52 (54)
32 PLN03086 PRLI-interacting fact 97.5 0.00028 6E-09 39.3 4.1 55 2-64 477-541 (567)
33 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00078 1.7E-08 21.8 1.8 16 10-26 5-20 (24)
34 PRK04860 hypothetical protein; 97.0 0.00062 1.3E-08 32.4 1.9 38 3-49 119-156 (160)
35 PF12874 zf-met: Zinc-finger o 96.8 0.00099 2.2E-08 21.6 1.2 16 42-57 6-21 (25)
36 PF12756 zf-C2H2_2: C2H2 type 96.5 0.0029 6.3E-08 27.2 1.9 49 6-59 2-73 (100)
37 PHA00732 hypothetical protein 96.4 0.0027 5.9E-08 26.8 1.6 22 35-58 2-23 (79)
38 PF12171 zf-C2H2_jaz: Zinc-fin 96.0 0.0017 3.6E-08 21.6 -0.1 20 4-25 2-21 (27)
39 PF13913 zf-C2HC_2: zinc-finge 95.9 0.011 2.3E-07 19.5 1.8 19 36-57 4-22 (25)
40 COG5048 FOG: Zn-finger [Genera 95.1 0.003 6.5E-08 33.3 -1.0 58 3-63 289-350 (467)
41 smart00451 ZnF_U1 U1-like zinc 94.9 0.032 6.9E-07 19.4 1.7 22 3-26 3-24 (35)
42 KOG3993|consensus 94.7 0.0031 6.8E-08 34.3 -1.6 51 4-59 268-318 (500)
43 PF12756 zf-C2H2_2: C2H2 type 94.3 0.074 1.6E-06 22.7 2.4 26 3-30 50-75 (100)
44 KOG2893|consensus 94.2 0.018 3.9E-07 29.4 0.5 39 10-55 15-53 (341)
45 COG5048 FOG: Zn-finger [Genera 92.5 0.14 3.1E-06 27.2 2.1 57 2-61 32-88 (467)
46 COG4049 Uncharacterized protei 92.1 0.082 1.8E-06 20.9 0.8 21 4-26 18-38 (65)
47 COG5189 SFP1 Putative transcri 91.4 0.14 3E-06 27.4 1.3 26 31-57 347-372 (423)
48 KOG1146|consensus 90.4 0.31 6.8E-06 30.7 2.3 52 2-58 464-540 (1406)
49 PF12013 DUF3505: Protein of u 84.3 1.1 2.3E-05 20.0 1.7 25 35-61 81-109 (109)
50 cd00350 rubredoxin_like Rubred 82.2 1.2 2.7E-05 15.4 1.2 24 4-44 2-25 (33)
51 PF15269 zf-C2H2_7: Zinc-finge 81.6 1.5 3.3E-05 16.6 1.4 22 4-27 21-42 (54)
52 KOG4167|consensus 80.7 0.3 6.5E-06 29.0 -0.9 24 4-29 793-816 (907)
53 PF04959 ARS2: Arsenite-resist 77.8 1.9 4.1E-05 21.9 1.4 24 3-28 77-100 (214)
54 PF09538 FYDLN_acid: Protein o 76.2 2.6 5.7E-05 19.1 1.5 30 4-49 10-39 (108)
55 PF05443 ROS_MUCR: ROS/MUCR tr 74.2 2.1 4.6E-05 20.1 1.0 23 35-62 73-95 (132)
56 KOG1146|consensus 72.7 1.9 4.2E-05 27.6 0.9 54 2-61 1283-1353(1406)
57 PHA00626 hypothetical protein 71.3 2.1 4.7E-05 17.1 0.6 14 3-18 23-36 (59)
58 COG2879 Uncharacterized small 71.1 5.9 0.00013 16.2 1.8 19 48-66 24-42 (65)
59 smart00614 ZnF_BED BED zinc fi 70.8 5.2 0.00011 15.1 1.6 21 35-57 19-44 (50)
60 PF07754 DUF1610: Domain of un 70.1 2.5 5.4E-05 13.8 0.6 8 3-12 16-23 (24)
61 PF09845 DUF2072: Zn-ribbon co 69.4 3.1 6.6E-05 19.6 1.0 15 3-19 1-15 (131)
62 smart00834 CxxC_CXXC_SSSS Puta 68.0 2.4 5.3E-05 15.0 0.4 12 4-17 6-17 (41)
63 PRK09678 DNA-binding transcrip 67.4 1.7 3.8E-05 18.2 -0.0 44 4-52 2-45 (72)
64 TIGR00373 conserved hypothetic 66.8 5.3 0.00011 19.2 1.5 31 4-48 110-140 (158)
65 PF13719 zinc_ribbon_5: zinc-r 66.7 6.2 0.00014 14.0 1.5 33 5-47 4-36 (37)
66 smart00659 RPOLCX RNA polymera 66.6 5.7 0.00012 14.9 1.3 26 4-45 3-28 (44)
67 KOG2071|consensus 66.4 6.1 0.00013 23.3 1.9 26 2-29 417-442 (579)
68 PF13451 zf-trcl: Probable zin 65.2 2.9 6.3E-05 16.2 0.4 16 2-19 3-18 (49)
69 PF09723 Zn-ribbon_8: Zinc rib 64.0 2.9 6.3E-05 15.3 0.3 29 4-44 6-34 (42)
70 KOG2932|consensus 63.1 7.6 0.00016 21.2 1.7 27 35-61 145-172 (389)
71 KOG3408|consensus 62.6 4 8.6E-05 19.0 0.6 22 35-58 58-79 (129)
72 PF10571 UPF0547: Uncharacteri 62.5 5.5 0.00012 13.1 0.8 6 10-15 19-24 (26)
73 PRK06266 transcription initiat 61.1 6.9 0.00015 19.3 1.3 32 3-48 117-148 (178)
74 smart00154 ZnF_AN1 AN1-like Zi 60.8 4.7 0.0001 14.6 0.6 13 3-17 12-24 (39)
75 COG1592 Rubrerythrin [Energy p 60.2 8.3 0.00018 19.0 1.5 23 4-44 135-157 (166)
76 KOG4173|consensus 59.9 3.1 6.7E-05 21.2 0.1 50 5-57 108-167 (253)
77 TIGR02605 CxxC_CxxC_SSSS putat 59.5 4.1 8.8E-05 15.4 0.4 12 4-17 6-17 (52)
78 COG3357 Predicted transcriptio 58.0 5.5 0.00012 17.6 0.7 14 2-17 57-70 (97)
79 TIGR02098 MJ0042_CXXC MJ0042 f 57.1 9.8 0.00021 13.3 1.2 34 4-47 3-36 (38)
80 TIGR02300 FYDLN_acid conserved 54.2 15 0.00033 17.3 1.8 30 4-49 10-39 (129)
81 smart00734 ZnF_Rad18 Rad18-lik 54.2 10 0.00022 12.4 1.4 18 36-56 3-20 (26)
82 PF01428 zf-AN1: AN1-like Zinc 54.1 4.4 9.5E-05 14.9 0.0 13 3-17 13-25 (43)
83 PF04780 DUF629: Protein of un 52.9 15 0.00032 21.3 1.9 25 4-30 58-83 (466)
84 PF13453 zf-TFIIB: Transcripti 51.9 14 0.0003 13.3 1.8 19 4-24 20-38 (41)
85 KOG2186|consensus 50.9 7.4 0.00016 20.6 0.6 46 4-57 4-49 (276)
86 PLN02294 cytochrome c oxidase 50.0 8.9 0.00019 19.0 0.7 14 2-17 140-153 (174)
87 PF13717 zinc_ribbon_4: zinc-r 48.7 16 0.00034 12.9 1.4 32 5-46 4-35 (36)
88 COG4957 Predicted transcriptio 47.8 11 0.00023 18.0 0.8 24 5-33 78-101 (148)
89 PF09986 DUF2225: Uncharacteri 47.6 9 0.0002 19.4 0.6 23 1-25 3-25 (214)
90 smart00531 TFIIE Transcription 47.0 30 0.00066 16.4 2.2 36 3-47 99-134 (147)
91 COG3364 Zn-ribbon containing p 47.0 10 0.00022 17.2 0.6 14 3-18 2-15 (112)
92 KOG2231|consensus 46.7 23 0.00049 21.6 2.0 17 10-26 187-203 (669)
93 PRK00398 rpoP DNA-directed RNA 46.0 11 0.00023 14.0 0.5 31 2-47 2-32 (46)
94 PF08790 zf-LYAR: LYAR-type C2 45.8 4.5 9.7E-05 13.7 -0.4 6 10-15 5-10 (28)
95 COG3677 Transposase and inacti 45.6 11 0.00024 17.6 0.7 14 3-18 53-66 (129)
96 COG1997 RPL43A Ribosomal prote 45.0 8.3 0.00018 16.9 0.2 31 3-48 35-65 (89)
97 PF11789 zf-Nse: Zinc-finger o 44.2 10 0.00023 15.0 0.4 7 10-16 29-35 (57)
98 PF04606 Ogr_Delta: Ogr/Delta- 42.9 11 0.00023 14.2 0.3 13 4-16 26-38 (47)
99 PF02892 zf-BED: BED zinc fing 42.4 22 0.00047 12.8 1.7 21 35-57 17-41 (45)
100 COG1773 Rubredoxin [Energy pro 42.2 12 0.00025 14.9 0.4 15 2-18 2-16 (55)
101 COG2888 Predicted Zn-ribbon RN 42.2 26 0.00055 14.3 1.3 8 4-13 28-35 (61)
102 KOG0717|consensus 40.0 18 0.00038 21.1 1.0 21 35-57 293-313 (508)
103 KOG0227|consensus 38.6 15 0.00033 18.7 0.5 19 35-55 54-72 (222)
104 cd00729 rubredoxin_SM Rubredox 38.6 16 0.00035 12.7 0.5 25 3-44 2-26 (34)
105 KOG1994|consensus 38.3 15 0.00033 19.2 0.5 19 35-55 240-258 (268)
106 KOG2482|consensus 37.6 33 0.00071 19.3 1.7 23 4-28 196-218 (423)
107 PF03604 DNA_RNApol_7kD: DNA d 37.4 14 0.00031 12.8 0.3 26 4-45 1-26 (32)
108 PRK00464 nrdR transcriptional 35.8 14 0.00031 17.9 0.2 13 4-18 29-41 (154)
109 KOG2593|consensus 35.3 32 0.00069 19.8 1.5 16 3-20 128-143 (436)
110 cd00730 rubredoxin Rubredoxin; 35.1 23 0.0005 13.7 0.7 13 4-18 2-14 (50)
111 KOG2785|consensus 33.2 99 0.0021 17.7 3.3 52 3-58 166-242 (390)
112 KOG2807|consensus 32.0 89 0.0019 17.6 2.7 21 32-55 289-309 (378)
113 PTZ00043 cytochrome c oxidase 29.6 31 0.00067 18.2 0.8 15 2-18 180-194 (268)
114 KOG4124|consensus 29.3 20 0.00043 20.1 0.1 22 30-55 210-231 (442)
115 smart00440 ZnF_C2C2 C2C2 Zinc 29.2 28 0.0006 12.6 0.5 10 4-15 29-38 (40)
116 PTZ00448 hypothetical protein; 28.9 68 0.0015 18.2 2.0 23 3-27 314-336 (373)
117 KOG1842|consensus 28.4 39 0.00084 19.7 1.1 25 35-61 16-40 (505)
118 PF10426 zf-RAG1: Recombinatio 27.9 41 0.00089 11.6 0.8 7 37-43 5-11 (30)
119 PF01927 Mut7-C: Mut7-C RNAse 27.5 29 0.00062 16.5 0.5 10 4-15 125-134 (147)
120 COG3809 Uncharacterized protei 27.4 67 0.0015 13.9 1.5 21 6-28 24-44 (88)
121 PF04328 DUF466: Protein of un 26.5 62 0.0013 13.3 1.9 12 54-65 30-41 (65)
122 PF07975 C1_4: TFIIH C1-like d 26.1 8 0.00017 15.1 -1.2 13 4-18 22-34 (51)
123 PF10013 DUF2256: Uncharacteri 26.1 39 0.00084 12.7 0.6 11 6-18 11-21 (42)
124 PF06858 NOG1: Nucleolar GTP-b 25.6 54 0.0012 13.2 1.0 23 42-64 27-49 (58)
125 PF08792 A2L_zn_ribbon: A2L zi 25.4 33 0.00071 12.0 0.4 6 10-15 26-31 (33)
126 PF10276 zf-CHCC: Zinc-finger 24.8 24 0.00053 13.0 -0.0 6 10-15 34-39 (40)
127 KOG4385|consensus 24.0 57 0.0012 19.3 1.2 23 5-27 211-233 (581)
128 PF00301 Rubredoxin: Rubredoxi 23.9 26 0.00055 13.4 -0.0 13 4-18 2-14 (47)
129 PLN03238 probable histone acet 23.7 1.4E+02 0.003 16.5 2.5 23 3-27 48-70 (290)
130 cd00974 DSRD Desulforedoxin (D 23.6 39 0.00084 11.5 0.4 11 3-15 4-14 (34)
131 KOG2295|consensus 23.6 84 0.0018 19.1 1.8 26 2-27 508-533 (648)
132 KOG4377|consensus 23.5 92 0.002 18.1 1.9 28 3-30 271-298 (480)
133 TIGR00319 desulf_FeS4 desulfof 23.4 38 0.00082 11.5 0.4 11 3-15 7-17 (34)
134 PRK03824 hypA hydrogenase nick 23.3 28 0.0006 16.4 0.0 14 3-18 70-83 (135)
135 TIGR03831 YgiT_finger YgiT-typ 22.9 44 0.00096 11.8 0.6 10 4-15 33-42 (46)
136 KOG4727|consensus 22.4 44 0.00096 16.8 0.6 21 35-57 76-96 (193)
137 COG5216 Uncharacterized conser 22.0 47 0.001 13.5 0.6 29 4-43 23-51 (67)
138 PF01215 COX5B: Cytochrome c o 21.9 19 0.00042 17.1 -0.6 13 2-16 111-123 (136)
139 PF04423 Rad50_zn_hook: Rad50 21.7 37 0.00081 13.0 0.3 12 5-18 22-33 (54)
140 COG5236 Uncharacterized conser 21.7 1.3E+02 0.0027 17.3 2.2 20 6-27 223-242 (493)
141 COG1996 RPC10 DNA-directed RNA 21.4 30 0.00066 13.4 -0.0 11 3-15 6-16 (49)
142 TIGR00622 ssl1 transcription f 21.3 90 0.002 14.5 1.4 23 35-59 82-104 (112)
143 COG4530 Uncharacterized protei 21.2 87 0.0019 14.6 1.3 12 2-15 25-36 (129)
144 PF01286 XPA_N: XPA protein N- 21.2 35 0.00076 12.1 0.1 12 5-18 5-16 (34)
145 PF06397 Desulfoferrod_N: Desu 21.1 35 0.00076 12.3 0.1 11 3-15 6-16 (36)
146 PF14353 CpXC: CpXC protein 20.5 49 0.0011 15.1 0.5 13 4-18 39-51 (128)
147 KOG2636|consensus 20.4 96 0.0021 18.3 1.6 27 26-55 394-421 (497)
148 PF13878 zf-C2H2_3: zinc-finge 20.2 71 0.0015 11.6 2.6 23 4-28 14-38 (41)
149 TIGR00244 transcriptional regu 20.2 54 0.0012 16.0 0.6 13 5-19 30-42 (147)
150 PF14690 zf-ISL3: zinc-finger 20.0 65 0.0014 11.6 0.8 9 3-13 2-10 (47)
No 1
>KOG2462|consensus
Probab=99.78 E-value=1.2e-19 Score=88.88 Aligned_cols=59 Identities=36% Similarity=0.672 Sum_probs=55.3
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHhhCCCCCC
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHSTNKIT 66 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~~~~~~ 66 (66)
|.+|. .||+.|+..+-|+-|+++|+|++| |.|.. |++.|...++|..|++||.+.|+|+
T Consensus 187 ~c~C~--iCGKaFSRPWLLQGHiRTHTGEKP-F~C~h--C~kAFADRSNLRAHmQTHS~~K~~q 245 (279)
T KOG2462|consen 187 PCECG--ICGKAFSRPWLLQGHIRTHTGEKP-FSCPH--CGKAFADRSNLRAHMQTHSDVKKHQ 245 (279)
T ss_pred Ccccc--cccccccchHHhhcccccccCCCC-ccCCc--ccchhcchHHHHHHHHhhcCCcccc
Confidence 56677 999999999999999999999999 99988 9999999999999999999999885
No 2
>KOG2462|consensus
Probab=99.60 E-value=6.8e-16 Score=75.94 Aligned_cols=53 Identities=38% Similarity=0.739 Sum_probs=50.4
Q ss_pred CCcccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHH
Q psy1778 1 MRMFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKH 58 (66)
Q Consensus 1 ~~~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~ 58 (66)
||||.|. .|++.|..+++|..||++|.+.+. |+|.. |+++|...+.|..|...
T Consensus 213 EKPF~C~--hC~kAFADRSNLRAHmQTHS~~K~-~qC~~--C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 213 EKPFSCP--HCGKAFADRSNLRAHMQTHSDVKK-HQCPR--CGKSFALKSYLNKHSES 265 (279)
T ss_pred CCCccCC--cccchhcchHHHHHHHHhhcCCcc-ccCcc--hhhHHHHHHHHHHhhhh
Confidence 7999999 999999999999999999999999 99987 99999999999999763
No 3
>KOG3623|consensus
Probab=99.42 E-value=4.6e-14 Score=77.05 Aligned_cols=51 Identities=35% Similarity=0.729 Sum_probs=26.1
Q ss_pred CcccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHH
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLK 57 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~ 57 (66)
|||.|. .|.+.|..+-+|..|++.|.|++| |+|.. |+++|+.+.++.+||.
T Consensus 921 RPyqC~--iCkKAFKHKHHLtEHkRLHSGEKP-fQCdK--ClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 921 RPYQCI--ICKKAFKHKHHLTEHKRLHSGEKP-FQCDK--CLKRFSHSGSYSQHMN 971 (1007)
T ss_pred CCcccc--hhhHhhhhhhhhhhhhhhccCCCc-chhhh--hhhhcccccchHhhhc
Confidence 455555 555555555555555555555555 55533 5555555555555543
No 4
>KOG3623|consensus
Probab=99.35 E-value=3.3e-13 Score=73.84 Aligned_cols=59 Identities=24% Similarity=0.600 Sum_probs=56.8
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHhhCCCCCC
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHSTNKIT 66 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~~~~~~ 66 (66)
+|.|. .|++.|.-.+.|.+|.--|+|++| ++|.+ |.+.|.....|..|.|.|.|||||+
T Consensus 894 myaCD--qCDK~FqKqSSLaRHKYEHsGqRP-yqC~i--CkKAFKHKHHLtEHkRLHSGEKPfQ 952 (1007)
T KOG3623|consen 894 MYACD--QCDKAFQKQSSLARHKYEHSGQRP-YQCII--CKKAFKHKHHLTEHKRLHSGEKPFQ 952 (1007)
T ss_pred cchHH--HHHHHHHhhHHHHHhhhhhcCCCC-cccch--hhHhhhhhhhhhhhhhhccCCCcch
Confidence 68899 999999999999999999999999 99988 9999999999999999999999996
No 5
>PHA02768 hypothetical protein; Provisional
Probab=99.24 E-value=7.9e-12 Score=48.75 Aligned_cols=43 Identities=19% Similarity=0.580 Sum_probs=37.7
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHH
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLY 53 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~ 53 (66)
|.|+ .||+.|.+..+|..|+++|+ ++ +.|.. |++.|...+.|.
T Consensus 6 y~C~--~CGK~Fs~~~~L~~H~r~H~--k~-~kc~~--C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECP--ICGEIYIKRKSMITHLRKHN--TN-LKLSN--CKRISLRTGEYI 48 (55)
T ss_pred cCcc--hhCCeeccHHHHHHHHHhcC--Cc-ccCCc--ccceecccceeE
Confidence 6788 99999999999999999998 57 88966 999998777654
No 6
>KOG1074|consensus
Probab=99.19 E-value=2.8e-12 Score=70.91 Aligned_cols=56 Identities=27% Similarity=0.539 Sum_probs=51.3
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHhhCCC
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHSTN 63 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~~~ 63 (66)
+++|. .|.+.|...+.|+.|.+.|++++| |+|.+ |+..|+...+|..|...|...-
T Consensus 353 khkCr--~CakvfgS~SaLqiHlRSHTGERP-fqCnv--CG~~FSTkGNLKvH~~rH~e~~ 408 (958)
T KOG1074|consen 353 KHKCR--FCAKVFGSDSALQIHLRSHTGERP-FQCNV--CGNRFSTKGNLKVHFQRHREKY 408 (958)
T ss_pred cchhh--hhHhhcCchhhhhhhhhccCCCCC-eeecc--cccccccccceeeeeeeccccC
Confidence 36788 999999999999999999999999 99988 9999999999999988776554
No 7
>KOG3576|consensus
Probab=99.16 E-value=9.3e-12 Score=59.82 Aligned_cols=54 Identities=33% Similarity=0.698 Sum_probs=47.9
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHhhC
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHS 61 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~ 61 (66)
-+.|. .||+.|.....|.+|+++|++.+| |.|.. |++.|.+.-+|..|++..+|
T Consensus 145 r~lct--~cgkgfndtfdlkrh~rthtgvrp-ykc~~--c~kaftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 145 RHLCT--FCGKGFNDTFDLKRHTRTHTGVRP-YKCSL--CEKAFTQRCSLESHLKKVHG 198 (267)
T ss_pred HHHHh--hccCcccchhhhhhhhccccCccc-cchhh--hhHHHHhhccHHHHHHHHcC
Confidence 46677 899999999999999999999999 99988 99999999999999886654
No 8
>PHA00733 hypothetical protein
Probab=99.09 E-value=4.2e-10 Score=51.06 Aligned_cols=53 Identities=25% Similarity=0.493 Sum_probs=46.8
Q ss_pred CcccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHhhC
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHS 61 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~ 61 (66)
+||.|. .|++.|.....|..|+.++ ..+ +.|.. |++.|.....|..|+...++
T Consensus 72 kPy~C~--~Cgk~Fss~s~L~~H~r~h--~~~-~~C~~--CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 72 SPYVCP--LCLMPFSSSVSLKQHIRYT--EHS-KVCPV--CGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCccCC--CCCCcCCCHHHHHHHHhcC--CcC-ccCCC--CCCccCCHHHHHHHHHHhcC
Confidence 689999 9999999999999999876 357 89987 99999999999999887654
No 9
>KOG1074|consensus
Probab=99.08 E-value=6.4e-11 Score=65.78 Aligned_cols=56 Identities=30% Similarity=0.618 Sum_probs=51.5
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHhhCCCC
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHSTNK 64 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~~~~ 64 (66)
..|. .|++.|.....|..|+++|++++| |.|.+ |.+.|....+|..||.+|....+
T Consensus 880 h~C~--vCgk~FsSSsALqiH~rTHtg~KP-F~C~f--C~~aFttrgnLKvHMgtH~w~q~ 935 (958)
T KOG1074|consen 880 HVCN--VCGKQFSSSAALEIHMRTHTGPKP-FFCHF--CEEAFTTRGNLKVHMGTHMWVQP 935 (958)
T ss_pred hhhc--cchhcccchHHHHHhhhcCCCCCC-ccchh--hhhhhhhhhhhhhhhccccccCC
Confidence 4677 999999999999999999999999 99988 99999999999999999875544
No 10
>KOG3576|consensus
Probab=98.94 E-value=1.1e-10 Score=56.29 Aligned_cols=58 Identities=24% Similarity=0.491 Sum_probs=53.8
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHhhCCCCCC
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHSTNKIT 66 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~~~~~~ 66 (66)
+.|. .|++.|....-|.+|++.|...+. +.|.. |++.|...-.|..|+++|+|.+||.
T Consensus 118 ftCr--vCgK~F~lQRmlnrh~kch~~vkr-~lct~--cgkgfndtfdlkrh~rthtgvrpyk 175 (267)
T KOG3576|consen 118 FTCR--VCGKKFGLQRMLNRHLKCHSDVKR-HLCTF--CGKGFNDTFDLKRHTRTHTGVRPYK 175 (267)
T ss_pred eeee--hhhhhhhHHHHHHHHhhhccHHHH-HHHhh--ccCcccchhhhhhhhccccCccccc
Confidence 6688 999999999999999999999888 89988 9999999999999999999999983
No 11
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.89 E-value=2.2e-09 Score=36.21 Aligned_cols=26 Identities=42% Similarity=0.979 Sum_probs=22.9
Q ss_pred HHHHHHHHhcCCCCCccCCcccccccccc
Q psy1778 20 HLQEHMLQHNENKPKFTCPYQDCLMSYVA 48 (66)
Q Consensus 20 ~l~~~~~~~~~~~~~~~c~~~~c~~~f~~ 48 (66)
+|..|+++|++++| |.|.. |++.|.+
T Consensus 1 ~l~~H~~~H~~~k~-~~C~~--C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP-YKCPY--CGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSS-EEESS--SSEEESS
T ss_pred CHHHHhhhcCCCCC-CCCCC--CcCeeCc
Confidence 47899999999999 99987 9998863
No 12
>PHA00616 hypothetical protein
Probab=98.87 E-value=1.9e-09 Score=40.36 Aligned_cols=34 Identities=29% Similarity=0.693 Sum_probs=29.3
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCCCCCccCCc
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPY 39 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~ 39 (66)
||.|. .||+.|...+++..|++.++++++ +.|..
T Consensus 1 pYqC~--~CG~~F~~~s~l~~H~r~~hg~~~-~~~~~ 34 (44)
T PHA00616 1 MYQCL--RCGGIFRKKKEVIEHLLSVHKQNK-LTLEY 34 (44)
T ss_pred CCccc--hhhHHHhhHHHHHHHHHHhcCCCc-cceeE
Confidence 68888 999999999999999999998888 77653
No 13
>PHA00616 hypothetical protein
Probab=98.70 E-value=1.1e-08 Score=38.29 Aligned_cols=30 Identities=33% Similarity=0.568 Sum_probs=27.4
Q ss_pred ccCCcccccccccccchHHHHHHHhhCCCCCC
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLKHVHSTNKIT 66 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~~~~~~~~~~ 66 (66)
++|.. |+..|.....+..|++.|++++++.
T Consensus 2 YqC~~--CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 2 YQCLR--CGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred Cccch--hhHHHhhHHHHHHHHHHhcCCCccc
Confidence 78976 9999999999999999999998863
No 14
>KOG3608|consensus
Probab=98.67 E-value=4.1e-08 Score=50.93 Aligned_cols=55 Identities=25% Similarity=0.571 Sum_probs=38.1
Q ss_pred CcccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHhh
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVH 60 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~ 60 (66)
|||+|. .|.+.+...+.|.+|..+|+ +.. |.|..++|...+.....+..|.+.++
T Consensus 291 kpfKCd--~Cd~~c~~esdL~kH~~~HS-~~~-y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 291 KPFKCD--ECDTRCVRESDLAKHVQVHS-KTV-YQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred CCcccc--chhhhhccHHHHHHHHHhcc-ccc-eecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 677777 77777777777777777665 344 67776677777777777777766555
No 15
>PHA00732 hypothetical protein
Probab=98.56 E-value=1e-07 Score=40.04 Aligned_cols=44 Identities=36% Similarity=0.706 Sum_probs=36.1
Q ss_pred cccCCccccCccccChHHHHHHHHH-hcCCCCCccCCcccccccccccchHHHHHH
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQ-HNENKPKFTCPYQDCLMSYVAKSSLYAHLK 57 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~-~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~ 57 (66)
||.|. .|++.|.+...|..|++. |. + +.|.. |++.|. .+..|..
T Consensus 1 py~C~--~Cgk~F~s~s~Lk~H~r~~H~---~-~~C~~--CgKsF~---~l~~H~~ 45 (79)
T PHA00732 1 MFKCP--ICGFTTVTLFALKQHARRNHT---L-TKCPV--CNKSYR---RLNQHFY 45 (79)
T ss_pred CccCC--CCCCccCCHHHHHHHhhcccC---C-CccCC--CCCEeC---Chhhhhc
Confidence 68899 999999999999999984 54 4 68977 999987 4666654
No 16
>KOG3993|consensus
Probab=98.40 E-value=1.7e-07 Score=49.57 Aligned_cols=53 Identities=25% Similarity=0.485 Sum_probs=44.5
Q ss_pred ccCCccccCccccChHHHHHHHHHhcC---------------------------------CCCCccCCcccccccccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNE---------------------------------NKPKFTCPYQDCLMSYVAKS 50 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~---------------------------------~~~~~~c~~~~c~~~f~~~~ 50 (66)
|+|+ +|++.|+...+|..|.+.|.. +.. |.|.. |++.|....
T Consensus 296 YrCP--EC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi-~~C~~--C~KkFrRqA 370 (500)
T KOG3993|consen 296 YRCP--ECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGI-FSCHT--CGKKFRRQA 370 (500)
T ss_pred ecCC--cccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCce-eecHH--hhhhhHHHH
Confidence 7899 999999999999999986621 113 67877 999999999
Q ss_pred hHHHHHHHhhC
Q psy1778 51 SLYAHLKHVHS 61 (66)
Q Consensus 51 ~l~~h~~~~~~ 61 (66)
+|..|+.+|+.
T Consensus 371 YLrKHqlthq~ 381 (500)
T KOG3993|consen 371 YLRKHQLTHQR 381 (500)
T ss_pred HHHHhHHhhhc
Confidence 99999888764
No 17
>KOG3608|consensus
Probab=98.33 E-value=1.3e-06 Score=45.62 Aligned_cols=52 Identities=29% Similarity=0.617 Sum_probs=42.9
Q ss_pred ccCCccccCccccChHHHHHHHHH-hcCCCCCccCCcccccccccccchHHHHHHHhh
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQ-HNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVH 60 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~-~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~ 60 (66)
|+|+ .|.......+.|..|++. |..++| |+|.- |+..+...+.|..|..+|.
T Consensus 264 ykCp--lCdmtc~~~ssL~~H~r~rHs~dkp-fKCd~--Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 264 YKCP--LCDMTCSSASSLTTHIRYRHSKDKP-FKCDE--CDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred cccc--ccccCCCChHHHHHHHHhhhccCCC-ccccc--hhhhhccHHHHHHHHHhcc
Confidence 6788 888888888888888774 677888 89966 9999999999999988654
No 18
>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=98.31 E-value=5.8e-07 Score=29.15 Aligned_cols=21 Identities=48% Similarity=1.001 Sum_probs=11.8
Q ss_pred cCCccccCccccChHHHHHHHHH
Q psy1778 5 PCPLVTCGKSFLRSEHLQEHMLQ 27 (66)
Q Consensus 5 ~c~~~~c~~~~~~~~~l~~~~~~ 27 (66)
.|. .|++.|.....|..|++.
T Consensus 2 ~C~--~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCP--ICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EET--TTTEEESSHHHHHHHHHH
T ss_pred CCC--CCCCccCCHHHHHHHHhH
Confidence 455 555666655555555543
No 19
>PHA02768 hypothetical protein; Provisional
Probab=98.19 E-value=1.3e-06 Score=34.21 Aligned_cols=24 Identities=29% Similarity=0.797 Sum_probs=22.6
Q ss_pred ccCCcccccccccccchHHHHHHHhh
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLKHVH 60 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~~~~ 60 (66)
|.|.. |++.|...+.|..|+++|+
T Consensus 6 y~C~~--CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 6 YECPI--CGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred cCcch--hCCeeccHHHHHHHHHhcC
Confidence 78977 9999999999999999988
No 20
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.19 E-value=6.4e-07 Score=46.12 Aligned_cols=54 Identities=31% Similarity=0.667 Sum_probs=44.6
Q ss_pred CCcccCCccccCccccChHHHHHHHHH-h------------------cCCCCCccCCcccccccccccchHHHHHH
Q psy1778 1 MRMFPCPLVTCGKSFLRSEHLQEHMLQ-H------------------NENKPKFTCPYQDCLMSYVAKSSLYAHLK 57 (66)
Q Consensus 1 ~~~~~c~~~~c~~~~~~~~~l~~~~~~-~------------------~~~~~~~~c~~~~c~~~f~~~~~l~~h~~ 57 (66)
+|||+|+++.|++.+.....|.-|+.- | ...+| |.|.+ |++++.....|.-|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KP-YrCev--C~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKP-YRCEV--CDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCc-eeccc--cchhhccCccceeccc
Confidence 489999999999999999888888652 1 12478 99999 9999999999987743
No 21
>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=27.44 Aligned_cols=23 Identities=35% Similarity=0.788 Sum_probs=19.9
Q ss_pred ccCCcccccccccccchHHHHHHHh
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLKHV 59 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~~~ 59 (66)
|.|.. |++.|.....|..|++.|
T Consensus 1 y~C~~--C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPI--CGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETT--TTEEESSHHHHHHHHHHH
T ss_pred CCCCC--CCCccCCHHHHHHHHhHC
Confidence 46866 999999999999999864
No 22
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.06 E-value=3.5e-05 Score=30.13 Aligned_cols=51 Identities=35% Similarity=0.681 Sum_probs=36.9
Q ss_pred cccCCccccCccccChHHHHHHHHH-hcCC-CCCccCCcccccccccccchHHHHHHHhhC
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQ-HNEN-KPKFTCPYQDCLMSYVAKSSLYAHLKHVHS 61 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~-~~~~-~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~ 61 (66)
.|.|+ .|++ ......|..|... |..+ +. +.|.+ |...+. .+|..|+...++
T Consensus 2 ~f~CP--~C~~-~~~~~~L~~H~~~~H~~~~~~-v~CPi--C~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCP--YCGK-GFSESSLVEHCEDEHRSESKN-VVCPI--CSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCC--CCCC-ccCHHHHHHHHHhHCcCCCCC-ccCCC--chhhhh--hHHHHHHHHhcC
Confidence 47899 9999 4557789999664 5443 45 89977 987544 488889876653
No 23
>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=97.95 E-value=4.7e-06 Score=27.97 Aligned_cols=22 Identities=41% Similarity=0.813 Sum_probs=10.5
Q ss_pred ccCCccccCccccChHHHHHHHHH
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQ 27 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~ 27 (66)
|.|. .|++.|.....|..|++.
T Consensus 2 ~~C~--~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 2 FECD--ECGKTFSSLSALREHKRS 23 (27)
T ss_dssp EEET--TTTEEESSHHHHHHHHCT
T ss_pred CCCC--ccCCccCChhHHHHHhHH
Confidence 4444 455555555444444443
No 24
>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=97.91 E-value=1.1e-05 Score=25.97 Aligned_cols=18 Identities=44% Similarity=0.805 Sum_probs=8.7
Q ss_pred ccCccccChHHHHHHHHH
Q psy1778 10 TCGKSFLRSEHLQEHMLQ 27 (66)
Q Consensus 10 ~c~~~~~~~~~l~~~~~~ 27 (66)
.|+..|.....+..|+..
T Consensus 5 ~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 5 ICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp STS-EESSHHHHHHHHHH
T ss_pred CCCCcCCcHHHHHHHHHh
Confidence 455555555555555443
No 25
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.90 E-value=3.1e-05 Score=42.83 Aligned_cols=53 Identities=21% Similarity=0.524 Sum_probs=28.6
Q ss_pred CcccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHhhCCCC
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHSTNK 64 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~~~~ 64 (66)
+++.|. .|+..|. ...+..|+.++. ++ +.| + |+..+ ....|..|+.++.++++
T Consensus 452 ~H~~C~--~Cgk~f~-~s~LekH~~~~H--kp-v~C--p-Cg~~~-~R~~L~~H~~thCp~Kp 504 (567)
T PLN03086 452 NHVHCE--KCGQAFQ-QGEMEKHMKVFH--EP-LQC--P-CGVVL-EKEQMVQHQASTCPLRL 504 (567)
T ss_pred cCccCC--CCCCccc-hHHHHHHHHhcC--CC-ccC--C-CCCCc-chhHHHhhhhccCCCCc
Confidence 345666 6766664 455666666542 45 556 2 55433 34555556555554444
No 26
>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=97.88 E-value=2e-05 Score=25.33 Aligned_cols=24 Identities=42% Similarity=0.837 Sum_probs=19.1
Q ss_pred ccCCcccccccccccchHHHHHHHhh
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLKHVH 60 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~~~~ 60 (66)
|.|.. |+..|.....|..|+.+++
T Consensus 1 ~~C~~--C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPI--CGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SS--TS-EESSHHHHHHHHHHHS
T ss_pred CCCcC--CCCcCCcHHHHHHHHHhhC
Confidence 46877 9999999999999998764
No 27
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.86 E-value=2.6e-05 Score=30.07 Aligned_cols=33 Identities=27% Similarity=0.402 Sum_probs=21.9
Q ss_pred CCCCCccCCcccccccccccchHHHHHHHhhCCCCC
Q psy1778 30 ENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHSTNKI 65 (66)
Q Consensus 30 ~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~~~~~ 65 (66)
+..| -.|.. |+..+.+..+|..|+..+++.||-
T Consensus 21 S~~P-atCP~--C~a~~~~srnLrRHle~~H~~k~~ 53 (54)
T PF09237_consen 21 SEQP-ATCPI--CGAVIRQSRNLRRHLEIRHFKKPG 53 (54)
T ss_dssp TS---EE-TT--T--EESSHHHHHHHHHHHTTTS--
T ss_pred cCCC-CCCCc--chhhccchhhHHHHHHHHhcccCC
Confidence 4567 78966 999999999999999888887763
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.86 E-value=5.5e-06 Score=27.81 Aligned_cols=25 Identities=28% Similarity=0.482 Sum_probs=21.8
Q ss_pred ccCCcccccccccccchHHHHHHHhhC
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLKHVHS 61 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~~~~~ 61 (66)
+.|.. |+..|.....|..|++.|.+
T Consensus 2 ~~C~~--C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 2 FECDE--CGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp EEETT--TTEEESSHHHHHHHHCTTTT
T ss_pred CCCCc--cCCccCChhHHHHHhHHhcC
Confidence 78977 99999999999999987653
No 29
>PHA00733 hypothetical protein
Probab=97.78 E-value=1.1e-05 Score=36.87 Aligned_cols=53 Identities=23% Similarity=0.504 Sum_probs=37.3
Q ss_pred CcccCCccccCccccChHHHHHH--H---HHhcCCCCCccCCcccccccccccchHHHHHHHh
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEH--M---LQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHV 59 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~--~---~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~ 59 (66)
+++.|. .|...|.....+..+ + ..+.+.+| +.|.. |+..|.....|..|++.+
T Consensus 39 ~~~~~~--~~~~~~~~~~~l~~~~~l~~~~~~~~~kP-y~C~~--Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 39 KRLIRA--VVKTLIYNPQLLDESSYLYKLLTSKAVSP-YVCPL--CLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred hhHHHH--HHhhhccChhhhcchHHHHhhcccCCCCC-ccCCC--CCCcCCCHHHHHHHHhcC
Confidence 456666 677666665555444 1 12234678 99977 999999999999998854
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.70 E-value=9.9e-05 Score=23.91 Aligned_cols=22 Identities=50% Similarity=0.996 Sum_probs=13.0
Q ss_pred cCCccccCccccChHHHHHHHHHh
Q psy1778 5 PCPLVTCGKSFLRSEHLQEHMLQH 28 (66)
Q Consensus 5 ~c~~~~c~~~~~~~~~l~~~~~~~ 28 (66)
.|. .|++.|.....+..|+..|
T Consensus 2 ~C~--~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCP--ECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCC--CCcchhCCHHHHHHHHHHh
Confidence 455 5666666666666665544
No 31
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.66 E-value=6.7e-05 Score=28.96 Aligned_cols=30 Identities=30% Similarity=0.619 Sum_probs=21.6
Q ss_pred CcccCCccccCccccChHHHHHHHHHhcCCCC
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHNENKP 33 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~ 33 (66)
.|..|+ .|+..+.+..+|.+|+.+..+.+|
T Consensus 23 ~PatCP--~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 23 QPATCP--ICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp --EE-T--TT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCC--cchhhccchhhHHHHHHHHhcccC
Confidence 577899 999999999999999988777665
No 32
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.51 E-value=0.00028 Score=39.33 Aligned_cols=55 Identities=18% Similarity=0.384 Sum_probs=39.4
Q ss_pred CcccCCccccCccccChHHHHHHHHHhcCCCCCccCCccccccccc----------ccchHHHHHHHhhCCCC
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYV----------AKSSLYAHLKHVHSTNK 64 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~----------~~~~l~~h~~~~~~~~~ 64 (66)
+|+.|+ |+..+ .+..|..|+..+...++ +.|.. |+..+. ....|..|+.+ .|.++
T Consensus 477 kpv~Cp---Cg~~~-~R~~L~~H~~thCp~Kp-i~C~f--C~~~v~~g~~~~d~~d~~s~Lt~HE~~-CG~rt 541 (567)
T PLN03086 477 EPLQCP---CGVVL-EKEQMVQHQASTCPLRL-ITCRF--CGDMVQAGGSAMDVRDRLRGMSEHESI-CGSRT 541 (567)
T ss_pred CCccCC---CCCCc-chhHHHhhhhccCCCCc-eeCCC--CCCccccCccccchhhhhhhHHHHHHh-cCCcc
Confidence 456775 88654 66888889888888888 89987 988774 13467788775 35444
No 33
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.04 E-value=0.00078 Score=21.77 Aligned_cols=16 Identities=25% Similarity=0.449 Sum_probs=6.7
Q ss_pred ccCccccChHHHHHHHH
Q psy1778 10 TCGKSFLRSEHLQEHML 26 (66)
Q Consensus 10 ~c~~~~~~~~~l~~~~~ 26 (66)
.|+.... ...|..|++
T Consensus 5 ~C~y~t~-~~~l~~H~~ 20 (24)
T PF13909_consen 5 HCSYSTS-KSNLKRHLK 20 (24)
T ss_dssp SSS-EES-HHHHHHHHH
T ss_pred CCCCcCC-HHHHHHHHH
Confidence 4444443 444444444
No 34
>PRK04860 hypothetical protein; Provisional
Probab=97.01 E-value=0.00062 Score=32.36 Aligned_cols=38 Identities=18% Similarity=0.411 Sum_probs=29.8
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCCCCCccCCccccccccccc
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAK 49 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~ 49 (66)
+|.|. |+. ....+..|.+++.+.++ |.|.. |...|...
T Consensus 119 ~Y~C~---C~~---~~~~~rrH~ri~~g~~~-YrC~~--C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK---CQE---HQLTVRRHNRVVRGEAV-YRCRR--CGETLVFK 156 (160)
T ss_pred EEEcC---CCC---eeCHHHHHHHHhcCCcc-EECCC--CCceeEEe
Confidence 46774 765 55678899999999999 99977 98877654
No 35
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.76 E-value=0.00099 Score=21.65 Aligned_cols=16 Identities=38% Similarity=0.698 Sum_probs=8.3
Q ss_pred ccccccccchHHHHHH
Q psy1778 42 CLMSYVAKSSLYAHLK 57 (66)
Q Consensus 42 c~~~f~~~~~l~~h~~ 57 (66)
|...|.+...+..|++
T Consensus 6 C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 6 CNKSFSSENSLRQHLR 21 (25)
T ss_dssp TTEEESSHHHHHHHHT
T ss_pred CCCCcCCHHHHHHHHC
Confidence 5555555555555543
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.45 E-value=0.0029 Score=27.16 Aligned_cols=49 Identities=31% Similarity=0.748 Sum_probs=19.7
Q ss_pred CCccccCccccChHHHHHHHHH-hcC----------------------CCCCccCCcccccccccccchHHHHHHHh
Q psy1778 6 CPLVTCGKSFLRSEHLQEHMLQ-HNE----------------------NKPKFTCPYQDCLMSYVAKSSLYAHLKHV 59 (66)
Q Consensus 6 c~~~~c~~~~~~~~~l~~~~~~-~~~----------------------~~~~~~c~~~~c~~~f~~~~~l~~h~~~~ 59 (66)
|. .|+..|.....+..|+.. |.- ... +.|.. |...|.+...|..|++.+
T Consensus 2 C~--~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~-~~C~~--C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 2 CL--FCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKES-FRCPY--CNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -------------------------------------------------SS-EEBSS--SS-EESSHHHHHHHHHHT
T ss_pred cc--ccccccccccccccccccccccccccccccccccccccccccccCCC-CCCCc--cCCCCcCHHHHHHHHcCc
Confidence 55 788888888787777642 210 012 57877 999999999999999864
No 37
>PHA00732 hypothetical protein
Probab=96.40 E-value=0.0027 Score=26.81 Aligned_cols=22 Identities=32% Similarity=0.664 Sum_probs=19.9
Q ss_pred ccCCcccccccccccchHHHHHHH
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLKH 58 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~~ 58 (66)
+.|.. |+..|.....|..|++.
T Consensus 2 y~C~~--Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 2 FKCPI--CGFTTVTLFALKQHARR 23 (79)
T ss_pred ccCCC--CCCccCCHHHHHHHhhc
Confidence 78977 99999999999999974
No 38
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.98 E-value=0.0017 Score=21.65 Aligned_cols=20 Identities=40% Similarity=0.878 Sum_probs=10.4
Q ss_pred ccCCccccCccccChHHHHHHH
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHM 25 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~ 25 (66)
|.|. .|++.|.....+..|+
T Consensus 2 ~~C~--~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCD--ACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBT--TTTBBBSSHHHHHCCT
T ss_pred CCcc--cCCCCcCCHHHHHHHH
Confidence 3455 5555555555555443
No 39
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.91 E-value=0.011 Score=19.50 Aligned_cols=19 Identities=32% Similarity=0.628 Sum_probs=9.4
Q ss_pred cCCcccccccccccchHHHHHH
Q psy1778 36 TCPYQDCLMSYVAKSSLYAHLK 57 (66)
Q Consensus 36 ~c~~~~c~~~f~~~~~l~~h~~ 57 (66)
.|.. |++.| ....|..|+.
T Consensus 4 ~C~~--CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPI--CGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCC--CCCEE-CHHHHHHHHH
Confidence 4544 55555 4444555543
No 40
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.12 E-value=0.003 Score=33.32 Aligned_cols=58 Identities=31% Similarity=0.560 Sum_probs=47.3
Q ss_pred cccCCccccCccccChHHHHHHHH--HhcCC--CCCccCCcccccccccccchHHHHHHHhhCCC
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHML--QHNEN--KPKFTCPYQDCLMSYVAKSSLYAHLKHVHSTN 63 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~--~~~~~--~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~~~ 63 (66)
++.|. .|...|.....+..|.. .|.++ ++ +.|....|+..|.....+..|..+|.+..
T Consensus 289 ~~~~~--~~~~~~s~~~~l~~~~~~~~h~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~~~~~~ 350 (467)
T COG5048 289 PIKSK--QCNISFSRSSPLTRHLRSVNHSGESLKP-FSCPYSLCGKLFSRNDALKRHILLHTSIS 350 (467)
T ss_pred CCCCc--cccCCccccccccccccccccccccCCc-eeeeccCCCccccccccccCCcccccCCC
Confidence 45666 88999999999999999 79988 89 89972249999999999988887776544
No 41
>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=94.88 E-value=0.032 Score=19.41 Aligned_cols=22 Identities=23% Similarity=0.525 Sum_probs=12.2
Q ss_pred cccCCccccCccccChHHHHHHHH
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHML 26 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~ 26 (66)
+|.|. .|+..|.....+..|+.
T Consensus 3 ~~~C~--~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCK--LCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEcc--ccCCccCCHHHHHHHHC
Confidence 34555 66666665555555543
No 42
>KOG3993|consensus
Probab=94.67 E-value=0.0031 Score=34.26 Aligned_cols=51 Identities=16% Similarity=0.408 Sum_probs=36.9
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHh
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHV 59 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~ 59 (66)
|.|. .|...|.....|.+|.-.--...- |.| ++|++.|+=..+|..|.|=|
T Consensus 268 yiCq--LCK~kYeD~F~LAQHrC~RIV~vE-YrC--PEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 268 YICQ--LCKEKYEDAFALAQHRCPRIVHVE-YRC--PECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHH--HHHHhhhhHHHHhhccCCeeEEee-ecC--CcccccccCchhhhhhhccc
Confidence 5677 777777777778877542211223 899 45999999999999997744
No 43
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.27 E-value=0.074 Score=22.72 Aligned_cols=26 Identities=46% Similarity=0.852 Sum_probs=21.5
Q ss_pred cccCCccccCccccChHHHHHHHHHhcC
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNE 30 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~ 30 (66)
.+.|. .|+..|.....+..|+..+..
T Consensus 50 ~~~C~--~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 50 SFRCP--YCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp SEEBS--SSS-EESSHHHHHHHHHHTTT
T ss_pred CCCCC--ccCCCCcCHHHHHHHHcCccC
Confidence 47788 999999999999999997643
No 44
>KOG2893|consensus
Probab=94.21 E-value=0.018 Score=29.37 Aligned_cols=39 Identities=23% Similarity=0.463 Sum_probs=28.9
Q ss_pred ccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHH
Q psy1778 10 TCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAH 55 (66)
Q Consensus 10 ~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h 55 (66)
.|++.|.....|.+|+++. . |+|.+ |.+..-+-..|..|
T Consensus 15 ycnrefddekiliqhqkak----h-fkchi--chkkl~sgpglsih 53 (341)
T KOG2893|consen 15 YCNREFDDEKILIQHQKAK----H-FKCHI--CHKKLFSGPGLSIH 53 (341)
T ss_pred ecccccchhhhhhhhhhhc----c-ceeee--ehhhhccCCCceee
Confidence 7999999999999998854 3 89977 87655444444444
No 45
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.45 E-value=0.14 Score=27.20 Aligned_cols=57 Identities=39% Similarity=0.711 Sum_probs=46.6
Q ss_pred CcccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHHHhhC
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHS 61 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~ 61 (66)
+++.|. .|...|....+...|...+.+.++ ..|....|...+.....+..+...+..
T Consensus 32 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (467)
T COG5048 32 RPDSCP--NCTDSFSRLEHLTRHIRSHTGEKP-SQCSYSGCDKSFSRPLELSRHLRTHHN 88 (467)
T ss_pred chhhcc--cccccccccchhhhhcccccccCC-ccccccccccccCCcchhhhhcccccc
Confidence 346677 888999999999999999999999 888877788888888888888776543
No 46
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=92.15 E-value=0.082 Score=20.93 Aligned_cols=21 Identities=33% Similarity=0.789 Sum_probs=17.0
Q ss_pred ccCCccccCccccChHHHHHHHH
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHML 26 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~ 26 (66)
+.|+ .|+..|.....+.+|..
T Consensus 18 lrCP--RC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 18 LRCP--RCGMVFRRRKDYIRHVN 38 (65)
T ss_pred eeCC--chhHHHHHhHHHHHHhh
Confidence 5677 89999988888888854
No 47
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=91.38 E-value=0.14 Score=27.41 Aligned_cols=26 Identities=31% Similarity=0.749 Sum_probs=23.8
Q ss_pred CCCCccCCcccccccccccchHHHHHH
Q psy1778 31 NKPKFTCPYQDCLMSYVAKSSLYAHLK 57 (66)
Q Consensus 31 ~~~~~~c~~~~c~~~f~~~~~l~~h~~ 57 (66)
++| |.|.+++|.+.+.....|.-|+.
T Consensus 347 ~Kp-ykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 347 GKP-YKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred Cce-ecCCCCCchhhhccccchhhhhh
Confidence 489 99999999999999999999975
No 48
>KOG1146|consensus
Probab=90.41 E-value=0.31 Score=30.65 Aligned_cols=52 Identities=27% Similarity=0.600 Sum_probs=41.4
Q ss_pred CcccCCccccCccccChHHHHHHHHHhc-------------------------CCCCCccCCcccccccccccchHHHHH
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHN-------------------------ENKPKFTCPYQDCLMSYVAKSSLYAHL 56 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~-------------------------~~~~~~~c~~~~c~~~f~~~~~l~~h~ 56 (66)
|.+.|. .|+..+.....|..|++... +.++ +.|.. |...+.....|..|+
T Consensus 464 kt~~cp--kc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p-~~C~~--C~~stttng~Lsihl 538 (1406)
T KOG1146|consen 464 KTLKCP--KCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP-YPCRA--CNYSTTTNGNLSIHL 538 (1406)
T ss_pred ccccCC--ccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc-cccee--eeeeeecchHHHHHH
Confidence 467888 99999999999999998611 1245 67866 999999999999997
Q ss_pred HH
Q psy1778 57 KH 58 (66)
Q Consensus 57 ~~ 58 (66)
..
T Consensus 539 qS 540 (1406)
T KOG1146|consen 539 QS 540 (1406)
T ss_pred HH
Confidence 73
No 49
>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=84.26 E-value=1.1 Score=19.98 Aligned_cols=25 Identities=24% Similarity=0.569 Sum_probs=20.0
Q ss_pred ccC----CcccccccccccchHHHHHHHhhC
Q psy1778 35 FTC----PYQDCLMSYVAKSSLYAHLKHVHS 61 (66)
Q Consensus 35 ~~c----~~~~c~~~f~~~~~l~~h~~~~~~ 61 (66)
+.| .. |.....+...+..|.+..+|
T Consensus 81 ~~C~~~~~~--C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPH--CGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCC--CCcEeccHHHHHHHHHHhcC
Confidence 567 55 99888899999999887664
No 50
>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=82.24 E-value=1.2 Score=15.42 Aligned_cols=24 Identities=38% Similarity=1.050 Sum_probs=15.8
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLM 44 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~ 44 (66)
|.|. .||..+.... .+ ..|.. |+.
T Consensus 2 ~~C~--~CGy~y~~~~------------~~-~~CP~--Cg~ 25 (33)
T cd00350 2 YVCP--VCGYIYDGEE------------AP-WVCPV--CGA 25 (33)
T ss_pred EECC--CCCCEECCCc------------CC-CcCcC--CCC
Confidence 6777 8887764332 46 78866 865
No 51
>PF15269 zf-C2H2_7: Zinc-finger
Probab=81.59 E-value=1.5 Score=16.60 Aligned_cols=22 Identities=27% Similarity=0.486 Sum_probs=15.8
Q ss_pred ccCCccccCccccChHHHHHHHHH
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQ 27 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~ 27 (66)
|+|- +|..+...+++|..||+-
T Consensus 21 ykcf--qcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCF--QCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceee--cCCcccchHHHHHHHHHH
Confidence 4455 777777778888888763
No 52
>KOG4167|consensus
Probab=80.72 E-value=0.3 Score=29.02 Aligned_cols=24 Identities=42% Similarity=0.962 Sum_probs=20.8
Q ss_pred ccCCccccCccccChHHHHHHHHHhc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHN 29 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~ 29 (66)
|.|. +|++.|.-...+..||+.|.
T Consensus 793 FpCr--eC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCR--ECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehH--HHHHHHHHHhhhhHHHHHHH
Confidence 6788 99999998888889988875
No 53
>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=77.80 E-value=1.9 Score=21.92 Aligned_cols=24 Identities=33% Similarity=0.866 Sum_probs=18.3
Q ss_pred cccCCccccCccccChHHHHHHHHHh
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQH 28 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~ 28 (66)
.|.|. .|++.|.-......|+...
T Consensus 77 K~~C~--lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 77 KWRCP--LCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp EEEE---SSS-EESSHHHHHHHHHHH
T ss_pred EECCC--CCCcccCChHHHHHHHhhc
Confidence 58888 9999999999888887643
No 54
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=76.23 E-value=2.6 Score=19.06 Aligned_cols=30 Identities=30% Similarity=0.869 Sum_probs=20.9
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCccccccccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAK 49 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~ 49 (66)
..|+ .||..|-. ....| ..|.. |+..|...
T Consensus 10 R~Cp--~CG~kFYD-----------Lnk~P-ivCP~--CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCP--SCGAKFYD-----------LNKDP-IVCPK--CGTEFPPE 39 (108)
T ss_pred ccCC--CCcchhcc-----------CCCCC-ccCCC--CCCccCcc
Confidence 4577 89987742 23467 88965 99888766
No 55
>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=74.20 E-value=2.1 Score=20.10 Aligned_cols=23 Identities=26% Similarity=0.486 Sum_probs=13.4
Q ss_pred ccCCcccccccccccchHHHHHHHhhCC
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLKHVHST 62 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~~~~~~ 62 (66)
+.|.. |++.|.. |..|+++|+|-
T Consensus 73 i~cle--cGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 73 IICLE--CGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp EE-TB--T--EESB---HHHHHHHTT-S
T ss_pred eEEcc--CCcccch---HHHHHHHccCC
Confidence 56766 8887754 47888888664
No 56
>KOG1146|consensus
Probab=72.71 E-value=1.9 Score=27.61 Aligned_cols=54 Identities=17% Similarity=0.354 Sum_probs=39.1
Q ss_pred CcccCCccccCccccChHHHHHHHHHhc-----------------CCCCCccCCcccccccccccchHHHHHHHhhC
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHN-----------------ENKPKFTCPYQDCLMSYVAKSSLYAHLKHVHS 61 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~-----------------~~~~~~~c~~~~c~~~f~~~~~l~~h~~~~~~ 61 (66)
.+|.|. .|...|.....+..|.+.-. ...+ + |.. |...|+....|..|++....
T Consensus 1283 ~~~~~~--~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~-~-c~~--c~~~~~~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1283 HRYLCR--QCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTY-H-CLA--CEVLLSGREALQIHMRSSAH 1353 (1406)
T ss_pred hhHHHH--HHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCccccc-c-chH--HHhhcchhHHHHHHHHHhhh
Confidence 467787 88888988888888874210 1122 3 766 98999999999999986543
No 57
>PHA00626 hypothetical protein
Probab=71.34 E-value=2.1 Score=17.05 Aligned_cols=14 Identities=21% Similarity=0.529 Sum_probs=10.8
Q ss_pred cccCCccccCccccCh
Q psy1778 3 MFPCPLVTCGKSFLRS 18 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~ 18 (66)
.|.|. .||..|+..
T Consensus 23 rYkCk--dCGY~ft~~ 36 (59)
T PHA00626 23 DYVCC--DCGYNDSKD 36 (59)
T ss_pred ceEcC--CCCCeechh
Confidence 58888 999887643
No 58
>COG2879 Uncharacterized small protein [Function unknown]
Probab=71.11 E-value=5.9 Score=16.21 Aligned_cols=19 Identities=11% Similarity=0.207 Sum_probs=13.3
Q ss_pred ccchHHHHHHHhhCCCCCC
Q psy1778 48 AKSSLYAHLKHVHSTNKIT 66 (66)
Q Consensus 48 ~~~~l~~h~~~~~~~~~~~ 66 (66)
.-+....|++.++.++|.+
T Consensus 24 dYdnYVehmr~~hPd~p~m 42 (65)
T COG2879 24 DYDNYVEHMRKKHPDKPPM 42 (65)
T ss_pred cHHHHHHHHHHhCcCCCcc
Confidence 3456677888888777753
No 59
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=70.84 E-value=5.2 Score=15.14 Aligned_cols=21 Identities=33% Similarity=0.607 Sum_probs=14.4
Q ss_pred ccCCccccccccccc-----chHHHHHH
Q psy1778 35 FTCPYQDCLMSYVAK-----SSLYAHLK 57 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~-----~~l~~h~~ 57 (66)
..|.. |+..+... +.|..|+.
T Consensus 19 a~C~~--C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKY--CGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecC--CCCEeeeCCCCCcHHHHHHHH
Confidence 46766 87766554 57778877
No 60
>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=70.12 E-value=2.5 Score=13.79 Aligned_cols=8 Identities=75% Similarity=2.074 Sum_probs=4.9
Q ss_pred cccCCccccC
Q psy1778 3 MFPCPLVTCG 12 (66)
Q Consensus 3 ~~~c~~~~c~ 12 (66)
+|.|+ .||
T Consensus 16 ~f~CP--nCG 23 (24)
T PF07754_consen 16 PFPCP--NCG 23 (24)
T ss_pred eEeCC--CCC
Confidence 46666 665
No 61
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=69.38 E-value=3.1 Score=19.58 Aligned_cols=15 Identities=27% Similarity=0.740 Sum_probs=11.9
Q ss_pred cccCCccccCccccChH
Q psy1778 3 MFPCPLVTCGKSFLRSE 19 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~ 19 (66)
|+.|. .||+.|..-+
T Consensus 1 PH~Ct--~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCT--KCGRVFEDGS 15 (131)
T ss_pred CcccC--cCCCCcCCCc
Confidence 68898 9999987543
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=67.97 E-value=2.4 Score=15.03 Aligned_cols=12 Identities=33% Similarity=1.043 Sum_probs=9.1
Q ss_pred ccCCccccCccccC
Q psy1778 4 FPCPLVTCGKSFLR 17 (66)
Q Consensus 4 ~~c~~~~c~~~~~~ 17 (66)
|.|. .||..|..
T Consensus 6 y~C~--~Cg~~fe~ 17 (41)
T smart00834 6 YRCE--DCGHTFEV 17 (41)
T ss_pred EEcC--CCCCEEEE
Confidence 6787 99987753
No 63
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=67.44 E-value=1.7 Score=18.18 Aligned_cols=44 Identities=16% Similarity=0.441 Sum_probs=22.6
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchH
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSL 52 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l 52 (66)
+.|+ .|+........-... ....+.- ++|...+|+.+|.....+
T Consensus 2 m~CP--~Cg~~a~irtSr~~s--~~~~~~Y-~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCP--LCQHAAHARTSRYIT--DTTKERY-HQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCC--CCCCccEEEEChhcC--hhhheee-eecCCCCCCCEEEEEEEE
Confidence 3577 888654322211111 1122333 678755699888765443
No 64
>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=66.78 E-value=5.3 Score=19.24 Aligned_cols=31 Identities=32% Similarity=0.577 Sum_probs=21.4
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVA 48 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~ 48 (66)
|.|+ .|+..|+....+. .. |.|.. |+.....
T Consensus 110 Y~Cp--~c~~r~tf~eA~~---------~~-F~Cp~--Cg~~L~~ 140 (158)
T TIGR00373 110 FICP--NMCVRFTFNEAME---------LN-FTCPR--CGAMLDY 140 (158)
T ss_pred EECC--CCCcEeeHHHHHH---------cC-CcCCC--CCCEeee
Confidence 6788 8988877665553 24 89966 9876543
No 65
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=66.65 E-value=6.2 Score=14.02 Aligned_cols=33 Identities=21% Similarity=0.584 Sum_probs=19.7
Q ss_pred cCCccccCccccChHHHHHHHHHhcCCCCCccCCccccccccc
Q psy1778 5 PCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYV 47 (66)
Q Consensus 5 ~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~ 47 (66)
.|+ .|+..|.-...- +..+... ..|.. |...|.
T Consensus 4 ~CP--~C~~~f~v~~~~-----l~~~~~~-vrC~~--C~~~f~ 36 (37)
T PF13719_consen 4 TCP--NCQTRFRVPDDK-----LPAGGRK-VRCPK--CGHVFR 36 (37)
T ss_pred ECC--CCCceEEcCHHH-----cccCCcE-EECCC--CCcEee
Confidence 467 888887655431 2223334 78866 877663
No 66
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=66.59 E-value=5.7 Score=14.88 Aligned_cols=26 Identities=19% Similarity=0.505 Sum_probs=17.2
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCccccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMS 45 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~ 45 (66)
|.|. .||..|... ...+ ..|.. |+..
T Consensus 3 Y~C~--~Cg~~~~~~-----------~~~~-irC~~--CG~r 28 (44)
T smart00659 3 YICG--ECGRENEIK-----------SKDV-VRCRE--CGYR 28 (44)
T ss_pred EECC--CCCCEeecC-----------CCCc-eECCC--CCce
Confidence 7788 999877533 2345 78854 8754
No 67
>KOG2071|consensus
Probab=66.39 E-value=6.1 Score=23.26 Aligned_cols=26 Identities=35% Similarity=0.552 Sum_probs=20.2
Q ss_pred CcccCCccccCccccChHHHHHHHHHhc
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHN 29 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~ 29 (66)
+|-.|. .||.+|........||..|.
T Consensus 417 ~pnqC~--~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 417 SPNQCK--SCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred Ccchhc--ccccccccchhhhhHhhhhh
Confidence 456788 89999988888777777664
No 68
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=65.19 E-value=2.9 Score=16.17 Aligned_cols=16 Identities=25% Similarity=0.835 Sum_probs=11.3
Q ss_pred CcccCCccccCccccChH
Q psy1778 2 RMFPCPLVTCGKSFLRSE 19 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~ 19 (66)
+++.|. +||..|.-..
T Consensus 3 k~l~C~--dCg~~FvfTa 18 (49)
T PF13451_consen 3 KTLTCK--DCGAEFVFTA 18 (49)
T ss_pred eeEEcc--cCCCeEEEeh
Confidence 567888 9998665443
No 69
>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=63.96 E-value=2.9 Score=15.34 Aligned_cols=29 Identities=28% Similarity=0.770 Sum_probs=17.1
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLM 44 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~ 44 (66)
|.|. .||..|..... +.. ..+ ..|.. |+.
T Consensus 6 y~C~--~Cg~~fe~~~~------~~~-~~~-~~CP~--Cg~ 34 (42)
T PF09723_consen 6 YRCE--ECGHEFEVLQS------ISE-DDP-VPCPE--CGS 34 (42)
T ss_pred EEeC--CCCCEEEEEEE------cCC-CCC-CcCCC--CCC
Confidence 6788 99987754322 111 334 67754 875
No 70
>KOG2932|consensus
Probab=63.10 E-value=7.6 Score=21.22 Aligned_cols=27 Identities=37% Similarity=0.844 Sum_probs=21.3
Q ss_pred ccCCcc-cccccccccchHHHHHHHhhC
Q psy1778 35 FTCPYQ-DCLMSYVAKSSLYAHLKHVHS 61 (66)
Q Consensus 35 ~~c~~~-~c~~~f~~~~~l~~h~~~~~~ 61 (66)
|.|..+ +|.++|.+...|..|+...++
T Consensus 145 FmC~~~~GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 145 FMCAAPHGCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred EEeecchhHHHHHhhHHHHHHHhhhhhc
Confidence 777654 599999999999999875443
No 71
>KOG3408|consensus
Probab=62.56 E-value=4 Score=18.99 Aligned_cols=22 Identities=27% Similarity=0.608 Sum_probs=18.8
Q ss_pred ccCCcccccccccccchHHHHHHH
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLKH 58 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~~ 58 (66)
+.|.. |.+-|.....|..|.++
T Consensus 58 fyCi~--CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 58 FYCIE--CARYFIDAKALKTHFKT 79 (129)
T ss_pred eehhh--hhhhhcchHHHHHHHhc
Confidence 67877 99999999999988764
No 72
>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=62.46 E-value=5.5 Score=13.13 Aligned_cols=6 Identities=50% Similarity=1.287 Sum_probs=3.5
Q ss_pred ccCccc
Q psy1778 10 TCGKSF 15 (66)
Q Consensus 10 ~c~~~~ 15 (66)
.||..|
T Consensus 19 ~CG~~F 24 (26)
T PF10571_consen 19 HCGYDF 24 (26)
T ss_pred CCCCCC
Confidence 566555
No 73
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=61.09 E-value=6.9 Score=19.30 Aligned_cols=32 Identities=31% Similarity=0.675 Sum_probs=21.7
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccc
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVA 48 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~ 48 (66)
-|.|+ .|+..|+....+. .. |.|.. |+.....
T Consensus 117 ~Y~Cp--~C~~rytf~eA~~---------~~-F~Cp~--Cg~~L~~ 148 (178)
T PRK06266 117 FFFCP--NCHIRFTFDEAME---------YG-FRCPQ--CGEMLEE 148 (178)
T ss_pred EEECC--CCCcEEeHHHHhh---------cC-CcCCC--CCCCCee
Confidence 37788 8998887665432 24 89966 9876543
No 74
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=60.78 E-value=4.7 Score=14.61 Aligned_cols=13 Identities=38% Similarity=0.884 Sum_probs=8.3
Q ss_pred cccCCccccCccccC
Q psy1778 3 MFPCPLVTCGKSFLR 17 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~ 17 (66)
|+.|. .|++.|-.
T Consensus 12 ~f~C~--~C~~~FC~ 24 (39)
T smart00154 12 GFKCR--HCGNLFCG 24 (39)
T ss_pred CeECC--ccCCcccc
Confidence 56676 67776653
No 75
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=60.17 E-value=8.3 Score=18.96 Aligned_cols=23 Identities=35% Similarity=0.976 Sum_probs=15.3
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLM 44 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~ 44 (66)
|.|. .||..+ .+.-| -.|.+ |+.
T Consensus 135 ~vC~--vCGy~~-------------~ge~P-~~CPi--Cga 157 (166)
T COG1592 135 WVCP--VCGYTH-------------EGEAP-EVCPI--CGA 157 (166)
T ss_pred EEcC--CCCCcc-------------cCCCC-CcCCC--CCC
Confidence 7787 887653 34557 78866 863
No 76
>KOG4173|consensus
Probab=59.93 E-value=3.1 Score=21.23 Aligned_cols=50 Identities=20% Similarity=0.511 Sum_probs=30.2
Q ss_pred cCCccccCccccChHHHHHHHH-Hh---------cCCCCCccCCcccccccccccchHHHHHH
Q psy1778 5 PCPLVTCGKSFLRSEHLQEHML-QH---------NENKPKFTCPYQDCLMSYVAKSSLYAHLK 57 (66)
Q Consensus 5 ~c~~~~c~~~~~~~~~l~~~~~-~~---------~~~~~~~~c~~~~c~~~f~~~~~l~~h~~ 57 (66)
.|. .|.+.|.+..-|..|+. .| .|..- |+|.+.+|.-.|.....-..|+-
T Consensus 108 sCs--~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dM-y~ClvEgCt~KFkT~r~RkdH~I 167 (253)
T KOG4173|consen 108 SCS--FCKRAFPTGHLLDAHILEWHDSLFQALVERGQDM-YQCLVEGCTEKFKTSRDRKDHMI 167 (253)
T ss_pred hhH--HHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccH-HHHHHHhhhhhhhhhhhhhhHHH
Confidence 455 77777777666665543 11 22222 67766677777777766666654
No 77
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=59.50 E-value=4.1 Score=15.43 Aligned_cols=12 Identities=33% Similarity=1.029 Sum_probs=9.3
Q ss_pred ccCCccccCccccC
Q psy1778 4 FPCPLVTCGKSFLR 17 (66)
Q Consensus 4 ~~c~~~~c~~~~~~ 17 (66)
|.|. .|+..|..
T Consensus 6 y~C~--~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCT--ACGHRFEV 17 (52)
T ss_pred EEeC--CCCCEeEE
Confidence 6788 99987763
No 78
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=58.02 E-value=5.5 Score=17.58 Aligned_cols=14 Identities=36% Similarity=0.705 Sum_probs=11.4
Q ss_pred CcccCCccccCccccC
Q psy1778 2 RMFPCPLVTCGKSFLR 17 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~ 17 (66)
+|-.|. .||..|..
T Consensus 57 ~Pa~Ck--kCGfef~~ 70 (97)
T COG3357 57 RPARCK--KCGFEFRD 70 (97)
T ss_pred cChhhc--ccCccccc
Confidence 577888 99998865
No 79
>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=57.12 E-value=9.8 Score=13.30 Aligned_cols=34 Identities=21% Similarity=0.468 Sum_probs=19.3
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCccccccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYV 47 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~ 47 (66)
..|+ .|+..|.-..... ...... +.|.. |+..|.
T Consensus 3 ~~CP--~C~~~~~v~~~~~-----~~~~~~-v~C~~--C~~~~~ 36 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQL-----GANGGK-VRCGK--CGHVWY 36 (38)
T ss_pred EECC--CCCCEEEeCHHHc-----CCCCCE-EECCC--CCCEEE
Confidence 4577 8888776543321 112223 67866 887664
No 80
>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=54.24 E-value=15 Score=17.31 Aligned_cols=30 Identities=23% Similarity=0.518 Sum_probs=20.0
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCccccccccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAK 49 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~ 49 (66)
..|+ .||+.|-. ....| ..|.. |+..|...
T Consensus 10 r~Cp--~cg~kFYD-----------Lnk~p-~vcP~--cg~~~~~~ 39 (129)
T TIGR02300 10 RICP--NTGSKFYD-----------LNRRP-AVSPY--TGEQFPPE 39 (129)
T ss_pred ccCC--CcCccccc-----------cCCCC-ccCCC--cCCccCcc
Confidence 4577 88887742 23457 88865 98877554
No 81
>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=54.24 E-value=10 Score=12.39 Aligned_cols=18 Identities=28% Similarity=0.772 Sum_probs=8.6
Q ss_pred cCCcccccccccccchHHHHH
Q psy1778 36 TCPYQDCLMSYVAKSSLYAHL 56 (66)
Q Consensus 36 ~c~~~~c~~~f~~~~~l~~h~ 56 (66)
.|.+ |...+ ....+..|+
T Consensus 3 ~CPi--C~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPV--CFREV-PENLINSHL 20 (26)
T ss_pred cCCC--CcCcc-cHHHHHHHH
Confidence 4544 65554 334444444
No 82
>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=54.12 E-value=4.4 Score=14.90 Aligned_cols=13 Identities=54% Similarity=1.060 Sum_probs=6.3
Q ss_pred cccCCccccCccccC
Q psy1778 3 MFPCPLVTCGKSFLR 17 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~ 17 (66)
|+.|. .|+..|-.
T Consensus 13 ~~~C~--~C~~~FC~ 25 (43)
T PF01428_consen 13 PFKCK--HCGKSFCL 25 (43)
T ss_dssp HEE-T--TTS-EE-T
T ss_pred CeECC--CCCcccCc
Confidence 45666 77776653
No 83
>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=52.90 E-value=15 Score=21.26 Aligned_cols=25 Identities=36% Similarity=0.741 Sum_probs=20.5
Q ss_pred ccCCccccCccccChHHHHHHHH-HhcC
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHML-QHNE 30 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~-~~~~ 30 (66)
|.|+ .|.+.|.....+..|+. -|.+
T Consensus 58 WiCp--~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 58 WICP--RCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eeCC--cccceeCCHHHHHHHHHHhhhh
Confidence 6788 89999999999999976 3443
No 84
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=51.89 E-value=14 Score=13.32 Aligned_cols=19 Identities=26% Similarity=0.711 Sum_probs=12.7
Q ss_pred ccCCccccCccccChHHHHHH
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEH 24 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~ 24 (66)
..|. .|+..|.....+...
T Consensus 20 d~C~--~C~G~W~d~~el~~~ 38 (41)
T PF13453_consen 20 DVCP--SCGGIWFDAGELEKL 38 (41)
T ss_pred EECC--CCCeEEccHHHHHHH
Confidence 3466 788887777766543
No 85
>KOG2186|consensus
Probab=50.92 E-value=7.4 Score=20.55 Aligned_cols=46 Identities=30% Similarity=0.652 Sum_probs=29.4
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccccchHHHHHH
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVAKSSLYAHLK 57 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~~~~l~~h~~ 57 (66)
|.|. .||....- ..+..|+..-.+ .. |.|. +|+.+|.. ..+..|..
T Consensus 4 FtCn--vCgEsvKK-p~vekH~srCrn-~~-fSCI--DC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCN--VCGESVKK-PQVEKHMSRCRN-AY-FSCI--DCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehh--hhhhhccc-cchHHHHHhccC-Ce-eEEe--eccccccc-chhhhhhh
Confidence 4566 88876543 345567765554 44 8884 49999988 44555654
No 86
>PLN02294 cytochrome c oxidase subunit Vb
Probab=50.02 E-value=8.9 Score=18.99 Aligned_cols=14 Identities=36% Similarity=0.925 Sum_probs=9.7
Q ss_pred CcccCCccccCccccC
Q psy1778 2 RMFPCPLVTCGKSFLR 17 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~ 17 (66)
+|..|. +||..|..
T Consensus 140 kp~RCp--eCG~~fkL 153 (174)
T PLN02294 140 KSFECP--VCTQYFEL 153 (174)
T ss_pred CceeCC--CCCCEEEE
Confidence 567777 78877653
No 87
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=48.73 E-value=16 Score=12.95 Aligned_cols=32 Identities=16% Similarity=0.529 Sum_probs=18.3
Q ss_pred cCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccc
Q psy1778 5 PCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSY 46 (66)
Q Consensus 5 ~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f 46 (66)
.|+ .|+..|.-.... +-..... ..|.. |+..|
T Consensus 4 ~Cp--~C~~~y~i~d~~-----ip~~g~~-v~C~~--C~~~f 35 (36)
T PF13717_consen 4 TCP--NCQAKYEIDDEK-----IPPKGRK-VRCSK--CGHVF 35 (36)
T ss_pred ECC--CCCCEEeCCHHH-----CCCCCcE-EECCC--CCCEe
Confidence 466 888777655432 2222333 67865 87665
No 88
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=47.81 E-value=11 Score=18.03 Aligned_cols=24 Identities=33% Similarity=0.553 Sum_probs=17.6
Q ss_pred cCCccccCccccChHHHHHHHHHhcCCCC
Q psy1778 5 PCPLVTCGKSFLRSEHLQEHMLQHNENKP 33 (66)
Q Consensus 5 ~c~~~~c~~~~~~~~~l~~~~~~~~~~~~ 33 (66)
.|- ++|+.|. .|.+|+.+|-+-.|
T Consensus 78 icL--EDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 78 ICL--EDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEe--ccCcchH---HHHHHHhcccCCCH
Confidence 466 8888886 48889888766544
No 89
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=47.63 E-value=9 Score=19.43 Aligned_cols=23 Identities=26% Similarity=0.642 Sum_probs=16.6
Q ss_pred CCcccCCccccCccccChHHHHHHH
Q psy1778 1 MRMFPCPLVTCGKSFLRSEHLQEHM 25 (66)
Q Consensus 1 ~~~~~c~~~~c~~~~~~~~~l~~~~ 25 (66)
++...|+ .|+..|..........
T Consensus 3 ~k~~~CP--vC~~~F~~~~vrs~~~ 25 (214)
T PF09986_consen 3 DKKITCP--VCGKEFKTKKVRSGKI 25 (214)
T ss_pred CCceECC--CCCCeeeeeEEEcCCc
Confidence 3567898 9999998875554443
No 90
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=47.00 E-value=30 Score=16.40 Aligned_cols=36 Identities=28% Similarity=0.565 Sum_probs=20.7
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCCCCCccCCccccccccc
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYV 47 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~ 47 (66)
-|.|+ .|+..|.....+.. .. .... |.|.. |+....
T Consensus 99 ~Y~Cp--~C~~~y~~~ea~~~---~d-~~~~-f~Cp~--Cg~~l~ 134 (147)
T smart00531 99 YYKCP--NCQSKYTFLEANQL---LD-MDGT-FTCPR--CGEELE 134 (147)
T ss_pred EEECc--CCCCEeeHHHHHHh---cC-CCCc-EECCC--CCCEEE
Confidence 36788 89988775433221 01 1233 88865 887554
No 91
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=47.00 E-value=10 Score=17.16 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=11.5
Q ss_pred cccCCccccCccccCh
Q psy1778 3 MFPCPLVTCGKSFLRS 18 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~ 18 (66)
|+.|. .||..|..-
T Consensus 2 pH~Ct--rCG~vf~~g 15 (112)
T COG3364 2 PHQCT--RCGEVFDDG 15 (112)
T ss_pred Cceec--ccccccccc
Confidence 67888 999998763
No 92
>KOG2231|consensus
Probab=46.71 E-value=23 Score=21.56 Aligned_cols=17 Identities=29% Similarity=0.637 Sum_probs=11.2
Q ss_pred ccCccccChHHHHHHHH
Q psy1778 10 TCGKSFLRSEHLQEHML 26 (66)
Q Consensus 10 ~c~~~~~~~~~l~~~~~ 26 (66)
.|...|.....+..|++
T Consensus 187 ~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 187 FCHERFLDDDELYRHLR 203 (669)
T ss_pred hhhhhhccHHHHHHhhc
Confidence 66666666666666665
No 93
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=46.00 E-value=11 Score=13.99 Aligned_cols=31 Identities=26% Similarity=0.694 Sum_probs=19.2
Q ss_pred CcccCCccccCccccChHHHHHHHHHhcCCCCCccCCccccccccc
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYV 47 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~ 47 (66)
..|.|+ .||..+.-.. .... +.|.. |+..+.
T Consensus 2 ~~y~C~--~CG~~~~~~~----------~~~~-~~Cp~--CG~~~~ 32 (46)
T PRK00398 2 AEYKCA--RCGREVELDE----------YGTG-VRCPY--CGYRIL 32 (46)
T ss_pred CEEECC--CCCCEEEECC----------CCCc-eECCC--CCCeEE
Confidence 357888 9998764321 1115 78866 886544
No 94
>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=45.83 E-value=4.5 Score=13.74 Aligned_cols=6 Identities=50% Similarity=1.254 Sum_probs=3.0
Q ss_pred ccCccc
Q psy1778 10 TCGKSF 15 (66)
Q Consensus 10 ~c~~~~ 15 (66)
+|++.|
T Consensus 5 DC~~~F 10 (28)
T PF08790_consen 5 DCSKDF 10 (28)
T ss_dssp TTTEEE
T ss_pred cCCCCc
Confidence 455544
No 95
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.60 E-value=11 Score=17.59 Aligned_cols=14 Identities=29% Similarity=0.923 Sum_probs=10.9
Q ss_pred cccCCccccCccccCh
Q psy1778 3 MFPCPLVTCGKSFLRS 18 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~ 18 (66)
-|.|+ .|++.|...
T Consensus 53 RyrC~--~C~~tf~~~ 66 (129)
T COG3677 53 RYKCK--SCGSTFTVE 66 (129)
T ss_pred ccccC--CcCcceeee
Confidence 47888 999888655
No 96
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=44.98 E-value=8.3 Score=16.89 Aligned_cols=31 Identities=19% Similarity=0.542 Sum_probs=17.5
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccccccc
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMSYVA 48 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~f~~ 48 (66)
+|.|+ .|++.-. .++.+ .. +.|.. |+..|.-
T Consensus 35 ~~~Cp--~C~~~~V--------kR~a~--GI-W~C~k--Cg~~fAG 65 (89)
T COG1997 35 KHVCP--FCGRTTV--------KRIAT--GI-WKCRK--CGAKFAG 65 (89)
T ss_pred CCcCC--CCCCcce--------eeecc--Ce-EEcCC--CCCeecc
Confidence 56777 8876411 12222 24 77866 8877753
No 97
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=44.20 E-value=10 Score=14.97 Aligned_cols=7 Identities=43% Similarity=1.165 Sum_probs=2.4
Q ss_pred ccCcccc
Q psy1778 10 TCGKSFL 16 (66)
Q Consensus 10 ~c~~~~~ 16 (66)
.|+-.|.
T Consensus 29 ~C~H~fe 35 (57)
T PF11789_consen 29 KCGHTFE 35 (57)
T ss_dssp SS--EEE
T ss_pred CCCCeec
Confidence 4555554
No 98
>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=42.93 E-value=11 Score=14.19 Aligned_cols=13 Identities=31% Similarity=0.889 Sum_probs=6.9
Q ss_pred ccCCccccCcccc
Q psy1778 4 FPCPLVTCGKSFL 16 (66)
Q Consensus 4 ~~c~~~~c~~~~~ 16 (66)
+.|...+||..|.
T Consensus 26 ~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 26 CQCTNPECGHTFV 38 (47)
T ss_pred EEECCCcCCCEEE
Confidence 4455455665554
No 99
>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=42.36 E-value=22 Score=12.81 Aligned_cols=21 Identities=38% Similarity=0.545 Sum_probs=12.1
Q ss_pred ccCCcccccccccc----cchHHHHHH
Q psy1778 35 FTCPYQDCLMSYVA----KSSLYAHLK 57 (66)
Q Consensus 35 ~~c~~~~c~~~f~~----~~~l~~h~~ 57 (66)
..|.. |...+.. .+.|..|++
T Consensus 17 a~C~~--C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 17 AKCKY--CGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp EEETT--TTEE-----SSTHHHHHHHH
T ss_pred EEeCC--CCeEEeeCCCcHHHHHHhhh
Confidence 67766 8776655 366777763
No 100
>COG1773 Rubredoxin [Energy production and conversion]
Probab=42.17 E-value=12 Score=14.92 Aligned_cols=15 Identities=20% Similarity=0.689 Sum_probs=11.2
Q ss_pred CcccCCccccCccccCh
Q psy1778 2 RMFPCPLVTCGKSFLRS 18 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~ 18 (66)
+.|.|. .||..|...
T Consensus 2 ~~~~C~--~CG~vYd~e 16 (55)
T COG1773 2 KRWRCS--VCGYVYDPE 16 (55)
T ss_pred CceEec--CCceEeccc
Confidence 457888 899887654
No 101
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=42.17 E-value=26 Score=14.28 Aligned_cols=8 Identities=75% Similarity=2.224 Sum_probs=4.5
Q ss_pred ccCCccccCc
Q psy1778 4 FPCPLVTCGK 13 (66)
Q Consensus 4 ~~c~~~~c~~ 13 (66)
|.|+ .||.
T Consensus 28 F~CP--nCGe 35 (61)
T COG2888 28 FPCP--NCGE 35 (61)
T ss_pred eeCC--CCCc
Confidence 4555 6664
No 102
>KOG0717|consensus
Probab=39.97 E-value=18 Score=21.05 Aligned_cols=21 Identities=24% Similarity=0.471 Sum_probs=18.2
Q ss_pred ccCCcccccccccccchHHHHHH
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLK 57 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~ 57 (66)
+.|.+ |.++|.+...+..|..
T Consensus 293 lyC~v--CnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVV--CNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEee--ccccccchHHHHhhHH
Confidence 57877 9999999999998865
No 103
>KOG0227|consensus
Probab=38.62 E-value=15 Score=18.67 Aligned_cols=19 Identities=32% Similarity=0.635 Sum_probs=14.4
Q ss_pred ccCCcccccccccccchHHHH
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAH 55 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h 55 (66)
|.|.+ |.....+..+...|
T Consensus 54 yeCkL--ClT~H~ne~Syl~H 72 (222)
T KOG0227|consen 54 YECKL--CLTLHNNEGSYLAH 72 (222)
T ss_pred eeehh--hhhhhcchhhhhhh
Confidence 78988 98877777776655
No 104
>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=38.55 E-value=16 Score=12.72 Aligned_cols=25 Identities=32% Similarity=0.828 Sum_probs=16.2
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCCCCCccCCcccccc
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLM 44 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~ 44 (66)
.|.|. .||..+... ..| ..|.+ |+.
T Consensus 2 ~~~C~--~CG~i~~g~------------~~p-~~CP~--Cg~ 26 (34)
T cd00729 2 VWVCP--VCGYIHEGE------------EAP-EKCPI--CGA 26 (34)
T ss_pred eEECC--CCCCEeECC------------cCC-CcCcC--CCC
Confidence 47888 899765321 246 67866 865
No 105
>KOG1994|consensus
Probab=38.26 E-value=15 Score=19.19 Aligned_cols=19 Identities=32% Similarity=0.898 Sum_probs=16.9
Q ss_pred ccCCcccccccccccchHHHH
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAH 55 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h 55 (66)
|.|.+ |+..|.....|..|
T Consensus 240 ~YC~f--CG~~y~~~edl~eh 258 (268)
T KOG1994|consen 240 YYCFF--CGIKYKDEEDLYEH 258 (268)
T ss_pred eEEEE--eccccCCHHHHHHh
Confidence 88988 99999999988876
No 106
>KOG2482|consensus
Probab=37.55 E-value=33 Score=19.27 Aligned_cols=23 Identities=35% Similarity=0.652 Sum_probs=18.4
Q ss_pred ccCCccccCccccChHHHHHHHHHh
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQH 28 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~ 28 (66)
+.|- .|.+.|..+..|..||+-.
T Consensus 196 ~~CL--yCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 196 LRCL--YCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred heee--eeccccCCcHHHHHHHHhc
Confidence 4566 8889999999999888744
No 107
>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=37.39 E-value=14 Score=12.83 Aligned_cols=26 Identities=27% Similarity=0.720 Sum_probs=14.4
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCccccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCLMS 45 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~~~ 45 (66)
|.|. .|+..+... ...+ ..|.. |+..
T Consensus 1 Y~C~--~Cg~~~~~~-----------~~~~-irC~~--CG~R 26 (32)
T PF03604_consen 1 YICG--ECGAEVELK-----------PGDP-IRCPE--CGHR 26 (32)
T ss_dssp EBES--SSSSSE-BS-----------TSST-SSBSS--SS-S
T ss_pred CCCC--cCCCeeEcC-----------CCCc-EECCc--CCCe
Confidence 5677 888765421 1235 78855 8754
No 108
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=35.79 E-value=14 Score=17.87 Aligned_cols=13 Identities=38% Similarity=0.766 Sum_probs=10.3
Q ss_pred ccCCccccCccccCh
Q psy1778 4 FPCPLVTCGKSFLRS 18 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~ 18 (66)
+.|+ .||++|..-
T Consensus 29 ~~c~--~c~~~f~~~ 41 (154)
T PRK00464 29 RECL--ACGKRFTTF 41 (154)
T ss_pred eecc--ccCCcceEe
Confidence 7788 999888754
No 109
>KOG2593|consensus
Probab=35.33 E-value=32 Score=19.80 Aligned_cols=16 Identities=31% Similarity=0.781 Sum_probs=10.6
Q ss_pred cccCCccccCccccChHH
Q psy1778 3 MFPCPLVTCGKSFLRSEH 20 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~ 20 (66)
-|.|+ .|.+.|..-..
T Consensus 128 ~Y~Cp--~C~kkyt~Lea 143 (436)
T KOG2593|consen 128 GYVCP--NCQKKYTSLEA 143 (436)
T ss_pred cccCC--ccccchhhhHH
Confidence 36777 88877765443
No 110
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=35.08 E-value=23 Score=13.68 Aligned_cols=13 Identities=23% Similarity=0.772 Sum_probs=10.1
Q ss_pred ccCCccccCccccCh
Q psy1778 4 FPCPLVTCGKSFLRS 18 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~ 18 (66)
|.|. .||..+...
T Consensus 2 y~C~--~CgyiYd~~ 14 (50)
T cd00730 2 YECR--ICGYIYDPA 14 (50)
T ss_pred cCCC--CCCeEECCC
Confidence 6788 899887754
No 111
>KOG2785|consensus
Probab=33.23 E-value=99 Score=17.73 Aligned_cols=52 Identities=23% Similarity=0.466 Sum_probs=36.7
Q ss_pred cccCCccccCccccChHHHHHHHHHhcCC-CC---------------------CccCCccccc---ccccccchHHHHHH
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNEN-KP---------------------KFTCPYQDCL---MSYVAKSSLYAHLK 57 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~~-~~---------------------~~~c~~~~c~---~~f~~~~~l~~h~~ 57 (66)
|--|- .|+..+..-.....||..+.+- .| -+.|.. |. ..|.+......||.
T Consensus 166 Pt~CL--fC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~--CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 166 PTDCL--FCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLF--CNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred Cccee--ecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEE--eccccCcccccHHHHHHHh
Confidence 44566 8998888888888888765432 11 045655 66 88999999999987
Q ss_pred H
Q psy1778 58 H 58 (66)
Q Consensus 58 ~ 58 (66)
.
T Consensus 242 ~ 242 (390)
T KOG2785|consen 242 D 242 (390)
T ss_pred h
Confidence 3
No 112
>KOG2807|consensus
Probab=32.02 E-value=89 Score=17.61 Aligned_cols=21 Identities=29% Similarity=0.703 Sum_probs=13.4
Q ss_pred CCCccCCcccccccccccchHHHH
Q psy1778 32 KPKFTCPYQDCLMSYVAKSSLYAH 55 (66)
Q Consensus 32 ~~~~~c~~~~c~~~f~~~~~l~~h 55 (66)
.| ..|.. |+-+......|..-
T Consensus 289 LP-~eCpi--C~ltLVss~hLARS 309 (378)
T KOG2807|consen 289 LP-IECPI--CSLTLVSSPHLARS 309 (378)
T ss_pred CC-ccCCc--cceeEecchHHHHH
Confidence 35 66755 77777666666644
No 113
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=29.58 E-value=31 Score=18.15 Aligned_cols=15 Identities=20% Similarity=0.700 Sum_probs=11.6
Q ss_pred CcccCCccccCccccCh
Q psy1778 2 RMFPCPLVTCGKSFLRS 18 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~ 18 (66)
++..|. +||..|...
T Consensus 180 kpqRCp--ECGqVFKLV 194 (268)
T PTZ00043 180 FLYRCG--ECDQIFMLV 194 (268)
T ss_pred CCccCC--CCCcEEEEE
Confidence 577898 999888653
No 114
>KOG4124|consensus
Probab=29.33 E-value=20 Score=20.12 Aligned_cols=22 Identities=23% Similarity=0.247 Sum_probs=12.5
Q ss_pred CCCCCccCCcccccccccccchHHHH
Q psy1778 30 ENKPKFTCPYQDCLMSYVAKSSLYAH 55 (66)
Q Consensus 30 ~~~~~~~c~~~~c~~~f~~~~~l~~h 55 (66)
..+| |.|. |+........|..|
T Consensus 210 ~~~p-~k~~---~~~~~~T~~~l~~H 231 (442)
T KOG4124|consen 210 TGTP-KKMP---ESLVMDTSSPLSDH 231 (442)
T ss_pred ccCC-ccCc---ccccccccchhhhc
Confidence 3456 6664 55666666665544
No 115
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=29.22 E-value=28 Score=12.60 Aligned_cols=10 Identities=30% Similarity=1.235 Sum_probs=4.7
Q ss_pred ccCCccccCccc
Q psy1778 4 FPCPLVTCGKSF 15 (66)
Q Consensus 4 ~~c~~~~c~~~~ 15 (66)
|.|. .|+..|
T Consensus 29 y~C~--~C~~~w 38 (40)
T smart00440 29 YVCT--KCGHRW 38 (40)
T ss_pred EEeC--CCCCEe
Confidence 3444 555444
No 116
>PTZ00448 hypothetical protein; Provisional
Probab=28.92 E-value=68 Score=18.22 Aligned_cols=23 Identities=17% Similarity=0.553 Sum_probs=17.1
Q ss_pred cccCCccccCccccChHHHHHHHHH
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQ 27 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~ 27 (66)
.|.|. .|+-.|........|.++
T Consensus 314 ~~tC~--~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCR--KCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred Ccccc--ccccccCCHHHHHHHhhh
Confidence 36688 888888777777777664
No 117
>KOG1842|consensus
Probab=28.39 E-value=39 Score=19.70 Aligned_cols=25 Identities=40% Similarity=0.721 Sum_probs=19.5
Q ss_pred ccCCcccccccccccchHHHHHHHhhC
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLKHVHS 61 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~~~~~ 61 (66)
|.|.+ |...|.....|..|.-.-|+
T Consensus 16 flCPi--C~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 16 FLCPI--CLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred ccCch--HhhhhhhHHHHHHHHhhhcc
Confidence 78876 99999988888888765443
No 118
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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 domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=27.88 E-value=41 Score=11.62 Aligned_cols=7 Identities=57% Similarity=1.507 Sum_probs=1.2
Q ss_pred CCccccc
Q psy1778 37 CPYQDCL 43 (66)
Q Consensus 37 c~~~~c~ 43 (66)
|.+.+|.
T Consensus 5 CPvkdC~ 11 (30)
T PF10426_consen 5 CPVKDCD 11 (30)
T ss_dssp --STT--
T ss_pred cccccCc
Confidence 4333443
No 119
>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=27.48 E-value=29 Score=16.46 Aligned_cols=10 Identities=50% Similarity=1.507 Sum_probs=5.8
Q ss_pred ccCCccccCccc
Q psy1778 4 FPCPLVTCGKSF 15 (66)
Q Consensus 4 ~~c~~~~c~~~~ 15 (66)
|.|+ .|++.|
T Consensus 125 ~~C~--~C~kiy 134 (147)
T PF01927_consen 125 WRCP--GCGKIY 134 (147)
T ss_pred EECC--CCCCEe
Confidence 4566 666654
No 120
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.36 E-value=67 Score=13.93 Aligned_cols=21 Identities=24% Similarity=0.623 Sum_probs=16.7
Q ss_pred CCccccCccccChHHHHHHHHHh
Q psy1778 6 CPLVTCGKSFLRSEHLQEHMLQH 28 (66)
Q Consensus 6 c~~~~c~~~~~~~~~l~~~~~~~ 28 (66)
|+ .|+.+|...+.|-.-+...
T Consensus 24 CP--rCrGVWLDrGELdKli~r~ 44 (88)
T COG3809 24 CP--RCRGVWLDRGELDKLIERS 44 (88)
T ss_pred CC--ccccEeecchhHHHHHHHh
Confidence 66 8999999999988776543
No 121
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=26.48 E-value=62 Score=13.26 Aligned_cols=12 Identities=17% Similarity=0.396 Sum_probs=6.5
Q ss_pred HHHHHhhCCCCC
Q psy1778 54 AHLKHVHSTNKI 65 (66)
Q Consensus 54 ~h~~~~~~~~~~ 65 (66)
.|++.++.+.|.
T Consensus 30 ~H~~~~HP~~p~ 41 (65)
T PF04328_consen 30 EHMRRHHPDEPP 41 (65)
T ss_pred HHHHHHCcCCCC
Confidence 455656655543
No 122
>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=26.13 E-value=8 Score=15.09 Aligned_cols=13 Identities=31% Similarity=0.973 Sum_probs=4.7
Q ss_pred ccCCccccCccccCh
Q psy1778 4 FPCPLVTCGKSFLRS 18 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~ 18 (66)
|.|+ .|...|-..
T Consensus 22 y~C~--~C~~~FC~d 34 (51)
T PF07975_consen 22 YRCP--KCKNHFCID 34 (51)
T ss_dssp E--T--TTT--B-HH
T ss_pred EECC--CCCCccccC
Confidence 6666 676666433
No 123
>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=26.11 E-value=39 Score=12.69 Aligned_cols=11 Identities=45% Similarity=1.337 Sum_probs=7.9
Q ss_pred CCccccCccccCh
Q psy1778 6 CPLVTCGKSFLRS 18 (66)
Q Consensus 6 c~~~~c~~~~~~~ 18 (66)
|. .|++.|.-.
T Consensus 11 C~--~C~rpf~WR 21 (42)
T PF10013_consen 11 CP--VCGRPFTWR 21 (42)
T ss_pred Cc--ccCCcchHH
Confidence 66 888887654
No 124
>PF06858 NOG1: Nucleolar GTP-binding protein 1 (NOG1); InterPro: IPR010674 This domain represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). The NOG1 family includes eukaryotic, bacterial and archaeal proteins. In Saccharomyces cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. In particular, NOG1 is believed to be functionally linked to ribosome biogenesis, which occurs in the nucleolus. In eukaryotes, NOG1 mutants were found to disrupt the biogenesis of the 60S ribosomal subunit []. The DRG and OBG proteins as well as the prokaryotic NOG-like proteins are homologous throughout their length to the amino half of eukaryotic NOG1, which contains the GTP binding motifs (IPR006073 from INTERPRO); the N-terminal GTP-binding motif is required for function.; GO: 0005525 GTP binding; PDB: 2E87_A.
Probab=25.60 E-value=54 Score=13.23 Aligned_cols=23 Identities=22% Similarity=0.362 Sum_probs=12.8
Q ss_pred ccccccccchHHHHHHHhhCCCC
Q psy1778 42 CLMSYVAKSSLYAHLKHVHSTNK 64 (66)
Q Consensus 42 c~~~f~~~~~l~~h~~~~~~~~~ 64 (66)
|+.+....-.|....+..-+++|
T Consensus 27 CGysie~Q~~L~~~ik~~F~~~P 49 (58)
T PF06858_consen 27 CGYSIEEQLSLFKEIKPLFPNKP 49 (58)
T ss_dssp TSS-HHHHHHHHHHHHHHTTTS-
T ss_pred CCCCHHHHHHHHHHHHHHcCCCC
Confidence 76666666666666655554554
No 125
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=25.38 E-value=33 Score=11.96 Aligned_cols=6 Identities=67% Similarity=1.398 Sum_probs=3.0
Q ss_pred ccCccc
Q psy1778 10 TCGKSF 15 (66)
Q Consensus 10 ~c~~~~ 15 (66)
.|+.+|
T Consensus 26 ~Cg~~~ 31 (33)
T PF08792_consen 26 FCGSSF 31 (33)
T ss_pred cCCcEe
Confidence 555443
No 126
>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=24.75 E-value=24 Score=12.98 Aligned_cols=6 Identities=33% Similarity=1.176 Sum_probs=2.8
Q ss_pred ccCccc
Q psy1778 10 TCGKSF 15 (66)
Q Consensus 10 ~c~~~~ 15 (66)
.|+..|
T Consensus 34 YCg~~y 39 (40)
T PF10276_consen 34 YCGTRY 39 (40)
T ss_dssp TTTEEE
T ss_pred CCCCEE
Confidence 555443
No 127
>KOG4385|consensus
Probab=24.00 E-value=57 Score=19.33 Aligned_cols=23 Identities=13% Similarity=0.212 Sum_probs=19.1
Q ss_pred cCCccccCccccChHHHHHHHHH
Q psy1778 5 PCPLVTCGKSFLRSEHLQEHMLQ 27 (66)
Q Consensus 5 ~c~~~~c~~~~~~~~~l~~~~~~ 27 (66)
.|.|+.|+..+.....+..|...
T Consensus 211 vckwpgcE~~~ed~~~flKhln~ 233 (581)
T KOG4385|consen 211 VCKWPGCEAVCEDFGSFLKHLNT 233 (581)
T ss_pred ccCCCchhhhccchHHHHHhhcc
Confidence 58888999999888888888664
No 128
>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=23.92 E-value=26 Score=13.38 Aligned_cols=13 Identities=31% Similarity=1.009 Sum_probs=9.2
Q ss_pred ccCCccccCccccCh
Q psy1778 4 FPCPLVTCGKSFLRS 18 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~ 18 (66)
|.|. .|+..+...
T Consensus 2 y~C~--~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCP--VCGYVYDPE 14 (47)
T ss_dssp EEET--TTSBEEETT
T ss_pred cCCC--CCCEEEcCC
Confidence 6677 888777654
No 129
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=23.67 E-value=1.4e+02 Score=16.46 Aligned_cols=23 Identities=22% Similarity=0.550 Sum_probs=18.8
Q ss_pred cccCCccccCccccChHHHHHHHHH
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQ 27 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~ 27 (66)
-|.|. .|-+-|.....+..|+..
T Consensus 48 lyiCe--~Clky~~~~~~l~~H~~~ 70 (290)
T PLN03238 48 LYICE--YCLKYMRKKKSLLRHLAK 70 (290)
T ss_pred EEEcC--CCcchhCCHHHHHHHHHh
Confidence 46788 898888899999999773
No 130
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=23.62 E-value=39 Score=11.55 Aligned_cols=11 Identities=27% Similarity=1.020 Sum_probs=7.5
Q ss_pred cccCCccccCccc
Q psy1778 3 MFPCPLVTCGKSF 15 (66)
Q Consensus 3 ~~~c~~~~c~~~~ 15 (66)
-|+|. .|+...
T Consensus 4 ~ykC~--~CGniv 14 (34)
T cd00974 4 VYKCE--ICGNIV 14 (34)
T ss_pred EEEcC--CCCcEE
Confidence 46777 787654
No 131
>KOG2295|consensus
Probab=23.61 E-value=84 Score=19.08 Aligned_cols=26 Identities=31% Similarity=0.699 Sum_probs=20.7
Q ss_pred CcccCCccccCccccChHHHHHHHHH
Q psy1778 2 RMFPCPLVTCGKSFLRSEHLQEHMLQ 27 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~~~~~l~~~~~~ 27 (66)
..|.|+...|.+.|.-......|+..
T Consensus 508 dKy~C~lsgc~KlF~gpEFvrKHi~~ 533 (648)
T KOG2295|consen 508 DKYLCPLSGCAKLFKGPEFVRKHINK 533 (648)
T ss_pred ccccCCCcchHhhccCHHHHHHHHHH
Confidence 35889877788999988888888764
No 132
>KOG4377|consensus
Probab=23.46 E-value=92 Score=18.15 Aligned_cols=28 Identities=14% Similarity=0.191 Sum_probs=21.5
Q ss_pred cccCCccccCccccChHHHHHHHHHhcC
Q psy1778 3 MFPCPLVTCGKSFLRSEHLQEHMLQHNE 30 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~~~l~~~~~~~~~ 30 (66)
-|.|..+.|+.-+.++..+.+|..+|.-
T Consensus 271 hyhcl~e~C~ykr~~k~DvirH~~~hkk 298 (480)
T KOG4377|consen 271 HYHCLNEYCFYKRGQKNDVIRHVEIHKK 298 (480)
T ss_pred hhcccCccccccccchhhhHHHHHHHhh
Confidence 4667777898877778888899887753
No 133
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=23.35 E-value=38 Score=11.55 Aligned_cols=11 Identities=27% Similarity=1.038 Sum_probs=7.4
Q ss_pred cccCCccccCccc
Q psy1778 3 MFPCPLVTCGKSF 15 (66)
Q Consensus 3 ~~~c~~~~c~~~~ 15 (66)
-|+|. .|+...
T Consensus 7 ~ykC~--~Cgniv 17 (34)
T TIGR00319 7 VYKCE--VCGNIV 17 (34)
T ss_pred EEEcC--CCCcEE
Confidence 46777 787654
No 134
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.33 E-value=28 Score=16.40 Aligned_cols=14 Identities=21% Similarity=0.776 Sum_probs=10.1
Q ss_pred cccCCccccCccccCh
Q psy1778 3 MFPCPLVTCGKSFLRS 18 (66)
Q Consensus 3 ~~~c~~~~c~~~~~~~ 18 (66)
.+.|. .||..|...
T Consensus 70 ~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCR--NCGNEWSLK 83 (135)
T ss_pred EEECC--CCCCEEecc
Confidence 36788 999877653
No 135
>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=22.90 E-value=44 Score=11.85 Aligned_cols=10 Identities=40% Similarity=1.461 Sum_probs=5.5
Q ss_pred ccCCccccCccc
Q psy1778 4 FPCPLVTCGKSF 15 (66)
Q Consensus 4 ~~c~~~~c~~~~ 15 (66)
+.|. .||..+
T Consensus 33 ~~C~--~CGE~~ 42 (46)
T TIGR03831 33 LVCP--QCGEEY 42 (46)
T ss_pred cccc--cCCCEe
Confidence 3466 666544
No 136
>KOG4727|consensus
Probab=22.41 E-value=44 Score=16.79 Aligned_cols=21 Identities=14% Similarity=0.412 Sum_probs=16.4
Q ss_pred ccCCcccccccccccchHHHHHH
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLK 57 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~ 57 (66)
|.|.+ |.-.+..+.++..|+.
T Consensus 76 yyCdV--CdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 76 YYCDV--CDCVVKDSINFLDHIN 96 (193)
T ss_pred eeeee--cceeehhhHHHHHHhc
Confidence 77988 9888888877776653
No 137
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=21.98 E-value=47 Score=13.48 Aligned_cols=29 Identities=38% Similarity=0.819 Sum_probs=15.4
Q ss_pred ccCCccccCccccChHHHHHHHHHhcCCCCCccCCccccc
Q psy1778 4 FPCPLVTCGKSFLRSEHLQEHMLQHNENKPKFTCPYQDCL 43 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~~~l~~~~~~~~~~~~~~~c~~~~c~ 43 (66)
|.|+ ||.+|.-... -...|++. -.|.. |.
T Consensus 23 yPCP---CGDRFeIsLe-----Dl~~GE~V-ArCPS--CS 51 (67)
T COG5216 23 YPCP---CGDRFEISLE-----DLRNGEVV-ARCPS--CS 51 (67)
T ss_pred ecCC---CCCEeEEEHH-----HhhCCceE-EEcCC--ce
Confidence 5675 8877753311 12345555 56754 64
No 138
>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=21.93 E-value=19 Score=17.15 Aligned_cols=13 Identities=38% Similarity=1.007 Sum_probs=7.8
Q ss_pred CcccCCccccCcccc
Q psy1778 2 RMFPCPLVTCGKSFL 16 (66)
Q Consensus 2 ~~~~c~~~~c~~~~~ 16 (66)
+|..|. +||..|.
T Consensus 111 ~~~RCp--eCG~~fk 123 (136)
T PF01215_consen 111 KPQRCP--ECGQVFK 123 (136)
T ss_dssp SEEEET--TTEEEEE
T ss_pred CccCCC--CCCeEEE
Confidence 355666 6776654
No 139
>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=21.73 E-value=37 Score=12.98 Aligned_cols=12 Identities=33% Similarity=0.957 Sum_probs=5.4
Q ss_pred cCCccccCccccCh
Q psy1778 5 PCPLVTCGKSFLRS 18 (66)
Q Consensus 5 ~c~~~~c~~~~~~~ 18 (66)
.|+ .|++.|...
T Consensus 22 ~CP--lC~r~l~~e 33 (54)
T PF04423_consen 22 CCP--LCGRPLDEE 33 (54)
T ss_dssp E-T--TT--EE-HH
T ss_pred cCC--CCCCCCCHH
Confidence 577 888877654
No 140
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=21.69 E-value=1.3e+02 Score=17.25 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=14.3
Q ss_pred CCccccCccccChHHHHHHHHH
Q psy1778 6 CPLVTCGKSFLRSEHLQEHMLQ 27 (66)
Q Consensus 6 c~~~~c~~~~~~~~~l~~~~~~ 27 (66)
|. .|...|-....|..|++.
T Consensus 223 C~--FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 223 CI--FCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hh--hccceecChHHHHHHHHh
Confidence 55 677777777777777764
No 141
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=21.38 E-value=30 Score=13.42 Aligned_cols=11 Identities=27% Similarity=1.066 Sum_probs=8.9
Q ss_pred cccCCccccCccc
Q psy1778 3 MFPCPLVTCGKSF 15 (66)
Q Consensus 3 ~~~c~~~~c~~~~ 15 (66)
-|.|. .||+.+
T Consensus 6 ~Y~C~--~Cg~~~ 16 (49)
T COG1996 6 EYKCA--RCGREV 16 (49)
T ss_pred EEEhh--hcCCee
Confidence 47888 999887
No 142
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.34 E-value=90 Score=14.47 Aligned_cols=23 Identities=13% Similarity=0.504 Sum_probs=13.6
Q ss_pred ccCCcccccccccccchHHHHHHHh
Q psy1778 35 FTCPYQDCLMSYVAKSSLYAHLKHV 59 (66)
Q Consensus 35 ~~c~~~~c~~~f~~~~~l~~h~~~~ 59 (66)
|.|.. |...|...-....|...|
T Consensus 82 y~C~~--C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 82 YVCAV--CKNVFCVDCDVFVHESLH 104 (112)
T ss_pred eeCCC--CCCccccccchhhhhhcc
Confidence 55654 666666666666665443
No 143
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.23 E-value=87 Score=14.56 Aligned_cols=12 Identities=33% Similarity=0.526 Sum_probs=8.0
Q ss_pred CcccCCccccCccc
Q psy1778 2 RMFPCPLVTCGKSF 15 (66)
Q Consensus 2 ~~~~c~~~~c~~~~ 15 (66)
.|..|+ .||++|
T Consensus 25 dPiVsP--ytG~s~ 36 (129)
T COG4530 25 DPIVSP--YTGKSY 36 (129)
T ss_pred CccccC--cccccc
Confidence 356666 777777
No 144
>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=21.19 E-value=35 Score=12.11 Aligned_cols=12 Identities=50% Similarity=1.207 Sum_probs=5.1
Q ss_pred cCCccccCccccCh
Q psy1778 5 PCPLVTCGKSFLRS 18 (66)
Q Consensus 5 ~c~~~~c~~~~~~~ 18 (66)
.|. +|++.|..+
T Consensus 5 ~C~--eC~~~f~dS 16 (34)
T PF01286_consen 5 KCD--ECGKPFMDS 16 (34)
T ss_dssp E-T--TT--EES-S
T ss_pred hHh--HhCCHHHHH
Confidence 466 788777543
No 145
>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=21.10 E-value=35 Score=12.28 Aligned_cols=11 Identities=27% Similarity=1.029 Sum_probs=5.5
Q ss_pred cccCCccccCccc
Q psy1778 3 MFPCPLVTCGKSF 15 (66)
Q Consensus 3 ~~~c~~~~c~~~~ 15 (66)
-|+|. .||...
T Consensus 6 ~YkC~--~CGniV 16 (36)
T PF06397_consen 6 FYKCE--HCGNIV 16 (36)
T ss_dssp EEE-T--TT--EE
T ss_pred EEEcc--CCCCEE
Confidence 47788 888654
No 146
>PF14353 CpXC: CpXC protein
Probab=20.51 E-value=49 Score=15.15 Aligned_cols=13 Identities=46% Similarity=1.262 Sum_probs=8.7
Q ss_pred ccCCccccCccccCh
Q psy1778 4 FPCPLVTCGKSFLRS 18 (66)
Q Consensus 4 ~~c~~~~c~~~~~~~ 18 (66)
+.|+ .||..+.-.
T Consensus 39 ~~CP--~Cg~~~~~~ 51 (128)
T PF14353_consen 39 FTCP--SCGHKFRLE 51 (128)
T ss_pred EECC--CCCCceecC
Confidence 5677 888766543
No 147
>KOG2636|consensus
Probab=20.40 E-value=96 Score=18.29 Aligned_cols=27 Identities=19% Similarity=0.450 Sum_probs=18.3
Q ss_pred HHhcCCCCCccCCccccc-ccccccchHHHH
Q psy1778 26 LQHNENKPKFTCPYQDCL-MSYVAKSSLYAH 55 (66)
Q Consensus 26 ~~~~~~~~~~~c~~~~c~-~~f~~~~~l~~h 55 (66)
+.|+.... |.|.+ |+ .++.-...+..|
T Consensus 394 KLHGL~~e-y~CEI--CGNy~Y~GrkaF~RH 421 (497)
T KOG2636|consen 394 KLHGLDIE-YNCEI--CGNYVYKGRKAFDRH 421 (497)
T ss_pred hhcCCCcc-cceee--ccCccccCcHHHHHH
Confidence 45666677 88887 87 666666666655
No 148
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=20.21 E-value=71 Score=11.62 Aligned_cols=23 Identities=35% Similarity=0.628 Sum_probs=12.4
Q ss_pred ccCCccccCccccC--hHHHHHHHHHh
Q psy1778 4 FPCPLVTCGKSFLR--SEHLQEHMLQH 28 (66)
Q Consensus 4 ~~c~~~~c~~~~~~--~~~l~~~~~~~ 28 (66)
-.|. .||..+.. ......|.+-|
T Consensus 14 ~~C~--~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCP--TCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCC--CCCCEECCCCHHHHHHHHHHH
Confidence 3566 78765443 34445555544
No 149
>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=20.19 E-value=54 Score=15.97 Aligned_cols=13 Identities=31% Similarity=0.667 Sum_probs=9.1
Q ss_pred cCCccccCccccChH
Q psy1778 5 PCPLVTCGKSFLRSE 19 (66)
Q Consensus 5 ~c~~~~c~~~~~~~~ 19 (66)
.|. .|++.|.+-.
T Consensus 30 eC~--~C~~RFTTyE 42 (147)
T TIGR00244 30 ECL--ECHERFTTFE 42 (147)
T ss_pred cCC--ccCCccceee
Confidence 466 8888887643
No 150
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=20.03 E-value=65 Score=11.59 Aligned_cols=9 Identities=44% Similarity=1.106 Sum_probs=5.8
Q ss_pred cccCCccccCc
Q psy1778 3 MFPCPLVTCGK 13 (66)
Q Consensus 3 ~~~c~~~~c~~ 13 (66)
|..|+ .||.
T Consensus 2 ~~~Cp--~Cg~ 10 (47)
T PF14690_consen 2 PPRCP--HCGS 10 (47)
T ss_pred CccCC--CcCC
Confidence 55666 7774
Done!