Query psy8140
Match_columns 108
No_of_seqs 117 out of 448
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 19:39:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8140.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8140hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2169|consensus 99.9 3.8E-27 8.3E-32 201.4 7.0 105 4-108 266-373 (636)
2 PF02891 zf-MIZ: MIZ/SP-RING z 99.9 3.8E-27 8.2E-32 143.2 2.5 50 40-89 1-50 (50)
3 PF11789 zf-Nse: Zinc-finger o 99.5 7.1E-15 1.5E-19 91.4 2.8 53 31-85 1-53 (57)
4 KOG2979|consensus 98.8 1.2E-09 2.5E-14 85.6 0.6 60 31-92 166-227 (262)
5 smart00504 Ubox Modified RING 98.4 2.8E-07 6.1E-12 56.3 3.6 57 42-103 2-58 (63)
6 COG5627 MMS21 DNA repair prote 98.2 5.9E-07 1.3E-11 70.2 1.0 69 31-101 179-249 (275)
7 PF04564 U-box: U-box domain; 98.0 7.3E-06 1.6E-10 52.5 3.4 57 41-101 4-60 (73)
8 PLN03208 E3 ubiquitin-protein 96.9 0.001 2.3E-08 50.5 3.5 68 27-96 5-84 (193)
9 COG5222 Uncharacterized conser 96.5 0.0021 4.6E-08 52.4 3.2 77 18-98 251-329 (427)
10 PF04641 Rtf2: Rtf2 RING-finge 96.5 0.0031 6.7E-08 49.0 3.6 55 38-97 110-167 (260)
11 PF14835 zf-RING_6: zf-RING of 96.0 0.005 1.1E-07 39.4 2.1 58 41-104 7-64 (65)
12 KOG2164|consensus 96.0 0.0044 9.6E-08 52.9 2.4 55 41-96 186-241 (513)
13 cd00162 RING RING-finger (Real 95.5 0.016 3.4E-07 31.6 2.6 44 44-90 2-45 (45)
14 PF13923 zf-C3HC4_2: Zinc fing 94.8 0.022 4.7E-07 31.9 1.9 39 44-86 1-39 (39)
15 PF13445 zf-RING_UBOX: RING-ty 93.4 0.058 1.3E-06 31.5 1.8 39 44-84 1-43 (43)
16 PF00097 zf-C3HC4: Zinc finger 92.5 0.093 2E-06 29.1 1.7 41 44-86 1-41 (41)
17 PF15227 zf-C3HC4_4: zinc fing 92.4 0.076 1.6E-06 30.6 1.3 42 44-86 1-42 (42)
18 TIGR00599 rad18 DNA repair pro 92.0 0.22 4.8E-06 41.5 4.1 63 37-104 22-84 (397)
19 PF13639 zf-RING_2: Ring finge 91.4 0.14 3.1E-06 29.0 1.7 40 44-87 3-44 (44)
20 cd00350 rubredoxin_like Rubred 91.3 0.069 1.5E-06 29.3 0.3 12 79-90 16-27 (33)
21 PF04810 zf-Sec23_Sec24: Sec23 90.8 0.029 6.3E-07 32.1 -1.6 21 70-90 14-34 (40)
22 PF13920 zf-C3HC4_3: Zinc fing 89.9 0.35 7.6E-06 28.2 2.5 44 43-91 4-48 (50)
23 COG5574 PEX10 RING-finger-cont 88.2 0.24 5.2E-06 39.5 1.2 56 40-98 214-269 (271)
24 KOG0320|consensus 87.7 0.28 6E-06 37.2 1.2 50 42-95 132-182 (187)
25 PF13894 zf-C2H2_4: C2H2-type 87.2 0.27 5.9E-06 23.5 0.7 11 81-91 1-11 (24)
26 smart00531 TFIIE Transcription 86.4 0.74 1.6E-05 32.8 2.8 42 37-93 95-136 (147)
27 KOG0978|consensus 86.0 0.22 4.7E-06 44.3 -0.1 56 37-96 639-694 (698)
28 PF04423 Rad50_zn_hook: Rad50 85.7 0.57 1.2E-05 28.0 1.7 24 69-93 10-33 (54)
29 PF14634 zf-RING_5: zinc-RING 85.3 0.87 1.9E-05 25.9 2.3 33 52-88 12-44 (44)
30 PF12861 zf-Apc11: Anaphase-pr 85.0 0.68 1.5E-05 31.0 1.9 57 34-93 25-84 (85)
31 KOG2177|consensus 84.6 0.39 8.4E-06 34.7 0.6 43 41-88 13-55 (386)
32 smart00184 RING Ring finger. E 83.8 1.1 2.3E-05 23.1 2.0 39 44-86 1-39 (39)
33 PHA02929 N1R/p28-like protein; 82.0 1.5 3.3E-05 34.2 3.1 47 41-91 174-227 (238)
34 smart00734 ZnF_Rad18 Rad18-lik 81.0 0.44 9.6E-06 24.9 -0.2 11 82-92 3-13 (26)
35 KOG3113|consensus 79.5 1.5 3.3E-05 35.1 2.3 56 36-97 106-164 (293)
36 PF00096 zf-C2H2: Zinc finger, 79.5 0.76 1.7E-05 22.3 0.4 11 81-91 1-11 (23)
37 KOG0801|consensus 79.3 0.96 2.1E-05 34.2 1.1 20 79-98 137-156 (205)
38 cd00730 rubredoxin Rubredoxin; 77.9 0.93 2E-05 27.3 0.5 13 77-89 31-43 (50)
39 PF00301 Rubredoxin: Rubredoxi 77.2 1.4 3E-05 26.2 1.2 14 76-89 30-43 (47)
40 PF13465 zf-H2C2_2: Zinc-finge 77.1 2.6 5.6E-05 21.6 2.0 18 74-91 8-25 (26)
41 KOG1493|consensus 75.5 0.76 1.6E-05 30.6 -0.3 36 55-93 47-83 (84)
42 PF05605 zf-Di19: Drought indu 73.2 0.92 2E-05 27.0 -0.4 16 80-95 2-17 (54)
43 TIGR00570 cdk7 CDK-activating 72.7 3.8 8.3E-05 33.3 3.0 51 43-96 5-59 (309)
44 COG5533 UBP5 Ubiquitin C-termi 72.6 1.4 3.1E-05 36.4 0.5 37 53-89 257-293 (415)
45 PF00641 zf-RanBP: Zn-finger i 70.7 2.4 5.3E-05 22.3 1.0 11 78-88 2-12 (30)
46 PF14447 Prok-RING_4: Prokaryo 70.2 3.6 7.8E-05 25.5 1.8 37 48-95 18-54 (55)
47 PLN00162 transport protein sec 69.7 1.1 2.5E-05 39.9 -0.7 34 53-90 52-85 (761)
48 PF13913 zf-C2HC_2: zinc-finge 69.4 1.1 2.4E-05 23.0 -0.5 16 80-95 2-17 (25)
49 COG1592 Rubrerythrin [Energy p 68.0 4.5 9.7E-05 30.1 2.2 12 79-90 133-144 (166)
50 PF09889 DUF2116: Uncharacteri 67.6 2.5 5.5E-05 26.4 0.7 16 81-96 4-19 (59)
51 KOG0311|consensus 67.3 0.37 8E-06 40.0 -3.9 66 33-101 33-101 (381)
52 KOG2817|consensus 66.9 4.3 9.3E-05 34.1 2.1 54 40-94 333-388 (394)
53 KOG1813|consensus 66.6 3.2 7E-05 33.7 1.3 54 33-91 233-286 (313)
54 PF12874 zf-met: Zinc-finger o 66.0 2.5 5.4E-05 20.8 0.4 11 81-91 1-11 (25)
55 KOG0317|consensus 64.4 7 0.00015 31.6 2.9 50 42-96 240-289 (293)
56 COG3024 Uncharacterized protei 64.2 3.4 7.5E-05 26.4 0.9 17 77-93 4-20 (65)
57 PF04710 Pellino: Pellino; In 64.0 2.3 4.9E-05 35.9 0.0 54 42-97 278-345 (416)
58 KOG0823|consensus 63.9 6.9 0.00015 30.6 2.6 54 41-96 47-100 (230)
59 PF03119 DNA_ligase_ZBD: NAD-d 63.3 1.6 3.5E-05 23.1 -0.7 10 82-91 1-10 (28)
60 PF02228 Gag_p19: Major core p 63.3 4.2 9E-05 27.3 1.2 20 67-86 45-64 (92)
61 PF04641 Rtf2: Rtf2 RING-finge 62.9 6.3 0.00014 30.6 2.3 32 41-74 34-65 (260)
62 PRK00418 DNA gyrase inhibitor; 62.6 4.2 9.1E-05 25.7 1.0 14 79-92 5-18 (62)
63 cd00729 rubredoxin_SM Rubredox 61.9 4.1 8.8E-05 22.4 0.8 11 80-90 2-12 (34)
64 cd01408 SIRT1 SIRT1: Eukaryoti 59.8 12 0.00025 28.7 3.2 37 59-97 121-157 (235)
65 PF14353 CpXC: CpXC protein 59.8 1.8 3.9E-05 29.8 -1.1 22 78-99 36-59 (128)
66 PRK01343 zinc-binding protein; 59.6 4.6 9.9E-05 25.1 0.8 16 76-91 5-20 (57)
67 TIGR01206 lysW lysine biosynth 59.3 4.4 9.5E-05 24.8 0.7 18 80-97 2-19 (54)
68 PF03966 Trm112p: Trm112p-like 58.9 9.3 0.0002 23.7 2.2 17 77-93 50-66 (68)
69 PF11793 FANCL_C: FANCL C-term 58.3 6.7 0.00015 24.7 1.4 14 80-93 55-68 (70)
70 PF03884 DUF329: Domain of unk 57.7 4.6 9.9E-05 25.0 0.6 13 80-92 2-14 (57)
71 PF12678 zf-rbx1: RING-H2 zinc 57.6 10 0.00023 23.9 2.3 31 53-87 43-73 (73)
72 COG4068 Uncharacterized protei 57.0 5.6 0.00012 25.2 0.9 18 79-96 7-24 (64)
73 cd00085 HNHc HNH nucleases; HN 55.5 7.2 0.00016 21.8 1.2 20 81-100 12-31 (57)
74 PRK00398 rpoP DNA-directed RNA 55.1 5.9 0.00013 22.8 0.7 13 80-92 21-33 (46)
75 KOG1986|consensus 54.2 4 8.6E-05 36.7 -0.2 33 54-90 53-85 (745)
76 KOG0287|consensus 53.9 4.1 8.8E-05 34.1 -0.1 59 40-104 22-81 (442)
77 PF13395 HNH_4: HNH endonuclea 52.8 6.8 0.00015 23.3 0.8 18 83-100 1-23 (54)
78 COG1773 Rubredoxin [Energy pro 51.4 6.1 0.00013 24.4 0.4 11 78-88 34-44 (55)
79 PF13453 zf-TFIIB: Transcripti 51.1 7.6 0.00017 21.8 0.8 9 82-90 1-9 (41)
80 PF14255 Cys_rich_CPXG: Cystei 50.8 7.2 0.00016 23.7 0.7 14 82-98 2-15 (52)
81 KOG4172|consensus 50.2 5.5 0.00012 25.0 0.1 38 51-91 14-54 (62)
82 COG5109 Uncharacterized conser 50.2 15 0.00032 30.5 2.6 52 41-94 336-390 (396)
83 KOG0289|consensus 50.1 11 0.00024 32.4 1.9 51 42-96 1-51 (506)
84 PF04780 DUF629: Protein of un 49.2 10 0.00022 32.5 1.5 23 68-90 45-67 (466)
85 PF14446 Prok-RING_1: Prokaryo 49.0 11 0.00023 23.3 1.2 19 80-98 5-24 (54)
86 PF13397 DUF4109: Domain of un 49.0 10 0.00022 26.3 1.3 43 34-93 21-63 (105)
87 smart00451 ZnF_U1 U1-like zinc 48.6 11 0.00025 19.6 1.2 13 79-91 2-14 (35)
88 PF12171 zf-C2H2_jaz: Zinc-fin 48.5 9.8 0.00021 19.2 0.9 12 80-91 1-12 (27)
89 PF06750 DiS_P_DiS: Bacterial 48.5 10 0.00022 25.2 1.2 19 78-96 31-49 (92)
90 smart00547 ZnF_RBZ Zinc finger 48.5 8.2 0.00018 19.3 0.6 10 79-88 1-10 (26)
91 COG2051 RPS27A Ribosomal prote 48.0 9.2 0.0002 24.6 0.8 25 58-90 23-48 (67)
92 PHA02926 zinc finger-like prot 47.3 20 0.00043 28.3 2.8 49 41-91 170-230 (242)
93 KOG0297|consensus 47.0 11 0.00025 31.0 1.5 56 38-97 18-73 (391)
94 COG4391 Uncharacterized protei 45.7 5.4 0.00012 25.3 -0.5 45 33-92 16-60 (62)
95 TIGR00100 hypA hydrogenase nic 45.2 15 0.00032 25.3 1.6 32 59-100 75-110 (115)
96 smart00507 HNHc HNH nucleases. 44.7 13 0.00029 20.2 1.1 18 81-99 11-28 (52)
97 PF06416 DUF1076: Protein of u 44.3 15 0.00033 25.8 1.5 35 40-77 39-79 (113)
98 COG5540 RING-finger-containing 43.6 17 0.00036 30.1 1.9 14 79-92 360-373 (374)
99 PF10571 UPF0547: Uncharacteri 43.3 11 0.00023 19.7 0.5 11 82-92 2-12 (26)
100 PF00645 zf-PARP: Poly(ADP-rib 42.3 22 0.00047 22.4 2.0 22 77-98 4-25 (82)
101 KOG0828|consensus 42.3 6.6 0.00014 34.3 -0.6 52 41-92 571-635 (636)
102 COG1579 Zn-ribbon protein, pos 42.1 17 0.00038 28.5 1.7 41 52-94 192-235 (239)
103 TIGR03831 YgiT_finger YgiT-typ 41.6 11 0.00025 20.7 0.5 14 77-90 29-42 (46)
104 PTZ00410 NAD-dependent SIR2; P 41.4 39 0.00085 27.8 3.8 35 60-96 153-187 (349)
105 TIGR02605 CxxC_CxxC_SSSS putat 41.0 4.9 0.00011 23.3 -1.1 26 58-88 9-34 (52)
106 PF13248 zf-ribbon_3: zinc-rib 40.3 15 0.00033 18.7 0.8 12 81-92 3-14 (26)
107 COG5047 SEC23 Vesicle coat com 40.3 8.7 0.00019 34.3 -0.2 16 75-90 71-86 (755)
108 KOG3800|consensus 39.9 10 0.00022 30.8 0.1 40 53-100 21-60 (300)
109 PF05191 ADK_lid: Adenylate ki 39.8 12 0.00026 20.9 0.4 13 80-92 1-13 (36)
110 KOG2879|consensus 38.9 28 0.0006 28.2 2.4 53 37-91 235-287 (298)
111 PRK14138 NAD-dependent deacety 38.8 29 0.00063 26.6 2.5 37 60-98 125-161 (244)
112 PF12230 PRP21_like_P: Pre-mRN 38.7 10 0.00022 28.7 0.0 18 78-95 166-183 (229)
113 KOG2932|consensus 38.4 9 0.00019 31.7 -0.4 50 49-108 98-147 (389)
114 PF04959 ARS2: Arsenite-resist 38.4 14 0.00029 28.5 0.6 18 77-94 74-91 (214)
115 PF10497 zf-4CXXC_R1: Zinc-fin 38.3 17 0.00036 24.8 1.0 12 77-88 58-69 (105)
116 PF14311 DUF4379: Domain of un 38.3 16 0.00034 21.6 0.8 13 77-89 25-37 (55)
117 PF10367 Vps39_2: Vacuolar sor 38.0 20 0.00044 23.0 1.3 19 79-97 77-95 (109)
118 PF02146 SIR2: Sir2 family; I 37.8 22 0.00048 25.5 1.6 33 59-93 110-142 (178)
119 smart00355 ZnF_C2H2 zinc finge 37.4 14 0.00031 17.1 0.4 11 81-91 1-11 (26)
120 KOG1312|consensus 36.9 15 0.00033 30.1 0.7 15 47-61 152-166 (341)
121 PRK07218 replication factor A; 36.7 47 0.001 28.0 3.6 63 20-101 268-330 (423)
122 PRK05452 anaerobic nitric oxid 36.5 14 0.00031 31.1 0.6 12 78-89 456-467 (479)
123 KOG2419|consensus 36.5 7.6 0.00016 35.2 -1.1 22 77-98 585-606 (975)
124 PF08209 Sgf11: Sgf11 (transcr 36.3 19 0.00042 19.8 0.9 14 78-91 2-15 (33)
125 PF07282 OrfB_Zn_ribbon: Putat 35.6 49 0.0011 20.0 2.8 51 20-91 7-57 (69)
126 COG3478 Predicted nucleic-acid 35.4 17 0.00037 23.3 0.6 13 78-90 2-14 (68)
127 PF02945 Endonuclease_7: Recom 35.3 17 0.00036 23.8 0.6 19 80-98 22-42 (81)
128 TIGR00375 conserved hypothetic 35.2 15 0.00033 30.5 0.5 11 80-91 259-269 (374)
129 PF01927 Mut7-C: Mut7-C RNAse 35.2 19 0.00041 25.5 0.9 13 78-90 122-134 (147)
130 PF13240 zinc_ribbon_2: zinc-r 35.0 23 0.00049 17.8 0.9 11 82-92 1-11 (23)
131 PF10058 DUF2296: Predicted in 34.9 20 0.00044 21.7 0.9 11 78-88 42-52 (54)
132 PF00628 PHD: PHD-finger; Int 34.4 4.5 9.7E-05 23.2 -2.1 26 61-87 24-49 (51)
133 KOG3039|consensus 34.0 31 0.00066 27.8 2.0 65 29-97 209-276 (303)
134 KOG3002|consensus 33.8 16 0.00034 29.5 0.4 44 41-91 48-91 (299)
135 COG4338 Uncharacterized protei 33.8 12 0.00025 22.9 -0.3 14 79-92 11-24 (54)
136 PF09237 GAGA: GAGA factor; I 33.1 17 0.00037 22.4 0.3 14 78-91 22-35 (54)
137 PF01844 HNH: HNH endonuclease 32.9 20 0.00043 19.8 0.6 17 83-99 1-18 (47)
138 PHA02565 49 recombination endo 32.6 26 0.00055 26.0 1.3 21 78-98 18-40 (157)
139 smart00746 TRASH metallochaper 32.4 28 0.0006 16.8 1.1 9 83-91 1-9 (39)
140 smart00659 RPOLCX RNA polymera 32.2 26 0.00056 20.3 1.0 15 77-91 16-30 (44)
141 PF10013 DUF2256: Uncharacteri 31.8 22 0.00047 20.9 0.6 15 78-92 6-20 (42)
142 PF09723 Zn-ribbon_8: Zinc rib 31.7 6.5 0.00014 22.4 -1.6 27 57-88 8-34 (42)
143 PF07754 DUF1610: Domain of un 31.6 31 0.00066 17.8 1.1 11 78-88 14-24 (24)
144 KOG4739|consensus 31.4 32 0.0007 26.9 1.7 37 52-95 15-52 (233)
145 PF10276 zf-CHCC: Zinc-finger 31.1 7 0.00015 22.5 -1.5 19 71-89 20-38 (40)
146 KOG0824|consensus 30.6 27 0.00057 28.7 1.1 47 41-91 7-53 (324)
147 COG0723 QcrA Rieske Fe-S prote 30.0 18 0.00039 26.2 0.1 29 55-87 103-131 (177)
148 cd01410 SIRT7 SIRT7: Eukaryoti 29.7 71 0.0015 23.9 3.3 38 59-98 100-138 (206)
149 COG5432 RAD18 RING-finger-cont 29.6 22 0.00048 29.3 0.6 52 40-96 24-75 (391)
150 COG0675 Transposase and inacti 29.6 59 0.0013 24.5 2.8 15 77-91 319-333 (364)
151 PRK00564 hypA hydrogenase nick 29.1 14 0.0003 25.5 -0.6 21 81-101 89-113 (117)
152 KOG2893|consensus 28.8 30 0.00065 27.9 1.2 30 59-90 15-44 (341)
153 PF14471 DUF4428: Domain of un 28.7 24 0.00051 21.1 0.4 13 82-94 1-13 (51)
154 PF13719 zinc_ribbon_5: zinc-r 28.7 25 0.00054 19.4 0.5 14 81-94 3-16 (37)
155 PF12756 zf-C2H2_2: C2H2 type 28.4 29 0.00062 21.6 0.8 13 79-91 49-61 (100)
156 TIGR02098 MJ0042_CXXC MJ0042 f 28.2 23 0.00051 19.1 0.3 13 81-93 3-15 (38)
157 PF14205 Cys_rich_KTR: Cystein 28.0 32 0.0007 21.3 0.9 11 80-90 4-14 (55)
158 KOG2660|consensus 27.7 33 0.00072 28.2 1.3 62 41-106 15-80 (331)
159 PF07812 TfuA: TfuA-like prote 27.4 58 0.0013 23.1 2.3 45 1-48 31-81 (120)
160 PRK12496 hypothetical protein; 26.7 26 0.00056 25.6 0.4 12 81-92 144-155 (164)
161 PRK00762 hypA hydrogenase nick 26.6 26 0.00057 24.4 0.4 22 79-100 91-116 (124)
162 PF04606 Ogr_Delta: Ogr/Delta- 26.5 28 0.00062 20.1 0.5 10 82-91 1-10 (47)
163 PF09538 FYDLN_acid: Protein o 26.5 30 0.00064 23.9 0.7 10 80-89 9-18 (108)
164 KOG4265|consensus 26.5 37 0.00081 28.1 1.3 12 80-91 325-336 (349)
165 PHA02768 hypothetical protein; 26.3 22 0.00047 21.9 -0.0 11 81-91 6-16 (55)
166 KOG1705|consensus 26.3 34 0.00073 23.6 0.9 18 79-96 26-43 (110)
167 COG3677 Transposase and inacti 26.3 30 0.00064 24.4 0.7 16 78-93 51-66 (129)
168 PF03854 zf-P11: P-11 zinc fin 26.0 25 0.00054 21.3 0.2 14 78-91 33-46 (50)
169 COG2956 Predicted N-acetylgluc 25.9 30 0.00066 28.9 0.7 16 76-91 364-379 (389)
170 smart00249 PHD PHD zinc finger 25.6 18 0.0004 19.3 -0.4 11 76-86 37-47 (47)
171 PRK00420 hypothetical protein; 25.5 44 0.00096 23.3 1.4 18 77-94 37-54 (112)
172 COG5243 HRD1 HRD ubiquitin lig 25.5 59 0.0013 27.7 2.3 41 45-93 304-347 (491)
173 smart00834 CxxC_CXXC_SSSS Puta 24.9 37 0.0008 18.3 0.8 28 58-90 9-36 (41)
174 COG4306 Uncharacterized protei 24.8 37 0.00081 24.7 1.0 23 70-92 29-51 (160)
175 KOG4623|consensus 24.7 30 0.00064 30.4 0.5 16 77-92 44-59 (611)
176 COG1379 PHP family phosphoeste 24.6 29 0.00064 29.0 0.4 14 78-91 263-276 (403)
177 KOG1984|consensus 24.1 20 0.00044 33.3 -0.6 36 51-90 335-370 (1007)
178 COG1655 Uncharacterized protei 23.8 35 0.00076 27.1 0.7 19 78-96 17-35 (267)
179 KOG3970|consensus 23.4 62 0.0013 25.8 2.0 44 52-95 57-110 (299)
180 PF06676 DUF1178: Protein of u 23.2 50 0.0011 24.1 1.4 14 75-88 27-40 (148)
181 PF12660 zf-TFIIIC: Putative z 23.1 28 0.0006 23.4 0.0 17 81-97 15-31 (99)
182 PRK12380 hydrogenase nickel in 23.0 35 0.00076 23.4 0.5 32 59-100 75-110 (113)
183 PF08274 PhnA_Zn_Ribbon: PhnA 22.9 26 0.00055 18.9 -0.2 11 82-92 4-14 (30)
184 PF09082 DUF1922: Domain of un 22.5 34 0.00074 22.0 0.4 21 76-97 16-36 (68)
185 PF09779 Ima1_N: Ima1 N-termin 22.3 53 0.0012 23.0 1.3 16 77-92 17-32 (131)
186 KOG0827|consensus 22.2 47 0.001 28.3 1.2 27 59-87 25-52 (465)
187 KOG0804|consensus 22.2 40 0.00087 29.1 0.8 40 43-88 177-219 (493)
188 PF14149 YhfH: YhfH-like prote 22.0 17 0.00036 20.8 -1.1 20 71-90 4-23 (37)
189 PF06170 DUF983: Protein of un 21.7 46 0.00099 22.0 0.8 15 80-94 8-22 (86)
190 KOG1952|consensus 21.5 60 0.0013 30.2 1.8 33 59-93 212-252 (950)
191 TIGR00416 sms DNA repair prote 21.2 44 0.00094 28.1 0.8 18 77-94 18-35 (454)
192 cd07692 Ig_CD3_epsilon Immunog 21.2 88 0.0019 19.8 2.0 20 33-52 3-22 (65)
193 PF04475 DUF555: Protein of un 21.1 49 0.0011 22.9 0.9 19 78-96 45-63 (102)
194 PF08271 TF_Zn_Ribbon: TFIIB z 20.9 51 0.0011 18.5 0.8 9 82-90 2-10 (43)
195 PF03660 PHF5: PHF5-like prote 20.7 36 0.00078 23.7 0.2 16 80-95 27-42 (106)
196 PF14354 Lar_restr_allev: Rest 20.6 46 0.001 19.6 0.6 9 82-90 5-13 (61)
197 KOG1973|consensus 20.6 34 0.00074 26.9 0.0 48 38-90 218-269 (274)
198 PRK11823 DNA repair protein Ra 20.5 46 0.001 27.8 0.8 18 77-94 18-35 (446)
199 COG4888 Uncharacterized Zn rib 20.5 49 0.0011 22.9 0.8 12 78-89 20-31 (104)
200 PF09256 BaffR-Tall_bind: BAFF 20.0 47 0.001 18.2 0.5 11 58-68 2-12 (31)
No 1
>KOG2169|consensus
Probab=99.94 E-value=3.8e-27 Score=201.40 Aligned_cols=105 Identities=41% Similarity=0.678 Sum_probs=100.0
Q ss_pred hHHHHhccCCCh--HHHH-HHHHHhccCCCCceeeeeeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCc
Q psy8140 4 IVSLIAHLMRDI--AFSR-YIKEKYNSENDSEIKTLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPK 80 (108)
Q Consensus 4 l~~l~~~~~~~~--~~~~-~i~~~~~~~~Dddi~~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~ 80 (108)
|++++.++.++. +.++ .|++++.+++|.||+.+...|||.|||+++||.+|+|+..|+|+||||+..|+++|+++++
T Consensus 266 lq~~~~~~~~~~~~~~s~~~~~~~l~~~~d~~i~tt~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~~lq~n~~~pT 345 (636)
T KOG2169|consen 266 LQRLKQNGKINRNLSQSDALIKKKLTAGPDSEIATTSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDALSYLQMNEQKPT 345 (636)
T ss_pred HHHHhccCCccCchhHhHHHhhcccccCCcccceeccceeEecCCcccceeecCCcccccccceecchhhhHHhccCCCe
Confidence 788999999998 7777 8888898899999999999999999999999999999999999999999999999999999
Q ss_pred eecccCCCcccCCCeeehhhhhhhhhcC
Q psy8140 81 WNCPVCDKVGHLILLCMAMIESVCLFLC 108 (108)
Q Consensus 81 W~CPiC~~~~~~~dL~iD~~~~~~l~~~ 108 (108)
|+||||++.+.+++|+||+|++.||.-|
T Consensus 346 W~CPVC~~~~~~e~l~iD~~~~~iL~~~ 373 (636)
T KOG2169|consen 346 WRCPVCQKAAPFEGLIIDGYFLNILQSC 373 (636)
T ss_pred eeCccCCccccccchhhhHHHHHHHhhc
Confidence 9999999999999999999999999754
No 2
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=99.93 E-value=3.8e-27 Score=143.22 Aligned_cols=50 Identities=46% Similarity=1.073 Sum_probs=36.4
Q ss_pred eeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCc
Q psy8140 40 SSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKV 89 (108)
Q Consensus 40 vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~ 89 (108)
|||+||||+++|++||||++|+|+||||+++||+++++++.|+||+|+++
T Consensus 1 vsL~CPls~~~i~~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 1 VSLRCPLSFQRIRIPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp EESB-TTTSSB-SSEEEETT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred CeeeCCCCCCEEEeCccCCcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 79999999999999999999999999999999999999999999999974
No 3
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=99.51 E-value=7.1e-15 Score=91.43 Aligned_cols=53 Identities=26% Similarity=0.466 Sum_probs=38.5
Q ss_pred CceeeeeeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceeccc
Q psy8140 31 SEIKTLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPV 85 (108)
Q Consensus 31 ddi~~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPi 85 (108)
|||+++...++++||||++.++.|++++.|.|. ||.++++++-++.+.-+||+
T Consensus 1 ddi~i~~~~~~~~CPiT~~~~~~PV~s~~C~H~--fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 1 DDIVIEGGTISLKCPITLQPFEDPVKSKKCGHT--FEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp S-----SSB--SB-TTTSSB-SSEEEESSS--E--EEHHHHHHHCTTTS-EE-SC
T ss_pred CceEEeccEeccCCCCcCChhhCCcCcCCCCCe--ecHHHHHHHHHhcCCCCCCC
Confidence 689999999999999999999999999999998 99999999988889999999
No 4
>KOG2979|consensus
Probab=98.79 E-value=1.2e-09 Score=85.64 Aligned_cols=60 Identities=20% Similarity=0.328 Sum_probs=53.5
Q ss_pred CceeeeeeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceeccc--CCCcccC
Q psy8140 31 SEIKTLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPV--CDKVGHL 92 (108)
Q Consensus 31 ddi~~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPi--C~~~~~~ 92 (108)
+++.+.+..+|++||+|++.|.+|++++.|.|+ ||.++.+++-....+.+||+ |..+...
T Consensus 166 ~e~~i~~e~fs~rdPis~~~I~nPviSkkC~Hv--ydrDsI~~~l~~~~~i~CPv~gC~~~~~~ 227 (262)
T KOG2979|consen 166 DEELIGQEVFSNRDPISKKPIVNPVISKKCGHV--YDRDSIMQILCDEITIRCPVLGCENPYYI 227 (262)
T ss_pred HHHHhhhhhhcccCchhhhhhhchhhhcCcCcc--hhhhhHHHHhccCceeecccccCCccccc
Confidence 457788999999999999999999999999999 99999999988888999999 7744443
No 5
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.42 E-value=2.8e-07 Score=56.25 Aligned_cols=57 Identities=14% Similarity=0.085 Sum_probs=48.7
Q ss_pred ecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCeeehhhhhh
Q psy8140 42 LICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCMAMIESV 103 (108)
Q Consensus 42 L~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~iD~~~~~ 103 (108)
+.|||++..|+.|+.. .|.|. |+.+.+.++..+ ...||+|++.++.++|+-+..+..
T Consensus 2 ~~Cpi~~~~~~~Pv~~-~~G~v--~~~~~i~~~~~~--~~~cP~~~~~~~~~~l~~~~~l~~ 58 (63)
T smart00504 2 FLCPISLEVMKDPVIL-PSGQT--YERRAIEKWLLS--HGTDPVTGQPLTHEDLIPNLALKS 58 (63)
T ss_pred cCCcCCCCcCCCCEEC-CCCCE--EeHHHHHHHHHH--CCCCCCCcCCCChhhceeCHHHHH
Confidence 6899999999999987 67888 999999988765 458999999999999988765543
No 6
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=98.16 E-value=5.9e-07 Score=70.22 Aligned_cols=69 Identities=19% Similarity=0.202 Sum_probs=62.6
Q ss_pred CceeeeeeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceeccc--CCCcccCCCeeehhhh
Q psy8140 31 SEIKTLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPV--CDKVGHLILLCMAMIE 101 (108)
Q Consensus 31 ddi~~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPi--C~~~~~~~dL~iD~~~ 101 (108)
|+|.+.+..++++||||.+++..|.-++.|+|. ||.+.+...-+-.++--||. |++....+.++-|.++
T Consensus 179 d~i~I~~~~~~nrCpitl~p~~~pils~kcnh~--~e~D~I~~~lq~~~trvcp~~~Csq~~~~~~~v~d~Il 249 (275)
T COG5627 179 DKILIHQELLSNRCPITLNPDFYPILSSKCNHK--PEMDLINKKLQVECTRVCPRLICSQKEVVDPYVCDHIL 249 (275)
T ss_pred hhhhhhhhhhcccCCcccCcchhHHHHhhhccc--ccHHHHHHHhcCCceeecchhhcchheeccchhhhHHH
Confidence 678999999999999999999999999999999 99999988877778889998 9998888888877665
No 7
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=97.99 E-value=7.3e-06 Score=52.48 Aligned_cols=57 Identities=14% Similarity=0.094 Sum_probs=43.1
Q ss_pred eecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCeeehhhh
Q psy8140 41 SLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCMAMIE 101 (108)
Q Consensus 41 sL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~iD~~~ 101 (108)
.|.||||+..|+.||....+ |. ||..++.....+ ..-.||+|+++++.++|+-+.-+
T Consensus 4 ~f~CpIt~~lM~dPVi~~~G-~t--yer~~I~~~l~~-~~~~~P~t~~~l~~~~l~pn~~L 60 (73)
T PF04564_consen 4 EFLCPITGELMRDPVILPSG-HT--YERSAIERWLEQ-NGGTDPFTRQPLSESDLIPNRAL 60 (73)
T ss_dssp GGB-TTTSSB-SSEEEETTS-EE--EEHHHHHHHHCT-TSSB-TTT-SB-SGGGSEE-HHH
T ss_pred ccCCcCcCcHhhCceeCCcC-CE--EcHHHHHHHHHc-CCCCCCCCCCcCCcccceECHHH
Confidence 37899999999999998766 87 999999887766 56799999999999999876544
No 8
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=96.89 E-value=0.001 Score=50.47 Aligned_cols=68 Identities=18% Similarity=0.320 Sum_probs=47.3
Q ss_pred cCCCCceeeeeeeeeecCCCccccccccccccccCccceecHH-HHHHHh-----------cCCCceecccCCCcccCCC
Q psy8140 27 SENDSEIKTLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGA-TFIKMN-----------ELKPKWNCPVCDKVGHLIL 94 (108)
Q Consensus 27 ~~~Dddi~~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~-~fl~~~-----------~~~~~W~CPiC~~~~~~~d 94 (108)
+|+||...+.. .=.+.|||-+..++.|+-. .|.|.-|+.-. .|+... ..++..+||+|...++..+
T Consensus 5 ~~~~~~~~~~~-~~~~~CpICld~~~dPVvT-~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 5 KDEDDTTLVDS-GGDFDCNICLDQVRDPVVT-LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred cccccceeccC-CCccCCccCCCcCCCcEEc-CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 34444444332 2358999999999999885 79999777644 355432 1345689999999998877
Q ss_pred ee
Q psy8140 95 LC 96 (108)
Q Consensus 95 L~ 96 (108)
|+
T Consensus 83 Lv 84 (193)
T PLN03208 83 LV 84 (193)
T ss_pred EE
Confidence 75
No 9
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.55 E-value=0.0021 Score=52.39 Aligned_cols=77 Identities=23% Similarity=0.317 Sum_probs=51.5
Q ss_pred HHHHHHHhccCCCCcee-eeeeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCC-cccCCCe
Q psy8140 18 SRYIKEKYNSENDSEIK-TLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDK-VGHLILL 95 (108)
Q Consensus 18 ~~~i~~~~~~~~Dddi~-~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~-~~~~~dL 95 (108)
.|+-++.+..++|. |- ...-.+||+||+....+++|+|..-|.|. |--+. ++...-..-++||.|.+ .+-++.|
T Consensus 251 Yq~r~~a~~~~~Dq-v~k~~~~~i~LkCplc~~Llrnp~kT~cC~~~--fc~ec-i~~al~dsDf~CpnC~rkdvlld~l 326 (427)
T COG5222 251 YQQRTKAVAEIPDQ-VYKMQPPNISLKCPLCHCLLRNPMKTPCCGHT--FCDEC-IGTALLDSDFKCPNCSRKDVLLDGL 326 (427)
T ss_pred HHHHHHhhhhCchh-hhccCCCCccccCcchhhhhhCcccCccccch--HHHHH-HhhhhhhccccCCCcccccchhhcc
Confidence 33334444445554 43 33456899999999999999999999999 65553 33334456699999986 4444544
Q ss_pred eeh
Q psy8140 96 CMA 98 (108)
Q Consensus 96 ~iD 98 (108)
.-|
T Consensus 327 ~pD 329 (427)
T COG5222 327 TPD 329 (427)
T ss_pred Ccc
Confidence 443
No 10
>PF04641 Rtf2: Rtf2 RING-finger
Probab=96.47 E-value=0.0031 Score=49.04 Aligned_cols=55 Identities=18% Similarity=0.312 Sum_probs=42.8
Q ss_pred eeeeecCCCccccccc---cccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCeee
Q psy8140 38 LTSSLICPLGKMRMAF---PTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCM 97 (108)
Q Consensus 38 ~~vsL~CPlS~~ri~~---P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~i 97 (108)
....+.||+|+..|.- -+=-..|.|+ |-..++-++. ..|.||+|++++.-+|+++
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V--~s~~alke~k---~~~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCV--FSEKALKELK---KSKKCPVCGKPFTEEDIIP 167 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCE--eeHHHHHhhc---ccccccccCCccccCCEEE
Confidence 4567899999998832 2223589998 7777777763 5799999999999998874
No 11
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.01 E-value=0.005 Score=39.36 Aligned_cols=58 Identities=17% Similarity=0.280 Sum_probs=25.2
Q ss_pred eecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCeeehhhhhhh
Q psy8140 41 SLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCMAMIESVC 104 (108)
Q Consensus 41 sL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~iD~~~~~~ 104 (108)
.|+|+.-...|+.|+--..|.|.-|=.-. ...-+ -.||+|..++...|+++..-+..+
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci-----~~~~~-~~CPvC~~Paw~qD~~~NrqLd~~ 64 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCI-----RDCIG-SECPVCHTPAWIQDIQINRQLDSM 64 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTG-----GGGTT-TB-SSS--B-S-SS----HHHHHH
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHh-----HHhcC-CCCCCcCChHHHHHHHhhhhhhcc
Confidence 48999999999999998899998332111 11222 359999999999999998766543
No 12
>KOG2164|consensus
Probab=96.00 E-value=0.0044 Score=52.89 Aligned_cols=55 Identities=22% Similarity=0.501 Sum_probs=45.1
Q ss_pred eecCCCccccccccccccccCccceec-HHHHHHHhcCCCceecccCCCcccCCCee
Q psy8140 41 SLICPLGKMRMAFPTKASTCAHLQCFD-GATFIKMNELKPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 41 sL~CPlS~~ri~~P~Rg~~C~H~qCFD-l~~fl~~~~~~~~W~CPiC~~~~~~~dL~ 96 (108)
...|||=+-.-..|+|.. |.|+-||. +-.|+......+.-.||+|...+++.||.
T Consensus 186 ~~~CPICL~~~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~ 241 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLL 241 (513)
T ss_pred CCcCCcccCCCCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhcccccee
Confidence 899999999999999998 99997664 34455555445667899999999998876
No 13
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=95.48 E-value=0.016 Score=31.63 Aligned_cols=44 Identities=25% Similarity=0.449 Sum_probs=29.4
Q ss_pred CCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcc
Q psy8140 44 CPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 44 CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~ 90 (108)
||+=...+..|+.-..|.|. |-..-+..+.++ +..+||+|++.+
T Consensus 2 C~iC~~~~~~~~~~~~C~H~--~c~~C~~~~~~~-~~~~Cp~C~~~~ 45 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHV--FCRSCIDKWLKS-GKNTCPLCRTPI 45 (45)
T ss_pred CCcCchhhhCceEecCCCCh--hcHHHHHHHHHh-CcCCCCCCCCcC
Confidence 66666667778887789999 444433333322 567899998753
No 14
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=94.83 E-value=0.022 Score=31.86 Aligned_cols=39 Identities=31% Similarity=0.634 Sum_probs=27.3
Q ss_pred CCCccccccccccccccCccceecHHHHHHHhcCCCceecccC
Q psy8140 44 CPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVC 86 (108)
Q Consensus 44 CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC 86 (108)
|||=+..++.|+....|.|+-| .+=+.++.+. ..+||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC--~~C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFC--KECIEKYLEK--NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEE--HHHHHHHHHC--TSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchh--HHHHHHHHHC--cCCCcCC
Confidence 5677788889999999999944 4445555444 3799998
No 15
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=93.41 E-value=0.058 Score=31.53 Aligned_cols=39 Identities=26% Similarity=0.652 Sum_probs=16.8
Q ss_pred CCCccccccc----cccccccCccceecHHHHHHHhcCCCceecc
Q psy8140 44 CPLGKMRMAF----PTKASTCAHLQCFDGATFIKMNELKPKWNCP 84 (108)
Q Consensus 44 CPlS~~ri~~----P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CP 84 (108)
||+++. +.. |+.=. |.|.-|.+.-.=|..+...++.+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence 788888 766 77754 9999554444333333335789998
No 16
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=92.50 E-value=0.093 Score=29.14 Aligned_cols=41 Identities=27% Similarity=0.495 Sum_probs=30.1
Q ss_pred CCCccccccccccccccCccceecHHHHHHHhcCCCceecccC
Q psy8140 44 CPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVC 86 (108)
Q Consensus 44 CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC 86 (108)
|||=...+..|.+...|.|. |-..=+.++.+..+.-+||.|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~--fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHS--FCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEE--EEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCc--chHHHHHHHHHhcCCccCCcC
Confidence 45666777888889999999 655555555444677889988
No 17
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=92.38 E-value=0.076 Score=30.57 Aligned_cols=42 Identities=21% Similarity=0.463 Sum_probs=23.6
Q ss_pred CCCccccccccccccccCccceecHHHHHHHhcCCCceecccC
Q psy8140 44 CPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVC 86 (108)
Q Consensus 44 CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC 86 (108)
|||=+..++.|+. ..|.|.-|+.=-.=+........+.||.|
T Consensus 1 CpiC~~~~~~Pv~-l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVS-LPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccc-cCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 6777888889987 69999966553322222222333899998
No 18
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.02 E-value=0.22 Score=41.51 Aligned_cols=63 Identities=22% Similarity=0.320 Sum_probs=44.9
Q ss_pred eeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCeeehhhhhhh
Q psy8140 37 ELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCMAMIESVC 104 (108)
Q Consensus 37 ~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~iD~~~~~~ 104 (108)
...-.+.||+=+..+..|+. ..|.|.-|..--. ..... ...||+|...+....|+-+..+..+
T Consensus 22 ~Le~~l~C~IC~d~~~~Pvi-tpCgH~FCs~CI~--~~l~~--~~~CP~Cr~~~~~~~Lr~N~~L~~i 84 (397)
T TIGR00599 22 PLDTSLRCHICKDFFDVPVL-TSCSHTFCSLCIR--RCLSN--QPKCPLCRAEDQESKLRSNWLVSEI 84 (397)
T ss_pred ccccccCCCcCchhhhCccC-CCCCCchhHHHHH--HHHhC--CCCCCCCCCccccccCccchHHHHH
Confidence 34457899999999999995 6899996554322 22222 2489999999987788766655544
No 19
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=91.38 E-value=0.14 Score=29.01 Aligned_cols=40 Identities=23% Similarity=0.525 Sum_probs=24.8
Q ss_pred CCCcccccc--ccccccccCccceecHHHHHHHhcCCCceecccCC
Q psy8140 44 CPLGKMRMA--FPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCD 87 (108)
Q Consensus 44 CPlS~~ri~--~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~ 87 (108)
|||-+..+. ..+....|.|. |-.+=+.++.+++ .+||+|.
T Consensus 3 C~IC~~~~~~~~~~~~l~C~H~--fh~~Ci~~~~~~~--~~CP~CR 44 (44)
T PF13639_consen 3 CPICLEEFEDGEKVVKLPCGHV--FHRSCIKEWLKRN--NSCPVCR 44 (44)
T ss_dssp ETTTTCBHHTTSCEEEETTSEE--EEHHHHHHHHHHS--SB-TTTH
T ss_pred CcCCChhhcCCCeEEEccCCCe--eCHHHHHHHHHhC--CcCCccC
Confidence 555555552 34445569998 7777777665543 3999993
No 20
>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=91.29 E-value=0.069 Score=29.29 Aligned_cols=12 Identities=42% Similarity=1.179 Sum_probs=9.8
Q ss_pred CceecccCCCcc
Q psy8140 79 PKWNCPVCDKVG 90 (108)
Q Consensus 79 ~~W~CPiC~~~~ 90 (108)
..|.||+|+..-
T Consensus 16 ~~~~CP~Cg~~~ 27 (33)
T cd00350 16 APWVCPVCGAPK 27 (33)
T ss_pred CCCcCcCCCCcH
Confidence 779999998743
No 21
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=90.82 E-value=0.029 Score=32.10 Aligned_cols=21 Identities=19% Similarity=0.643 Sum_probs=13.3
Q ss_pred HHHHHhcCCCceecccCCCcc
Q psy8140 70 TFIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 70 ~fl~~~~~~~~W~CPiC~~~~ 90 (108)
.|.++.....+|.||+|+..-
T Consensus 14 p~~~~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 14 PFCQFDDGGKTWICNFCGTKN 34 (40)
T ss_dssp TTSEEETTTTEEEETTT--EE
T ss_pred CcceEcCCCCEEECcCCCCcC
Confidence 344445567899999999754
No 22
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=89.90 E-value=0.35 Score=28.18 Aligned_cols=44 Identities=23% Similarity=0.414 Sum_probs=26.0
Q ss_pred cCCCccccccccccccccCcc-ceecHHHHHHHhcCCCceecccCCCccc
Q psy8140 43 ICPLGKMRMAFPTKASTCAHL-QCFDGATFIKMNELKPKWNCPVCDKVGH 91 (108)
Q Consensus 43 ~CPlS~~ri~~P~Rg~~C~H~-qCFDl~~fl~~~~~~~~W~CPiC~~~~~ 91 (108)
.|++=+.....+ --..|+|. -|++ =+.++.+ ...+||+|.+++.
T Consensus 4 ~C~iC~~~~~~~-~~~pCgH~~~C~~--C~~~~~~--~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRDV-VLLPCGHLCFCEE--CAERLLK--RKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSSE-EEETTCEEEEEHH--HHHHHHH--TTSBBTTTTBB-S
T ss_pred CCccCCccCCce-EEeCCCChHHHHH--HhHHhcc--cCCCCCcCChhhc
Confidence 455555555543 33469998 4444 3333333 6789999999874
No 23
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.18 E-value=0.24 Score=39.45 Aligned_cols=56 Identities=20% Similarity=0.245 Sum_probs=45.7
Q ss_pred eeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCeeeh
Q psy8140 40 SSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCMA 98 (108)
Q Consensus 40 vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~iD 98 (108)
-+.+|+|=...+..|++. .|.|+ |-+.=.+.+...+..-.||.|...+.+.++.|+
T Consensus 214 ~d~kC~lC~e~~~~ps~t-~CgHl--FC~~Cl~~~~t~~k~~~CplCRak~~pk~viil 269 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCT-PCGHL--FCLSCLLISWTKKKYEFCPLCRAKVYPKKVIIL 269 (271)
T ss_pred cccceeeeecccCCcccc-cccch--hhHHHHHHHHHhhccccCchhhhhccchhhhee
Confidence 367899999999999986 89999 777777776555555669999999999888665
No 24
>KOG0320|consensus
Probab=87.68 E-value=0.28 Score=37.18 Aligned_cols=50 Identities=26% Similarity=0.477 Sum_probs=33.6
Q ss_pred ecCCCccccccccc-cccccCccceecHHHHHHHhcCCCceecccCCCcccCCCe
Q psy8140 42 LICPLGKMRMAFPT-KASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILL 95 (108)
Q Consensus 42 L~CPlS~~ri~~P~-Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL 95 (108)
.+||+=+....-=+ -+..|.|+ |-..= ++ ...+..-+||+|++.++-.++
T Consensus 132 ~~CPiCl~~~sek~~vsTkCGHv--FC~~C-ik-~alk~~~~CP~C~kkIt~k~~ 182 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVPVSTKCGHV--FCSQC-IK-DALKNTNKCPTCRKKITHKQF 182 (187)
T ss_pred cCCCceecchhhccccccccchh--HHHHH-HH-HHHHhCCCCCCcccccchhhh
Confidence 89998876665544 45899999 43332 11 223567899999998765543
No 25
>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=87.22 E-value=0.27 Score=23.48 Aligned_cols=11 Identities=36% Similarity=1.081 Sum_probs=7.5
Q ss_pred eecccCCCccc
Q psy8140 81 WNCPVCDKVGH 91 (108)
Q Consensus 81 W~CPiC~~~~~ 91 (108)
|+||+|++.+.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 79999998764
No 26
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=86.42 E-value=0.74 Score=32.84 Aligned_cols=42 Identities=14% Similarity=0.350 Sum_probs=29.2
Q ss_pred eeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCC
Q psy8140 37 ELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLI 93 (108)
Q Consensus 37 ~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~ 93 (108)
.......|| +|.+. |+....+......+...||.|+..+...
T Consensus 95 ~~~~~Y~Cp-------------~C~~~--y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 95 TNNAYYKCP-------------NCQSK--YTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred cCCcEEECc-------------CCCCE--eeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 334567888 58765 7766666553346779999999987544
No 27
>KOG0978|consensus
Probab=86.05 E-value=0.22 Score=44.31 Aligned_cols=56 Identities=18% Similarity=0.329 Sum_probs=40.8
Q ss_pred eeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCee
Q psy8140 37 ELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 37 ~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~ 96 (108)
...=-|+||.=..|-+.-|- ..|.|+-||+- ++.....+.-+||.|+..+...|+.
T Consensus 639 ~yK~~LkCs~Cn~R~Kd~vI-~kC~H~FC~~C---vq~r~etRqRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 639 EYKELLKCSVCNTRWKDAVI-TKCGHVFCEEC---VQTRYETRQRKCPKCNAAFGANDVH 694 (698)
T ss_pred HHHhceeCCCccCchhhHHH-HhcchHHHHHH---HHHHHHHhcCCCCCCCCCCCccccc
Confidence 34556999998877766554 48999977763 3333345566899999999998874
No 28
>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=85.71 E-value=0.57 Score=27.98 Aligned_cols=24 Identities=17% Similarity=0.326 Sum_probs=11.1
Q ss_pred HHHHHHhcCCCceecccCCCcccCC
Q psy8140 69 ATFIKMNELKPKWNCPVCDKVGHLI 93 (108)
Q Consensus 69 ~~fl~~~~~~~~W~CPiC~~~~~~~ 93 (108)
..++..-..... .||+|++++..+
T Consensus 10 ~k~i~~l~~~~~-~CPlC~r~l~~e 33 (54)
T PF04423_consen 10 KKYIEELKEAKG-CCPLCGRPLDEE 33 (54)
T ss_dssp HHHHHHHTT-SE-E-TTT--EE-HH
T ss_pred HHHHHHHhcCCC-cCCCCCCCCCHH
Confidence 334444444443 999999988643
No 29
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=85.31 E-value=0.87 Score=25.94 Aligned_cols=33 Identities=24% Similarity=0.640 Sum_probs=22.2
Q ss_pred cccccccccCccceecHHHHHHHhcCCCceecccCCC
Q psy8140 52 AFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDK 88 (108)
Q Consensus 52 ~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~ 88 (108)
+.+.+-..|.|. |=.+=+..+. ...-.||+|++
T Consensus 12 ~~~~~l~~CgH~--~C~~C~~~~~--~~~~~CP~C~k 44 (44)
T PF14634_consen 12 ERRPRLTSCGHI--FCEKCLKKLK--GKSVKCPICRK 44 (44)
T ss_pred CCCeEEcccCCH--HHHHHHHhhc--CCCCCCcCCCC
Confidence 456778899998 4333333333 56789999985
No 30
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=84.97 E-value=0.68 Score=30.99 Aligned_cols=57 Identities=21% Similarity=0.360 Sum_probs=34.3
Q ss_pred eeeeeeeeecCCCccccc-ccc-ccccccCccceecHHHHHHH-hcCCCceecccCCCcccCC
Q psy8140 34 KTLELTSSLICPLGKMRM-AFP-TKASTCAHLQCFDGATFIKM-NELKPKWNCPVCDKVGHLI 93 (108)
Q Consensus 34 ~~~~~~vsL~CPlS~~ri-~~P-~Rg~~C~H~qCFDl~~fl~~-~~~~~~W~CPiC~~~~~~~ 93 (108)
.+=...+.-.||--+.+= .-| +.| .|+|. |-+-=+++. +.++.+-+||.|.+...+.
T Consensus 25 gICr~~fdg~Cp~Ck~Pgd~Cplv~g-~C~H~--FH~hCI~kWl~~~~~~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 25 GICRMPFDGCCPDCKFPGDDCPLVWG-KCSHN--FHMHCILKWLSTQSSKGQCPMCRQPWKFK 84 (85)
T ss_pred eeEecccccCCCCccCCCCCCceeec-cCccH--HHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence 344555666676432211 112 333 49997 888777764 3334567999999987654
No 31
>KOG2177|consensus
Probab=84.62 E-value=0.39 Score=34.74 Aligned_cols=43 Identities=30% Similarity=0.494 Sum_probs=33.2
Q ss_pred eecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCC
Q psy8140 41 SLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDK 88 (108)
Q Consensus 41 sL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~ 88 (108)
-+.|||-...++.| +...|.|.-|..-..= ... ....||.|..
T Consensus 13 ~~~C~iC~~~~~~p-~~l~C~H~~c~~C~~~--~~~--~~~~Cp~cr~ 55 (386)
T KOG2177|consen 13 ELTCPICLEYFREP-VLLPCGHNFCRACLTR--SWE--GPLSCPVCRP 55 (386)
T ss_pred cccChhhHHHhhcC-ccccccchHhHHHHHH--hcC--CCcCCcccCC
Confidence 47899999999999 8888999955544332 222 6699999994
No 32
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=83.76 E-value=1.1 Score=23.09 Aligned_cols=39 Identities=23% Similarity=0.562 Sum_probs=20.2
Q ss_pred CCCccccccccccccccCccceecHHHHHHHhcCCCceecccC
Q psy8140 44 CPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVC 86 (108)
Q Consensus 44 CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC 86 (108)
||+-+...+ +..-..|.|.-|++ -+-.+.. ....+||+|
T Consensus 1 C~iC~~~~~-~~~~~~C~H~~c~~--C~~~~~~-~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELK-DPVVLPCGHTFCRS--CIRKWLK-SGNNTCPIC 39 (39)
T ss_pred CCcCccCCC-CcEEecCCChHHHH--HHHHHHH-hCcCCCCCC
Confidence 344444433 33334699984433 3333222 455679987
No 33
>PHA02929 N1R/p28-like protein; Provisional
Probab=82.00 E-value=1.5 Score=34.21 Aligned_cols=47 Identities=21% Similarity=0.264 Sum_probs=31.4
Q ss_pred eecCCCccccccccc-------cccccCccceecHHHHHHHhcCCCceecccCCCccc
Q psy8140 41 SLICPLGKMRMAFPT-------KASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGH 91 (108)
Q Consensus 41 sL~CPlS~~ri~~P~-------Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~ 91 (108)
...|||-+..+..|. .-..|.|. |...=+.....+ .-.||+|.+.+.
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~--FC~~CI~~Wl~~--~~tCPlCR~~~~ 227 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHV--FCIECIDIWKKE--KNTCPVCRTPFI 227 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCc--ccHHHHHHHHhc--CCCCCCCCCEee
Confidence 368999988876542 23479998 666644444333 347999998764
No 34
>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=80.98 E-value=0.44 Score=24.90 Aligned_cols=11 Identities=36% Similarity=0.721 Sum_probs=9.1
Q ss_pred ecccCCCcccC
Q psy8140 82 NCPVCDKVGHL 92 (108)
Q Consensus 82 ~CPiC~~~~~~ 92 (108)
.||||++.++.
T Consensus 3 ~CPiC~~~v~~ 13 (26)
T smart00734 3 QCPVCFREVPE 13 (26)
T ss_pred cCCCCcCcccH
Confidence 69999998843
No 35
>KOG3113|consensus
Probab=79.54 E-value=1.5 Score=35.09 Aligned_cols=56 Identities=16% Similarity=0.294 Sum_probs=42.7
Q ss_pred eeeeeeecCCCccccccccccc---cccCccceecHHHHHHHhcCCCceecccCCCcccCCCeee
Q psy8140 36 LELTSSLICPLGKMRMAFPTKA---STCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCM 97 (108)
Q Consensus 36 ~~~~vsL~CPlS~~ri~~P~Rg---~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~i 97 (108)
+....-.+||+++-.|.---|. ..|.|+ |...+.-+. +.-.|++|+....-+|.+|
T Consensus 106 D~~~a~fiCPvtgleMng~~~F~~l~~CGcV--~SerAlKei----kas~C~~C~a~y~~~dvIv 164 (293)
T KOG3113|consen 106 DTQRARFICPVTGLEMNGKYRFCALRCCGCV--FSERALKEI----KASVCHVCGAAYQEDDVIV 164 (293)
T ss_pred ccccceeecccccceecceEEEEEEecccee--ccHHHHHHh----hhccccccCCcccccCeEe
Confidence 3456779999999887654443 568998 888885443 4678999999999888876
No 36
>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=79.48 E-value=0.76 Score=22.29 Aligned_cols=11 Identities=36% Similarity=1.074 Sum_probs=9.3
Q ss_pred eecccCCCccc
Q psy8140 81 WNCPVCDKVGH 91 (108)
Q Consensus 81 W~CPiC~~~~~ 91 (108)
|+||.|++.+.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 68999998775
No 37
>KOG0801|consensus
Probab=79.34 E-value=0.96 Score=34.18 Aligned_cols=20 Identities=30% Similarity=0.390 Sum_probs=17.0
Q ss_pred CceecccCCCcccCCCeeeh
Q psy8140 79 PKWNCPVCDKVGHLILLCMA 98 (108)
Q Consensus 79 ~~W~CPiC~~~~~~~dL~iD 98 (108)
.-.+||||+|.+..+|+++-
T Consensus 137 ~g~KCPvC~K~V~sDd~e~H 156 (205)
T KOG0801|consen 137 SGMKCPVCHKVVPSDDAEIH 156 (205)
T ss_pred CCccCCccccccCCCcceEE
Confidence 34899999999999998764
No 38
>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=77.89 E-value=0.93 Score=27.30 Aligned_cols=13 Identities=46% Similarity=1.168 Sum_probs=10.2
Q ss_pred CCCceecccCCCc
Q psy8140 77 LKPKWNCPVCDKV 89 (108)
Q Consensus 77 ~~~~W~CPiC~~~ 89 (108)
....|.||+|+..
T Consensus 31 Lp~~w~CP~C~a~ 43 (50)
T cd00730 31 LPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCCCCc
Confidence 3457999999864
No 39
>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=77.20 E-value=1.4 Score=26.23 Aligned_cols=14 Identities=43% Similarity=1.184 Sum_probs=8.4
Q ss_pred cCCCceecccCCCc
Q psy8140 76 ELKPKWNCPVCDKV 89 (108)
Q Consensus 76 ~~~~~W~CPiC~~~ 89 (108)
.....|.||+|+..
T Consensus 30 ~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 30 DLPDDWVCPVCGAP 43 (47)
T ss_dssp GS-TT-B-TTTSSB
T ss_pred HCCCCCcCcCCCCc
Confidence 34568999999865
No 40
>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=77.08 E-value=2.6 Score=21.56 Aligned_cols=18 Identities=22% Similarity=0.508 Sum_probs=12.9
Q ss_pred HhcCCCceecccCCCccc
Q psy8140 74 MNELKPKWNCPVCDKVGH 91 (108)
Q Consensus 74 ~~~~~~~W~CPiC~~~~~ 91 (108)
.......++||.|++.+.
T Consensus 8 ~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 8 THTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHSSSSSEEESSSSEEES
T ss_pred hcCCCCCCCCCCCcCeeC
Confidence 334456799999998653
No 41
>KOG1493|consensus
Probab=75.54 E-value=0.76 Score=30.56 Aligned_cols=36 Identities=22% Similarity=0.530 Sum_probs=27.2
Q ss_pred ccccccCccceecHHHHHH-HhcCCCceecccCCCcccCC
Q psy8140 55 TKASTCAHLQCFDGATFIK-MNELKPKWNCPVCDKVGHLI 93 (108)
Q Consensus 55 ~Rg~~C~H~qCFDl~~fl~-~~~~~~~W~CPiC~~~~~~~ 93 (108)
+-| .|.|. |-+--.++ .+..+++-+||.|.+...+.
T Consensus 47 v~G-~C~h~--fh~hCI~~wl~~~tsq~~CPmcRq~~~~~ 83 (84)
T KOG1493|consen 47 VWG-YCLHA--FHAHCILKWLNTPTSQGQCPMCRQTWQFK 83 (84)
T ss_pred HHH-HHHHH--HHHHHHHHHhcCccccccCCcchheeEec
Confidence 345 89997 77776666 46678889999999877654
No 42
>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=73.20 E-value=0.92 Score=27.03 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=9.6
Q ss_pred ceecccCCCcccCCCe
Q psy8140 80 KWNCPVCDKVGHLILL 95 (108)
Q Consensus 80 ~W~CPiC~~~~~~~dL 95 (108)
.+.||+|++.+...+|
T Consensus 2 ~f~CP~C~~~~~~~~L 17 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSL 17 (54)
T ss_pred CcCCCCCCCccCHHHH
Confidence 4567777775544443
No 43
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.72 E-value=3.8 Score=33.28 Aligned_cols=51 Identities=22% Similarity=0.413 Sum_probs=30.6
Q ss_pred cCCCccc-cccccc---cccccCccceecHHHHHHHhcCCCceecccCCCcccCCCee
Q psy8140 43 ICPLGKM-RMAFPT---KASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 43 ~CPlS~~-ri~~P~---Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~ 96 (108)
.||+=+. +...|- -...|.|.-|- +-+...-..+.-.||+|++.+...++.
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~---sCv~~l~~~~~~~CP~C~~~lrk~~fr 59 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTLCE---SCVDLLFVRGSGSCPECDTPLRKNNFR 59 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcccH---HHHHHHhcCCCCCCCCCCCccchhhcc
Confidence 5676544 233443 22269998553 334332344567999999999888743
No 44
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=72.65 E-value=1.4 Score=36.45 Aligned_cols=37 Identities=24% Similarity=0.428 Sum_probs=27.3
Q ss_pred ccccccccCccceecHHHHHHHhcCCCceecccCCCc
Q psy8140 53 FPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKV 89 (108)
Q Consensus 53 ~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~ 89 (108)
-|-+-+.|.-.+|||.-.=-+.-+-...|.||.|++.
T Consensus 257 p~~~v~~~~l~eC~~~f~~~e~L~g~d~W~CpkC~~k 293 (415)
T COG5533 257 PPYEVVQLGLQECIDRFYEEEKLEGKDAWRCPKCGRK 293 (415)
T ss_pred ccchheeecHHHHHHHhhhHHhhcCcccccCchhccc
Confidence 3557788887779886554444556789999999964
No 45
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=70.75 E-value=2.4 Score=22.27 Aligned_cols=11 Identities=36% Similarity=1.253 Sum_probs=9.0
Q ss_pred CCceecccCCC
Q psy8140 78 KPKWNCPVCDK 88 (108)
Q Consensus 78 ~~~W~CPiC~~ 88 (108)
.+.|.||.|..
T Consensus 2 ~g~W~C~~C~~ 12 (30)
T PF00641_consen 2 EGDWKCPSCTF 12 (30)
T ss_dssp SSSEEETTTTE
T ss_pred CcCccCCCCcC
Confidence 46899999974
No 46
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=70.20 E-value=3.6 Score=25.46 Aligned_cols=37 Identities=22% Similarity=0.444 Sum_probs=25.5
Q ss_pred cccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCe
Q psy8140 48 KMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILL 95 (108)
Q Consensus 48 ~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL 95 (108)
.+....|.--..|.+ |||++. .--||+|++++...+.
T Consensus 18 ~~~~~~pCgH~I~~~--~f~~~r---------YngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 18 TKGTVLPCGHLICDN--CFPGER---------YNGCPFCGTPFEFDDP 54 (55)
T ss_pred cccccccccceeecc--ccChhh---------ccCCCCCCCcccCCCC
Confidence 445555555555554 699986 3569999999987664
No 47
>PLN00162 transport protein sec23; Provisional
Probab=69.72 E-value=1.1 Score=39.93 Aligned_cols=34 Identities=21% Similarity=0.530 Sum_probs=22.9
Q ss_pred ccccccccCccceecHHHHHHHhcCCCceecccCCCcc
Q psy8140 53 FPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 53 ~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~ 90 (108)
.|+|=+.|+-. +..|.+.....+.|.||+|+..-
T Consensus 52 ~pvRC~~Cray----lNPf~~~d~~~~~W~C~~C~~~N 85 (761)
T PLN00162 52 DPLRCRTCRAV----LNPYCRVDFQAKIWICPFCFQRN 85 (761)
T ss_pred CCCccCCCcCE----ECCceEEecCCCEEEccCCCCCC
Confidence 46666666543 44455555667899999999754
No 48
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=69.38 E-value=1.1 Score=23.04 Aligned_cols=16 Identities=25% Similarity=0.436 Sum_probs=12.2
Q ss_pred ceecccCCCcccCCCe
Q psy8140 80 KWNCPVCDKVGHLILL 95 (108)
Q Consensus 80 ~W~CPiC~~~~~~~dL 95 (108)
.-.||+|++.+..+.|
T Consensus 2 l~~C~~CgR~F~~~~l 17 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRL 17 (25)
T ss_pred CCcCCCCCCEECHHHH
Confidence 3579999998876554
No 49
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=67.98 E-value=4.5 Score=30.09 Aligned_cols=12 Identities=42% Similarity=1.118 Sum_probs=8.7
Q ss_pred CceecccCCCcc
Q psy8140 79 PKWNCPVCDKVG 90 (108)
Q Consensus 79 ~~W~CPiC~~~~ 90 (108)
..|.||+||-..
T Consensus 133 ~~~vC~vCGy~~ 144 (166)
T COG1592 133 KVWVCPVCGYTH 144 (166)
T ss_pred CEEEcCCCCCcc
Confidence 478888888544
No 50
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=67.60 E-value=2.5 Score=26.37 Aligned_cols=16 Identities=31% Similarity=0.331 Sum_probs=12.8
Q ss_pred eecccCCCcccCCCee
Q psy8140 81 WNCPVCDKVGHLILLC 96 (108)
Q Consensus 81 W~CPiC~~~~~~~dL~ 96 (108)
=.||+||+++.+++..
T Consensus 4 kHC~~CG~~Ip~~~~f 19 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESF 19 (59)
T ss_pred CcCCcCCCcCCcchhh
Confidence 4699999999987544
No 51
>KOG0311|consensus
Probab=67.33 E-value=0.37 Score=39.97 Aligned_cols=66 Identities=23% Similarity=0.286 Sum_probs=51.1
Q ss_pred eeee--eeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcc-cCCCeeehhhh
Q psy8140 33 IKTL--ELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVG-HLILLCMAMIE 101 (108)
Q Consensus 33 i~~~--~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~-~~~dL~iD~~~ 101 (108)
+++. .+...+.||+-+..|+.-..-+.|-|--|||.- +. +.+.+.-.||-|.+.+ .-.+|++|.-+
T Consensus 33 i~~~l~~~~~~v~c~icl~llk~tmttkeClhrfc~~ci--~~-a~r~gn~ecptcRk~l~SkrsLr~Dp~f 101 (381)
T KOG0311|consen 33 IMVDLAMFDIQVICPICLSLLKKTMTTKECLHRFCFDCI--WK-ALRSGNNECPTCRKKLVSKRSLRIDPNF 101 (381)
T ss_pred heecHHHhhhhhccHHHHHHHHhhcccHHHHHHHHHHHH--HH-HHHhcCCCCchHHhhccccccCCCCccH
Confidence 5544 677899999999999999999999999888763 33 3344557899999876 56788888543
No 52
>KOG2817|consensus
Probab=66.86 E-value=4.3 Score=34.06 Aligned_cols=54 Identities=24% Similarity=0.369 Sum_probs=38.0
Q ss_pred eeecCCCccc--cccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCC
Q psy8140 40 SSLICPLGKM--RMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLIL 94 (108)
Q Consensus 40 vsL~CPlS~~--ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~d 94 (108)
-...||++++ -=.+|-.--.|.|+-+=|+.+=|..+-. .+.+||.|-....+++
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~-~sfKCPYCP~e~~~~~ 388 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGS-QSFKCPYCPVEQLASD 388 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCC-eeeeCCCCCcccCHHh
Confidence 4589999974 4578888899999965555554433322 2699999987665544
No 53
>KOG1813|consensus
Probab=66.62 E-value=3.2 Score=33.73 Aligned_cols=54 Identities=19% Similarity=0.246 Sum_probs=39.1
Q ss_pred eeeeeeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCccc
Q psy8140 33 IKTLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGH 91 (108)
Q Consensus 33 i~~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~ 91 (108)
+......|...|-|-++....||+. .|.|. |--...+.-.+ ..-+|++|++.+.
T Consensus 233 ~~~D~~~~Pf~c~icr~~f~~pVvt-~c~h~--fc~~ca~~~~q--k~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 233 KIEDIELLPFKCFICRKYFYRPVVT-KCGHY--FCEVCALKPYQ--KGEKCYVCSQQTH 286 (313)
T ss_pred ecCCcccCCccccccccccccchhh-cCCce--eehhhhccccc--cCCcceecccccc
Confidence 3334567888999999999999998 79998 44443333222 3468999999875
No 54
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=66.02 E-value=2.5 Score=20.77 Aligned_cols=11 Identities=27% Similarity=0.806 Sum_probs=9.2
Q ss_pred eecccCCCccc
Q psy8140 81 WNCPVCDKVGH 91 (108)
Q Consensus 81 W~CPiC~~~~~ 91 (108)
|.|.+|++.+.
T Consensus 1 ~~C~~C~~~f~ 11 (25)
T PF12874_consen 1 FYCDICNKSFS 11 (25)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCCcC
Confidence 78999998764
No 55
>KOG0317|consensus
Probab=64.41 E-value=7 Score=31.59 Aligned_cols=50 Identities=20% Similarity=0.433 Sum_probs=36.7
Q ss_pred ecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCee
Q psy8140 42 LICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 42 L~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~ 96 (108)
-+|-|=...+..|.- ..|.|+-| =.=.++....+. .||.|...+++.+++
T Consensus 240 ~kC~LCLe~~~~pSa-TpCGHiFC--WsCI~~w~~ek~--eCPlCR~~~~pskvi 289 (293)
T KOG0317|consen 240 RKCSLCLENRSNPSA-TPCGHIFC--WSCILEWCSEKA--ECPLCREKFQPSKVI 289 (293)
T ss_pred CceEEEecCCCCCCc-CcCcchHH--HHHHHHHHcccc--CCCcccccCCCccee
Confidence 567777788888875 58999944 444555555443 499999999998875
No 56
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.19 E-value=3.4 Score=26.37 Aligned_cols=17 Identities=29% Similarity=0.438 Sum_probs=12.9
Q ss_pred CCCceecccCCCcccCC
Q psy8140 77 LKPKWNCPVCDKVGHLI 93 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~~~ 93 (108)
...+-+||.|++++...
T Consensus 4 ~~~~v~CP~Cgkpv~w~ 20 (65)
T COG3024 4 LRITVPCPTCGKPVVWG 20 (65)
T ss_pred ccccccCCCCCCccccc
Confidence 34567899999988653
No 57
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=63.97 E-value=2.3 Score=35.86 Aligned_cols=54 Identities=28% Similarity=0.637 Sum_probs=0.0
Q ss_pred ecCCCcccccccccccc-------------ccCccceecHHHHHHHhc-CCCceecccCCCcccCCCeee
Q psy8140 42 LICPLGKMRMAFPTKAS-------------TCAHLQCFDGATFIKMNE-LKPKWNCPVCDKVGHLILLCM 97 (108)
Q Consensus 42 L~CPlS~~ri~~P~Rg~-------------~C~H~qCFDl~~fl~~~~-~~~~W~CPiC~~~~~~~dL~i 97 (108)
..||..+..+..|.++. +|.|+ +=...|-.... ......||+|.+.-++-.|.+
T Consensus 278 pQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHV--hG~h~Wg~~~~~~~~~r~CPlCr~~g~~V~L~m 345 (416)
T PF04710_consen 278 PQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHV--HGYHNWGQDSDRDPRSRTCPLCRQVGPYVPLWM 345 (416)
T ss_dssp ----------------------------------------------------------------------
T ss_pred CCCCcCCCccccccccccccccccCceeeccccce--eeecccccccccccccccCCCccccCCceeEee
Confidence 56888888888887776 89998 44445544322 235889999999887766654
No 58
>KOG0823|consensus
Probab=63.85 E-value=6.9 Score=30.64 Aligned_cols=54 Identities=19% Similarity=0.340 Sum_probs=37.8
Q ss_pred eecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCee
Q psy8140 41 SLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 41 sL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~ 96 (108)
..-|-|=+..-+-||-. .|.|+-|+--- |.....+...-.||||...++.+.++
T Consensus 47 ~FdCNICLd~akdPVvT-lCGHLFCWpCl-yqWl~~~~~~~~cPVCK~~Vs~~~vv 100 (230)
T KOG0823|consen 47 FFDCNICLDLAKDPVVT-LCGHLFCWPCL-YQWLQTRPNSKECPVCKAEVSIDTVV 100 (230)
T ss_pred ceeeeeeccccCCCEEe-ecccceehHHH-HHHHhhcCCCeeCCccccccccceEE
Confidence 35566767777777765 89999888643 33334455566789999988877664
No 59
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=63.30 E-value=1.6 Score=23.15 Aligned_cols=10 Identities=40% Similarity=0.886 Sum_probs=5.6
Q ss_pred ecccCCCccc
Q psy8140 82 NCPVCDKVGH 91 (108)
Q Consensus 82 ~CPiC~~~~~ 91 (108)
+||+|+..+.
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 5999998875
No 60
>PF02228 Gag_p19: Major core protein p19; InterPro: IPR003139 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from delta-retroviruses such as Human T-lymphotropic virus 1 and Human T-cell leukemia virus 2 (HTLV-2), both members of the human oncovirus subclass of retroviruses [, ].; GO: 0005198 structural molecule activity, 0019013 viral nucleocapsid; PDB: 1JVR_A.
Probab=63.26 E-value=4.2 Score=27.27 Aligned_cols=20 Identities=25% Similarity=0.522 Sum_probs=15.9
Q ss_pred cHHHHHHHhcCCCceecccC
Q psy8140 67 DGATFIKMNELKPKWNCPVC 86 (108)
Q Consensus 67 Dl~~fl~~~~~~~~W~CPiC 86 (108)
++..||.+..+++.|-|||=
T Consensus 45 qLr~flk~alkTpvwl~pi~ 64 (92)
T PF02228_consen 45 QLRNFLKLALKTPVWLNPIN 64 (92)
T ss_dssp HHHHHHHHHHT-TTSTTTT-
T ss_pred HHHHHHHHHHcCCeeecccc
Confidence 57788888889999999983
No 61
>PF04641 Rtf2: Rtf2 RING-finger
Probab=62.93 E-value=6.3 Score=30.58 Aligned_cols=32 Identities=13% Similarity=0.324 Sum_probs=27.1
Q ss_pred eecCCCccccccccccccccCccceecHHHHHHH
Q psy8140 41 SLICPLGKMRMAFPTKASTCAHLQCFDGATFIKM 74 (108)
Q Consensus 41 sL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~ 74 (108)
--.|+||+++++.|+=+-.-.++ |+.++.|++
T Consensus 34 w~~CaLS~~pL~~PiV~d~~G~L--ynKeaile~ 65 (260)
T PF04641_consen 34 WTHCALSQQPLEDPIVSDRLGRL--YNKEAILEF 65 (260)
T ss_pred cCcccCcCCccCCCeeeCCCCee--EcHHHHHHH
Confidence 45799999999999966666676 999999986
No 62
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=62.56 E-value=4.2 Score=25.71 Aligned_cols=14 Identities=36% Similarity=0.648 Sum_probs=11.2
Q ss_pred CceecccCCCcccC
Q psy8140 79 PKWNCPVCDKVGHL 92 (108)
Q Consensus 79 ~~W~CPiC~~~~~~ 92 (108)
..-+||+|++.+.+
T Consensus 5 ~~v~CP~C~k~~~w 18 (62)
T PRK00418 5 ITVNCPTCGKPVEW 18 (62)
T ss_pred ccccCCCCCCcccc
Confidence 45789999998754
No 63
>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=61.94 E-value=4.1 Score=22.41 Aligned_cols=11 Identities=45% Similarity=1.331 Sum_probs=7.9
Q ss_pred ceecccCCCcc
Q psy8140 80 KWNCPVCDKVG 90 (108)
Q Consensus 80 ~W~CPiC~~~~ 90 (108)
.|+|++||-..
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 58888888543
No 64
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=59.78 E-value=12 Score=28.67 Aligned_cols=37 Identities=16% Similarity=0.282 Sum_probs=24.2
Q ss_pred ccCccceecHHHHHHHhcCCCceecccCCCcccCCCeee
Q psy8140 59 TCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCM 97 (108)
Q Consensus 59 ~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~i 97 (108)
.|.|. ||.+.+..........+||.|+..+++.=+-.
T Consensus 121 ~C~~~--~~~~~~~~~~~~~~~p~C~~Cgg~lrP~Vv~F 157 (235)
T cd01408 121 KCKHK--YPGDWMREDIFNQEVPKCPRCGGLVKPDIVFF 157 (235)
T ss_pred cCCCc--CCHHHHHHHHhCCCCccCCCCCCCccCcEEEC
Confidence 38886 88766555433334578999998877654433
No 65
>PF14353 CpXC: CpXC protein
Probab=59.77 E-value=1.8 Score=29.77 Aligned_cols=22 Identities=23% Similarity=0.353 Sum_probs=15.2
Q ss_pred CCceecccCCCccc--CCCeeehh
Q psy8140 78 KPKWNCPVCDKVGH--LILLCMAM 99 (108)
Q Consensus 78 ~~~W~CPiC~~~~~--~~dL~iD~ 99 (108)
-..+.||.|+..+. +.-|+.|.
T Consensus 36 l~~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred cCEEECCCCCCceecCCCEEEEcC
Confidence 35899999998765 34455553
No 66
>PRK01343 zinc-binding protein; Provisional
Probab=59.62 E-value=4.6 Score=25.14 Aligned_cols=16 Identities=38% Similarity=0.868 Sum_probs=12.3
Q ss_pred cCCCceecccCCCccc
Q psy8140 76 ELKPKWNCPVCDKVGH 91 (108)
Q Consensus 76 ~~~~~W~CPiC~~~~~ 91 (108)
...+.-+||+|++.+.
T Consensus 5 ~~~p~~~CP~C~k~~~ 20 (57)
T PRK01343 5 PLRPTRPCPECGKPST 20 (57)
T ss_pred cCCCCCcCCCCCCcCc
Confidence 3456788999999865
No 67
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=59.29 E-value=4.4 Score=24.81 Aligned_cols=18 Identities=22% Similarity=0.431 Sum_probs=13.3
Q ss_pred ceecccCCCcccCCCeee
Q psy8140 80 KWNCPVCDKVGHLILLCM 97 (108)
Q Consensus 80 ~W~CPiC~~~~~~~dL~i 97 (108)
..+||.|+..+.+.+...
T Consensus 2 ~~~CP~CG~~iev~~~~~ 19 (54)
T TIGR01206 2 QFECPDCGAEIELENPEL 19 (54)
T ss_pred ccCCCCCCCEEecCCCcc
Confidence 358999999887766443
No 68
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=58.87 E-value=9.3 Score=23.69 Aligned_cols=17 Identities=18% Similarity=0.472 Sum_probs=13.6
Q ss_pred CCCceecccCCCcccCC
Q psy8140 77 LKPKWNCPVCDKVGHLI 93 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~~~ 93 (108)
..+...||.|+...+..
T Consensus 50 ~eg~L~Cp~c~r~YPI~ 66 (68)
T PF03966_consen 50 VEGELICPECGREYPIR 66 (68)
T ss_dssp TTTEEEETTTTEEEEEE
T ss_pred cCCEEEcCCCCCEEeCC
Confidence 46889999999877654
No 69
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=58.25 E-value=6.7 Score=24.70 Aligned_cols=14 Identities=21% Similarity=0.351 Sum_probs=9.6
Q ss_pred ceecccCCCcccCC
Q psy8140 80 KWNCPVCDKVGHLI 93 (108)
Q Consensus 80 ~W~CPiC~~~~~~~ 93 (108)
.++||.|+++++++
T Consensus 55 ~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 55 FGECPYCSSPISWS 68 (70)
T ss_dssp EEE-TTT-SEEEGG
T ss_pred ccCCcCCCCeeeEe
Confidence 58999999988754
No 70
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=57.72 E-value=4.6 Score=25.05 Aligned_cols=13 Identities=31% Similarity=0.767 Sum_probs=7.1
Q ss_pred ceecccCCCcccC
Q psy8140 80 KWNCPVCDKVGHL 92 (108)
Q Consensus 80 ~W~CPiC~~~~~~ 92 (108)
+-+||+|++.+.+
T Consensus 2 ~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 2 TVKCPICGKPVEW 14 (57)
T ss_dssp EEE-TTT--EEE-
T ss_pred cccCCCCCCeecc
Confidence 4589999998865
No 71
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=57.56 E-value=10 Score=23.88 Aligned_cols=31 Identities=23% Similarity=0.559 Sum_probs=18.7
Q ss_pred ccccccccCccceecHHHHHHHhcCCCceecccCC
Q psy8140 53 FPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCD 87 (108)
Q Consensus 53 ~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~ 87 (108)
.|+.-..|+|. |-..=+.+.-+... .||+|.
T Consensus 43 ~~i~~~~C~H~--FH~~Ci~~Wl~~~~--~CP~CR 73 (73)
T PF12678_consen 43 CPIVWGPCGHI--FHFHCISQWLKQNN--TCPLCR 73 (73)
T ss_dssp S-EEEETTSEE--EEHHHHHHHHTTSS--B-TTSS
T ss_pred cceEecccCCC--EEHHHHHHHHhcCC--cCCCCC
Confidence 34444569998 77766555444333 999995
No 72
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=57.00 E-value=5.6 Score=25.18 Aligned_cols=18 Identities=28% Similarity=0.366 Sum_probs=14.2
Q ss_pred CceecccCCCcccCCCee
Q psy8140 79 PKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 79 ~~W~CPiC~~~~~~~dL~ 96 (108)
|.-.||+|++.++.++-.
T Consensus 7 PH~HC~VCg~aIp~de~~ 24 (64)
T COG4068 7 PHRHCVVCGKAIPPDEQV 24 (64)
T ss_pred CCccccccCCcCCCccch
Confidence 455799999999987643
No 73
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=55.55 E-value=7.2 Score=21.77 Aligned_cols=20 Identities=35% Similarity=0.431 Sum_probs=15.9
Q ss_pred eecccCCCcccCCCeeehhh
Q psy8140 81 WNCPVCDKVGHLILLCMAMI 100 (108)
Q Consensus 81 W~CPiC~~~~~~~dL~iD~~ 100 (108)
++|++|+..+....+.+|-+
T Consensus 12 ~~C~~c~~~~~~~~~~v~Hi 31 (57)
T cd00085 12 GLCPYCGKPGGTEGLEVDHI 31 (57)
T ss_pred CcCccCCCcCCCCCceEEee
Confidence 79999999887777777643
No 74
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=55.11 E-value=5.9 Score=22.75 Aligned_cols=13 Identities=23% Similarity=0.455 Sum_probs=10.5
Q ss_pred ceecccCCCcccC
Q psy8140 80 KWNCPVCDKVGHL 92 (108)
Q Consensus 80 ~W~CPiC~~~~~~ 92 (108)
.++||.|+.++-+
T Consensus 21 ~~~Cp~CG~~~~~ 33 (46)
T PRK00398 21 GVRCPYCGYRILF 33 (46)
T ss_pred ceECCCCCCeEEE
Confidence 7999999987643
No 75
>KOG1986|consensus
Probab=54.16 E-value=4 Score=36.67 Aligned_cols=33 Identities=21% Similarity=0.660 Sum_probs=19.4
Q ss_pred cccccccCccceecHHHHHHHhcCCCceecccCCCcc
Q psy8140 54 PTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 54 P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~ 90 (108)
|+|=..|+-. +..|-..-.+.+.|.||+|.+.=
T Consensus 53 P~~C~~C~Av----lNPyc~vd~~a~~W~CpfC~qrN 85 (745)
T KOG1986|consen 53 PLRCSKCGAV----LNPYCSVDFRAKSWICPFCNQRN 85 (745)
T ss_pred Cchhccchhh----cCcceeecccCceEeccccccCC
Confidence 4454455443 22232334567899999999753
No 76
>KOG0287|consensus
Probab=53.94 E-value=4.1 Score=34.10 Aligned_cols=59 Identities=22% Similarity=0.269 Sum_probs=42.7
Q ss_pred eeecCCCccccccccccccccCccce-ecHHHHHHHhcCCCceecccCCCcccCCCeeehhhhhhh
Q psy8140 40 SSLICPLGKMRMAFPTKASTCAHLQC-FDGATFIKMNELKPKWNCPVCDKVGHLILLCMAMIESVC 104 (108)
Q Consensus 40 vsL~CPlS~~ri~~P~Rg~~C~H~qC-FDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~iD~~~~~~ 104 (108)
-.|+|-|-+.-+++|+-.- |.|.-| |-...|| +.+-+||.|-..++-.+|+=..++..|
T Consensus 22 ~lLRC~IC~eyf~ip~itp-CsHtfCSlCIR~~L-----~~~p~CP~C~~~~~Es~Lr~n~il~Ei 81 (442)
T KOG0287|consen 22 DLLRCGICFEYFNIPMITP-CSHTFCSLCIRKFL-----SYKPQCPTCCVTVTESDLRNNRILDEI 81 (442)
T ss_pred HHHHHhHHHHHhcCceecc-ccchHHHHHHHHHh-----ccCCCCCceecccchhhhhhhhHHHHH
Confidence 4689999999999999877 999833 2222222 445689999999998888865555444
No 77
>PF13395 HNH_4: HNH endonuclease
Probab=52.78 E-value=6.8 Score=23.30 Aligned_cols=18 Identities=28% Similarity=0.469 Sum_probs=14.6
Q ss_pred cccCCCcccCCC-----eeehhh
Q psy8140 83 CPVCDKVGHLIL-----LCMAMI 100 (108)
Q Consensus 83 CPiC~~~~~~~d-----L~iD~~ 100 (108)
||.|++.+..++ ..||-+
T Consensus 1 C~Y~g~~i~~~~l~~~~~~iDHi 23 (54)
T PF13395_consen 1 CPYCGKPISIENLFKNKYEIDHI 23 (54)
T ss_pred CCCCCCCCChhhcccCCceeEEE
Confidence 899999999998 466644
No 78
>COG1773 Rubredoxin [Energy production and conversion]
Probab=51.42 E-value=6.1 Score=24.41 Aligned_cols=11 Identities=36% Similarity=1.159 Sum_probs=9.1
Q ss_pred CCceecccCCC
Q psy8140 78 KPKWNCPVCDK 88 (108)
Q Consensus 78 ~~~W~CPiC~~ 88 (108)
...|.||+|+.
T Consensus 34 Pd~w~CP~Cg~ 44 (55)
T COG1773 34 PDDWVCPECGV 44 (55)
T ss_pred CCccCCCCCCC
Confidence 45799999994
No 79
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=51.10 E-value=7.6 Score=21.80 Aligned_cols=9 Identities=33% Similarity=0.862 Sum_probs=6.0
Q ss_pred ecccCCCcc
Q psy8140 82 NCPVCDKVG 90 (108)
Q Consensus 82 ~CPiC~~~~ 90 (108)
+||.|+..+
T Consensus 1 ~CP~C~~~l 9 (41)
T PF13453_consen 1 KCPRCGTEL 9 (41)
T ss_pred CcCCCCccc
Confidence 578887643
No 80
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=50.83 E-value=7.2 Score=23.67 Aligned_cols=14 Identities=21% Similarity=0.617 Sum_probs=10.4
Q ss_pred ecccCCCcccCCCeeeh
Q psy8140 82 NCPVCDKVGHLILLCMA 98 (108)
Q Consensus 82 ~CPiC~~~~~~~dL~iD 98 (108)
.||.|+..+ ++.||
T Consensus 2 ~CPyCge~~---~~~iD 15 (52)
T PF14255_consen 2 QCPYCGEPI---EILID 15 (52)
T ss_pred CCCCCCCee---EEEEe
Confidence 699999887 45555
No 81
>KOG4172|consensus
Probab=50.25 E-value=5.5 Score=24.98 Aligned_cols=38 Identities=21% Similarity=0.579 Sum_probs=22.7
Q ss_pred cccccccc--ccCccc-eecHHHHHHHhcCCCceecccCCCccc
Q psy8140 51 MAFPTKAS--TCAHLQ-CFDGATFIKMNELKPKWNCPVCDKVGH 91 (108)
Q Consensus 51 i~~P~Rg~--~C~H~q-CFDl~~fl~~~~~~~~W~CPiC~~~~~ 91 (108)
++.|+-+. .|.|+= |||-.- ..- +.....||+|..+++
T Consensus 14 ye~pvdsVlYtCGHMCmCy~Cg~--rl~-~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 14 YEHPVDSVLYTCGHMCMCYACGL--RLK-KALHGCCPICRAPIK 54 (62)
T ss_pred ccCcchHHHHHcchHHhHHHHHH--HHH-HccCCcCcchhhHHH
Confidence 34555554 588873 555443 222 225678999998774
No 82
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=50.20 E-value=15 Score=30.51 Aligned_cols=52 Identities=19% Similarity=0.441 Sum_probs=38.6
Q ss_pred eecCCCcc--ccccccccccccCccceecHHHHHHHhcC-CCceecccCCCcccCCC
Q psy8140 41 SLICPLGK--MRMAFPTKASTCAHLQCFDGATFIKMNEL-KPKWNCPVCDKVGHLIL 94 (108)
Q Consensus 41 sL~CPlS~--~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~-~~~W~CPiC~~~~~~~d 94 (108)
-.+||.++ ..-++|--...|.|+ -..++.=...++ .-+++||.|-.....++
T Consensus 336 ~FiCPVlKe~~t~ENpP~ml~CgHV--Iskeal~~LS~nG~~~FKCPYCP~~~~~~~ 390 (396)
T COG5109 336 LFICPVLKELCTDENPPVMLECGHV--ISKEALSVLSQNGVLSFKCPYCPEMSKYEN 390 (396)
T ss_pred eeeccccHhhhcccCCCeeeeccce--eeHHHHHHHhhcCcEEeeCCCCCcchhhhh
Confidence 36899986 456789999999999 666665555443 45899999987665554
No 83
>KOG0289|consensus
Probab=50.12 E-value=11 Score=32.38 Aligned_cols=51 Identities=12% Similarity=0.186 Sum_probs=43.2
Q ss_pred ecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCee
Q psy8140 42 LICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 42 L~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~ 96 (108)
+.|-||+..=+.||-+..=.|+ |+..-+-++-.. +-+|||-+++++++||+
T Consensus 1 m~CaISgEvP~~PVvS~~Sg~v--fEkrLIEqyI~e--~G~DPIt~~pLs~eelV 51 (506)
T KOG0289|consen 1 MVCAISGEVPEEPVVSPVSGHV--FEKRLIEQYIAE--TGKDPITNEPLSIEELV 51 (506)
T ss_pred CeecccCCCCCCccccccccch--HHHHHHHHHHHH--cCCCCCCCCcCCHHHee
Confidence 4699999999999999999999 998866665544 45899999999999886
No 84
>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=49.21 E-value=10 Score=32.49 Aligned_cols=23 Identities=35% Similarity=0.583 Sum_probs=16.2
Q ss_pred HHHHHHHhcCCCceecccCCCcc
Q psy8140 68 GATFIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 68 l~~fl~~~~~~~~W~CPiC~~~~ 90 (108)
+.+|.+-+....-|.||.|.+.+
T Consensus 45 al~fak~n~sWrFWiCp~CskkF 67 (466)
T PF04780_consen 45 ALSFAKENKSWRFWICPRCSKKF 67 (466)
T ss_pred HHHHHHhcCceeEeeCCccccee
Confidence 34555556667789999999764
No 85
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=49.01 E-value=11 Score=23.27 Aligned_cols=19 Identities=26% Similarity=0.394 Sum_probs=13.9
Q ss_pred ceecccCCCccc-CCCeeeh
Q psy8140 80 KWNCPVCDKVGH-LILLCMA 98 (108)
Q Consensus 80 ~W~CPiC~~~~~-~~dL~iD 98 (108)
.-+||+|++.+. -+|+++-
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvC 24 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVC 24 (54)
T ss_pred CccChhhCCcccCCCCEEEC
Confidence 457999999886 5666653
No 86
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=49.01 E-value=10 Score=26.32 Aligned_cols=43 Identities=23% Similarity=0.416 Sum_probs=29.6
Q ss_pred eeeeeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCC
Q psy8140 34 KTLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLI 93 (108)
Q Consensus 34 ~~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~ 93 (108)
.+....|+..||-+..-... |-.+ ..--..|.||.|+......
T Consensus 21 ~apR~~v~Y~C~~Gh~~~v~------------Fa~e-----AevP~~WeC~~cG~~A~~~ 63 (105)
T PF13397_consen 21 FAPRQRVSYWCPNGHETEVP------------FAAE-----AEVPATWECPRCGLPAGRD 63 (105)
T ss_pred ccCceEEEEECCCCCEEecc------------cccc-----CCCCCceeCCCCCCccccc
Confidence 45688999999986543322 3332 2446789999999987654
No 87
>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=48.58 E-value=11 Score=19.64 Aligned_cols=13 Identities=15% Similarity=0.480 Sum_probs=11.0
Q ss_pred CceecccCCCccc
Q psy8140 79 PKWNCPVCDKVGH 91 (108)
Q Consensus 79 ~~W~CPiC~~~~~ 91 (108)
+.|.|.+|++.+.
T Consensus 2 ~~~~C~~C~~~~~ 14 (35)
T smart00451 2 GGFYCKLCNVTFT 14 (35)
T ss_pred cCeEccccCCccC
Confidence 5688999999876
No 88
>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=48.54 E-value=9.8 Score=19.21 Aligned_cols=12 Identities=33% Similarity=0.764 Sum_probs=9.3
Q ss_pred ceecccCCCccc
Q psy8140 80 KWNCPVCDKVGH 91 (108)
Q Consensus 80 ~W~CPiC~~~~~ 91 (108)
+|.|++|++.+.
T Consensus 1 q~~C~~C~k~f~ 12 (27)
T PF12171_consen 1 QFYCDACDKYFS 12 (27)
T ss_dssp -CBBTTTTBBBS
T ss_pred CCCcccCCCCcC
Confidence 478999998774
No 89
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=48.53 E-value=10 Score=25.24 Aligned_cols=19 Identities=26% Similarity=0.426 Sum_probs=15.5
Q ss_pred CCceecccCCCcccCCCee
Q psy8140 78 KPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 78 ~~~W~CPiC~~~~~~~dL~ 96 (108)
.++-.||.|++++++-|++
T Consensus 31 ~~rS~C~~C~~~L~~~~lI 49 (92)
T PF06750_consen 31 FPRSHCPHCGHPLSWWDLI 49 (92)
T ss_pred CCCCcCcCCCCcCcccccc
Confidence 4678899999998888775
No 90
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=48.47 E-value=8.2 Score=19.30 Aligned_cols=10 Identities=40% Similarity=1.378 Sum_probs=7.9
Q ss_pred CceecccCCC
Q psy8140 79 PKWNCPVCDK 88 (108)
Q Consensus 79 ~~W~CPiC~~ 88 (108)
+.|.||.|.-
T Consensus 1 g~W~C~~C~~ 10 (26)
T smart00547 1 GDWECPACTF 10 (26)
T ss_pred CcccCCCCCC
Confidence 4699999963
No 91
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=48.02 E-value=9.2 Score=24.57 Aligned_cols=25 Identities=24% Similarity=0.507 Sum_probs=18.3
Q ss_pred cccCccc-eecHHHHHHHhcCCCceecccCCCcc
Q psy8140 58 STCAHLQ-CFDGATFIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 58 ~~C~H~q-CFDl~~fl~~~~~~~~W~CPiC~~~~ 90 (108)
..|.|.| +|+-. ...-+|++|+..+
T Consensus 23 pdC~N~q~vFsha--------st~V~C~~CG~~l 48 (67)
T COG2051 23 PDCGNEQVVFSHA--------STVVTCLICGTTL 48 (67)
T ss_pred CCCCCEEEEeccC--------ceEEEecccccEE
Confidence 3788888 56543 3578999999765
No 92
>PHA02926 zinc finger-like protein; Provisional
Probab=47.34 E-value=20 Score=28.25 Aligned_cols=49 Identities=16% Similarity=0.295 Sum_probs=30.6
Q ss_pred eecCCCcccccccc--------ccccccCccceecHHHHHHHhc----CCCceecccCCCccc
Q psy8140 41 SLICPLGKMRMAFP--------TKASTCAHLQCFDGATFIKMNE----LKPKWNCPVCDKVGH 91 (108)
Q Consensus 41 sL~CPlS~~ri~~P--------~Rg~~C~H~qCFDl~~fl~~~~----~~~~W~CPiC~~~~~ 91 (108)
...|+|=+..+-.| +--..|.|.-|++ =+-+..+ .+....||+|...+.
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~--CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCIT--CINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCccCccccccccccccccccccCCCCchHHHH--HHHHHHHhccccCcCCcCCCCcceee
Confidence 46788877665332 3345999995554 3333332 234677999998764
No 93
>KOG0297|consensus
Probab=47.04 E-value=11 Score=31.02 Aligned_cols=56 Identities=23% Similarity=0.434 Sum_probs=41.3
Q ss_pred eeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCeee
Q psy8140 38 LTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCM 97 (108)
Q Consensus 38 ~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~i 97 (108)
..-+|.||+=...+..|.....|.|. |=..-....... .-.||.|......++.+-
T Consensus 18 ~~~~l~C~~C~~vl~~p~~~~~cgh~--fC~~C~~~~~~~--~~~cp~~~~~~~~~~~~~ 73 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPVQTTTCGHR--FCAGCLLESLSN--HQKCPVCRQELTQAEELP 73 (391)
T ss_pred CcccccCccccccccCCCCCCCCCCc--ccccccchhhcc--CcCCcccccccchhhccC
Confidence 45679999999999999999999998 333333322222 678999988877766653
No 94
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.73 E-value=5.4 Score=25.28 Aligned_cols=45 Identities=22% Similarity=0.332 Sum_probs=32.1
Q ss_pred eeeeeeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccC
Q psy8140 33 IKTLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHL 92 (108)
Q Consensus 33 i~~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~ 92 (108)
..+.....+|-||-.....-.| |+ ||.| ...+.-.||.|++..++
T Consensus 16 ~~I~~~~~~l~C~g~~~p~~HP-------rV-------~L~m-g~~gev~CPYC~t~y~l 60 (62)
T COG4391 16 ETIEIGDLPLMCPGPEPPNDHP-------RV-------FLDM-GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred eEEEeCCeeEEcCCCCCCCCCC-------EE-------EEEc-CCCCcEecCccccEEEe
Confidence 4455667788898776653333 33 7777 56788999999998765
No 95
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=45.23 E-value=15 Score=25.30 Aligned_cols=32 Identities=19% Similarity=0.353 Sum_probs=20.4
Q ss_pred ccCccceecHHHHHHHhcCCCceecccCCCc----ccCCCeeehhh
Q psy8140 59 TCAHLQCFDGATFIKMNELKPKWNCPVCDKV----GHLILLCMAMI 100 (108)
Q Consensus 59 ~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~----~~~~dL~iD~~ 100 (108)
.|.+. |....+ .+.||.|+.. ..=++|+|+.+
T Consensus 75 ~Cg~~--~~~~~~--------~~~CP~Cgs~~~~i~~G~El~I~~i 110 (115)
T TIGR00100 75 DCSEE--VSPEID--------LYRCPKCHGIMLQVRAGKELNLKSI 110 (115)
T ss_pred cCCCE--EecCCc--------CccCcCCcCCCcEEecCCeEEEEEE
Confidence 67665 655432 5889999963 34466666644
No 96
>smart00507 HNHc HNH nucleases.
Probab=44.65 E-value=13 Score=20.18 Aligned_cols=18 Identities=22% Similarity=0.216 Sum_probs=13.8
Q ss_pred eecccCCCcccCCCeeehh
Q psy8140 81 WNCPVCDKVGHLILLCMAM 99 (108)
Q Consensus 81 W~CPiC~~~~~~~dL~iD~ 99 (108)
+.|++|+..... .+.+|-
T Consensus 11 ~~C~~C~~~~~~-~~~v~H 28 (52)
T smart00507 11 GVCAYCGKPASE-GLEVDH 28 (52)
T ss_pred CCCcCCcCCCCC-CeEEEe
Confidence 899999998865 566653
No 97
>PF06416 DUF1076: Protein of unknown function (DUF1076); InterPro: IPR010489 This entry is represented by Bacteriophage 2851, Orf74 (EP2851_74). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2KKX_A 2KKY_A.
Probab=44.31 E-value=15 Score=25.83 Aligned_cols=35 Identities=17% Similarity=0.434 Sum_probs=24.1
Q ss_pred eeecCCCccc------cccccccccccCccceecHHHHHHHhcC
Q psy8140 40 SSLICPLGKM------RMAFPTKASTCAHLQCFDGATFIKMNEL 77 (108)
Q Consensus 40 vsL~CPlS~~------ri~~P~Rg~~C~H~qCFDl~~fl~~~~~ 77 (108)
-.|+||||+. =+++-..+..|. + ||.++|.++-..
T Consensus 39 e~L~CPITL~iPe~GVFvkNs~~S~VC~-L--yD~~Al~~Lv~~ 79 (113)
T PF06416_consen 39 EHLTCPITLCIPENGVFVKNSSGSDVCS-L--YDKEALSRLVRE 79 (113)
T ss_dssp HHH-BTTTTC--SCEEEEECTTTSSEEE-E--EEHHHHHHHHHC
T ss_pred HHcCCCeEEeecCCceEEecCCCCccce-e--cCHHHHHHHHHc
Confidence 3489999964 356666666774 3 999999997443
No 98
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.62 E-value=17 Score=30.11 Aligned_cols=14 Identities=29% Similarity=0.482 Sum_probs=11.4
Q ss_pred CceecccCCCcccC
Q psy8140 79 PKWNCPVCDKVGHL 92 (108)
Q Consensus 79 ~~W~CPiC~~~~~~ 92 (108)
-+-+||+|+..+++
T Consensus 360 y~~~CPvCrt~iPP 373 (374)
T COG5540 360 YSNKCPVCRTAIPP 373 (374)
T ss_pred hcccCCccCCCCCC
Confidence 45789999998865
No 99
>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=43.31 E-value=11 Score=19.69 Aligned_cols=11 Identities=27% Similarity=0.601 Sum_probs=8.0
Q ss_pred ecccCCCcccC
Q psy8140 82 NCPVCDKVGHL 92 (108)
Q Consensus 82 ~CPiC~~~~~~ 92 (108)
+||.|++.++.
T Consensus 2 ~CP~C~~~V~~ 12 (26)
T PF10571_consen 2 TCPECGAEVPE 12 (26)
T ss_pred cCCCCcCCchh
Confidence 58888887753
No 100
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=42.33 E-value=22 Score=22.44 Aligned_cols=22 Identities=18% Similarity=0.116 Sum_probs=18.5
Q ss_pred CCCceecccCCCcccCCCeeeh
Q psy8140 77 LKPKWNCPVCDKVGHLILLCMA 98 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~~~dL~iD 98 (108)
.+++-+|-.|++.+.-.+|+|-
T Consensus 4 ks~Ra~Ck~C~~~I~kg~lRiG 25 (82)
T PF00645_consen 4 KSGRAKCKGCKKKIAKGELRIG 25 (82)
T ss_dssp SSSTEBETTTSCBE-TTSEEEE
T ss_pred CCCCccCcccCCcCCCCCEEEE
Confidence 4678899999999999999984
No 101
>KOG0828|consensus
Probab=42.29 E-value=6.6 Score=34.33 Aligned_cols=52 Identities=15% Similarity=0.179 Sum_probs=35.2
Q ss_pred eecCCCccccccccccccccCccceecHHHHHHH-------------hcCCCceecccCCCcccC
Q psy8140 41 SLICPLGKMRMAFPTKASTCAHLQCFDGATFIKM-------------NELKPKWNCPVCDKVGHL 92 (108)
Q Consensus 41 sL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~-------------~~~~~~W~CPiC~~~~~~ 92 (108)
+--|||-.+.|.+=.++..|.|.+=+-..+|+-. ...+-+..||+|..++++
T Consensus 571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 3468888888888888888887755544444321 112356899999998764
No 102
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=42.09 E-value=17 Score=28.46 Aligned_cols=41 Identities=20% Similarity=0.383 Sum_probs=25.8
Q ss_pred cccccccccCccceecH---HHHHHHhcCCCceecccCCCcccCCC
Q psy8140 52 AFPTKASTCAHLQCFDG---ATFIKMNELKPKWNCPVCDKVGHLIL 94 (108)
Q Consensus 52 ~~P~Rg~~C~H~qCFDl---~~fl~~~~~~~~W~CPiC~~~~~~~d 94 (108)
..|++|..|.. ||=. ..+-.+.....--.||.||..+.+++
T Consensus 192 vvpl~g~~C~G--C~m~l~~~~~~~V~~~d~iv~CP~CgRILy~~e 235 (239)
T COG1579 192 VVPLEGRVCGG--CHMKLPSQTLSKVRKKDEIVFCPYCGRILYYDE 235 (239)
T ss_pred EEeecCCcccC--CeeeecHHHHHHHhcCCCCccCCccchHHHhhh
Confidence 34666777653 4422 12233445677899999999887654
No 103
>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=41.58 E-value=11 Score=20.74 Aligned_cols=14 Identities=29% Similarity=0.574 Sum_probs=11.2
Q ss_pred CCCceecccCCCcc
Q psy8140 77 LKPKWNCPVCDKVG 90 (108)
Q Consensus 77 ~~~~W~CPiC~~~~ 90 (108)
+-+-|.||.|+..+
T Consensus 29 ~vp~~~C~~CGE~~ 42 (46)
T TIGR03831 29 NVPALVCPQCGEEY 42 (46)
T ss_pred CCCccccccCCCEe
Confidence 45789999999765
No 104
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=41.44 E-value=39 Score=27.84 Aligned_cols=35 Identities=11% Similarity=0.160 Sum_probs=20.6
Q ss_pred cCccceecHHHHHHHhcCCCceecccCCCcccCCCee
Q psy8140 60 CAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 60 C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~ 96 (108)
|.+. ||.+............+||.|+-.++++=+-
T Consensus 153 C~~~--~~~~~~~~~~~~~~vP~C~~CgG~lRPdVVl 187 (349)
T PTZ00410 153 CHTP--YDIEQAYLEARSGKVPHCSTCGGIVKPDVVF 187 (349)
T ss_pred CCCC--cchhHHHHHhhcCCCCCCCCCCCccCCcEEe
Confidence 6555 6655433222233457899999887765443
No 105
>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=40.96 E-value=4.9 Score=23.35 Aligned_cols=26 Identities=35% Similarity=0.830 Sum_probs=16.9
Q ss_pred cccCccceecHHHHHHHhcCCCceecccCCC
Q psy8140 58 STCAHLQCFDGATFIKMNELKPKWNCPVCDK 88 (108)
Q Consensus 58 ~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~ 88 (108)
..|.|. |+... .+.. .....||.|+.
T Consensus 9 ~~Cg~~--fe~~~--~~~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 9 TACGHR--FEVLQ--KMSD-DPLATCPECGG 34 (52)
T ss_pred CCCCCE--eEEEE--ecCC-CCCCCCCCCCC
Confidence 467775 77542 2222 56788999997
No 106
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=40.30 E-value=15 Score=18.70 Aligned_cols=12 Identities=25% Similarity=0.437 Sum_probs=7.9
Q ss_pred eecccCCCcccC
Q psy8140 81 WNCPVCDKVGHL 92 (108)
Q Consensus 81 W~CPiC~~~~~~ 92 (108)
..||-|++.+..
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 568888875543
No 107
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=40.29 E-value=8.7 Score=34.27 Aligned_cols=16 Identities=31% Similarity=1.010 Sum_probs=12.8
Q ss_pred hcCCCceecccCCCcc
Q psy8140 75 NELKPKWNCPVCDKVG 90 (108)
Q Consensus 75 ~~~~~~W~CPiC~~~~ 90 (108)
..+...|.||+|++.-
T Consensus 71 d~r~~~W~CpfCnqrn 86 (755)
T COG5047 71 DERNQSWICPFCNQRN 86 (755)
T ss_pred ccCCceEecceecCCC
Confidence 4467789999999765
No 108
>KOG3800|consensus
Probab=39.87 E-value=10 Score=30.82 Aligned_cols=40 Identities=15% Similarity=0.200 Sum_probs=26.3
Q ss_pred ccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCeeehhh
Q psy8140 53 FPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCMAMI 100 (108)
Q Consensus 53 ~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~iD~~ 100 (108)
+|++...|.. |||.-- ..+..+||.|++.+.-.+.++-.|
T Consensus 21 n~C~H~lCEs--Cvd~iF------~~g~~~CpeC~~iLRk~nfr~q~f 60 (300)
T KOG3800|consen 21 NECGHRLCES--CVDRIF------SLGPAQCPECMVILRKNNFRVQTF 60 (300)
T ss_pred ccccchHHHH--HHHHHH------hcCCCCCCcccchhhhcccchhhc
Confidence 3444444432 566542 457899999999988777766544
No 109
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=39.82 E-value=12 Score=20.86 Aligned_cols=13 Identities=31% Similarity=0.971 Sum_probs=10.1
Q ss_pred ceecccCCCcccC
Q psy8140 80 KWNCPVCDKVGHL 92 (108)
Q Consensus 80 ~W~CPiC~~~~~~ 92 (108)
+|.||.|++..+.
T Consensus 1 Rr~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 1 RRICPKCGRIYHI 13 (36)
T ss_dssp EEEETTTTEEEET
T ss_pred CcCcCCCCCcccc
Confidence 5889999987653
No 110
>KOG2879|consensus
Probab=38.90 E-value=28 Score=28.25 Aligned_cols=53 Identities=21% Similarity=0.478 Sum_probs=39.2
Q ss_pred eeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCccc
Q psy8140 37 ELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGH 91 (108)
Q Consensus 37 ~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~ 91 (108)
..+.+..||+=+.+=.+|--+-.|.|.-||=-.. ....-.-...||-|+..+.
T Consensus 235 ~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~--ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 235 TGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIA--TSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cccCCceeeccCCCCCCCeeeccccceeehhhhh--hhhcchhhcccCccCCCCc
Confidence 4456678999999999999999999998863221 1111233578999999886
No 111
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=38.84 E-value=29 Score=26.63 Aligned_cols=37 Identities=14% Similarity=0.228 Sum_probs=24.8
Q ss_pred cCccceecHHHHHHHhcCCCceecccCCCcccCCCeeeh
Q psy8140 60 CAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCMA 98 (108)
Q Consensus 60 C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~iD 98 (108)
|.+. ||.+.+..+.......+||.|+..+++.=+-.+
T Consensus 125 C~~~--~~~~~~~~~~~~~~~p~Cp~Cgg~lrP~Vv~Fg 161 (244)
T PRK14138 125 CGKR--YTVEDVIEKLEKSDVPRCDDCSGLIRPNIVFFG 161 (244)
T ss_pred CCCc--ccHHHHHHHHhcCCCCCCCCCCCeECCCEEECC
Confidence 6665 888877765444445789999987776544333
No 112
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=38.68 E-value=10 Score=28.65 Aligned_cols=18 Identities=11% Similarity=0.161 Sum_probs=0.0
Q ss_pred CCceecccCCCcccCCCe
Q psy8140 78 KPKWNCPVCDKVGHLILL 95 (108)
Q Consensus 78 ~~~W~CPiC~~~~~~~dL 95 (108)
...-.||+||+.++.+++
T Consensus 166 ~~~~~cPitGe~IP~~e~ 183 (229)
T PF12230_consen 166 EKMIICPITGEMIPADEM 183 (229)
T ss_dssp ------------------
T ss_pred cccccccccccccccccc
Confidence 355899999999987765
No 113
>KOG2932|consensus
Probab=38.44 E-value=9 Score=31.71 Aligned_cols=50 Identities=24% Similarity=0.519 Sum_probs=33.2
Q ss_pred ccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCeeehhhhhhhhhcC
Q psy8140 49 MRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCMAMIESVCLFLC 108 (108)
Q Consensus 49 ~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~iD~~~~~~l~~~ 108 (108)
..|.+=.|=.-|+|+-|+|-.- ...--.||.|.-++ ++|.+..+--+|.|
T Consensus 98 ~PI~IYGRmIPCkHvFCl~CAr------~~~dK~Cp~C~d~V----qrIeq~~~g~iFmC 147 (389)
T KOG2932|consen 98 FPIAIYGRMIPCKHVFCLECAR------SDSDKICPLCDDRV----QRIEQIMMGGIFMC 147 (389)
T ss_pred Ccceeeecccccchhhhhhhhh------cCccccCcCcccHH----HHHHHhcccceEEe
Confidence 4566678899999997776543 22345799999776 34445555555554
No 114
>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=38.43 E-value=14 Score=28.53 Aligned_cols=18 Identities=33% Similarity=0.691 Sum_probs=11.8
Q ss_pred CCCceecccCCCcccCCC
Q psy8140 77 LKPKWNCPVCDKVGHLIL 94 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~~~d 94 (108)
...+|.||.|+|.++-.+
T Consensus 74 ~~~K~~C~lc~KlFkg~e 91 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPE 91 (214)
T ss_dssp SSEEEEE-SSS-EESSHH
T ss_pred cCCEECCCCCCcccCChH
Confidence 357899999998776433
No 115
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=38.33 E-value=17 Score=24.84 Aligned_cols=12 Identities=42% Similarity=1.348 Sum_probs=9.7
Q ss_pred CCCceecccCCC
Q psy8140 77 LKPKWNCPVCDK 88 (108)
Q Consensus 77 ~~~~W~CPiC~~ 88 (108)
..+.|.||.|..
T Consensus 58 ~~~~W~CP~Crg 69 (105)
T PF10497_consen 58 EDPNWKCPKCRG 69 (105)
T ss_pred cCCceECCCCCC
Confidence 467899999875
No 116
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=38.32 E-value=16 Score=21.62 Aligned_cols=13 Identities=38% Similarity=0.987 Sum_probs=9.6
Q ss_pred CCCceecccCCCc
Q psy8140 77 LKPKWNCPVCDKV 89 (108)
Q Consensus 77 ~~~~W~CPiC~~~ 89 (108)
..-.|+||.|+..
T Consensus 25 ~~v~W~C~~Cgh~ 37 (55)
T PF14311_consen 25 KKVWWKCPKCGHE 37 (55)
T ss_pred CEEEEECCCCCCe
Confidence 3446999999764
No 117
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=38.01 E-value=20 Score=23.00 Aligned_cols=19 Identities=21% Similarity=0.352 Sum_probs=13.5
Q ss_pred CceecccCCCcccCCCeee
Q psy8140 79 PKWNCPVCDKVGHLILLCM 97 (108)
Q Consensus 79 ~~W~CPiC~~~~~~~dL~i 97 (108)
..-.|++|++++....+.+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~ 95 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVV 95 (109)
T ss_pred CCCCccCcCCcCCCceEEE
Confidence 4567999999987654443
No 118
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=37.79 E-value=22 Score=25.52 Aligned_cols=33 Identities=15% Similarity=0.347 Sum_probs=23.7
Q ss_pred ccCccceecHHHHHHHhcCCCceecccCCCcccCC
Q psy8140 59 TCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLI 93 (108)
Q Consensus 59 ~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~ 93 (108)
.|.+. |+...+.........-+||.|+..+++.
T Consensus 110 ~C~~~--~~~~~~~~~~~~~~~~~C~~C~~~lrp~ 142 (178)
T PF02146_consen 110 KCGKE--YDREDIVDSIDEEEPPRCPKCGGLLRPD 142 (178)
T ss_dssp TTSBE--EEGHHHHHHHHTTSSCBCTTTSCBEEEE
T ss_pred CCCcc--ccchhhcccccccccccccccCccCCCC
Confidence 47776 7777776655555556999999977653
No 119
>smart00355 ZnF_C2H2 zinc finger.
Probab=37.44 E-value=14 Score=17.10 Aligned_cols=11 Identities=45% Similarity=1.065 Sum_probs=8.5
Q ss_pred eecccCCCccc
Q psy8140 81 WNCPVCDKVGH 91 (108)
Q Consensus 81 W~CPiC~~~~~ 91 (108)
++|+.|++.+.
T Consensus 1 ~~C~~C~~~f~ 11 (26)
T smart00355 1 YRCPECGKVFK 11 (26)
T ss_pred CCCCCCcchhC
Confidence 47999998764
No 120
>KOG1312|consensus
Probab=36.87 E-value=15 Score=30.10 Aligned_cols=15 Identities=13% Similarity=0.563 Sum_probs=13.4
Q ss_pred ccccccccccccccC
Q psy8140 47 GKMRMAFPTKASTCA 61 (108)
Q Consensus 47 S~~ri~~P~Rg~~C~ 61 (108)
|-.+|+-||||++|.
T Consensus 152 STCki~KPARSKHCs 166 (341)
T KOG1312|consen 152 STCKIRKPARSKHCS 166 (341)
T ss_pred ccccCCCccccccch
Confidence 678999999999985
No 121
>PRK07218 replication factor A; Provisional
Probab=36.69 E-value=47 Score=28.04 Aligned_cols=63 Identities=16% Similarity=0.094 Sum_probs=39.7
Q ss_pred HHHHHhccCCCCceeeeeeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCeeehh
Q psy8140 20 YIKEKYNSENDSEIKTLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCMAM 99 (108)
Q Consensus 20 ~i~~~~~~~~Dddi~~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~iD~ 99 (108)
.|.+....++.-++.+....+++.-. |.--=+.| .|+-. -.+|+||.|++.=...+|+|..
T Consensus 268 ~I~e~~~~~g~~~Vev~G~Iv~i~~g-sgli~rCP----~C~r~--------------v~~~~C~~hG~ve~~~dlrik~ 328 (423)
T PRK07218 268 KIREAVERGGIFDVELVGNIISVRDG-SGLIERCP----ECGRV--------------IQKGQCRSHGAVEGEDDLRIKA 328 (423)
T ss_pred chhhhhccCCcceEEEEEEEEEeccC-CcceecCc----Ccccc--------------ccCCcCCCCCCcCCeeeeEEEE
Confidence 56666655555567777777776644 11111223 25443 1349999999998899999865
Q ss_pred hh
Q psy8140 100 IE 101 (108)
Q Consensus 100 ~~ 101 (108)
.+
T Consensus 329 vL 330 (423)
T PRK07218 329 IL 330 (423)
T ss_pred EE
Confidence 43
No 122
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=36.53 E-value=14 Score=31.11 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=9.6
Q ss_pred CCceecccCCCc
Q psy8140 78 KPKWNCPVCDKV 89 (108)
Q Consensus 78 ~~~W~CPiC~~~ 89 (108)
...|.||+|+..
T Consensus 456 p~~~~cp~c~~~ 467 (479)
T PRK05452 456 PDNFLCPECSLG 467 (479)
T ss_pred CCCCcCcCCCCc
Confidence 347999999964
No 123
>KOG2419|consensus
Probab=36.49 E-value=7.6 Score=35.17 Aligned_cols=22 Identities=32% Similarity=0.652 Sum_probs=15.8
Q ss_pred CCCceecccCCCcccCCCeeeh
Q psy8140 77 LKPKWNCPVCDKVGHLILLCMA 98 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~~~dL~iD 98 (108)
-..-|+||+|++...+.-.+.+
T Consensus 585 ~~~i~nCP~C~~~~~~~~~~~~ 606 (975)
T KOG2419|consen 585 FKRIWNCPVCGEALQPTRDKLN 606 (975)
T ss_pred ceeecCCccHHhhhccchhhhh
Confidence 3568999999998876543333
No 124
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=36.31 E-value=19 Score=19.84 Aligned_cols=14 Identities=29% Similarity=0.695 Sum_probs=9.8
Q ss_pred CCceecccCCCccc
Q psy8140 78 KPKWNCPVCDKVGH 91 (108)
Q Consensus 78 ~~~W~CPiC~~~~~ 91 (108)
+....||.|++++.
T Consensus 2 ~~~~~C~nC~R~v~ 15 (33)
T PF08209_consen 2 SPYVECPNCGRPVA 15 (33)
T ss_dssp S-EEE-TTTSSEEE
T ss_pred CCeEECCCCcCCcc
Confidence 45689999999875
No 125
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=35.62 E-value=49 Score=19.98 Aligned_cols=51 Identities=18% Similarity=0.176 Sum_probs=28.0
Q ss_pred HHHHHhccCCCCceeeeeeeeeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCccc
Q psy8140 20 YIKEKYNSENDSEIKTLELTSSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGH 91 (108)
Q Consensus 20 ~i~~~~~~~~Dddi~~~~~~vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~ 91 (108)
.++.+....+-.-+.++..--|-.||.-+.+.+. ......|.||.|+....
T Consensus 7 ~L~yka~~~G~~v~~v~~~~TSq~C~~CG~~~~~---------------------~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 7 RLEYKAEEYGIQVVEVDEAYTSQTCPRCGHRNKK---------------------RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred HHHHHHHHhCCEEEEECCCCCccCccCccccccc---------------------ccccceEEcCCCCCEEC
Confidence 4444443333333344444456667755544443 33456899999987643
No 126
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.39 E-value=17 Score=23.32 Aligned_cols=13 Identities=31% Similarity=0.935 Sum_probs=9.8
Q ss_pred CCceecccCCCcc
Q psy8140 78 KPKWNCPVCDKVG 90 (108)
Q Consensus 78 ~~~W~CPiC~~~~ 90 (108)
+..|+||-|+..-
T Consensus 2 ~~~~kCpKCgn~~ 14 (68)
T COG3478 2 KNAFKCPKCGNTN 14 (68)
T ss_pred CccccCCCcCCcc
Confidence 3579999999643
No 127
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=35.34 E-value=17 Score=23.84 Aligned_cols=19 Identities=21% Similarity=0.314 Sum_probs=10.9
Q ss_pred ceecccCCCcc--cCCCeeeh
Q psy8140 80 KWNCPVCDKVG--HLILLCMA 98 (108)
Q Consensus 80 ~W~CPiC~~~~--~~~dL~iD 98 (108)
.+.||+|+++. ....+.+|
T Consensus 22 ~~~C~iC~~~~~~~~~~~~vD 42 (81)
T PF02945_consen 22 GGRCAICGKPLPGESRKLVVD 42 (81)
T ss_dssp TTE-TTT-SEEETTCGGCEEE
T ss_pred CCcCcCCCCCcccCCCcceec
Confidence 35999999833 34556665
No 128
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=35.21 E-value=15 Score=30.49 Aligned_cols=11 Identities=36% Similarity=0.640 Sum_probs=9.5
Q ss_pred ceecccCCCccc
Q psy8140 80 KWNCPVCDKVGH 91 (108)
Q Consensus 80 ~W~CPiC~~~~~ 91 (108)
.|+|| |+++++
T Consensus 259 ~~~Cp-CG~~i~ 269 (374)
T TIGR00375 259 CANCP-CGGRIK 269 (374)
T ss_pred CCCCC-CCCcce
Confidence 59999 999865
No 129
>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=35.16 E-value=19 Score=25.51 Aligned_cols=13 Identities=38% Similarity=1.048 Sum_probs=10.3
Q ss_pred CCceecccCCCcc
Q psy8140 78 KPKWNCPVCDKVG 90 (108)
Q Consensus 78 ~~~W~CPiC~~~~ 90 (108)
..-|+||.|++..
T Consensus 122 ~~f~~C~~C~kiy 134 (147)
T PF01927_consen 122 DEFWRCPGCGKIY 134 (147)
T ss_pred CeEEECCCCCCEe
Confidence 3479999999853
No 130
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=34.96 E-value=23 Score=17.79 Aligned_cols=11 Identities=27% Similarity=0.507 Sum_probs=8.2
Q ss_pred ecccCCCcccC
Q psy8140 82 NCPVCDKVGHL 92 (108)
Q Consensus 82 ~CPiC~~~~~~ 92 (108)
.||.|++.+.-
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 48888887753
No 131
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=34.86 E-value=20 Score=21.69 Aligned_cols=11 Identities=27% Similarity=1.020 Sum_probs=9.0
Q ss_pred CCceecccCCC
Q psy8140 78 KPKWNCPVCDK 88 (108)
Q Consensus 78 ~~~W~CPiC~~ 88 (108)
.-+|+||.|+.
T Consensus 42 ~i~y~C~~Cg~ 52 (54)
T PF10058_consen 42 EIQYRCPYCGA 52 (54)
T ss_pred ceEEEcCCCCC
Confidence 34899999985
No 132
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=34.39 E-value=4.5 Score=23.18 Aligned_cols=26 Identities=23% Similarity=0.561 Sum_probs=16.6
Q ss_pred CccceecHHHHHHHhcCCCceecccCC
Q psy8140 61 AHLQCFDGATFIKMNELKPKWNCPVCD 87 (108)
Q Consensus 61 ~H~qCFDl~~fl~~~~~~~~W~CPiC~ 87 (108)
.|..|.+...-...... ..|.||.|.
T Consensus 24 ~H~~C~~~~~~~~~~~~-~~w~C~~C~ 49 (51)
T PF00628_consen 24 YHQECVGPPEKAEEIPS-GDWYCPNCR 49 (51)
T ss_dssp EETTTSTSSHSHHSHHS-SSBSSHHHH
T ss_pred hCcccCCCChhhccCCC-CcEECcCCc
Confidence 47777777654433322 389999885
No 133
>KOG3039|consensus
Probab=33.98 E-value=31 Score=27.81 Aligned_cols=65 Identities=17% Similarity=0.217 Sum_probs=43.3
Q ss_pred CCCceeeeeeeeeecCCCccccccccccc---cccCccceecHHHHHHHhcCCCceecccCCCcccCCCeee
Q psy8140 29 NDSEIKTLELTSSLICPLGKMRMAFPTKA---STCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLCM 97 (108)
Q Consensus 29 ~Dddi~~~~~~vsL~CPlS~~ri~~P~Rg---~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~i 97 (108)
++++.-...-.-+..||++...+.+-.+- +.|.|+-|++-..=| -..--.||||+++++-.||+.
T Consensus 209 ~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEkl----ir~D~v~pv~d~plkdrdiI~ 276 (303)
T KOG3039|consen 209 EETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKL----IRKDMVDPVTDKPLKDRDIIG 276 (303)
T ss_pred chhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHh----ccccccccCCCCcCcccceEe
Confidence 33444222334678999999888876553 568888666544311 134578999999999888864
No 134
>KOG3002|consensus
Probab=33.83 E-value=16 Score=29.46 Aligned_cols=44 Identities=27% Similarity=0.388 Sum_probs=36.7
Q ss_pred eecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCccc
Q psy8140 41 SLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGH 91 (108)
Q Consensus 41 sL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~ 91 (108)
=|-||+=...|..|+.--.=.|+-|.+-.. +-.-+||.|..++.
T Consensus 48 lleCPvC~~~l~~Pi~QC~nGHlaCssC~~-------~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPIFQCDNGHLACSSCRT-------KVSNKCPTCRLPIG 91 (299)
T ss_pred hccCchhhccCcccceecCCCcEehhhhhh-------hhcccCCccccccc
Confidence 378999999999999988778998876554 55678999998885
No 135
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.78 E-value=12 Score=22.89 Aligned_cols=14 Identities=36% Similarity=0.750 Sum_probs=11.1
Q ss_pred CceecccCCCcccC
Q psy8140 79 PKWNCPVCDKVGHL 92 (108)
Q Consensus 79 ~~W~CPiC~~~~~~ 92 (108)
+.-.||+|+.++..
T Consensus 11 p~KICpvCqRPFsW 24 (54)
T COG4338 11 PDKICPVCQRPFSW 24 (54)
T ss_pred chhhhhhhcCchHH
Confidence 55679999998864
No 136
>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=33.15 E-value=17 Score=22.38 Aligned_cols=14 Identities=29% Similarity=0.719 Sum_probs=7.1
Q ss_pred CCceecccCCCccc
Q psy8140 78 KPKWNCPVCDKVGH 91 (108)
Q Consensus 78 ~~~W~CPiC~~~~~ 91 (108)
...-.||+|+..++
T Consensus 22 ~~PatCP~C~a~~~ 35 (54)
T PF09237_consen 22 EQPATCPICGAVIR 35 (54)
T ss_dssp S--EE-TTT--EES
T ss_pred CCCCCCCcchhhcc
Confidence 34589999998775
No 137
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=32.95 E-value=20 Score=19.76 Aligned_cols=17 Identities=29% Similarity=0.450 Sum_probs=8.2
Q ss_pred cccCCCcccCC-Ceeehh
Q psy8140 83 CPVCDKVGHLI-LLCMAM 99 (108)
Q Consensus 83 CPiC~~~~~~~-dL~iD~ 99 (108)
|++|++.+... .+.+|-
T Consensus 1 C~~C~~~~~~~~~~~v~H 18 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHH 18 (47)
T ss_dssp -TTT--B--GG-GEEEEE
T ss_pred CCCCCCcCccCcceEeEC
Confidence 88999988664 666663
No 138
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=32.63 E-value=26 Score=26.01 Aligned_cols=21 Identities=14% Similarity=0.306 Sum_probs=14.2
Q ss_pred CCceecccCCCccc--CCCeeeh
Q psy8140 78 KPKWNCPVCDKVGH--LILLCMA 98 (108)
Q Consensus 78 ~~~W~CPiC~~~~~--~~dL~iD 98 (108)
...+.||+|+.++. ..-+.||
T Consensus 18 ~Q~G~CaiC~~~l~~~~~~~~vD 40 (157)
T PHA02565 18 AQNGICPLCKRELDGDVSKNHLD 40 (157)
T ss_pred HhCCcCCCCCCccCCCccccccC
Confidence 34589999998864 2345555
No 139
>smart00746 TRASH metallochaperone-like domain.
Probab=32.43 E-value=28 Score=16.81 Aligned_cols=9 Identities=33% Similarity=0.637 Sum_probs=7.8
Q ss_pred cccCCCccc
Q psy8140 83 CPVCDKVGH 91 (108)
Q Consensus 83 CPiC~~~~~ 91 (108)
||+|++.+.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 899999886
No 140
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=32.23 E-value=26 Score=20.35 Aligned_cols=15 Identities=20% Similarity=0.140 Sum_probs=11.4
Q ss_pred CCCceecccCCCccc
Q psy8140 77 LKPKWNCPVCDKVGH 91 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~ 91 (108)
.....+||.|+..+-
T Consensus 16 ~~~~irC~~CG~rIl 30 (44)
T smart00659 16 SKDVVRCRECGYRIL 30 (44)
T ss_pred CCCceECCCCCceEE
Confidence 456799999997663
No 141
>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=31.84 E-value=22 Score=20.86 Aligned_cols=15 Identities=33% Similarity=0.625 Sum_probs=11.5
Q ss_pred CCceecccCCCcccC
Q psy8140 78 KPKWNCPVCDKVGHL 92 (108)
Q Consensus 78 ~~~W~CPiC~~~~~~ 92 (108)
-+.=.||+|+.+++.
T Consensus 6 lp~K~C~~C~rpf~W 20 (42)
T PF10013_consen 6 LPSKICPVCGRPFTW 20 (42)
T ss_pred CCCCcCcccCCcchH
Confidence 355689999998863
No 142
>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=31.71 E-value=6.5 Score=22.38 Aligned_cols=27 Identities=26% Similarity=0.651 Sum_probs=18.5
Q ss_pred ccccCccceecHHHHHHHhcCCCceecccCCC
Q psy8140 57 ASTCAHLQCFDGATFIKMNELKPKWNCPVCDK 88 (108)
Q Consensus 57 g~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~ 88 (108)
-..|.|. |+... .+.. .....||.|+.
T Consensus 8 C~~Cg~~--fe~~~--~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 8 CEECGHE--FEVLQ--SISE-DDPVPCPECGS 34 (42)
T ss_pred eCCCCCE--EEEEE--EcCC-CCCCcCCCCCC
Confidence 3467776 66543 3344 67899999998
No 143
>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=31.59 E-value=31 Score=17.81 Aligned_cols=11 Identities=27% Similarity=0.760 Sum_probs=8.5
Q ss_pred CCceecccCCC
Q psy8140 78 KPKWNCPVCDK 88 (108)
Q Consensus 78 ~~~W~CPiC~~ 88 (108)
...+.||-|+.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 56788999974
No 144
>KOG4739|consensus
Probab=31.40 E-value=32 Score=26.93 Aligned_cols=37 Identities=27% Similarity=0.436 Sum_probs=25.6
Q ss_pred cccccccccCccceecHHHHHHHhcCCCce-ecccCCCcccCCCe
Q psy8140 52 AFPTKASTCAHLQCFDGATFIKMNELKPKW-NCPVCDKVGHLILL 95 (108)
Q Consensus 52 ~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W-~CPiC~~~~~~~dL 95 (108)
..|-.=..|.|+ |-+-+.....- .||+|+++++..+|
T Consensus 15 ~~~f~LTaC~Hv-------fC~~C~k~~~~~~C~lCkk~ir~i~l 52 (233)
T KOG4739|consen 15 QDPFFLTACRHV-------FCEPCLKASSPDVCPLCKKSIRIIQL 52 (233)
T ss_pred CCceeeeechhh-------hhhhhcccCCccccccccceeeeeec
Confidence 666677889998 55544444434 99999999765444
No 145
>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=31.05 E-value=7 Score=22.51 Aligned_cols=19 Identities=16% Similarity=0.592 Sum_probs=12.2
Q ss_pred HHHHhcCCCceecccCCCc
Q psy8140 71 FIKMNELKPKWNCPVCDKV 89 (108)
Q Consensus 71 fl~~~~~~~~W~CPiC~~~ 89 (108)
||.+......-.||.|+..
T Consensus 20 yl~l~~~~~~~~CpYCg~~ 38 (40)
T PF10276_consen 20 YLNLDDEPGPVVCPYCGTR 38 (40)
T ss_dssp EEE-TTTTCEEEETTTTEE
T ss_pred EEecCCCCCeEECCCCCCE
Confidence 4444444456899999865
No 146
>KOG0824|consensus
Probab=30.61 E-value=27 Score=28.68 Aligned_cols=47 Identities=23% Similarity=0.268 Sum_probs=33.9
Q ss_pred eecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCccc
Q psy8140 41 SLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGH 91 (108)
Q Consensus 41 sL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~ 91 (108)
.=.|||=++.+..| -.-.|.|.-||- -++-......-.||+|..++.
T Consensus 7 ~~eC~IC~nt~n~P-v~l~C~HkFCyi---CiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 7 KKECLICYNTGNCP-VNLYCFHKFCYI---CIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred CCcceeeeccCCcC-ccccccchhhhh---hhcchhhcCCCCCceecCCCC
Confidence 34688999999999 556999985542 223344456667999999885
No 147
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=29.97 E-value=18 Score=26.18 Aligned_cols=29 Identities=24% Similarity=0.557 Sum_probs=21.3
Q ss_pred ccccccCccceecHHHHHHHhcCCCceecccCC
Q psy8140 55 TKASTCAHLQCFDGATFIKMNELKPKWNCPVCD 87 (108)
Q Consensus 55 ~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~ 87 (108)
+-+..|.|+.|.=.-. .....+.|.|| |.
T Consensus 103 a~~~iCtHlGC~~~~~---~~~~~~~~~CP-CH 131 (177)
T COG0723 103 AYSAICTHLGCTVPWN---NAGAEGGFFCP-CH 131 (177)
T ss_pred EEeeeccCCCCccCcc---cCCCCCeEEcc-CC
Confidence 7888999999975443 12456899999 54
No 148
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=29.69 E-value=71 Score=23.86 Aligned_cols=38 Identities=8% Similarity=0.294 Sum_probs=23.4
Q ss_pred ccCccceecHHHHHHHh-cCCCceecccCCCcccCCCeeeh
Q psy8140 59 TCAHLQCFDGATFIKMN-ELKPKWNCPVCDKVGHLILLCMA 98 (108)
Q Consensus 59 ~C~H~qCFDl~~fl~~~-~~~~~W~CPiC~~~~~~~dL~iD 98 (108)
.|.+. |+.+.++... ......+||.|+..+++.=+-.+
T Consensus 100 ~C~~~--~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~VV~Fg 138 (206)
T cd01410 100 SCGPE--YVRDDVVETRGDKETGRRCHACGGILKDTIVDFG 138 (206)
T ss_pred CCCCc--cchHHHHHHhhcCCCCCcCCCCcCccCCcEEECC
Confidence 47766 6666655432 23345789999988776544433
No 149
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=29.58 E-value=22 Score=29.30 Aligned_cols=52 Identities=29% Similarity=0.483 Sum_probs=36.8
Q ss_pred eeecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCcccCCCee
Q psy8140 40 SSLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 40 vsL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~~~dL~ 96 (108)
-.|+|-|-..+|++|+-. .|.|.-|+ |--.......=.||+|.......-|+
T Consensus 24 s~lrC~IC~~~i~ip~~T-tCgHtFCs----lCIR~hL~~qp~CP~Cr~~~~esrlr 75 (391)
T COG5432 24 SMLRCRICDCRISIPCET-TCGHTFCS----LCIRRHLGTQPFCPVCREDPCESRLR 75 (391)
T ss_pred hHHHhhhhhheeecceec-ccccchhH----HHHHHHhcCCCCCccccccHHhhhcc
Confidence 468999999999999975 89998442 22223335567899999776554444
No 150
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.56 E-value=59 Score=24.47 Aligned_cols=15 Identities=27% Similarity=0.578 Sum_probs=11.7
Q ss_pred CCCceecccCCCccc
Q psy8140 77 LKPKWNCPVCDKVGH 91 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~ 91 (108)
..+.|.||.|+....
T Consensus 319 ~~r~~~C~~cg~~~~ 333 (364)
T COG0675 319 SGRLFKCPRCGFVHD 333 (364)
T ss_pred cceeEECCCCCCeeh
Confidence 467899999997653
No 151
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.06 E-value=14 Score=25.52 Aligned_cols=21 Identities=14% Similarity=0.172 Sum_probs=13.9
Q ss_pred eecccCCCc----ccCCCeeehhhh
Q psy8140 81 WNCPVCDKV----GHLILLCMAMIE 101 (108)
Q Consensus 81 W~CPiC~~~----~~~~dL~iD~~~ 101 (108)
.+||.|+.. ..=++|+|+.+.
T Consensus 89 ~~CP~Cgs~~~~i~~G~El~I~~iE 113 (117)
T PRK00564 89 GVCEKCHSKNVIITQGNEMRLLSLE 113 (117)
T ss_pred CcCcCCCCCceEEecCCEEEEEEEE
Confidence 469999964 344577776543
No 152
>KOG2893|consensus
Probab=28.77 E-value=30 Score=27.86 Aligned_cols=30 Identities=20% Similarity=0.523 Sum_probs=26.4
Q ss_pred ccCccceecHHHHHHHhcCCCceecccCCCcc
Q psy8140 59 TCAHLQCFDGATFIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 59 ~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~ 90 (108)
.|+.- ||-+-+|-..++.+.++|-||.+.+
T Consensus 15 ycnre--fddekiliqhqkakhfkchichkkl 44 (341)
T KOG2893|consen 15 YCNRE--FDDEKILIQHQKAKHFKCHICHKKL 44 (341)
T ss_pred ecccc--cchhhhhhhhhhhccceeeeehhhh
Confidence 57766 9999999999999999999999876
No 153
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=28.70 E-value=24 Score=21.08 Aligned_cols=13 Identities=31% Similarity=0.662 Sum_probs=10.0
Q ss_pred ecccCCCcccCCC
Q psy8140 82 NCPVCDKVGHLIL 94 (108)
Q Consensus 82 ~CPiC~~~~~~~d 94 (108)
+|++|++.+.+-.
T Consensus 1 ~C~iCg~kigl~~ 13 (51)
T PF14471_consen 1 KCAICGKKIGLFK 13 (51)
T ss_pred CCCcccccccccc
Confidence 5999999886544
No 154
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=28.66 E-value=25 Score=19.39 Aligned_cols=14 Identities=21% Similarity=0.399 Sum_probs=10.7
Q ss_pred eecccCCCcccCCC
Q psy8140 81 WNCPVCDKVGHLIL 94 (108)
Q Consensus 81 W~CPiC~~~~~~~d 94 (108)
..||-|+....+.+
T Consensus 3 i~CP~C~~~f~v~~ 16 (37)
T PF13719_consen 3 ITCPNCQTRFRVPD 16 (37)
T ss_pred EECCCCCceEEcCH
Confidence 57999998776554
No 155
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=28.42 E-value=29 Score=21.59 Aligned_cols=13 Identities=31% Similarity=0.866 Sum_probs=9.7
Q ss_pred CceecccCCCccc
Q psy8140 79 PKWNCPVCDKVGH 91 (108)
Q Consensus 79 ~~W~CPiC~~~~~ 91 (108)
..|.|++|++...
T Consensus 49 ~~~~C~~C~~~f~ 61 (100)
T PF12756_consen 49 ESFRCPYCNKTFR 61 (100)
T ss_dssp SSEEBSSSS-EES
T ss_pred CCCCCCccCCCCc
Confidence 3699999998763
No 156
>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=28.23 E-value=23 Score=19.12 Aligned_cols=13 Identities=23% Similarity=0.697 Sum_probs=8.9
Q ss_pred eecccCCCcccCC
Q psy8140 81 WNCPVCDKVGHLI 93 (108)
Q Consensus 81 W~CPiC~~~~~~~ 93 (108)
..||-|++...+.
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 5688888766544
No 157
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=28.00 E-value=32 Score=21.26 Aligned_cols=11 Identities=27% Similarity=0.712 Sum_probs=7.2
Q ss_pred ceecccCCCcc
Q psy8140 80 KWNCPVCDKVG 90 (108)
Q Consensus 80 ~W~CPiC~~~~ 90 (108)
...||+|+...
T Consensus 4 Wi~CP~CgnKT 14 (55)
T PF14205_consen 4 WILCPICGNKT 14 (55)
T ss_pred EEECCCCCCcc
Confidence 34688888554
No 158
>KOG2660|consensus
Probab=27.74 E-value=33 Score=28.23 Aligned_cols=62 Identities=24% Similarity=0.358 Sum_probs=48.2
Q ss_pred eecCCCccccccccccccccCccceecHHHHHHHhcCCCceecccCCCccc----CCCeeehhhhhhhhh
Q psy8140 41 SLICPLGKMRMAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVGH----LILLCMAMIESVCLF 106 (108)
Q Consensus 41 sL~CPlS~~ri~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~~----~~dL~iD~~~~~~l~ 106 (108)
-+.|+|=...|..+.--..|-|. |-..=++..-.. .-.||.|+..++ ...|.-|..+++|.+
T Consensus 15 ~itC~LC~GYliDATTI~eCLHT--FCkSCivk~l~~--~~~CP~C~i~ih~t~pl~ni~~DrtlqdiVy 80 (331)
T KOG2660|consen 15 HITCRLCGGYLIDATTITECLHT--FCKSCIVKYLEE--SKYCPTCDIVIHKTHPLLNIRSDRTLQDIVY 80 (331)
T ss_pred ceehhhccceeecchhHHHHHHH--HHHHHHHHHHHH--hccCCccceeccCccccccCCcchHHHHHHH
Confidence 35688888888888889999998 777766666555 567999997664 567888998888753
No 159
>PF07812 TfuA: TfuA-like protein; InterPro: IPR012924 This domain consists of a group of sequences that are similar to the core of TfuA protein (Q52872 from SWISSPROT). This protein is involved in the production of trifolitoxin (TFX), a gene-encoded, post-translationally modified peptide antibiotic []. The role of TfuA in TFX synthesis is unknown, and it may be involved in other cellular processes [].
Probab=27.42 E-value=58 Score=23.07 Aligned_cols=45 Identities=31% Similarity=0.415 Sum_probs=25.6
Q ss_pred CcchH--HHHhccCCChHHHHHHHHHhc---cCCCCceeeeeeeeee-cCCCcc
Q psy8140 1 MGSIV--SLIAHLMRDIAFSRYIKEKYN---SENDSEIKTLELTSSL-ICPLGK 48 (108)
Q Consensus 1 ~~~l~--~l~~~~~~~~~~~~~i~~~~~---~~~Dddi~~~~~~vsL-~CPlS~ 48 (108)
||+|. +|..-+|+..- .|=+.+. -++||||.+....-.+ -.|||-
T Consensus 31 MGALRAaEl~~fGM~GvG---~If~~Yr~G~i~~DDEVAv~~~p~~~g~~~ls~ 81 (120)
T PF07812_consen 31 MGALRAAELAPFGMIGVG---RIFEWYRDGEIEDDDEVAVLHGPAELGYRPLSE 81 (120)
T ss_pred HHHHHHHHhHhcCCEeeh---HHHHHHhcCCcCCccceeeeecCcccCCccccH
Confidence 45553 45556666555 2223332 2678899887665555 556654
No 160
>PRK12496 hypothetical protein; Provisional
Probab=26.70 E-value=26 Score=25.58 Aligned_cols=12 Identities=17% Similarity=0.327 Sum_probs=9.3
Q ss_pred eecccCCCcccC
Q psy8140 81 WNCPVCDKVGHL 92 (108)
Q Consensus 81 W~CPiC~~~~~~ 92 (108)
-.||+||.++..
T Consensus 144 ~~C~~CG~~~~r 155 (164)
T PRK12496 144 DVCEICGSPVKR 155 (164)
T ss_pred CcCCCCCChhhh
Confidence 469999988753
No 161
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.62 E-value=26 Score=24.37 Aligned_cols=22 Identities=23% Similarity=0.305 Sum_probs=14.2
Q ss_pred CceecccCCC----cccCCCeeehhh
Q psy8140 79 PKWNCPVCDK----VGHLILLCMAMI 100 (108)
Q Consensus 79 ~~W~CPiC~~----~~~~~dL~iD~~ 100 (108)
+.|.||.|+. .+.=++|+|+.+
T Consensus 91 ~~~~CP~Cgs~~~~i~~G~El~i~~I 116 (124)
T PRK00762 91 AVIECPVCGNKRAHILGGRECNVKNI 116 (124)
T ss_pred cCCcCcCCCCCCCEEecCCeEEEEEE
Confidence 3588999994 234466666543
No 162
>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=26.50 E-value=28 Score=20.09 Aligned_cols=10 Identities=30% Similarity=0.949 Sum_probs=7.8
Q ss_pred ecccCCCccc
Q psy8140 82 NCPVCDKVGH 91 (108)
Q Consensus 82 ~CPiC~~~~~ 91 (108)
+||.|+..+.
T Consensus 1 ~CP~Cg~~a~ 10 (47)
T PF04606_consen 1 RCPHCGSKAR 10 (47)
T ss_pred CcCCCCCeeE
Confidence 5999998664
No 163
>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=26.46 E-value=30 Score=23.86 Aligned_cols=10 Identities=40% Similarity=0.989 Sum_probs=4.6
Q ss_pred ceecccCCCc
Q psy8140 80 KWNCPVCDKV 89 (108)
Q Consensus 80 ~W~CPiC~~~ 89 (108)
++.||.||+.
T Consensus 9 KR~Cp~CG~k 18 (108)
T PF09538_consen 9 KRTCPSCGAK 18 (108)
T ss_pred cccCCCCcch
Confidence 3445444443
No 164
>KOG4265|consensus
Probab=26.45 E-value=37 Score=28.15 Aligned_cols=12 Identities=33% Similarity=0.814 Sum_probs=9.6
Q ss_pred ceecccCCCccc
Q psy8140 80 KWNCPVCDKVGH 91 (108)
Q Consensus 80 ~W~CPiC~~~~~ 91 (108)
.-+||||.+++.
T Consensus 325 ~n~CPICRqpi~ 336 (349)
T KOG4265|consen 325 TNNCPICRQPIE 336 (349)
T ss_pred hcCCCccccchH
Confidence 347999999884
No 165
>PHA02768 hypothetical protein; Provisional
Probab=26.33 E-value=22 Score=21.90 Aligned_cols=11 Identities=27% Similarity=1.117 Sum_probs=8.8
Q ss_pred eecccCCCccc
Q psy8140 81 WNCPVCDKVGH 91 (108)
Q Consensus 81 W~CPiC~~~~~ 91 (108)
.+||.|++.+.
T Consensus 6 y~C~~CGK~Fs 16 (55)
T PHA02768 6 YECPICGEIYI 16 (55)
T ss_pred cCcchhCCeec
Confidence 58999998775
No 166
>KOG1705|consensus
Probab=26.30 E-value=34 Score=23.59 Aligned_cols=18 Identities=22% Similarity=0.349 Sum_probs=14.2
Q ss_pred CceecccCCCcccCCCee
Q psy8140 79 PKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 79 ~~W~CPiC~~~~~~~dL~ 96 (108)
---+||||...+.+..|+
T Consensus 26 CDgkC~ICDS~VRP~tlV 43 (110)
T KOG1705|consen 26 CDGKCVICDSYVRPCTLV 43 (110)
T ss_pred cCCcccccccccccceee
Confidence 346899999998887664
No 167
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.27 E-value=30 Score=24.41 Aligned_cols=16 Identities=13% Similarity=0.484 Sum_probs=12.9
Q ss_pred CCceecccCCCcccCC
Q psy8140 78 KPKWNCPVCDKVGHLI 93 (108)
Q Consensus 78 ~~~W~CPiC~~~~~~~ 93 (108)
..+|+||.|++....+
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4689999999987644
No 168
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=26.02 E-value=25 Score=21.31 Aligned_cols=14 Identities=29% Similarity=0.575 Sum_probs=9.7
Q ss_pred CCceecccCCCccc
Q psy8140 78 KPKWNCPVCDKVGH 91 (108)
Q Consensus 78 ~~~W~CPiC~~~~~ 91 (108)
+..-.||||+++++
T Consensus 33 ~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 33 SRSDRCPICGKPLP 46 (50)
T ss_dssp SSSSEETTTTEE--
T ss_pred ccccCCCcccCcCc
Confidence 44578999998875
No 169
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=25.90 E-value=30 Score=28.93 Aligned_cols=16 Identities=25% Similarity=0.717 Sum_probs=11.8
Q ss_pred cCCCceecccCCCccc
Q psy8140 76 ELKPKWNCPVCDKVGH 91 (108)
Q Consensus 76 ~~~~~W~CPiC~~~~~ 91 (108)
..+-.|.||-|++=-+
T Consensus 364 a~~l~W~CPsC~~W~T 379 (389)
T COG2956 364 AHTLYWHCPSCRAWET 379 (389)
T ss_pred ceeeeeeCCCcccccc
Confidence 3456899999996443
No 170
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PRK00420 hypothetical protein; Validated
Probab=25.54 E-value=44 Score=23.29 Aligned_cols=18 Identities=28% Similarity=0.233 Sum_probs=13.7
Q ss_pred CCCceecccCCCcccCCC
Q psy8140 77 LKPKWNCPVCDKVGHLIL 94 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~~~d 94 (108)
+.+.-.||.|++....++
T Consensus 37 k~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 37 KDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCceECCCCCCeeeecc
Confidence 567899999998765443
No 172
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=25.48 E-value=59 Score=27.74 Aligned_cols=41 Identities=20% Similarity=0.484 Sum_probs=22.4
Q ss_pred CCccccccccccccccCccceecHH---HHHHHhcCCCceecccCCCcccCC
Q psy8140 45 PLGKMRMAFPTKASTCAHLQCFDGA---TFIKMNELKPKWNCPVCDKVGHLI 93 (108)
Q Consensus 45 PlS~~ri~~P~Rg~~C~H~qCFDl~---~fl~~~~~~~~W~CPiC~~~~~~~ 93 (108)
|+-+..=+.|-| -.|.|. |.++ +|++.+ -.||||..++-++
T Consensus 304 ~~~~~~~~~pKr-LpCGHi--lHl~CLknW~ERq-----QTCPICr~p~ifd 347 (491)
T COG5243 304 PLPRGLDMTPKR-LPCGHI--LHLHCLKNWLERQ-----QTCPICRRPVIFD 347 (491)
T ss_pred cCcccccCCccc-ccccce--eeHHHHHHHHHhc-----cCCCcccCccccc
Confidence 333333333433 357774 5554 444433 3599999986543
No 173
>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=24.93 E-value=37 Score=18.28 Aligned_cols=28 Identities=29% Similarity=0.517 Sum_probs=16.8
Q ss_pred cccCccceecHHHHHHHhcCCCceecccCCCcc
Q psy8140 58 STCAHLQCFDGATFIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 58 ~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~ 90 (108)
..|.|. |+...-. .......||.|+..+
T Consensus 9 ~~Cg~~--fe~~~~~---~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 9 EDCGHT--FEVLQKI---SDDPLATCPECGGDV 36 (41)
T ss_pred CCCCCE--EEEEEec---CCCCCCCCCCCCCcc
Confidence 456665 5543211 125678999999854
No 174
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.79 E-value=37 Score=24.72 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=14.6
Q ss_pred HHHHHhcCCCceecccCCCcccC
Q psy8140 70 TFIKMNELKPKWNCPVCDKVGHL 92 (108)
Q Consensus 70 ~fl~~~~~~~~W~CPiC~~~~~~ 92 (108)
+|-.-.-...--+||+|+.+++-
T Consensus 29 afcskcgeati~qcp~csasirg 51 (160)
T COG4306 29 AFCSKCGEATITQCPICSASIRG 51 (160)
T ss_pred HHHhhhchHHHhcCCccCCcccc
Confidence 34333333456789999998863
No 175
>KOG4623|consensus
Probab=24.72 E-value=30 Score=30.43 Aligned_cols=16 Identities=25% Similarity=0.955 Sum_probs=12.2
Q ss_pred CCCceecccCCCcccC
Q psy8140 77 LKPKWNCPVCDKVGHL 92 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~~ 92 (108)
.++.|.||.|.+.=.+
T Consensus 44 ~rNswTCpsCEQyNgf 59 (611)
T KOG4623|consen 44 GRNSWTCPSCEQYNGF 59 (611)
T ss_pred CCCCCcCCcHHhhCCC
Confidence 4678999999875443
No 176
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=24.59 E-value=29 Score=28.98 Aligned_cols=14 Identities=29% Similarity=0.888 Sum_probs=11.2
Q ss_pred CCceecccCCCccc
Q psy8140 78 KPKWNCPVCDKVGH 91 (108)
Q Consensus 78 ~~~W~CPiC~~~~~ 91 (108)
...|+||-|+..++
T Consensus 263 ~~~wrCpkCGg~ik 276 (403)
T COG1379 263 SLRWRCPKCGGKIK 276 (403)
T ss_pred hhcccCcccccchh
Confidence 46799999998654
No 177
>KOG1984|consensus
Probab=24.09 E-value=20 Score=33.28 Aligned_cols=36 Identities=17% Similarity=0.392 Sum_probs=28.1
Q ss_pred ccccccccccCccceecHHHHHHHhcCCCceecccCCCcc
Q psy8140 51 MAFPTKASTCAHLQCFDGATFIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 51 i~~P~Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~~ 90 (108)
...|+|=..|+-- ..-|+++....++|.|++|+..-
T Consensus 335 ~sgPvRC~RCkaY----inPFmqF~~~gr~f~Cn~C~~~n 370 (1007)
T KOG1984|consen 335 ESGPVRCNRCKAY----INPFMQFIDGGRKFICNFCGSKN 370 (1007)
T ss_pred CCCCcchhhhhhh----cCcceEEecCCceEEecCCCccc
Confidence 4569999999875 33577777778899999999654
No 178
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.83 E-value=35 Score=27.14 Aligned_cols=19 Identities=26% Similarity=0.408 Sum_probs=14.1
Q ss_pred CCceecccCCCcccCCCee
Q psy8140 78 KPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 78 ~~~W~CPiC~~~~~~~dL~ 96 (108)
..+..||||+..+.-++..
T Consensus 17 kk~ieCPvC~tkFkkeev~ 35 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVK 35 (267)
T ss_pred hceeccCcccchhhhhhee
Confidence 4578999999877655543
No 179
>KOG3970|consensus
Probab=23.42 E-value=62 Score=25.84 Aligned_cols=44 Identities=23% Similarity=0.433 Sum_probs=29.4
Q ss_pred cccccccccCccceecHHHHHHHhcC---------CCceecccCCCccc-CCCe
Q psy8140 52 AFPTKASTCAHLQCFDGATFIKMNEL---------KPKWNCPVCDKVGH-LILL 95 (108)
Q Consensus 52 ~~P~Rg~~C~H~qCFDl~~fl~~~~~---------~~~W~CPiC~~~~~-~~dL 95 (108)
.+|--+..|.-+-||++-.|--++++ ..-.+||-|+..+- ..+|
T Consensus 57 ~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~Nl 110 (299)
T KOG3970|consen 57 NTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINL 110 (299)
T ss_pred CCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccc
Confidence 34555667777778887776655543 24589999998764 3444
No 180
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=23.18 E-value=50 Score=24.09 Aligned_cols=14 Identities=29% Similarity=0.778 Sum_probs=11.3
Q ss_pred hcCCCceecccCCC
Q psy8140 75 NELKPKWNCPVCDK 88 (108)
Q Consensus 75 ~~~~~~W~CPiC~~ 88 (108)
+...+...||+|+.
T Consensus 27 Q~~~glv~CP~Cgs 40 (148)
T PF06676_consen 27 QQARGLVSCPVCGS 40 (148)
T ss_pred HHHcCCccCCCCCC
Confidence 44568899999995
No 181
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=23.08 E-value=28 Score=23.37 Aligned_cols=17 Identities=24% Similarity=0.306 Sum_probs=1.5
Q ss_pred eecccCCCcccCCCeee
Q psy8140 81 WNCPVCDKVGHLILLCM 97 (108)
Q Consensus 81 W~CPiC~~~~~~~dL~i 97 (108)
=+||+|+..+.+++...
T Consensus 15 E~C~~C~~~i~~~~~~~ 31 (99)
T PF12660_consen 15 EKCPICGAPIPFDDLDE 31 (99)
T ss_dssp --------------SSE
T ss_pred ccccccccccccCCcCE
Confidence 68999999998877643
No 182
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=22.99 E-value=35 Score=23.35 Aligned_cols=32 Identities=19% Similarity=0.333 Sum_probs=19.7
Q ss_pred ccCccceecHHHHHHHhcCCCceecccCCCc----ccCCCeeehhh
Q psy8140 59 TCAHLQCFDGATFIKMNELKPKWNCPVCDKV----GHLILLCMAMI 100 (108)
Q Consensus 59 ~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~~----~~~~dL~iD~~ 100 (108)
.|.+. |.... ..+.||.|+.. ..=++|+|+.+
T Consensus 75 ~Cg~~--~~~~~--------~~~~CP~Cgs~~~~i~~G~El~i~~i 110 (113)
T PRK12380 75 DCSQV--VEIHQ--------HDAQCPHCHGERLRVDTGDSLIVKSI 110 (113)
T ss_pred cCCCE--EecCC--------cCccCcCCCCCCcEEccCCeEEEEEE
Confidence 67655 55432 45779999953 34466666643
No 183
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=22.88 E-value=26 Score=18.94 Aligned_cols=11 Identities=27% Similarity=0.824 Sum_probs=3.4
Q ss_pred ecccCCCcccC
Q psy8140 82 NCPVCDKVGHL 92 (108)
Q Consensus 82 ~CPiC~~~~~~ 92 (108)
+||.|+....+
T Consensus 4 ~Cp~C~se~~y 14 (30)
T PF08274_consen 4 KCPLCGSEYTY 14 (30)
T ss_dssp --TTT-----E
T ss_pred CCCCCCCccee
Confidence 79999987765
No 184
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=22.51 E-value=34 Score=21.98 Aligned_cols=21 Identities=24% Similarity=0.264 Sum_probs=14.2
Q ss_pred cCCCceecccCCCcccCCCeee
Q psy8140 76 ELKPKWNCPVCDKVGHLILLCM 97 (108)
Q Consensus 76 ~~~~~W~CPiC~~~~~~~dL~i 97 (108)
....+-+| +||+.+.+++.+|
T Consensus 16 e~~kTkkC-~CG~~l~vk~~rI 36 (68)
T PF09082_consen 16 EGAKTKKC-VCGKTLKVKERRI 36 (68)
T ss_dssp TT-SEEEE-TTTEEEE--SSS-
T ss_pred CCcceeEe-cCCCeeeeeeEEE
Confidence 34567899 8999999988876
No 185
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=22.29 E-value=53 Score=23.03 Aligned_cols=16 Identities=25% Similarity=0.982 Sum_probs=11.4
Q ss_pred CCCceecccCCCcccC
Q psy8140 77 LKPKWNCPVCDKVGHL 92 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~~ 92 (108)
+...|.||.|++.=.+
T Consensus 17 ~~~~w~C~~C~q~N~f 32 (131)
T PF09779_consen 17 RNSNWTCPHCEQYNGF 32 (131)
T ss_pred CCCeeECCCCCCccCc
Confidence 3445999999975443
No 186
>KOG0827|consensus
Probab=22.21 E-value=47 Score=28.34 Aligned_cols=27 Identities=33% Similarity=0.855 Sum_probs=22.1
Q ss_pred ccCccceecHHHHHHHhcCCCc-eecccCC
Q psy8140 59 TCAHLQCFDGATFIKMNELKPK-WNCPVCD 87 (108)
Q Consensus 59 ~C~H~qCFDl~~fl~~~~~~~~-W~CPiC~ 87 (108)
.|.|. |+.--..+....-|. -.||+|.
T Consensus 25 ~cGhi--fh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 25 TCGHI--FHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred chhhH--HHHHHHHHHHccCCccCCCCcee
Confidence 49999 999988887776664 3899999
No 187
>KOG0804|consensus
Probab=22.19 E-value=40 Score=29.09 Aligned_cols=40 Identities=30% Similarity=0.527 Sum_probs=27.3
Q ss_pred cCCCccccccccc---cccccCccceecHHHHHHHhcCCCceecccCCC
Q psy8140 43 ICPLGKMRMAFPT---KASTCAHLQCFDGATFIKMNELKPKWNCPVCDK 88 (108)
Q Consensus 43 ~CPlS~~ri~~P~---Rg~~C~H~qCFDl~~fl~~~~~~~~W~CPiC~~ 88 (108)
.||+=+-||---+ +...|.|. |...-.. +...-.||+|.-
T Consensus 177 TCpVCLERMD~s~~gi~t~~c~Hs--fh~~cl~----~w~~~scpvcR~ 219 (493)
T KOG0804|consen 177 TCPVCLERMDSSTTGILTILCNHS--FHCSCLM----KWWDSSCPVCRY 219 (493)
T ss_pred CcchhHhhcCccccceeeeecccc--cchHHHh----hcccCcChhhhh
Confidence 6888889998777 88899998 6655422 233345666653
No 188
>PF14149 YhfH: YhfH-like protein
Probab=22.01 E-value=17 Score=20.78 Aligned_cols=20 Identities=20% Similarity=0.360 Sum_probs=15.2
Q ss_pred HHHHhcCCCceecccCCCcc
Q psy8140 71 FIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 71 fl~~~~~~~~W~CPiC~~~~ 90 (108)
..++..+-|.=+||.||+.+
T Consensus 4 ~~eFfrnLp~K~C~~CG~~i 23 (37)
T PF14149_consen 4 IVEFFRNLPPKKCTECGKEI 23 (37)
T ss_pred HHHHHHhCCCcccHHHHHHH
Confidence 34556677888999999875
No 189
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=21.68 E-value=46 Score=21.96 Aligned_cols=15 Identities=20% Similarity=0.213 Sum_probs=11.8
Q ss_pred ceecccCCCcccCCC
Q psy8140 80 KWNCPVCDKVGHLIL 94 (108)
Q Consensus 80 ~W~CPiC~~~~~~~d 94 (108)
.=+||.|+.+....+
T Consensus 8 ~~~C~~CG~d~~~~~ 22 (86)
T PF06170_consen 8 APRCPHCGLDYSHAR 22 (86)
T ss_pred CCcccccCCccccCC
Confidence 457999999887655
No 190
>KOG1952|consensus
Probab=21.55 E-value=60 Score=30.21 Aligned_cols=33 Identities=27% Similarity=0.602 Sum_probs=23.4
Q ss_pred ccCccceecHHHHHHHhc-----CCCceecccCC---CcccCC
Q psy8140 59 TCAHLQCFDGATFIKMNE-----LKPKWNCPVCD---KVGHLI 93 (108)
Q Consensus 59 ~C~H~qCFDl~~fl~~~~-----~~~~W~CPiC~---~~~~~~ 93 (108)
.|-|+ |++.=+.++.. ....|+||-|. +.++..
T Consensus 212 sCYhV--FHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~~~~~ 252 (950)
T KOG1952|consen 212 SCYHV--FHLNCIKKWARSSEKTGQDGWRCPACQSVSKTVPKT 252 (950)
T ss_pred hhhhh--hhHHHHHHHHHHhhhccCccccCCcccchhccCCcc
Confidence 49998 99986666532 23679999999 444443
No 191
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=21.19 E-value=44 Score=28.12 Aligned_cols=18 Identities=22% Similarity=0.405 Sum_probs=12.8
Q ss_pred CCCceecccCCCcccCCC
Q psy8140 77 LKPKWNCPVCDKVGHLIL 94 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~~~d 94 (108)
.+-.|+||-|+.--++.+
T Consensus 18 ~~~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 18 PKWQGKCPACHAWNTITE 35 (454)
T ss_pred ccccEECcCCCCccccch
Confidence 455799999997554444
No 192
>cd07692 Ig_CD3_epsilon Immunoglobulin (Ig)-like domain of CD3 epsilon chain. Ig_CD3_epsilon; immunoglobulin (Ig)-like domain of CD3 epsilon chain. CD3 is a T cell surface receptor that is associated with alpha/beta T cell receptors (TCRs). The CD3 complex consists of one gamma, one delta, two epsilon, and two zeta chains. The CD3 subunits form heterodimers as gamma/epsilon, delta/epsilon, and zeta/zeta. The gamma, delta, and epsilon chains each contain an extracellular Ig domain, whereas the extracellular domains of the zeta chains are very small and have unknown structure. The CD3 domain participates in intracellular signalling once the TCR has bound an MHC/antigen complex.
Probab=21.19 E-value=88 Score=19.75 Aligned_cols=20 Identities=20% Similarity=0.398 Sum_probs=14.9
Q ss_pred eeeeeeeeeecCCCcccccc
Q psy8140 33 IKTLELTSSLICPLGKMRMA 52 (108)
Q Consensus 33 i~~~~~~vsL~CPlS~~ri~ 52 (108)
|-++...|.|.||.....|+
T Consensus 3 VsisGTtVtlTCP~~~~~i~ 22 (65)
T cd07692 3 VSISGTTVTVTCPLSGDDIK 22 (65)
T ss_pred EEEeccEEEEECCCCCCCce
Confidence 56778899999997654444
No 193
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=21.07 E-value=49 Score=22.87 Aligned_cols=19 Identities=16% Similarity=0.284 Sum_probs=14.0
Q ss_pred CCceecccCCCcccCCCee
Q psy8140 78 KPKWNCPVCDKVGHLILLC 96 (108)
Q Consensus 78 ~~~W~CPiC~~~~~~~dL~ 96 (108)
-+.+.||.|+..+..--+.
T Consensus 45 vG~~~cP~Cge~~~~a~vv 63 (102)
T PF04475_consen 45 VGDTICPKCGEELDSAFVV 63 (102)
T ss_pred cCcccCCCCCCccCceEEE
Confidence 4678999999988654333
No 194
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=20.92 E-value=51 Score=18.47 Aligned_cols=9 Identities=33% Similarity=0.995 Sum_probs=6.5
Q ss_pred ecccCCCcc
Q psy8140 82 NCPVCDKVG 90 (108)
Q Consensus 82 ~CPiC~~~~ 90 (108)
+||.|+..-
T Consensus 2 ~Cp~Cg~~~ 10 (43)
T PF08271_consen 2 KCPNCGSKE 10 (43)
T ss_dssp SBTTTSSSE
T ss_pred CCcCCcCCc
Confidence 688888743
No 195
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=20.69 E-value=36 Score=23.69 Aligned_cols=16 Identities=25% Similarity=0.526 Sum_probs=4.9
Q ss_pred ceecccCCCcccCCCe
Q psy8140 80 KWNCPVCDKVGHLILL 95 (108)
Q Consensus 80 ~W~CPiC~~~~~~~dL 95 (108)
--+||||+..+.+..+
T Consensus 27 dGkCpiCDS~Vrp~~~ 42 (106)
T PF03660_consen 27 DGKCPICDSYVRPCTK 42 (106)
T ss_dssp TT--TTT-------EE
T ss_pred CCcccccCCccCCcce
Confidence 3689999988876544
No 196
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=20.61 E-value=46 Score=19.65 Aligned_cols=9 Identities=33% Similarity=1.117 Sum_probs=6.8
Q ss_pred ecccCCCcc
Q psy8140 82 NCPVCDKVG 90 (108)
Q Consensus 82 ~CPiC~~~~ 90 (108)
.||.||...
T Consensus 5 PCPFCG~~~ 13 (61)
T PF14354_consen 5 PCPFCGSAD 13 (61)
T ss_pred CCCCCCCcc
Confidence 599998543
No 197
>KOG1973|consensus
Probab=20.56 E-value=34 Score=26.88 Aligned_cols=48 Identities=23% Similarity=0.495 Sum_probs=29.8
Q ss_pred eeeeecCCCccccccccccccccC----ccceecHHHHHHHhcCCCceecccCCCcc
Q psy8140 38 LTSSLICPLGKMRMAFPTKASTCA----HLQCFDGATFIKMNELKPKWNCPVCDKVG 90 (108)
Q Consensus 38 ~~vsL~CPlS~~ri~~P~Rg~~C~----H~qCFDl~~fl~~~~~~~~W~CPiC~~~~ 90 (108)
...--.|+-..-=--+=+-+.+|. |+.|--|. ..-+++|.||-|....
T Consensus 218 e~~yC~Cnqvsyg~Mi~CDn~~C~~eWFH~~CVGL~-----~~PkgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 218 EPTYCICNQVSYGKMIGCDNPGCPIEWFHFTCVGLK-----TKPKGKWYCPRCKAEN 269 (274)
T ss_pred CCEEEEecccccccccccCCCCCCcceEEEeccccc-----cCCCCcccchhhhhhh
Confidence 334445553222223446777788 88777766 3457789999998643
No 198
>PRK11823 DNA repair protein RadA; Provisional
Probab=20.51 E-value=46 Score=27.82 Aligned_cols=18 Identities=28% Similarity=0.377 Sum_probs=12.9
Q ss_pred CCCceecccCCCcccCCC
Q psy8140 77 LKPKWNCPVCDKVGHLIL 94 (108)
Q Consensus 77 ~~~~W~CPiC~~~~~~~d 94 (108)
.+-.|+||-|+.--++.+
T Consensus 18 ~~~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 18 PKWLGRCPECGAWNTLVE 35 (446)
T ss_pred cccCeeCcCCCCccceee
Confidence 455799999997555544
No 199
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=20.51 E-value=49 Score=22.92 Aligned_cols=12 Identities=25% Similarity=0.844 Sum_probs=9.7
Q ss_pred CCceecccCCCc
Q psy8140 78 KPKWNCPVCDKV 89 (108)
Q Consensus 78 ~~~W~CPiC~~~ 89 (108)
..++.||.|+..
T Consensus 20 ~k~FtCp~Cghe 31 (104)
T COG4888 20 PKTFTCPRCGHE 31 (104)
T ss_pred CceEecCccCCe
Confidence 467999999964
No 200
>PF09256 BaffR-Tall_bind: BAFF-R, TALL-1 binding; InterPro: IPR015336 Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [, , ]. Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [, ]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide []. There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. The domain represented by this entry is predominantly found in the tumour necrosis factor receptor superfamily member 13c, BAFF-R and is required for binding to tumour necrosis factor ligand TALL-1 []. ; PDB: 1P0T_c 2HFG_R 1OSX_A 1OQE_N.
Probab=20.04 E-value=47 Score=18.23 Aligned_cols=11 Identities=36% Similarity=1.102 Sum_probs=6.9
Q ss_pred cccCccceecH
Q psy8140 58 STCAHLQCFDG 68 (108)
Q Consensus 58 ~~C~H~qCFDl 68 (108)
..|.-.||||.
T Consensus 2 t~C~q~~CFDp 12 (31)
T PF09256_consen 2 TQCVQAECFDP 12 (31)
T ss_dssp ---BTTEEEET
T ss_pred CcccchhhcCH
Confidence 35888899995
Done!