Query psy3656
Match_columns 185
No_of_seqs 163 out of 1335
Neff 9.0
Searched_HMMs 46136
Date Fri Aug 16 22:17:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3656.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3656hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.9 5E-26 1.1E-30 183.5 -3.3 104 80-184 272-377 (468)
2 KOG1701|consensus 99.9 1.2E-24 2.5E-29 175.6 1.2 98 83-180 335-440 (468)
3 KOG4577|consensus 99.9 3.9E-24 8.5E-29 164.7 -3.8 104 81-185 32-139 (383)
4 KOG1044|consensus 99.8 1.3E-21 2.7E-26 163.1 1.9 99 80-179 131-230 (670)
5 KOG2272|consensus 99.8 6.5E-21 1.4E-25 144.6 -3.5 101 83-183 13-115 (332)
6 KOG2272|consensus 99.8 4.5E-20 9.8E-25 140.1 -1.8 105 77-181 190-294 (332)
7 KOG1703|consensus 99.7 7.1E-19 1.5E-23 149.7 1.7 103 82-184 363-467 (479)
8 KOG1703|consensus 99.7 2.9E-17 6.2E-22 139.9 3.1 103 82-184 303-406 (479)
9 PF00412 LIM: LIM domain; Int 99.5 3.5E-14 7.5E-19 86.9 2.7 56 85-140 1-58 (58)
10 KOG1044|consensus 99.4 3.9E-13 8.4E-18 112.9 5.4 91 82-182 16-107 (670)
11 KOG1700|consensus 99.4 1.2E-13 2.6E-18 104.8 0.6 102 82-183 7-151 (200)
12 PF00412 LIM: LIM domain; Int 99.0 2.8E-10 6.1E-15 69.4 3.6 41 144-184 1-43 (58)
13 smart00132 LIM Zinc-binding do 99.0 5.5E-10 1.2E-14 62.3 2.8 36 143-178 1-38 (39)
14 smart00132 LIM Zinc-binding do 98.5 5.4E-08 1.2E-12 54.0 2.6 36 84-119 1-38 (39)
15 KOG4577|consensus 98.1 4.6E-07 9.9E-12 70.9 -0.1 64 82-145 92-159 (383)
16 KOG1700|consensus 98.1 7.3E-07 1.6E-11 67.8 0.5 61 80-140 106-167 (200)
17 KOG0490|consensus 98.0 1.1E-06 2.4E-11 68.2 -0.8 96 88-184 2-104 (235)
18 KOG1702|consensus 97.9 1.2E-06 2.6E-11 65.6 -1.0 58 83-140 5-63 (264)
19 PF14446 Prok-RING_1: Prokaryo 94.9 0.02 4.3E-07 34.0 1.9 38 140-177 4-51 (54)
20 PF14835 zf-RING_6: zf-RING of 90.5 0.33 7.1E-06 29.9 2.7 49 109-157 8-56 (65)
21 PF08394 Arc_trans_TRASH: Arch 86.9 0.45 9.7E-06 26.0 1.4 28 144-171 1-30 (37)
22 PF09943 DUF2175: Uncharacteri 85.6 0.25 5.3E-06 33.3 -0.0 28 143-170 4-33 (101)
23 PF10367 Vps39_2: Vacuolar sor 85.5 0.77 1.7E-05 30.8 2.4 28 142-169 79-108 (109)
24 KOG0320|consensus 84.2 0.35 7.5E-06 35.9 0.3 48 106-153 129-179 (187)
25 PF10235 Cript: Microtubule-as 82.9 0.84 1.8E-05 30.1 1.6 36 110-153 46-81 (90)
26 PF10367 Vps39_2: Vacuolar sor 82.1 1.3 2.9E-05 29.6 2.5 32 79-110 75-108 (109)
27 KOG1813|consensus 80.8 0.83 1.8E-05 36.6 1.2 47 107-154 240-288 (313)
28 COG5152 Uncharacterized conser 78.7 0.39 8.4E-06 36.3 -1.2 51 106-157 194-246 (259)
29 smart00504 Ubox Modified RING 77.9 1.8 4E-05 25.9 1.9 44 109-153 2-47 (63)
30 PF06827 zf-FPG_IleRS: Zinc fi 76.3 0.77 1.7E-05 23.5 -0.1 27 141-167 1-27 (30)
31 PF05864 Chordopox_RPO7: Chord 75.4 0.33 7.1E-06 29.0 -1.9 17 169-185 6-22 (63)
32 PF11571 Med27: Mediator compl 75.1 1.4 3E-05 29.0 0.9 32 136-167 49-89 (90)
33 PRK14873 primosome assembly pr 74.7 2.3 5.1E-05 38.3 2.4 48 83-150 384-431 (665)
34 PF11781 RRN7: RNA polymerase 74.7 1.4 3E-05 23.8 0.6 23 110-136 10-32 (36)
35 PF12773 DZR: Double zinc ribb 73.7 3.8 8.2E-05 23.5 2.4 6 144-149 32-37 (50)
36 PHA03082 DNA-dependent RNA pol 73.2 0.39 8.4E-06 28.7 -1.9 17 169-185 6-22 (63)
37 smart00504 Ubox Modified RING 72.3 2.7 5.8E-05 25.1 1.6 39 143-181 3-49 (63)
38 PF00645 zf-PARP: Poly(ADP-rib 72.2 1.2 2.6E-05 28.6 -0.0 32 138-169 4-47 (82)
39 PF07191 zinc-ribbons_6: zinc- 70.3 1.9 4.1E-05 27.0 0.5 51 128-184 16-67 (70)
40 PF10083 DUF2321: Uncharacteri 69.9 2 4.3E-05 31.2 0.7 50 126-177 25-78 (158)
41 PF13920 zf-C3HC4_3: Zinc fing 69.9 2.9 6.2E-05 24.0 1.3 42 110-152 4-48 (50)
42 TIGR00595 priA primosomal prot 69.7 3.6 7.9E-05 35.9 2.4 38 110-150 224-262 (505)
43 PF13240 zinc_ribbon_2: zinc-r 66.8 3.9 8.5E-05 19.7 1.2 8 144-151 2-9 (23)
44 PF14634 zf-RING_5: zinc-RING 66.4 4.3 9.2E-05 22.7 1.5 39 111-149 2-44 (44)
45 PF06677 Auto_anti-p27: Sjogre 64.9 4.7 0.0001 22.5 1.4 10 125-134 30-39 (41)
46 KOG4443|consensus 63.4 4.5 9.8E-05 36.0 1.7 21 159-179 107-127 (694)
47 PF14471 DUF4428: Domain of un 63.2 3.6 7.8E-05 24.1 0.8 29 110-139 1-30 (51)
48 COG4847 Uncharacterized protei 62.8 2.3 5E-05 28.2 -0.1 34 142-175 7-42 (103)
49 cd00162 RING RING-finger (Real 62.3 4.2 9.1E-05 21.8 0.9 24 127-150 18-44 (45)
50 COG1645 Uncharacterized Zn-fin 61.7 4.9 0.00011 28.4 1.3 21 111-136 31-51 (131)
51 PLN03208 E3 ubiquitin-protein 60.3 8.7 0.00019 29.1 2.5 12 142-153 69-80 (193)
52 KOG2462|consensus 60.3 5.5 0.00012 31.8 1.5 37 143-179 217-255 (279)
53 PF10886 DUF2685: Protein of u 59.4 6.5 0.00014 23.3 1.4 24 142-165 2-26 (54)
54 PF05502 Dynactin_p62: Dynacti 59.3 6.3 0.00014 34.2 1.9 12 166-177 51-62 (483)
55 PRK14559 putative protein seri 58.6 11 0.00023 34.1 3.3 49 83-152 2-52 (645)
56 COG2191 Formylmethanofuran deh 57.5 4.9 0.00011 30.6 0.8 31 109-139 173-203 (206)
57 PF06906 DUF1272: Protein of u 57.2 14 0.00031 22.0 2.6 43 111-153 8-53 (57)
58 KOG0823|consensus 55.7 9.4 0.0002 29.7 2.1 50 104-154 43-97 (230)
59 PF07754 DUF1610: Domain of un 52.8 9.1 0.0002 18.7 1.1 10 144-153 1-10 (24)
60 PRK00420 hypothetical protein; 52.2 9.5 0.00021 26.3 1.5 10 83-92 24-33 (112)
61 PF13248 zf-ribbon_3: zinc-rib 51.6 11 0.00024 18.5 1.3 9 84-92 4-12 (26)
62 COG0266 Nei Formamidopyrimidin 51.5 9.5 0.00021 30.6 1.6 27 141-167 245-271 (273)
63 PF05502 Dynactin_p62: Dynacti 50.6 9.7 0.00021 33.1 1.6 37 83-119 27-63 (483)
64 COG1198 PriA Primosomal protei 50.0 14 0.0003 33.8 2.6 39 109-150 445-484 (730)
65 KOG2462|consensus 48.2 12 0.00026 29.9 1.7 14 166-179 214-227 (279)
66 PF13923 zf-C3HC4_2: Zinc fing 48.0 3.2 6.9E-05 22.4 -1.1 27 112-138 2-28 (39)
67 PF00096 zf-C2H2: Zinc finger, 46.9 7.7 0.00017 18.0 0.3 12 168-179 1-12 (23)
68 PRK12495 hypothetical protein; 46.9 13 0.00028 28.7 1.6 10 109-118 43-52 (226)
69 KOG4739|consensus 46.8 15 0.00033 28.7 2.0 34 120-153 15-49 (233)
70 PF08209 Sgf11: Sgf11 (transcr 45.6 3.9 8.4E-05 21.7 -1.0 15 168-182 5-19 (33)
71 cd02340 ZZ_NBR1_like Zinc fing 45.3 8.7 0.00019 21.5 0.4 10 144-153 3-12 (43)
72 PF12171 zf-C2H2_jaz: Zinc-fin 44.9 10 0.00022 18.6 0.6 13 168-180 2-14 (27)
73 KOG2114|consensus 44.1 9.3 0.0002 35.2 0.6 35 143-177 842-882 (933)
74 KOG3579|consensus 43.9 11 0.00024 30.3 0.9 47 83-134 269-316 (352)
75 PF08790 zf-LYAR: LYAR-type C2 43.9 4.5 9.8E-05 20.6 -0.8 15 168-182 1-15 (28)
76 COG0068 HypF Hydrogenase matur 43.0 16 0.00034 33.2 1.8 83 81-177 100-183 (750)
77 PF14569 zf-UDP: Zinc-binding 42.6 13 0.00029 23.8 0.9 50 81-150 8-60 (80)
78 PF02069 Metallothio_Pro: Prok 42.5 14 0.0003 21.8 0.9 25 110-134 9-33 (52)
79 PRK05580 primosome assembly pr 42.5 20 0.00044 32.5 2.4 38 110-150 392-430 (679)
80 smart00184 RING Ring finger. E 42.3 10 0.00022 19.3 0.4 26 144-169 1-26 (39)
81 PRK04016 DNA-directed RNA poly 42.2 5.4 0.00012 24.4 -0.8 11 169-179 6-16 (62)
82 PRK04023 DNA polymerase II lar 42.1 33 0.00072 32.6 3.7 52 80-153 624-675 (1121)
83 KOG3002|consensus 41.9 19 0.0004 29.3 1.9 43 109-152 49-91 (299)
84 PRK01103 formamidopyrimidine/5 41.4 17 0.00037 29.0 1.7 29 139-167 243-271 (274)
85 PHA02929 N1R/p28-like protein; 40.3 14 0.00031 28.9 1.0 36 142-177 175-226 (238)
86 cd02249 ZZ Zinc finger, ZZ typ 40.2 18 0.00039 20.3 1.2 11 143-153 2-12 (46)
87 PLN03208 E3 ubiquitin-protein 39.1 20 0.00043 27.2 1.6 30 108-138 18-47 (193)
88 PF01258 zf-dskA_traR: Prokary 38.7 2.3 4.9E-05 22.8 -2.6 13 84-96 5-17 (36)
89 PF12874 zf-met: Zinc-finger o 37.4 13 0.00029 17.5 0.3 13 168-180 1-13 (25)
90 PRK14810 formamidopyrimidine-D 36.8 22 0.00048 28.4 1.6 28 140-167 243-270 (272)
91 PF13894 zf-C2H2_4: C2H2-type 36.1 16 0.00035 16.5 0.5 11 168-178 1-11 (24)
92 KOG0978|consensus 35.8 11 0.00024 34.1 -0.3 27 125-151 659-688 (698)
93 PRK10445 endonuclease VIII; Pr 35.8 24 0.00051 28.1 1.6 29 139-167 233-261 (263)
94 PF06750 DiS_P_DiS: Bacterial 35.5 54 0.0012 21.6 3.1 11 82-92 33-43 (92)
95 PRK00807 50S ribosomal protein 35.3 30 0.00065 20.3 1.6 29 142-170 2-34 (52)
96 KOG3970|consensus 35.2 19 0.0004 28.0 0.9 53 99-154 44-107 (299)
97 PF03107 C1_2: C1 domain; Int 34.9 28 0.00062 17.6 1.3 9 144-152 3-11 (30)
98 PRK14811 formamidopyrimidine-D 34.7 26 0.00056 28.0 1.7 27 141-167 235-261 (269)
99 KOG0978|consensus 34.4 7.8 0.00017 35.1 -1.4 44 142-185 644-696 (698)
100 TIGR00577 fpg formamidopyrimid 33.9 26 0.00057 27.9 1.6 27 141-167 245-271 (272)
101 PF07649 C1_3: C1-like domain; 33.5 26 0.00055 17.7 1.0 9 144-152 3-11 (30)
102 PF00130 C1_1: Phorbol esters/ 33.5 53 0.0011 18.7 2.5 28 142-169 12-44 (53)
103 cd02341 ZZ_ZZZ3 Zinc finger, Z 33.5 26 0.00056 20.2 1.1 9 144-152 3-12 (48)
104 PRK14890 putative Zn-ribbon RN 33.1 31 0.00066 20.9 1.4 11 142-152 8-18 (59)
105 PF13912 zf-C2H2_6: C2H2-type 32.7 17 0.00038 17.5 0.3 12 168-179 2-13 (27)
106 TIGR00599 rad18 DNA repair pro 31.4 19 0.00041 30.5 0.5 44 108-152 26-71 (397)
107 TIGR00599 rad18 DNA repair pro 31.0 27 0.00058 29.6 1.3 37 82-118 26-70 (397)
108 COG3813 Uncharacterized protei 30.8 43 0.00093 21.1 1.8 42 111-152 8-52 (84)
109 COG4357 Zinc finger domain con 30.5 7.5 0.00016 25.9 -1.6 43 85-127 38-81 (105)
110 KOG2932|consensus 30.5 24 0.00053 28.8 0.9 43 110-152 92-134 (389)
111 TIGR00570 cdk7 CDK-activating 30.4 41 0.00089 27.5 2.2 28 126-153 25-55 (309)
112 PRK13945 formamidopyrimidine-D 30.3 33 0.00071 27.5 1.6 27 141-167 254-280 (282)
113 PF01927 Mut7-C: Mut7-C RNAse 30.3 93 0.002 22.2 3.9 36 82-117 91-133 (147)
114 PF13695 zf-3CxxC: Zinc-bindin 30.1 59 0.0013 21.5 2.6 13 138-150 35-47 (98)
115 KOG2186|consensus 30.0 12 0.00025 29.6 -1.0 41 83-123 4-44 (276)
116 PF06524 NOA36: NOA36 protein; 29.7 38 0.00082 27.0 1.8 11 142-152 210-220 (314)
117 smart00531 TFIIE Transcription 29.3 40 0.00086 24.2 1.8 35 82-119 99-134 (147)
118 cd02336 ZZ_RSC8 Zinc finger, Z 29.1 38 0.00082 19.2 1.3 29 110-138 2-32 (45)
119 KOG3039|consensus 29.0 36 0.00079 26.9 1.6 75 82-156 183-274 (303)
120 PF12677 DUF3797: Domain of un 28.5 48 0.001 19.2 1.6 26 142-167 14-42 (49)
121 COG4306 Uncharacterized protei 28.2 35 0.00075 24.0 1.2 11 143-153 41-51 (160)
122 PF04570 DUF581: Protein of un 27.8 33 0.00071 20.7 0.9 9 170-178 19-27 (58)
123 TIGR00143 hypF [NiFe] hydrogen 27.8 43 0.00093 30.7 2.1 83 81-177 67-150 (711)
124 PF02591 DUF164: Putative zinc 27.4 22 0.00048 20.9 0.1 14 80-93 20-33 (56)
125 PRK14891 50S ribosomal protein 27.2 45 0.00097 23.5 1.6 30 142-171 5-38 (131)
126 smart00746 TRASH metallochaper 27.1 64 0.0014 15.6 2.0 21 144-164 1-25 (39)
127 smart00547 ZnF_RBZ Zinc finger 27.1 45 0.00098 15.9 1.3 19 132-150 5-25 (26)
128 PF08746 zf-RING-like: RING-li 26.9 12 0.00026 21.0 -1.1 8 85-92 1-8 (43)
129 PHA02768 hypothetical protein; 26.9 10 0.00022 22.6 -1.4 11 109-119 6-16 (55)
130 smart00291 ZnF_ZZ Zinc-binding 26.6 42 0.00091 18.6 1.2 12 142-153 5-16 (44)
131 TIGR02420 dksA RNA polymerase- 26.5 12 0.00026 25.5 -1.3 28 142-174 81-108 (110)
132 PF13901 DUF4206: Domain of un 26.3 43 0.00094 25.4 1.6 42 131-174 144-196 (202)
133 PF01194 RNA_pol_N: RNA polyme 26.2 31 0.00067 20.9 0.6 9 170-178 7-15 (60)
134 COG1656 Uncharacterized conser 26.0 30 0.00064 25.6 0.6 36 142-177 98-140 (165)
135 TIGR00373 conserved hypothetic 25.9 56 0.0012 23.8 2.1 30 82-119 109-139 (158)
136 PF00628 PHD: PHD-finger; Int 25.5 73 0.0016 17.8 2.2 10 160-169 21-30 (51)
137 PF04997 RNA_pol_Rpb1_1: RNA p 25.0 1.1E+02 0.0024 24.2 3.9 52 126-177 39-104 (337)
138 PF01873 eIF-5_eIF-2B: Domain 24.8 49 0.0011 23.2 1.5 28 142-171 94-121 (125)
139 PF04810 zf-Sec23_Sec24: Sec23 24.6 63 0.0014 17.5 1.7 29 83-116 3-32 (40)
140 PRK14714 DNA polymerase II lar 24.5 83 0.0018 30.8 3.3 48 84-153 669-721 (1337)
141 KOG3576|consensus 24.5 4.2 9.1E-05 31.1 -4.1 10 83-92 118-127 (267)
142 PF13465 zf-H2C2_2: Zinc-finge 24.3 31 0.00067 16.7 0.3 10 168-177 15-24 (26)
143 smart00355 ZnF_C2H2 zinc finge 24.2 39 0.00085 15.2 0.7 12 168-179 1-12 (26)
144 COG2174 RPL34A Ribosomal prote 24.0 41 0.0009 22.2 0.9 19 135-153 26-46 (93)
145 COG1571 Predicted DNA-binding 23.2 57 0.0012 27.9 1.9 33 141-182 350-382 (421)
146 COG2888 Predicted Zn-ribbon RN 23.2 61 0.0013 19.6 1.5 11 142-152 10-20 (61)
147 PF13639 zf-RING_2: Ring finge 22.6 23 0.0005 19.4 -0.4 27 143-169 2-31 (44)
148 PF13832 zf-HC5HC2H_2: PHD-zin 22.2 55 0.0012 21.9 1.4 29 139-168 53-85 (110)
149 PLN02638 cellulose synthase A 22.0 73 0.0016 30.6 2.4 30 82-118 17-46 (1079)
150 PRK03564 formate dehydrogenase 21.8 1.8E+02 0.0038 23.9 4.4 10 82-91 187-196 (309)
151 PLN02436 cellulose synthase A 21.6 79 0.0017 30.4 2.6 31 81-118 35-65 (1094)
152 cd00472 Ribosomal_L24e_L24 Rib 21.6 67 0.0014 19.0 1.4 25 142-166 4-32 (54)
153 PF12156 ATPase-cat_bd: Putati 21.6 45 0.00098 21.7 0.8 10 143-152 2-11 (88)
154 smart00249 PHD PHD zinc finger 21.5 69 0.0015 17.0 1.5 7 161-167 22-28 (47)
155 COG0846 SIR2 NAD-dependent pro 21.5 1.3E+02 0.0029 23.8 3.5 19 141-159 146-165 (250)
156 PF10080 DUF2318: Predicted me 21.5 52 0.0011 22.2 1.1 33 102-138 29-61 (102)
157 PF14279 HNH_5: HNH endonuclea 21.3 32 0.0007 21.5 0.1 22 157-179 21-42 (71)
158 PRK11595 DNA utilization prote 21.2 68 0.0015 24.7 1.9 10 83-92 6-15 (227)
159 PF11077 DUF2616: Protein of u 21.1 66 0.0014 24.0 1.7 18 123-140 154-171 (173)
160 PF13834 DUF4193: Domain of un 21.0 26 0.00055 23.6 -0.5 11 125-135 88-98 (99)
161 PF12647 RNHCP: RNHCP domain; 20.9 1.8E+02 0.0038 19.3 3.4 34 142-176 42-76 (92)
162 PLN02400 cellulose synthase 20.2 83 0.0018 30.3 2.4 31 81-118 35-65 (1085)
163 PRK04136 rpl40e 50S ribosomal 20.2 58 0.0013 18.8 0.9 22 128-149 13-36 (48)
164 PRK06266 transcription initiat 20.2 1E+02 0.0022 23.0 2.5 30 82-119 117-147 (178)
No 1
>KOG1701|consensus
Probab=99.90 E-value=5e-26 Score=183.46 Aligned_cols=104 Identities=29% Similarity=0.749 Sum_probs=96.7
Q ss_pred CCCCccccccccccc--ceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEE
Q psy3656 80 TQKGCCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVT 157 (185)
Q Consensus 80 ~~~~~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~ 157 (185)
.+..+|.+|+|.|.+ ..+.+|++.||..||+|..|+++|.+..||..++++||+.||.... +||.+|++.|++++|+
T Consensus 272 ~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-ekC~~Cg~~I~d~iLr 350 (468)
T KOG1701|consen 272 DYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-EKCNKCGEPIMDRILR 350 (468)
T ss_pred hhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-HHHhhhhhHHHHHHHH
Confidence 345699999999964 4789999999999999999999999999999999999999998776 9999999999999999
Q ss_pred eCCCeecccCcccccCCCccCCCCeee
Q psy3656 158 ALEKTWHTEHFFCAQCGKQFGEAMVKF 184 (185)
Q Consensus 158 ~~~~~~H~~Cf~C~~C~~~l~~~~~~~ 184 (185)
|+|+.||+.||+|..|++.|++.-|.+
T Consensus 351 A~GkayHp~CF~Cv~C~r~ldgipFtv 377 (468)
T KOG1701|consen 351 ALGKAYHPGCFTCVVCARCLDGIPFTV 377 (468)
T ss_pred hcccccCCCceEEEEeccccCCccccc
Confidence 999999999999999999999988753
No 2
>KOG1701|consensus
Probab=99.89 E-value=1.2e-24 Score=175.63 Aligned_cols=98 Identities=36% Similarity=0.891 Sum_probs=90.9
Q ss_pred CcccccccccccceeeecCcccccCCccCCCCCCCCCCCCee-eeCCcCCCccchhhccCCCCCccCCcccCc-------
Q psy3656 83 GCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFF-ERDSRPYCEPDYHNLFSPRCSYCNGPILDK------- 154 (185)
Q Consensus 83 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~-~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~------- 154 (185)
.+|..|++.|.++++.++|+.||..||+|..|.+.|.+..|. ..++++||-+||+++|+++|+.|+++|+++
T Consensus 335 ekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etv 414 (468)
T KOG1701|consen 335 EKCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETV 414 (468)
T ss_pred HHHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceE
Confidence 478999999999999999999999999999999999888886 788999999999999999999999999842
Q ss_pred eEEeCCCeecccCcccccCCCccCCC
Q psy3656 155 CVTALEKTWHTEHFFCAQCGKQFGEA 180 (185)
Q Consensus 155 ~~~~~~~~~H~~Cf~C~~C~~~l~~~ 180 (185)
.|+++|+.||.+||+|..|+.+|+.+
T Consensus 415 Rvvamdr~fHv~CY~CEDCg~~LS~e 440 (468)
T KOG1701|consen 415 RVVAMDRDFHVNCYKCEDCGLLLSSE 440 (468)
T ss_pred EEEEccccccccceehhhcCcccccc
Confidence 46899999999999999999999743
No 3
>KOG4577|consensus
Probab=99.86 E-value=3.9e-24 Score=164.74 Aligned_cols=104 Identities=26% Similarity=0.680 Sum_probs=94.9
Q ss_pred CCCcccccccccccc-eeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCc-eE-E
Q psy3656 81 QKGCCSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDK-CV-T 157 (185)
Q Consensus 81 ~~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~-~~-~ 157 (185)
..++|++|.+.|.+. ++.++++.||..|++|+.|..+| ....+.++|.+||+++|.++||.+|..|..+|.+. +| .
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL-~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRk 110 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQL-ADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRK 110 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHH-HHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHH
Confidence 357899999999876 56799999999999999999999 45689999999999999999999999999999975 44 4
Q ss_pred eCCCeecccCcccccCCCcc-CCCCeeeC
Q psy3656 158 ALEKTWHTEHFFCAQCGKQF-GEAMVKFI 185 (185)
Q Consensus 158 ~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~ 185 (185)
|.+.+||.+||.|..|.++| .+|+|++|
T Consensus 111 Aqd~VYHl~CF~C~iC~R~L~TGdEFYLm 139 (383)
T KOG4577|consen 111 AQDFVYHLHCFACFICKRQLATGDEFYLM 139 (383)
T ss_pred hhcceeehhhhhhHhhhcccccCCeeEEe
Confidence 99999999999999999999 89999986
No 4
>KOG1044|consensus
Probab=99.83 E-value=1.3e-21 Score=163.05 Aligned_cols=99 Identities=34% Similarity=0.785 Sum_probs=93.5
Q ss_pred CCCCccccccccc-ccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEEe
Q psy3656 80 TQKGCCSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTA 158 (185)
Q Consensus 80 ~~~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~ 158 (185)
.+...|++|++.| .++.+.++++.||..||+|..|..-| .++|...+|.+||+.||...||.+|..|.+.|.|++|.|
T Consensus 131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL-~gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqa 209 (670)
T KOG1044|consen 131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVL-NGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQA 209 (670)
T ss_pred cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccc-cceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhc
Confidence 4567899999999 68999999999999999999999988 778999999999999999999999999999999999999
Q ss_pred CCCeecccCcccccCCCccCC
Q psy3656 159 LEKTWHTEHFFCAQCGKQFGE 179 (185)
Q Consensus 159 ~~~~~H~~Cf~C~~C~~~l~~ 179 (185)
.|+.|||.|-+|++|+.+|++
T Consensus 210 g~kh~HPtCARCsRCgqmF~e 230 (670)
T KOG1044|consen 210 GDKHFHPTCARCSRCGQMFGE 230 (670)
T ss_pred cCcccCcchhhhhhhcccccc
Confidence 999999999999999999943
No 5
>KOG2272|consensus
Probab=99.77 E-value=6.5e-21 Score=144.64 Aligned_cols=101 Identities=29% Similarity=0.785 Sum_probs=93.7
Q ss_pred Ccccccccccc--cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEEeCC
Q psy3656 83 GCCSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALE 160 (185)
Q Consensus 83 ~~C~~C~~~i~--~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~ 160 (185)
-.|..|..... ..++...|..||..||.|..|-.++.++.|+..+|+.||+.+|..+|+|.|..|++.|.|++|.+++
T Consensus 13 ~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVikamn 92 (332)
T KOG2272|consen 13 MVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIKAMN 92 (332)
T ss_pred HHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHHhhc
Confidence 35888988773 4578899999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeecccCcccccCCCccCCCCee
Q psy3656 161 KTWHTEHFFCAQCGKQFGEAMVK 183 (185)
Q Consensus 161 ~~~H~~Cf~C~~C~~~l~~~~~~ 183 (185)
..|||.||+|..|++.|.+.+|+
T Consensus 93 nSwHp~CF~Cd~Cn~~Lad~gf~ 115 (332)
T KOG2272|consen 93 NSWHPACFRCDLCNKHLADQGFY 115 (332)
T ss_pred cccCcccchhHHHHHHHhhhhhH
Confidence 99999999999999999877763
No 6
>KOG2272|consensus
Probab=99.75 E-value=4.5e-20 Score=140.09 Aligned_cols=105 Identities=36% Similarity=0.800 Sum_probs=98.0
Q ss_pred CCCCCCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceE
Q psy3656 77 VTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCV 156 (185)
Q Consensus 77 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~ 156 (185)
....+.++|..|.++|..+++.++|+-||.+.|+|+.|.+++.+-+.|.+.|..||+.||.++||..|..|++.|-|.++
T Consensus 190 hD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv 269 (332)
T KOG2272|consen 190 HDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVV 269 (332)
T ss_pred ccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHH
Confidence 33456789999999999889999999999999999999999988899999999999999999999999999999999999
Q ss_pred EeCCCeecccCcccccCCCccCCCC
Q psy3656 157 TALEKTWHTEHFFCAQCGKQFGEAM 181 (185)
Q Consensus 157 ~~~~~~~H~~Cf~C~~C~~~l~~~~ 181 (185)
.|.++.|.++||.|+.|++.|.-..
T Consensus 270 ~al~KawCv~cf~Cs~Cdkkl~~K~ 294 (332)
T KOG2272|consen 270 SALNKAWCVECFSCSTCDKKLTQKN 294 (332)
T ss_pred HHhhhhhcccccccccccccccccc
Confidence 9999999999999999999996544
No 7
>KOG1703|consensus
Probab=99.73 E-value=7.1e-19 Score=149.69 Aligned_cols=103 Identities=36% Similarity=0.863 Sum_probs=98.4
Q ss_pred CCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCccc--CceEEeC
Q psy3656 82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL--DKCVTAL 159 (185)
Q Consensus 82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~--~~~~~~~ 159 (185)
.+.|.+|+++|.++.|.+++..||.+||.|..|.+.|....|+..+|.+||+.||+.+++.+|..|.++|. +..+.++
T Consensus 363 ~p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~ 442 (479)
T KOG1703|consen 363 RPNCKRCLLPILEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEAD 442 (479)
T ss_pred CccccccCCchHHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhhcc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999987 7899999
Q ss_pred CCeecccCcccccCCCccCCCCeee
Q psy3656 160 EKTWHTEHFFCAQCGKQFGEAMVKF 184 (185)
Q Consensus 160 ~~~~H~~Cf~C~~C~~~l~~~~~~~ 184 (185)
+..||.+||+|+.|.+.|.++.|++
T Consensus 443 ~~~~h~~~F~c~~c~~~l~~~~~~~ 467 (479)
T KOG1703|consen 443 GSPFHGDCFRCANCMKKLTKKTFFE 467 (479)
T ss_pred CccccccceehhhhhccccCCceee
Confidence 9999999999999999999999876
No 8
>KOG1703|consensus
Probab=99.66 E-value=2.9e-17 Score=139.89 Aligned_cols=103 Identities=40% Similarity=0.785 Sum_probs=97.8
Q ss_pred CCccccccccccc-ceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEEeCC
Q psy3656 82 KGCCSSCDKPIVG-QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALE 160 (185)
Q Consensus 82 ~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~ 160 (185)
.+.|..|...|.+ +.+.++++.||+.+|.|..|...+..+.+...+|.+||..||...+.+.|..|+.+|.+++|.|.+
T Consensus 303 ~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~ 382 (479)
T KOG1703|consen 303 RPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALG 382 (479)
T ss_pred cccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhcc
Confidence 4789999999988 899999999999999999999999888888999999999999999999999999999999999999
Q ss_pred CeecccCcccccCCCccCCCCeee
Q psy3656 161 KTWHTEHFFCAQCGKQFGEAMVKF 184 (185)
Q Consensus 161 ~~~H~~Cf~C~~C~~~l~~~~~~~ 184 (185)
+.||++||.|..|++.|.+..|++
T Consensus 383 ~~wH~~cf~C~~C~~~~~~~~~~~ 406 (479)
T KOG1703|consen 383 RLWHPECFVCADCGKPLKNSSFFE 406 (479)
T ss_pred CeechhceeeecccCCCCCCcccc
Confidence 999999999999999998888764
No 9
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.46 E-value=3.5e-14 Score=86.94 Aligned_cols=56 Identities=45% Similarity=1.172 Sum_probs=50.4
Q ss_pred cccccccccc-cee-eecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhcc
Q psy3656 85 CSSCDKPIVG-QVI-TALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 140 (185)
Q Consensus 85 C~~C~~~i~~-~~~-~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~ 140 (185)
|..|+++|.+ +.+ .++|+.||.+||+|..|+..|....++..+|++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 7899999964 443 6999999999999999999999888999999999999999876
No 10
>KOG1044|consensus
Probab=99.39 E-value=3.9e-13 Score=112.86 Aligned_cols=91 Identities=26% Similarity=0.599 Sum_probs=79.3
Q ss_pred CCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEEeCCC
Q psy3656 82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVTALEK 161 (185)
Q Consensus 82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~~~~~ 161 (185)
...|..|.+.-.++++.+.++.||..||.|..|++.|..+.|+..++. ++++. ..|.+.|.+++|.++++
T Consensus 16 ~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~gevvsa~gk 85 (670)
T KOG1044|consen 16 GIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGEVVSTLGK 85 (670)
T ss_pred ceehhhhCCccccceeEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhccceeEecccc
Confidence 457999999999999999999999999999999999998888866554 34444 67899999999999999
Q ss_pred eecccCcccccCCCcc-CCCCe
Q psy3656 162 TWHTEHFFCAQCGKQF-GEAMV 182 (185)
Q Consensus 162 ~~H~~Cf~C~~C~~~l-~~~~~ 182 (185)
.||++||.|+.|..++ .+++.
T Consensus 86 tyh~~cf~cs~ck~pf~~g~~v 107 (670)
T KOG1044|consen 86 TYHPKCFSCSTCKSPFKSGDKV 107 (670)
T ss_pred eeccccceecccCCCCCCCCee
Confidence 9999999999999998 55443
No 11
>KOG1700|consensus
Probab=99.36 E-value=1.2e-13 Score=104.85 Aligned_cols=102 Identities=25% Similarity=0.603 Sum_probs=87.9
Q ss_pred CCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCC------------------
Q psy3656 82 KGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP------------------ 142 (185)
Q Consensus 82 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~------------------ 142 (185)
...|..|++.|+ .+.+..+|..||..||+|..|...|....+..+++.+||+.+|...+++
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKD 86 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcc
Confidence 357999999995 6777799999999999999999999988999999999999977666654
Q ss_pred -----------------------CCCccCCcccC-ceEEeCCCeecccCcccccCCCccCCCCee
Q psy3656 143 -----------------------RCSYCNGPILD-KCVTALEKTWHTEHFFCAQCGKQFGEAMVK 183 (185)
Q Consensus 143 -----------------------~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~ 183 (185)
.|..|.+.+.+ +.+...+..||..||+|+.|++.|....|.
T Consensus 87 ~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~ 151 (200)
T KOG1700|consen 87 GKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYA 151 (200)
T ss_pred cccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchh
Confidence 39999998874 566788999999999999999999766553
No 12
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.02 E-value=2.8e-10 Score=69.41 Aligned_cols=41 Identities=34% Similarity=0.790 Sum_probs=35.4
Q ss_pred CCccCCcccCceE--EeCCCeecccCcccccCCCccCCCCeee
Q psy3656 144 CSYCNGPILDKCV--TALEKTWHTEHFFCAQCGKQFGEAMVKF 184 (185)
Q Consensus 144 C~~C~~~i~~~~~--~~~~~~~H~~Cf~C~~C~~~l~~~~~~~ 184 (185)
|..|+++|.+..+ .+.++.||++||+|..|++.|.+..|+.
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~ 43 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYE 43 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEE
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEe
Confidence 7899999996433 5999999999999999999998887653
No 13
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.95 E-value=5.5e-10 Score=62.31 Aligned_cols=36 Identities=44% Similarity=1.018 Sum_probs=33.0
Q ss_pred CCCccCCcccC--ceEEeCCCeecccCcccccCCCccC
Q psy3656 143 RCSYCNGPILD--KCVTALEKTWHTEHFFCAQCGKQFG 178 (185)
Q Consensus 143 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~ 178 (185)
+|..|+++|.+ ..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58999999997 6778999999999999999999985
No 14
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.55 E-value=5.4e-08 Score=54.04 Aligned_cols=36 Identities=56% Similarity=1.238 Sum_probs=32.1
Q ss_pred ccccccccccc--ceeeecCcccccCCccCCCCCCCCC
Q psy3656 84 CCSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELG 119 (185)
Q Consensus 84 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~L~ 119 (185)
+|..|++.|.+ ..+.+.++.||..||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 48999999965 6788999999999999999999884
No 15
>KOG4577|consensus
Probab=98.13 E-value=4.6e-07 Score=70.91 Aligned_cols=64 Identities=31% Similarity=0.644 Sum_probs=52.2
Q ss_pred CCcccccccccc-ccee-eecCcccccCCccCCCCCCCCCCC-Cee-eeCCcCCCccchhhccCCCCC
Q psy3656 82 KGCCSSCDKPIV-GQVI-TALGKTWHPEHFICTHCNQELGTR-NFF-ERDSRPYCEPDYHNLFSPRCS 145 (185)
Q Consensus 82 ~~~C~~C~~~i~-~~~~-~~~~~~~H~~Cf~C~~C~~~L~~~-~~~-~~~g~~yC~~~~~~~~~~~C~ 145 (185)
..+|..|...|. .++| .+.+..||..||.|..|.++|..+ +|| ..++++.|+++|+..-..-|.
T Consensus 92 GTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~ 159 (383)
T KOG4577|consen 92 GTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCN 159 (383)
T ss_pred CCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhcccc
Confidence 358999999994 5554 588999999999999999999844 676 788999999999875545453
No 16
>KOG1700|consensus
Probab=98.11 E-value=7.3e-07 Score=67.84 Aligned_cols=61 Identities=30% Similarity=0.692 Sum_probs=54.4
Q ss_pred CCCCcccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhcc
Q psy3656 80 TQKGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 140 (185)
Q Consensus 80 ~~~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~ 140 (185)
.....|..|++.++ .+.+...+..||..||+|..|+..|....+...++.+||..++..+|
T Consensus 106 g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 106 GEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred ccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence 33578999999996 68899999999999999999999999999999999999998877655
No 17
>KOG0490|consensus
Probab=97.97 E-value=1.1e-06 Score=68.16 Aligned_cols=96 Identities=30% Similarity=0.701 Sum_probs=76.0
Q ss_pred cccccccc-eeeecCcccccCCccCCCCCCCCC-CCCeeeeCCcCCCccchhh--ccCCCCCccCCccc--CceEEeCCC
Q psy3656 88 CDKPIVGQ-VITALGKTWHPEHFICTHCNQELG-TRNFFERDSRPYCEPDYHN--LFSPRCSYCNGPIL--DKCVTALEK 161 (185)
Q Consensus 88 C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~~g~~yC~~~~~~--~~~~~C~~C~~~i~--~~~~~~~~~ 161 (185)
|+..|.+. .+...+..||..|.+|..|...|. ....+..+|..||..+|.+ .+..+|..|...|. ++...+.++
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~ 81 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEK 81 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcC
Confidence 55666543 345669999999999999999996 2344444999999999998 78899999999985 455667788
Q ss_pred eecccCcccccCCCcc-CCCCeee
Q psy3656 162 TWHTEHFFCAQCGKQF-GEAMVKF 184 (185)
Q Consensus 162 ~~H~~Cf~C~~C~~~l-~~~~~~~ 184 (185)
+ |-.||.|..|...+ .++++.+
T Consensus 82 ~-h~Pd~~~r~~la~~~~~~e~rV 104 (235)
T KOG0490|consen 82 V-HLPCFACRECLALLLTGDEFRV 104 (235)
T ss_pred C-CcCccchHHHHhhcCCCCeeee
Confidence 8 99999999999866 6666544
No 18
>KOG1702|consensus
Probab=97.95 E-value=1.2e-06 Score=65.56 Aligned_cols=58 Identities=29% Similarity=0.707 Sum_probs=51.9
Q ss_pred Ccccccccccc-cceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhcc
Q psy3656 83 GCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 140 (185)
Q Consensus 83 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~ 140 (185)
.-|..|++.++ .+.+..+++.||..||+|..|+.+|...++...+.++||..+|....
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 45889999995 68899999999999999999999999888889999999999997543
No 19
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=94.92 E-value=0.02 Score=33.98 Aligned_cols=38 Identities=24% Similarity=0.581 Sum_probs=29.0
Q ss_pred cCCCCCccCCccc--CceEE--eCCCeecccCc----cccc--CCCcc
Q psy3656 140 FSPRCSYCNGPIL--DKCVT--ALEKTWHTEHF----FCAQ--CGKQF 177 (185)
Q Consensus 140 ~~~~C~~C~~~i~--~~~~~--~~~~~~H~~Cf----~C~~--C~~~l 177 (185)
.+.+|..|++.|. +.+|. .-+..||.+|+ .|.. |+..+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 3588999999995 45554 45799999999 4877 76654
No 20
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=90.48 E-value=0.33 Score=29.89 Aligned_cols=49 Identities=14% Similarity=0.369 Sum_probs=23.0
Q ss_pred ccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccCceEE
Q psy3656 109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILDKCVT 157 (185)
Q Consensus 109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~~~ 157 (185)
++|+.|..-|..--....=...||..|-...++..|.+|+.|...+.+.
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~ 56 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDIQ 56 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS--
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHHH
Confidence 4677777766432223555678899998888888899999987655444
No 21
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=86.91 E-value=0.45 Score=25.96 Aligned_cols=28 Identities=29% Similarity=0.523 Sum_probs=21.0
Q ss_pred CCccCCcccCc--eEEeCCCeecccCcccc
Q psy3656 144 CSYCNGPILDK--CVTALEKTWHTEHFFCA 171 (185)
Q Consensus 144 C~~C~~~i~~~--~~~~~~~~~H~~Cf~C~ 171 (185)
|.-|++.|.++ .+...++.||--|=.|.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~ 30 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCL 30 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHH
Confidence 77899999865 45678999996665553
No 22
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=85.56 E-value=0.25 Score=33.26 Aligned_cols=28 Identities=29% Similarity=0.443 Sum_probs=21.9
Q ss_pred CCCccCCccc-CceEEe-CCCeecccCccc
Q psy3656 143 RCSYCNGPIL-DKCVTA-LEKTWHTEHFFC 170 (185)
Q Consensus 143 ~C~~C~~~i~-~~~~~~-~~~~~H~~Cf~C 170 (185)
+|..|+++|. |+..++ .+..-|-+||+=
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~ 33 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE 33 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence 6999999997 666664 457889999863
No 23
>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=85.51 E-value=0.77 Score=30.78 Aligned_cols=28 Identities=21% Similarity=0.373 Sum_probs=17.0
Q ss_pred CCCCccCCcccCc-eEEe-CCCeecccCcc
Q psy3656 142 PRCSYCNGPILDK-CVTA-LEKTWHTEHFF 169 (185)
Q Consensus 142 ~~C~~C~~~i~~~-~~~~-~~~~~H~~Cf~ 169 (185)
..|..|+++|... ++.+ .|..+|-.|++
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 5577777777643 3333 35667777753
No 24
>KOG0320|consensus
Probab=84.25 E-value=0.35 Score=35.90 Aligned_cols=48 Identities=13% Similarity=0.394 Sum_probs=37.2
Q ss_pred cCCccCCCCCCCCCCCC-eeeeCCcCCCccchhhc--cCCCCCccCCcccC
Q psy3656 106 PEHFICTHCNQELGTRN-FFERDSRPYCEPDYHNL--FSPRCSYCNGPILD 153 (185)
Q Consensus 106 ~~Cf~C~~C~~~L~~~~-~~~~~g~~yC~~~~~~~--~~~~C~~C~~~i~~ 153 (185)
..+|+|..|-....... +...-|++||..|-... .+.+|..|++.|..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 45689999977775443 55788999999998754 45899999998864
No 25
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=82.93 E-value=0.84 Score=30.12 Aligned_cols=36 Identities=25% Similarity=0.599 Sum_probs=25.1
Q ss_pred cCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccC
Q psy3656 110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 153 (185)
Q Consensus 110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~ 153 (185)
+|..|...+. ..|..||..|-.++ .+|+-|++.|++
T Consensus 46 ~C~~CK~~v~------q~g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 46 KCKICKTKVH------QPGAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred cccccccccc------cCCCccChhhhccc--CcccccCCeecc
Confidence 5666666552 22567999995543 689999999864
No 26
>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=82.05 E-value=1.3 Score=29.59 Aligned_cols=32 Identities=28% Similarity=0.453 Sum_probs=19.8
Q ss_pred CCCCCcccccccccccc--eeeecCcccccCCcc
Q psy3656 79 TTQKGCCSSCDKPIVGQ--VITALGKTWHPEHFI 110 (185)
Q Consensus 79 ~~~~~~C~~C~~~i~~~--~~~~~~~~~H~~Cf~ 110 (185)
......|..|++.|... .+--.|..+|..|++
T Consensus 75 i~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ECCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 34456788888888432 233446677777753
No 27
>KOG1813|consensus
Probab=80.77 E-value=0.83 Score=36.63 Aligned_cols=47 Identities=17% Similarity=0.388 Sum_probs=37.0
Q ss_pred CCccCCCCCCCCCCCCeeeeCCcCCCccchhhccC--CCCCccCCcccCc
Q psy3656 107 EHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS--PRCSYCNGPILDK 154 (185)
Q Consensus 107 ~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~--~~C~~C~~~i~~~ 154 (185)
--|.|..|.... -..+...-+..+|+.|....|. ++|..|++.+.|.
T Consensus 240 ~Pf~c~icr~~f-~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 240 LPFKCFICRKYF-YRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred CCcccccccccc-ccchhhcCCceeehhhhccccccCCcceecccccccc
Confidence 347888998877 3456677788899999887664 7899999998874
No 28
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=78.67 E-value=0.39 Score=36.28 Aligned_cols=51 Identities=12% Similarity=0.380 Sum_probs=39.0
Q ss_pred cCCccCCCCCCCCCCCCeeeeCCcCCCccchhhcc--CCCCCccCCcccCceEE
Q psy3656 106 PEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF--SPRCSYCNGPILDKCVT 157 (185)
Q Consensus 106 ~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~--~~~C~~C~~~i~~~~~~ 157 (185)
..-|.|..|..... ..+...-|..||..|+.+.+ ++.|..|++...|..-+
T Consensus 194 ~IPF~C~iCKkdy~-spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V 246 (259)
T COG5152 194 KIPFLCGICKKDYE-SPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWV 246 (259)
T ss_pred CCceeehhchhhcc-chhhhhcchhHHHHHHHHHhccCCcceecchhhccceeH
Confidence 34589999988773 34566778889999998776 48899999987776443
No 29
>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=77.93 E-value=1.8 Score=25.88 Aligned_cols=44 Identities=9% Similarity=0.192 Sum_probs=30.5
Q ss_pred ccCCCCCCCCCCCCeeeeCCcCCCccchhhcc--CCCCCccCCcccC
Q psy3656 109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLF--SPRCSYCNGPILD 153 (185)
Q Consensus 109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~--~~~C~~C~~~i~~ 153 (185)
|.|..|...+.. .+....|..||+.+..+.+ ...|..|++++..
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 467777777643 4666778889988766433 3578888887753
No 30
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=76.28 E-value=0.77 Score=23.54 Aligned_cols=27 Identities=15% Similarity=0.214 Sum_probs=13.0
Q ss_pred CCCCCccCCcccCceEEeCCCeecccC
Q psy3656 141 SPRCSYCNGPILDKCVTALEKTWHTEH 167 (185)
Q Consensus 141 ~~~C~~C~~~i~~~~~~~~~~~~H~~C 167 (185)
|.+|..|...|....+..+...|-+.|
T Consensus 1 G~~C~rC~~~~~~~~~~~r~~~~C~rC 27 (30)
T PF06827_consen 1 GEKCPRCWNYIEDIGINGRSTYLCPRC 27 (30)
T ss_dssp TSB-TTT--BBEEEEETTEEEEE-TTT
T ss_pred CCcCccCCCcceEeEecCCCCeECcCC
Confidence 467888888877554433334444444
No 31
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=75.35 E-value=0.33 Score=28.96 Aligned_cols=17 Identities=24% Similarity=0.884 Sum_probs=13.9
Q ss_pred ccccCCCccCCCCeeeC
Q psy3656 169 FCAQCGKQFGEAMVKFI 185 (185)
Q Consensus 169 ~C~~C~~~l~~~~~~~~ 185 (185)
.|++|++-|++++|.+|
T Consensus 6 vCSTCGrDlSeeRy~Ll 22 (63)
T PF05864_consen 6 VCSTCGRDLSEERYRLL 22 (63)
T ss_pred eecccCCcchHHHHHHH
Confidence 58899999999888754
No 32
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=75.14 E-value=1.4 Score=29.04 Aligned_cols=32 Identities=25% Similarity=0.472 Sum_probs=21.8
Q ss_pred hhhccCCCCCccCCcc--c---CceEE---eCC-CeecccC
Q psy3656 136 YHNLFSPRCSYCNGPI--L---DKCVT---ALE-KTWHTEH 167 (185)
Q Consensus 136 ~~~~~~~~C~~C~~~i--~---~~~~~---~~~-~~~H~~C 167 (185)
|..+|...|.+|++.+ . +...+ ... ..||+.|
T Consensus 49 Y~~lfs~pC~~C~klL~~~~~LPP~~r~~~~~~~~ayH~~C 89 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLLSSKAFLPPVRRPKDFRSWEAYHEGC 89 (90)
T ss_pred HhhhccchhhHHHhHhhhcccCCCeeecccCCCCcccCccc
Confidence 6778888999999988 2 22333 222 5888887
No 33
>PRK14873 primosome assembly protein PriA; Provisional
Probab=74.70 E-value=2.3 Score=38.34 Aligned_cols=48 Identities=27% Similarity=0.580 Sum_probs=34.8
Q ss_pred CcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCc
Q psy3656 83 GCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGP 150 (185)
Q Consensus 83 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~ 150 (185)
-.|..|+..+ +|..|+.+|. |....+.+.|.-|-......+|..|+..
T Consensus 384 l~C~~Cg~~~-----------------~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 384 LACARCRTPA-----------------RCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eEhhhCcCee-----------------ECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 4677777655 7888888772 3345667889988665556789999875
No 34
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=74.66 E-value=1.4 Score=23.82 Aligned_cols=23 Identities=26% Similarity=0.589 Sum_probs=15.8
Q ss_pred cCCCCCCCCCCCCeeeeCCcCCCccch
Q psy3656 110 ICTHCNQELGTRNFFERDSRPYCEPDY 136 (185)
Q Consensus 110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~ 136 (185)
.|..|+.. .+...+|..||..|-
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhCc
Confidence 46667654 366888888887663
No 35
>PF12773 DZR: Double zinc ribbon
Probab=73.69 E-value=3.8 Score=23.45 Aligned_cols=6 Identities=33% Similarity=1.270 Sum_probs=2.4
Q ss_pred CCccCC
Q psy3656 144 CSYCNG 149 (185)
Q Consensus 144 C~~C~~ 149 (185)
|..|+.
T Consensus 32 C~~Cg~ 37 (50)
T PF12773_consen 32 CPNCGA 37 (50)
T ss_pred CcCCcC
Confidence 444443
No 36
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=73.18 E-value=0.39 Score=28.66 Aligned_cols=17 Identities=24% Similarity=0.884 Sum_probs=13.9
Q ss_pred ccccCCCccCCCCeeeC
Q psy3656 169 FCAQCGKQFGEAMVKFI 185 (185)
Q Consensus 169 ~C~~C~~~l~~~~~~~~ 185 (185)
.|++|++-|++++|.+|
T Consensus 6 VCsTCGrDlSeeRy~Ll 22 (63)
T PHA03082 6 VCSTCGRDLSEERYRLL 22 (63)
T ss_pred eecccCcchhHHHHHHH
Confidence 58899999999888753
No 37
>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=72.33 E-value=2.7 Score=25.13 Aligned_cols=39 Identities=10% Similarity=0.117 Sum_probs=30.1
Q ss_pred CCCccCCcccCceEEeCCCeecccCcc--------cccCCCccCCCC
Q psy3656 143 RCSYCNGPILDKCVTALEKTWHTEHFF--------CAQCGKQFGEAM 181 (185)
Q Consensus 143 ~C~~C~~~i~~~~~~~~~~~~H~~Cf~--------C~~C~~~l~~~~ 181 (185)
.|..|++.+.+.++...|++|-.+|+. |..|+..|+.+.
T Consensus 3 ~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~ 49 (63)
T smart00504 3 LCPISLEVMKDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED 49 (63)
T ss_pred CCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence 588899988877777778888877654 888888886544
No 38
>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=72.17 E-value=1.2 Score=28.57 Aligned_cols=32 Identities=28% Similarity=0.451 Sum_probs=19.3
Q ss_pred hccCCCCCccCCcccCc------eEEeCC------CeecccCcc
Q psy3656 138 NLFSPRCSYCNGPILDK------CVTALE------KTWHTEHFF 169 (185)
Q Consensus 138 ~~~~~~C~~C~~~i~~~------~~~~~~------~~~H~~Cf~ 169 (185)
+.-..+|..|++.|.-. .+.... .=||.+||.
T Consensus 4 ks~Ra~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~ 47 (82)
T PF00645_consen 4 KSGRAKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFF 47 (82)
T ss_dssp SSSTEBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHH
T ss_pred CCCCccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccc
Confidence 33346899999999732 222222 367888886
No 39
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=70.28 E-value=1.9 Score=27.04 Aligned_cols=51 Identities=22% Similarity=0.511 Sum_probs=22.4
Q ss_pred CcCCCccchhhc-cCCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCeee
Q psy3656 128 SRPYCEPDYHNL-FSPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMVKF 184 (185)
Q Consensus 128 g~~yC~~~~~~~-~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~ 184 (185)
+..+|..|.... ....|..|++++. .|.|-|.+ =|.|..|+..++-.+..|
T Consensus 16 ~~~~C~~C~~~~~~~a~CPdC~~~Le--~LkACGAv----dYFC~~c~gLiSKkrV~f 67 (70)
T PF07191_consen 16 GHYHCEACQKDYKKEAFCPDCGQPLE--VLKACGAV----DYFCNHCHGLISKKRVRF 67 (70)
T ss_dssp TEEEETTT--EEEEEEE-TTT-SB-E--EEEETTEE----EEE-TTTT-EE-TTTSEE
T ss_pred CEEECccccccceecccCCCcccHHH--HHHHhccc----ceeeccCCceeecceEEE
Confidence 444555443221 1256777777764 45554421 145777777776665544
No 40
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=69.93 E-value=2 Score=31.24 Aligned_cols=50 Identities=22% Similarity=0.577 Sum_probs=33.4
Q ss_pred eCCcCCCccchhhccCCCCCccCCcccCce----EEeCCCeecccCcccccCCCcc
Q psy3656 126 RDSRPYCEPDYHNLFSPRCSYCNGPILDKC----VTALEKTWHTEHFFCAQCGKQF 177 (185)
Q Consensus 126 ~~g~~yC~~~~~~~~~~~C~~C~~~i~~~~----~~~~~~~~H~~Cf~C~~C~~~l 177 (185)
.-..-||..|-.+.. ..|..|+-+|.|.+ +...+..|++-- -|..|++++
T Consensus 25 ~~~~~fC~kCG~~tI-~~Cp~C~~~IrG~y~v~gv~~~g~~~~~Ps-YC~~CGkpy 78 (158)
T PF10083_consen 25 ELREKFCSKCGAKTI-TSCPNCSTPIRGDYHVEGVFGLGGHYEAPS-YCHNCGKPY 78 (158)
T ss_pred hHHHHHHHHhhHHHH-HHCcCCCCCCCCceecCCeeeeCCCCCCCh-hHHhCCCCC
Confidence 445678888876655 78999999999753 233456666322 277777765
No 41
>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=69.91 E-value=2.9 Score=24.00 Aligned_cols=42 Identities=21% Similarity=0.475 Sum_probs=27.7
Q ss_pred cCCCCCCCCCCCCeeeeCCcC-CCccchhhcc--CCCCCccCCccc
Q psy3656 110 ICTHCNQELGTRNFFERDSRP-YCEPDYHNLF--SPRCSYCNGPIL 152 (185)
Q Consensus 110 ~C~~C~~~L~~~~~~~~~g~~-yC~~~~~~~~--~~~C~~C~~~i~ 152 (185)
.|..|..... ...+..=|.. +|..|+.+.+ ..+|..|.++|.
T Consensus 4 ~C~iC~~~~~-~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPR-DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBS-SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCC-ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 4555655542 2344667777 8999987663 588999999885
No 42
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=69.68 E-value=3.6 Score=35.87 Aligned_cols=38 Identities=16% Similarity=0.523 Sum_probs=27.0
Q ss_pred cCCCCCCCCCCCCeeeeCCcCCCccchhh-ccCCCCCccCCc
Q psy3656 110 ICTHCNQELGTRNFFERDSRPYCEPDYHN-LFSPRCSYCNGP 150 (185)
Q Consensus 110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~-~~~~~C~~C~~~ 150 (185)
+|..|+..| .|....+.+.|..|-.. .+...|..|+..
T Consensus 224 ~C~~C~~~l---~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSL---TYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCce---EEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 677777766 34556778889888543 445789999874
No 43
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=66.81 E-value=3.9 Score=19.66 Aligned_cols=8 Identities=38% Similarity=1.099 Sum_probs=3.1
Q ss_pred CCccCCcc
Q psy3656 144 CSYCNGPI 151 (185)
Q Consensus 144 C~~C~~~i 151 (185)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 33344433
No 44
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=66.42 E-value=4.3 Score=22.65 Aligned_cols=39 Identities=23% Similarity=0.533 Sum_probs=23.7
Q ss_pred CCCCCCCCC--CCCeeeeCCcCCCccchhhcc--CCCCCccCC
Q psy3656 111 CTHCNQELG--TRNFFERDSRPYCEPDYHNLF--SPRCSYCNG 149 (185)
Q Consensus 111 C~~C~~~L~--~~~~~~~~g~~yC~~~~~~~~--~~~C~~C~~ 149 (185)
|..|..... ...+...=|..+|..|..+.. ...|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 445555552 122336667888888877766 466777753
No 45
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=64.91 E-value=4.7 Score=22.46 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=4.8
Q ss_pred eeCCcCCCcc
Q psy3656 125 ERDSRPYCEP 134 (185)
Q Consensus 125 ~~~g~~yC~~ 134 (185)
.++|+.||-.
T Consensus 30 ~k~g~~~Cv~ 39 (41)
T PF06677_consen 30 DKDGKIYCVS 39 (41)
T ss_pred ecCCCEECCC
Confidence 3455555543
No 46
>KOG4443|consensus
Probab=63.40 E-value=4.5 Score=36.04 Aligned_cols=21 Identities=14% Similarity=0.169 Sum_probs=14.3
Q ss_pred CCCeecccCcccccCCCccCC
Q psy3656 159 LEKTWHTEHFFCAQCGKQFGE 179 (185)
Q Consensus 159 ~~~~~H~~Cf~C~~C~~~l~~ 179 (185)
.+..+.++||+|-.|+..|.+
T Consensus 107 sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 107 SGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred CcccccHHHHhhhhccccccc
Confidence 456667777777777776643
No 47
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=63.15 E-value=3.6 Score=24.06 Aligned_cols=29 Identities=24% Similarity=0.538 Sum_probs=20.0
Q ss_pred cCCCCCCCCCCC-CeeeeCCcCCCccchhhc
Q psy3656 110 ICTHCNQELGTR-NFFERDSRPYCEPDYHNL 139 (185)
Q Consensus 110 ~C~~C~~~L~~~-~~~~~~g~~yC~~~~~~~ 139 (185)
.|..|+..++.- .+...+| ..|..|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 477888877643 3557777 5788888664
No 48
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=62.80 E-value=2.3 Score=28.17 Aligned_cols=34 Identities=24% Similarity=0.327 Sum_probs=23.7
Q ss_pred CCCCccCCccc-CceEEe-CCCeecccCcccccCCC
Q psy3656 142 PRCSYCNGPIL-DKCVTA-LEKTWHTEHFFCAQCGK 175 (185)
Q Consensus 142 ~~C~~C~~~i~-~~~~~~-~~~~~H~~Cf~C~~C~~ 175 (185)
-+|++|++.|. |+..++ ....-|-+||.=+.=++
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k 42 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKK 42 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcC
Confidence 37999999886 666654 45678888887554333
No 49
>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=62.26 E-value=4.2 Score=21.82 Aligned_cols=24 Identities=17% Similarity=0.573 Sum_probs=11.5
Q ss_pred CCcCCCccchhhcc---CCCCCccCCc
Q psy3656 127 DSRPYCEPDYHNLF---SPRCSYCNGP 150 (185)
Q Consensus 127 ~g~~yC~~~~~~~~---~~~C~~C~~~ 150 (185)
=|..||..|..+.+ ..+|..|+..
T Consensus 18 C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 18 CGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 45555655554322 2345555543
No 50
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=61.66 E-value=4.9 Score=28.43 Aligned_cols=21 Identities=29% Similarity=0.770 Sum_probs=12.4
Q ss_pred CCCCCCCCCCCCeeeeCCcCCCccch
Q psy3656 111 CTHCNQELGTRNFFERDSRPYCEPDY 136 (185)
Q Consensus 111 C~~C~~~L~~~~~~~~~g~~yC~~~~ 136 (185)
|..|+.+| | ..+|.+||.-|-
T Consensus 31 Cp~Cg~PL----F-~KdG~v~CPvC~ 51 (131)
T COG1645 31 CPKCGTPL----F-RKDGEVFCPVCG 51 (131)
T ss_pred CcccCCcc----e-eeCCeEECCCCC
Confidence 55566655 2 367777776553
No 51
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=60.32 E-value=8.7 Score=29.11 Aligned_cols=12 Identities=25% Similarity=1.021 Sum_probs=9.9
Q ss_pred CCCCccCCcccC
Q psy3656 142 PRCSYCNGPILD 153 (185)
Q Consensus 142 ~~C~~C~~~i~~ 153 (185)
.+|..|...|..
T Consensus 69 ~~CPvCR~~Is~ 80 (193)
T PLN03208 69 PKCPVCKSDVSE 80 (193)
T ss_pred CcCCCCCCcCCh
Confidence 679999998864
No 52
>KOG2462|consensus
Probab=60.30 E-value=5.5 Score=31.76 Aligned_cols=37 Identities=24% Similarity=0.631 Sum_probs=22.4
Q ss_pred CCCccCCcccCc-eEEe-CCCeecccCcccccCCCccCC
Q psy3656 143 RCSYCNGPILDK-CVTA-LEKTWHTEHFFCAQCGKQFGE 179 (185)
Q Consensus 143 ~C~~C~~~i~~~-~~~~-~~~~~H~~Cf~C~~C~~~l~~ 179 (185)
.|..|++...++ -|+| +...=+.+=|.|..|+|.|..
T Consensus 217 ~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 217 SCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred cCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHH
Confidence 488888877764 2222 222333456788888887653
No 53
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=59.41 E-value=6.5 Score=23.27 Aligned_cols=24 Identities=29% Similarity=0.443 Sum_probs=17.4
Q ss_pred CCCCccCCcccC-ceEEeCCCeecc
Q psy3656 142 PRCSYCNGPILD-KCVTALEKTWHT 165 (185)
Q Consensus 142 ~~C~~C~~~i~~-~~~~~~~~~~H~ 165 (185)
.+|.+|+++|.+ ..+...++.-|+
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCc
Confidence 479999999986 455555666665
No 54
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=59.28 E-value=6.3 Score=34.24 Aligned_cols=12 Identities=25% Similarity=0.562 Sum_probs=6.5
Q ss_pred cCcccccCCCcc
Q psy3656 166 EHFFCAQCGKQF 177 (185)
Q Consensus 166 ~Cf~C~~C~~~l 177 (185)
+||.|-.|...|
T Consensus 51 ~Cf~CP~C~~~L 62 (483)
T PF05502_consen 51 NCFDCPICFSPL 62 (483)
T ss_pred ccccCCCCCCcc
Confidence 555555555554
No 55
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=58.57 E-value=11 Score=34.05 Aligned_cols=49 Identities=16% Similarity=0.349 Sum_probs=26.1
Q ss_pred CcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhcc--CCCCCccCCccc
Q psy3656 83 GCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF--SPRCSYCNGPIL 152 (185)
Q Consensus 83 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~--~~~C~~C~~~i~ 152 (185)
.+|..|+..+.... --|..|+.+|.. ..|..|-...- ...|..|+..+.
T Consensus 2 ~~Cp~Cg~~n~~~a------------kFC~~CG~~l~~---------~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 2 LICPQCQFENPNNN------------RFCQKCGTSLTH---------KPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCcCCCCC------------ccccccCCCCCC---------CcCCCCCCCCCcccccccccCCccc
Confidence 35888887763211 135566666631 24666644322 145777777643
No 56
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=57.47 E-value=4.9 Score=30.61 Aligned_cols=31 Identities=16% Similarity=0.425 Sum_probs=23.5
Q ss_pred ccCCCCCCCCCCCCeeeeCCcCCCccchhhc
Q psy3656 109 FICTHCNQELGTRNFFERDSRPYCEPDYHNL 139 (185)
Q Consensus 109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~ 139 (185)
-+|..|+-..........+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 4777777766555566888999999998754
No 57
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=57.17 E-value=14 Score=22.01 Aligned_cols=43 Identities=16% Similarity=0.564 Sum_probs=26.4
Q ss_pred CCCCCCCCCCC---CeeeeCCcCCCccchhhccCCCCCccCCcccC
Q psy3656 111 CTHCNQELGTR---NFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 153 (185)
Q Consensus 111 C~~C~~~L~~~---~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~ 153 (185)
|..|.+.|... .+.-.-.=.||.+|....+..+|.-|+..+..
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv~ 53 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELVR 53 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCcccc
Confidence 45555555422 22222334578888888878889999887653
No 58
>KOG0823|consensus
Probab=55.72 E-value=9.4 Score=29.65 Aligned_cols=50 Identities=16% Similarity=0.310 Sum_probs=35.7
Q ss_pred cccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhcc-----CCCCCccCCcccCc
Q psy3656 104 WHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF-----SPRCSYCNGPILDK 154 (185)
Q Consensus 104 ~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~-----~~~C~~C~~~i~~~ 154 (185)
-....|-|.+|=... ...+...=|+|||..|..+-. ...|.+|+..|...
T Consensus 43 ~~~~~FdCNICLd~a-kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~ 97 (230)
T KOG0823|consen 43 RDGGFFDCNICLDLA-KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID 97 (230)
T ss_pred CCCCceeeeeecccc-CCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence 445567888885433 556788899999999976433 25689999888754
No 59
>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=52.83 E-value=9.1 Score=18.71 Aligned_cols=10 Identities=40% Similarity=1.055 Sum_probs=5.6
Q ss_pred CCccCCcccC
Q psy3656 144 CSYCNGPILD 153 (185)
Q Consensus 144 C~~C~~~i~~ 153 (185)
|.+|+..|.+
T Consensus 1 C~sC~~~i~~ 10 (24)
T PF07754_consen 1 CTSCGRPIAP 10 (24)
T ss_pred CccCCCcccC
Confidence 4556666554
No 60
>PRK00420 hypothetical protein; Validated
Probab=52.19 E-value=9.5 Score=26.28 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=5.5
Q ss_pred Cccccccccc
Q psy3656 83 GCCSSCDKPI 92 (185)
Q Consensus 83 ~~C~~C~~~i 92 (185)
..|..|+-++
T Consensus 24 ~~CP~Cg~pL 33 (112)
T PRK00420 24 KHCPVCGLPL 33 (112)
T ss_pred CCCCCCCCcc
Confidence 4466665544
No 61
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.56 E-value=11 Score=18.48 Aligned_cols=9 Identities=33% Similarity=0.988 Sum_probs=5.3
Q ss_pred ccccccccc
Q psy3656 84 CCSSCDKPI 92 (185)
Q Consensus 84 ~C~~C~~~i 92 (185)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 466666654
No 62
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=51.46 E-value=9.5 Score=30.55 Aligned_cols=27 Identities=15% Similarity=0.255 Sum_probs=22.8
Q ss_pred CCCCCccCCcccCceEEeCCCeecccC
Q psy3656 141 SPRCSYCNGPILDKCVTALEKTWHTEH 167 (185)
Q Consensus 141 ~~~C~~C~~~i~~~~~~~~~~~~H~~C 167 (185)
++-|..|+.+|.-..+.=++..|.|.|
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~C 271 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCC
Confidence 578999999999777777888888777
No 63
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=50.61 E-value=9.7 Score=33.11 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=27.8
Q ss_pred CcccccccccccceeeecCcccccCCccCCCCCCCCC
Q psy3656 83 GCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 119 (185)
Q Consensus 83 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 119 (185)
-.|..|-..+...-+...++...++||.|..|...|.
T Consensus 27 ~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 27 YYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred eECccccccCChhhheeccceeccccccCCCCCCcce
Confidence 4577777666433356677888889999999999985
No 64
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.99 E-value=14 Score=33.85 Aligned_cols=39 Identities=15% Similarity=0.392 Sum_probs=29.4
Q ss_pred ccCCCCCCCCCCCCeeeeCCcCCCccchhh-ccCCCCCccCCc
Q psy3656 109 FICTHCNQELGTRNFFERDSRPYCEPDYHN-LFSPRCSYCNGP 150 (185)
Q Consensus 109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~-~~~~~C~~C~~~ 150 (185)
++|..|...| .|....+.+.|..|-.+ .....|..|+..
T Consensus 445 ~~Cp~Cd~~l---t~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPL---TLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcce---EEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 3788888776 45566689999988655 445789999987
No 65
>KOG2462|consensus
Probab=48.16 E-value=12 Score=29.89 Aligned_cols=14 Identities=43% Similarity=1.156 Sum_probs=9.2
Q ss_pred cCcccccCCCccCC
Q psy3656 166 EHFFCAQCGKQFGE 179 (185)
Q Consensus 166 ~Cf~C~~C~~~l~~ 179 (185)
.=|.|..|+|.|.+
T Consensus 214 KPF~C~hC~kAFAD 227 (279)
T KOG2462|consen 214 KPFSCPHCGKAFAD 227 (279)
T ss_pred CCccCCcccchhcc
Confidence 34677778777643
No 66
>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=47.96 E-value=3.2 Score=22.44 Aligned_cols=27 Identities=15% Similarity=0.283 Sum_probs=13.7
Q ss_pred CCCCCCCCCCCeeeeCCcCCCccchhh
Q psy3656 112 THCNQELGTRNFFERDSRPYCEPDYHN 138 (185)
Q Consensus 112 ~~C~~~L~~~~~~~~~g~~yC~~~~~~ 138 (185)
..|...+........=|..||..|..+
T Consensus 2 ~iC~~~~~~~~~~~~CGH~fC~~C~~~ 28 (39)
T PF13923_consen 2 PICLDELRDPVVVTPCGHSFCKECIEK 28 (39)
T ss_dssp TTTTSB-SSEEEECTTSEEEEHHHHHH
T ss_pred CCCCCcccCcCEECCCCCchhHHHHHH
Confidence 445444433223456667777766554
No 67
>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=46.95 E-value=7.7 Score=17.96 Aligned_cols=12 Identities=42% Similarity=1.132 Sum_probs=9.1
Q ss_pred cccccCCCccCC
Q psy3656 168 FFCAQCGKQFGE 179 (185)
Q Consensus 168 f~C~~C~~~l~~ 179 (185)
|.|..|++.+..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 678888887754
No 68
>PRK12495 hypothetical protein; Provisional
Probab=46.87 E-value=13 Score=28.72 Aligned_cols=10 Identities=20% Similarity=0.750 Sum_probs=6.2
Q ss_pred ccCCCCCCCC
Q psy3656 109 FICTHCNQEL 118 (185)
Q Consensus 109 f~C~~C~~~L 118 (185)
+.|..|+.+|
T Consensus 43 ~hC~~CG~PI 52 (226)
T PRK12495 43 AHCDECGDPI 52 (226)
T ss_pred hhcccccCcc
Confidence 4566666666
No 69
>KOG4739|consensus
Probab=46.79 E-value=15 Score=28.66 Aligned_cols=34 Identities=24% Similarity=0.459 Sum_probs=27.0
Q ss_pred CCCee-eeCCcCCCccchhhccCCCCCccCCcccC
Q psy3656 120 TRNFF-ERDSRPYCEPDYHNLFSPRCSYCNGPILD 153 (185)
Q Consensus 120 ~~~~~-~~~g~~yC~~~~~~~~~~~C~~C~~~i~~ 153 (185)
...|+ .--+.++|..|...-.+..|..|++.|..
T Consensus 15 ~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 15 QDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred CCceeeeechhhhhhhhcccCCccccccccceeee
Confidence 34454 66778999999888887899999999764
No 70
>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=45.59 E-value=3.9 Score=21.68 Aligned_cols=15 Identities=20% Similarity=0.654 Sum_probs=10.1
Q ss_pred cccccCCCccCCCCe
Q psy3656 168 FFCAQCGKQFGEAMV 182 (185)
Q Consensus 168 f~C~~C~~~l~~~~~ 182 (185)
|.|..|++++...+|
T Consensus 5 ~~C~nC~R~v~a~Rf 19 (33)
T PF08209_consen 5 VECPNCGRPVAASRF 19 (33)
T ss_dssp EE-TTTSSEEEGGGH
T ss_pred EECCCCcCCcchhhh
Confidence 568888888766665
No 71
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=45.31 E-value=8.7 Score=21.52 Aligned_cols=10 Identities=50% Similarity=1.341 Sum_probs=5.0
Q ss_pred CCccCCcccC
Q psy3656 144 CSYCNGPILD 153 (185)
Q Consensus 144 C~~C~~~i~~ 153 (185)
|..|+++|.|
T Consensus 3 Cd~C~~~i~G 12 (43)
T cd02340 3 CDGCQGPIVG 12 (43)
T ss_pred CCCCCCcCcC
Confidence 4455554444
No 72
>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=44.88 E-value=10 Score=18.59 Aligned_cols=13 Identities=38% Similarity=1.122 Sum_probs=9.6
Q ss_pred cccccCCCccCCC
Q psy3656 168 FFCAQCGKQFGEA 180 (185)
Q Consensus 168 f~C~~C~~~l~~~ 180 (185)
|.|..|++.+.++
T Consensus 2 ~~C~~C~k~f~~~ 14 (27)
T PF12171_consen 2 FYCDACDKYFSSE 14 (27)
T ss_dssp CBBTTTTBBBSSH
T ss_pred CCcccCCCCcCCH
Confidence 6788888887654
No 73
>KOG2114|consensus
Probab=44.11 E-value=9.3 Score=35.23 Aligned_cols=35 Identities=23% Similarity=0.564 Sum_probs=27.4
Q ss_pred CCCccCCcccCceEE-eCCCeecccCcc-----cccCCCcc
Q psy3656 143 RCSYCNGPILDKCVT-ALEKTWHTEHFF-----CAQCGKQF 177 (185)
Q Consensus 143 ~C~~C~~~i~~~~~~-~~~~~~H~~Cf~-----C~~C~~~l 177 (185)
+|..|...+.-..|. .-++.||..||. |..|...+
T Consensus 842 kCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 842 KCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLPEL 882 (933)
T ss_pred eecccCCccccceeeeecccHHHHHhhccCcccCCccchhh
Confidence 699999988766665 458999999987 88887644
No 74
>KOG3579|consensus
Probab=43.95 E-value=11 Score=30.32 Aligned_cols=47 Identities=17% Similarity=0.421 Sum_probs=32.2
Q ss_pred Cccccccccccc-ceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCcc
Q psy3656 83 GCCSSCDKPIVG-QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 134 (185)
Q Consensus 83 ~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~ 134 (185)
-.|..|.+.+.| .+|..-.-.-|+.||-|+.=. +. -....|.+||..
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRes--IK---~Qg~sgevYCPS 316 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRES--IK---QQGASGEVYCPS 316 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCHHH--HH---hhcCCCceeCCC
Confidence 578999999975 578888888899999887321 11 112345778853
No 75
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=43.90 E-value=4.5 Score=20.57 Aligned_cols=15 Identities=33% Similarity=0.784 Sum_probs=11.7
Q ss_pred cccccCCCccCCCCe
Q psy3656 168 FFCAQCGKQFGEAMV 182 (185)
Q Consensus 168 f~C~~C~~~l~~~~~ 182 (185)
|.|..|++.|.++.|
T Consensus 1 ~sCiDC~~~F~~~~y 15 (28)
T PF08790_consen 1 FSCIDCSKDFDGDSY 15 (28)
T ss_dssp EEETTTTEEEEGGGT
T ss_pred CeeecCCCCcCcCCc
Confidence 678999998876654
No 76
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=43.04 E-value=16 Score=33.20 Aligned_cols=83 Identities=22% Similarity=0.606 Sum_probs=58.6
Q ss_pred CCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchh-hccCCCCCccCCcccCceEEeC
Q psy3656 81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH-NLFSPRCSYCNGPILDKCVTAL 159 (185)
Q Consensus 81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~-~~~~~~C~~C~~~i~~~~~~~~ 159 (185)
+..+|..|.+.|.+ -.++.||=---.|..|+-. |.+.+..+|=+.... +.| +-|..|.+ ++-...
T Consensus 100 D~a~C~~Cl~Ei~d----p~~rrY~YPF~~CT~CGPR-----fTIi~alPYDR~nTsM~~F-~lC~~C~~----EY~dP~ 165 (750)
T COG0068 100 DAATCEDCLEEIFD----PNSRRYLYPFINCTNCGPR-----FTIIEALPYDRENTSMADF-PLCPFCDK----EYKDPL 165 (750)
T ss_pred chhhhHHHHHHhcC----CCCcceeccccccCCCCcc-----eeeeccCCCCcccCccccC-cCCHHHHH----HhcCcc
Confidence 34679999887754 3456777666788989664 456666666544332 333 77888876 334457
Q ss_pred CCeecccCcccccCCCcc
Q psy3656 160 EKTWHTEHFFCAQCGKQF 177 (185)
Q Consensus 160 ~~~~H~~Cf~C~~C~~~l 177 (185)
++.||-+=..|..|+..+
T Consensus 166 nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 166 NRRFHAQPIACPKCGPHL 183 (750)
T ss_pred ccccccccccCcccCCCe
Confidence 899999999999999876
No 77
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=42.64 E-value=13 Score=23.75 Aligned_cols=50 Identities=22% Similarity=0.585 Sum_probs=18.2
Q ss_pred CCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchh--hccC-CCCCccCCc
Q psy3656 81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYH--NLFS-PRCSYCNGP 150 (185)
Q Consensus 81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~--~~~~-~~C~~C~~~ 150 (185)
...+|..|+..|- +...|..| -.|..|.-+ .|+.||. ++-+ ..|..|+.+
T Consensus 8 ~~qiCqiCGD~VG---l~~~Ge~F----VAC~eC~fP-------------vCr~CyEYErkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 8 NGQICQICGDDVG---LTENGEVF----VACHECAFP-------------VCRPCYEYERKEGNQVCPQCKTR 60 (80)
T ss_dssp SS-B-SSS--B-----B-SSSSB------S-SSS------------------HHHHHHHHHTS-SB-TTT--B
T ss_pred CCcccccccCccc---cCCCCCEE----EEEcccCCc-------------cchhHHHHHhhcCcccccccCCC
Confidence 3567888888771 22334433 245555444 4787775 3333 567777643
No 78
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=42.50 E-value=14 Score=21.77 Aligned_cols=25 Identities=20% Similarity=0.652 Sum_probs=13.4
Q ss_pred cCCCCCCCCCCCCeeeeCCcCCCcc
Q psy3656 110 ICTHCNQELGTRNFFERDSRPYCEP 134 (185)
Q Consensus 110 ~C~~C~~~L~~~~~~~~~g~~yC~~ 134 (185)
.|..|...+...+-...+|+.||-+
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~ 33 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSE 33 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSH
T ss_pred cCCCCEeEECchHhHHhCCEeeecH
Confidence 4667777776566678888888853
No 79
>PRK05580 primosome assembly protein PriA; Validated
Probab=42.47 E-value=20 Score=32.53 Aligned_cols=38 Identities=21% Similarity=0.484 Sum_probs=25.5
Q ss_pred cCCCCCCCCCCCCeeeeCCcCCCccchhh-ccCCCCCccCCc
Q psy3656 110 ICTHCNQELGTRNFFERDSRPYCEPDYHN-LFSPRCSYCNGP 150 (185)
Q Consensus 110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~-~~~~~C~~C~~~ 150 (185)
+|..|+..| .|....+.+.|..|-.. .+...|..|+..
T Consensus 392 ~C~~C~~~l---~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASL---TLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCCCce---eEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 667777666 33445677788888554 345689999775
No 80
>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=42.34 E-value=10 Score=19.30 Aligned_cols=26 Identities=19% Similarity=0.324 Sum_probs=13.7
Q ss_pred CCccCCcccCceEEeCCCeecccCcc
Q psy3656 144 CSYCNGPILDKCVTALEKTWHTEHFF 169 (185)
Q Consensus 144 C~~C~~~i~~~~~~~~~~~~H~~Cf~ 169 (185)
|..|.+......+..-+..||.+|+.
T Consensus 1 C~iC~~~~~~~~~~~C~H~~c~~C~~ 26 (39)
T smart00184 1 CPICLEELKDPVVLPCGHTFCRSCIR 26 (39)
T ss_pred CCcCccCCCCcEEecCCChHHHHHHH
Confidence 44555554434444456666666653
No 81
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=42.15 E-value=5.4 Score=24.37 Aligned_cols=11 Identities=45% Similarity=0.936 Sum_probs=5.6
Q ss_pred ccccCCCccCC
Q psy3656 169 FCAQCGKQFGE 179 (185)
Q Consensus 169 ~C~~C~~~l~~ 179 (185)
+|.+|++.+++
T Consensus 6 RCFTCGkvi~~ 16 (62)
T PRK04016 6 RCFTCGKVIAE 16 (62)
T ss_pred EecCCCCChHH
Confidence 34555555544
No 82
>PRK04023 DNA polymerase II large subunit; Validated
Probab=42.13 E-value=33 Score=32.57 Aligned_cols=52 Identities=17% Similarity=0.309 Sum_probs=35.7
Q ss_pred CCCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCcccC
Q psy3656 80 TQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPILD 153 (185)
Q Consensus 80 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~~ 153 (185)
.+...|..|+... .=|+|..|+.. .....+|..|-.......|..|+..+.+
T Consensus 624 Vg~RfCpsCG~~t--------------~~frCP~CG~~--------Te~i~fCP~CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 624 IGRRKCPSCGKET--------------FYRRCPFCGTH--------TEPVYRCPRCGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred ccCccCCCCCCcC--------------CcccCCCCCCC--------CCcceeCccccCcCCCCcCCCCCCCCCc
Confidence 3467899999863 11788999876 1223468888555555679999887763
No 83
>KOG3002|consensus
Probab=41.89 E-value=19 Score=29.33 Aligned_cols=43 Identities=23% Similarity=0.427 Sum_probs=28.9
Q ss_pred ccCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCccc
Q psy3656 109 FICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL 152 (185)
Q Consensus 109 f~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~ 152 (185)
+.|..|-..|..-.+.-.+|.+.|..|-.++ ..+|..|..+|.
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~-~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKV-SNKCPTCRLPIG 91 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhh-cccCCccccccc
Confidence 4566666666555566677788887775433 377888888775
No 84
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=41.39 E-value=17 Score=28.96 Aligned_cols=29 Identities=14% Similarity=0.150 Sum_probs=20.1
Q ss_pred ccCCCCCccCCcccCceEEeCCCeecccC
Q psy3656 139 LFSPRCSYCNGPILDKCVTALEKTWHTEH 167 (185)
Q Consensus 139 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~C 167 (185)
+.+..|..|+.+|.-..+.-+...|.|.|
T Consensus 243 R~g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (274)
T PRK01103 243 REGEPCRRCGTPIEKIKQGGRSTFFCPRC 271 (274)
T ss_pred CCCCCCCCCCCeeEEEEECCCCcEECcCC
Confidence 34578999999997555555566666655
No 85
>PHA02929 N1R/p28-like protein; Provisional
Probab=40.26 E-value=14 Score=28.92 Aligned_cols=36 Identities=22% Similarity=0.584 Sum_probs=22.6
Q ss_pred CCCCccCCcccCc--------eEEeCCCeecccCc--------ccccCCCcc
Q psy3656 142 PRCSYCNGPILDK--------CVTALEKTWHTEHF--------FCAQCGKQF 177 (185)
Q Consensus 142 ~~C~~C~~~i~~~--------~~~~~~~~~H~~Cf--------~C~~C~~~l 177 (185)
..|+.|...+.+. .+..-++.||.+|+ .|..|...+
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~ 226 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF 226 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence 4577777765532 22335677777777 577777665
No 86
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=40.24 E-value=18 Score=20.32 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=6.3
Q ss_pred CCCccCCcccC
Q psy3656 143 RCSYCNGPILD 153 (185)
Q Consensus 143 ~C~~C~~~i~~ 153 (185)
.|..|+++|.|
T Consensus 2 ~C~~C~~~i~g 12 (46)
T cd02249 2 SCDGCLKPIVG 12 (46)
T ss_pred CCcCCCCCCcC
Confidence 36666665554
No 87
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=39.11 E-value=20 Score=27.18 Aligned_cols=30 Identities=20% Similarity=0.449 Sum_probs=22.1
Q ss_pred CccCCCCCCCCCCCCeeeeCCcCCCccchhh
Q psy3656 108 HFICTHCNQELGTRNFFERDSRPYCEPDYHN 138 (185)
Q Consensus 108 Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~ 138 (185)
.|.|..|...+. ......=|..||..|..+
T Consensus 18 ~~~CpICld~~~-dPVvT~CGH~FC~~CI~~ 47 (193)
T PLN03208 18 DFDCNICLDQVR-DPVVTLCGHLFCWPCIHK 47 (193)
T ss_pred ccCCccCCCcCC-CcEEcCCCchhHHHHHHH
Confidence 478999987663 345567888999888754
No 88
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=38.71 E-value=2.3 Score=22.80 Aligned_cols=13 Identities=31% Similarity=0.836 Sum_probs=7.0
Q ss_pred cccccccccccce
Q psy3656 84 CCSSCDKPIVGQV 96 (185)
Q Consensus 84 ~C~~C~~~i~~~~ 96 (185)
.|..|++.|..++
T Consensus 5 ~C~~CGe~I~~~R 17 (36)
T PF01258_consen 5 ICEDCGEPIPEER 17 (36)
T ss_dssp B-TTTSSBEEHHH
T ss_pred CccccCChHHHHH
Confidence 3677777664433
No 89
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=37.35 E-value=13 Score=17.52 Aligned_cols=13 Identities=38% Similarity=1.134 Sum_probs=9.7
Q ss_pred cccccCCCccCCC
Q psy3656 168 FFCAQCGKQFGEA 180 (185)
Q Consensus 168 f~C~~C~~~l~~~ 180 (185)
|.|..|++.+.++
T Consensus 1 ~~C~~C~~~f~s~ 13 (25)
T PF12874_consen 1 FYCDICNKSFSSE 13 (25)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCCcCCH
Confidence 6788888887553
No 90
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=36.78 E-value=22 Score=28.36 Aligned_cols=28 Identities=18% Similarity=0.331 Sum_probs=20.5
Q ss_pred cCCCCCccCCcccCceEEeCCCeecccC
Q psy3656 140 FSPRCSYCNGPILDKCVTALEKTWHTEH 167 (185)
Q Consensus 140 ~~~~C~~C~~~i~~~~~~~~~~~~H~~C 167 (185)
-+..|..|+.+|.-..+.-+...|.|.|
T Consensus 243 ~g~pCprCG~~I~~~~~~gR~t~~CP~C 270 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVAGRSSHYCPHC 270 (272)
T ss_pred CCCcCCCCCCeeEEEEECCCccEECcCC
Confidence 3578999999997555555667777766
No 91
>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=36.12 E-value=16 Score=16.51 Aligned_cols=11 Identities=55% Similarity=1.265 Sum_probs=6.3
Q ss_pred cccccCCCccC
Q psy3656 168 FFCAQCGKQFG 178 (185)
Q Consensus 168 f~C~~C~~~l~ 178 (185)
|.|..|++.+.
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 57888887764
No 92
>KOG0978|consensus
Probab=35.80 E-value=11 Score=34.13 Aligned_cols=27 Identities=19% Similarity=0.587 Sum_probs=13.9
Q ss_pred eeCCcCCCccchhhccC---CCCCccCCcc
Q psy3656 125 ERDSRPYCEPDYHNLFS---PRCSYCNGPI 151 (185)
Q Consensus 125 ~~~g~~yC~~~~~~~~~---~~C~~C~~~i 151 (185)
..-+++||..|-..++. .+|..|+...
T Consensus 659 ~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 659 TKCGHVFCEECVQTRYETRQRKCPKCNAAF 688 (698)
T ss_pred HhcchHHHHHHHHHHHHHhcCCCCCCCCCC
Confidence 34444555555444443 4566666653
No 93
>PRK10445 endonuclease VIII; Provisional
Probab=35.75 E-value=24 Score=28.06 Aligned_cols=29 Identities=17% Similarity=0.313 Sum_probs=20.8
Q ss_pred ccCCCCCccCCcccCceEEeCCCeecccC
Q psy3656 139 LFSPRCSYCNGPILDKCVTALEKTWHTEH 167 (185)
Q Consensus 139 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~C 167 (185)
+.+..|..|+.+|.-..+.-+...|.|.|
T Consensus 233 r~g~~Cp~Cg~~I~~~~~~gR~t~~CP~C 261 (263)
T PRK10445 233 RDGEACERCGGIIEKTTLSSRPFYWCPGC 261 (263)
T ss_pred CCCCCCCCCCCEeEEEEECCCCcEECCCC
Confidence 34578999999997555555666776666
No 94
>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=35.47 E-value=54 Score=21.58 Aligned_cols=11 Identities=27% Similarity=1.093 Sum_probs=6.7
Q ss_pred CCccccccccc
Q psy3656 82 KGCCSSCDKPI 92 (185)
Q Consensus 82 ~~~C~~C~~~i 92 (185)
...|..|++++
T Consensus 33 rS~C~~C~~~L 43 (92)
T PF06750_consen 33 RSHCPHCGHPL 43 (92)
T ss_pred CCcCcCCCCcC
Confidence 34566666666
No 95
>PRK00807 50S ribosomal protein L24e; Validated
Probab=35.32 E-value=30 Score=20.26 Aligned_cols=29 Identities=24% Similarity=0.311 Sum_probs=19.8
Q ss_pred CCCCccCCccc-C--c-eEEeCCCeecccCccc
Q psy3656 142 PRCSYCNGPIL-D--K-CVTALEKTWHTEHFFC 170 (185)
Q Consensus 142 ~~C~~C~~~i~-~--~-~~~~~~~~~H~~Cf~C 170 (185)
..|..|+..|. | . .+...+++|.--+-+|
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC 34 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKC 34 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHH
Confidence 36888999887 3 2 3567788887555444
No 96
>KOG3970|consensus
Probab=35.20 E-value=19 Score=28.04 Aligned_cols=53 Identities=13% Similarity=0.209 Sum_probs=33.1
Q ss_pred ecCcccccCCccCCCCCCCCCCCCee-eeCCcCCCccchhhcc----------CCCCCccCCcccCc
Q psy3656 99 ALGKTWHPEHFICTHCNQELGTRNFF-ERDSRPYCEPDYHNLF----------SPRCSYCNGPILDK 154 (185)
Q Consensus 99 ~~~~~~H~~Cf~C~~C~~~L~~~~~~-~~~g~~yC~~~~~~~~----------~~~C~~C~~~i~~~ 154 (185)
..+..|..+| ..|+.+|..++.. ..--.++..+|+..+- |-+|..|++.|.+.
T Consensus 44 L~DsDY~pNC---~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp 107 (299)
T KOG3970|consen 44 LQDSDYNPNC---RLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP 107 (299)
T ss_pred HhhcCCCCCC---ceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence 3456666665 6677888755432 4444555566654432 23799999999864
No 97
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=34.93 E-value=28 Score=17.60 Aligned_cols=9 Identities=33% Similarity=0.781 Sum_probs=4.1
Q ss_pred CCccCCccc
Q psy3656 144 CSYCNGPIL 152 (185)
Q Consensus 144 C~~C~~~i~ 152 (185)
|..|++.+.
T Consensus 3 C~~C~~~~~ 11 (30)
T PF03107_consen 3 CDVCRRKID 11 (30)
T ss_pred CCCCCCCcC
Confidence 444444444
No 98
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.72 E-value=26 Score=27.96 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=17.7
Q ss_pred CCCCCccCCcccCceEEeCCCeecccC
Q psy3656 141 SPRCSYCNGPILDKCVTALEKTWHTEH 167 (185)
Q Consensus 141 ~~~C~~C~~~i~~~~~~~~~~~~H~~C 167 (185)
+..|..|+.+|.-..+.-+...|.|.|
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~C 261 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQC 261 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCC
Confidence 578999999987544444455554443
No 99
>KOG0978|consensus
Probab=34.44 E-value=7.8 Score=35.07 Aligned_cols=44 Identities=30% Similarity=0.540 Sum_probs=26.3
Q ss_pred CCCCccCCcccCceEEeCCCeecccCc---------ccccCCCccCCCCeeeC
Q psy3656 142 PRCSYCNGPILDKCVTALEKTWHTEHF---------FCAQCGKQFGEAMVKFI 185 (185)
Q Consensus 142 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf---------~C~~C~~~l~~~~~~~~ 185 (185)
-+|..|+..--+.+|.--+++|.-+|- +|..|+..||-..|+-|
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRI 696 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccccc
Confidence 457777744333343333333333332 48899999998888765
No 100
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.89 E-value=26 Score=27.90 Aligned_cols=27 Identities=19% Similarity=0.324 Sum_probs=20.1
Q ss_pred CCCCCccCCcccCceEEeCCCeecccC
Q psy3656 141 SPRCSYCNGPILDKCVTALEKTWHTEH 167 (185)
Q Consensus 141 ~~~C~~C~~~i~~~~~~~~~~~~H~~C 167 (185)
+..|..|+.+|.-..+.-+...|.|.|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 568999999997555555667777766
No 101
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=33.54 E-value=26 Score=17.68 Aligned_cols=9 Identities=44% Similarity=1.043 Sum_probs=2.0
Q ss_pred CCccCCccc
Q psy3656 144 CSYCNGPIL 152 (185)
Q Consensus 144 C~~C~~~i~ 152 (185)
|..|++++.
T Consensus 3 C~~C~~~~~ 11 (30)
T PF07649_consen 3 CDACGKPID 11 (30)
T ss_dssp -TTTS----
T ss_pred CCcCCCcCC
Confidence 445555544
No 102
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=33.48 E-value=53 Score=18.65 Aligned_cols=28 Identities=14% Similarity=0.169 Sum_probs=16.4
Q ss_pred CCCCccCCcccC---ceEE--eCCCeecccCcc
Q psy3656 142 PRCSYCNGPILD---KCVT--ALEKTWHTEHFF 169 (185)
Q Consensus 142 ~~C~~C~~~i~~---~~~~--~~~~~~H~~Cf~ 169 (185)
..|..|++.|.+ ..+. .-+...|.+|..
T Consensus 12 ~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~ 44 (53)
T PF00130_consen 12 TYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLS 44 (53)
T ss_dssp EB-TTSSSBECSSSSCEEEETTTT-EEETTGGC
T ss_pred CCCcccCcccCCCCCCeEEECCCCChHhhhhhh
Confidence 568888888843 3343 235677777764
No 103
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=33.47 E-value=26 Score=20.15 Aligned_cols=9 Identities=44% Similarity=0.992 Sum_probs=5.0
Q ss_pred CCccCC-ccc
Q psy3656 144 CSYCNG-PIL 152 (185)
Q Consensus 144 C~~C~~-~i~ 152 (185)
|..|+. +|.
T Consensus 3 Cd~C~~~pI~ 12 (48)
T cd02341 3 CDSCGIEPIP 12 (48)
T ss_pred CCCCCCCccc
Confidence 556655 554
No 104
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=33.09 E-value=31 Score=20.87 Aligned_cols=11 Identities=36% Similarity=0.942 Sum_probs=6.1
Q ss_pred CCCCccCCccc
Q psy3656 142 PRCSYCNGPIL 152 (185)
Q Consensus 142 ~~C~~C~~~i~ 152 (185)
++|.+|+..|.
T Consensus 8 ~~CtSCg~~i~ 18 (59)
T PRK14890 8 PKCTSCGIEIA 18 (59)
T ss_pred ccccCCCCccc
Confidence 44555655555
No 105
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=32.68 E-value=17 Score=17.46 Aligned_cols=12 Identities=50% Similarity=1.245 Sum_probs=8.8
Q ss_pred cccccCCCccCC
Q psy3656 168 FFCAQCGKQFGE 179 (185)
Q Consensus 168 f~C~~C~~~l~~ 179 (185)
|.|..|++.+..
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 578888887754
No 106
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.36 E-value=19 Score=30.48 Aligned_cols=44 Identities=18% Similarity=0.464 Sum_probs=29.9
Q ss_pred CccCCCCCCCCCCCCeeeeCCcCCCccchhhccC--CCCCccCCccc
Q psy3656 108 HFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS--PRCSYCNGPIL 152 (185)
Q Consensus 108 Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~--~~C~~C~~~i~ 152 (185)
-+.|..|...+. ..+...=|+.||..|....+. ..|..|...+.
T Consensus 26 ~l~C~IC~d~~~-~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDFFD-VPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchhhh-CccCCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 368888877663 234466788888888765443 46888888765
No 107
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.01 E-value=27 Score=29.62 Aligned_cols=37 Identities=22% Similarity=0.330 Sum_probs=20.6
Q ss_pred CCcccccccccccceeeecCcccccCCc--------cCCCCCCCC
Q psy3656 82 KGCCSSCDKPIVGQVITALGKTWHPEHF--------ICTHCNQEL 118 (185)
Q Consensus 82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf--------~C~~C~~~L 118 (185)
.-.|..|...+...++..-|..|...|+ .|..|...+
T Consensus 26 ~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~ 70 (397)
T TIGR00599 26 SLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAED 70 (397)
T ss_pred ccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCcc
Confidence 4579999987755444433433433333 255555544
No 108
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.78 E-value=43 Score=21.12 Aligned_cols=42 Identities=19% Similarity=0.500 Sum_probs=26.5
Q ss_pred CCCCCCCCCCCC---eeeeCCcCCCccchhhccCCCCCccCCccc
Q psy3656 111 CTHCNQELGTRN---FFERDSRPYCEPDYHNLFSPRCSYCNGPIL 152 (185)
Q Consensus 111 C~~C~~~L~~~~---~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~ 152 (185)
|.-|.+.|.... ..-.-.-.||-+|...+++..|.-|+..+.
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~g~CPnCGGelv 52 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENRLHGLCPNCGGELV 52 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHhhcCcCCCCCchhh
Confidence 444556664221 112223457888888888899999988654
No 109
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=30.51 E-value=7.5 Score=25.90 Aligned_cols=43 Identities=16% Similarity=0.354 Sum_probs=21.3
Q ss_pred ccccccccccc-eeeecCcccccCCccCCCCCCCCCCCCeeeeC
Q psy3656 85 CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERD 127 (185)
Q Consensus 85 C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~ 127 (185)
|..|...+... +....-..++..+..|..|...|.-.+|...+
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~ 81 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCG 81 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcC
Confidence 44444444322 22233355666666777776666444444333
No 110
>KOG2932|consensus
Probab=30.46 E-value=24 Score=28.79 Aligned_cols=43 Identities=12% Similarity=0.326 Sum_probs=26.6
Q ss_pred cCCCCCCCCCCCCeeeeCCcCCCccchhhccCCCCCccCCccc
Q psy3656 110 ICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPRCSYCNGPIL 152 (185)
Q Consensus 110 ~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~~C~~C~~~i~ 152 (185)
-|..|+.++.--.-.+.-...||.+|....-...|..|.+.|.
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQ 134 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHH
Confidence 4667777663222235556777777754333357999988875
No 111
>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=30.40 E-value=41 Score=27.49 Aligned_cols=28 Identities=25% Similarity=0.515 Sum_probs=18.1
Q ss_pred eCCcCCCccchhhccC---CCCCccCCcccC
Q psy3656 126 RDSRPYCEPDYHNLFS---PRCSYCNGPILD 153 (185)
Q Consensus 126 ~~g~~yC~~~~~~~~~---~~C~~C~~~i~~ 153 (185)
.=|+.+|..|..+.|. ..|..|+..+.-
T Consensus 25 ~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 3456667666665542 468888887763
No 112
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=30.31 E-value=33 Score=27.55 Aligned_cols=27 Identities=19% Similarity=0.443 Sum_probs=19.3
Q ss_pred CCCCCccCCcccCceEEeCCCeecccC
Q psy3656 141 SPRCSYCNGPILDKCVTALEKTWHTEH 167 (185)
Q Consensus 141 ~~~C~~C~~~i~~~~~~~~~~~~H~~C 167 (185)
+..|..|+.+|.-..+.-+...|.|.|
T Consensus 254 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 280 (282)
T PRK13945 254 GKPCRKCGTPIERIKLAGRSTHWCPNC 280 (282)
T ss_pred cCCCCcCCCeeEEEEECCCccEECCCC
Confidence 578999999997555544556666665
No 113
>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=30.30 E-value=93 Score=22.22 Aligned_cols=36 Identities=17% Similarity=0.385 Sum_probs=20.8
Q ss_pred CCcccccccccc-c--c----eeeecCcccccCCccCCCCCCC
Q psy3656 82 KGCCSSCDKPIV-G--Q----VITALGKTWHPEHFICTHCNQE 117 (185)
Q Consensus 82 ~~~C~~C~~~i~-~--~----~~~~~~~~~H~~Cf~C~~C~~~ 117 (185)
...|..|+..+. . + .+...-...+...++|..|++-
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCE
Confidence 468999998772 1 1 1222223334556788888764
No 114
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=30.05 E-value=59 Score=21.55 Aligned_cols=13 Identities=38% Similarity=0.894 Sum_probs=6.3
Q ss_pred hccCCCCCccCCc
Q psy3656 138 NLFSPRCSYCNGP 150 (185)
Q Consensus 138 ~~~~~~C~~C~~~ 150 (185)
+.|+.+|..|+..
T Consensus 35 rv~~Q~C~~C~~~ 47 (98)
T PF13695_consen 35 RVFGQRCKKCNPL 47 (98)
T ss_pred EEECCCCCCCCCC
Confidence 3445555555433
No 115
>KOG2186|consensus
Probab=30.03 E-value=12 Score=29.64 Aligned_cols=41 Identities=12% Similarity=0.374 Sum_probs=26.1
Q ss_pred CcccccccccccceeeecCcccccCCccCCCCCCCCCCCCe
Q psy3656 83 GCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF 123 (185)
Q Consensus 83 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~ 123 (185)
..|..|+..|.-..+.----..|..+|.|..|+..+....|
T Consensus 4 FtCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k~F~~~sY 44 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGKTFERVSY 44 (276)
T ss_pred EehhhhhhhccccchHHHHHhccCCeeEEeecccccccchh
Confidence 35899999884222221111235588999999999866444
No 116
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=29.73 E-value=38 Score=26.99 Aligned_cols=11 Identities=18% Similarity=0.350 Sum_probs=7.5
Q ss_pred CCCCccCCccc
Q psy3656 142 PRCSYCNGPIL 152 (185)
Q Consensus 142 ~~C~~C~~~i~ 152 (185)
..|..|+..+.
T Consensus 210 ~PCPKCg~et~ 220 (314)
T PF06524_consen 210 IPCPKCGYETQ 220 (314)
T ss_pred CCCCCCCCccc
Confidence 45777777665
No 117
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=29.32 E-value=40 Score=24.18 Aligned_cols=35 Identities=23% Similarity=0.462 Sum_probs=21.8
Q ss_pred CCcccccccccc-cceeeecCcccccCCccCCCCCCCCC
Q psy3656 82 KGCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELG 119 (185)
Q Consensus 82 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~L~ 119 (185)
.-.|..|+.... .+.....+. ..=|.|..|+..|.
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 457999998773 333222221 22289999998874
No 118
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=29.13 E-value=38 Score=19.18 Aligned_cols=29 Identities=14% Similarity=0.408 Sum_probs=15.2
Q ss_pred cCCCCCCCCCCCCee-e-eCCcCCCccchhh
Q psy3656 110 ICTHCNQELGTRNFF-E-RDSRPYCEPDYHN 138 (185)
Q Consensus 110 ~C~~C~~~L~~~~~~-~-~~g~~yC~~~~~~ 138 (185)
.|..|+..+..-.|. . ..+..+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 466666666432222 1 2234567777764
No 119
>KOG3039|consensus
Probab=28.99 E-value=36 Score=26.89 Aligned_cols=75 Identities=15% Similarity=0.232 Sum_probs=54.1
Q ss_pred CCcccccccccc-cc----eeeec-------CcccccCCccCCCCCCCCCCC---CeeeeCCcCCCccchhhccC--CCC
Q psy3656 82 KGCCSSCDKPIV-GQ----VITAL-------GKTWHPEHFICTHCNQELGTR---NFFERDSRPYCEPDYHNLFS--PRC 144 (185)
Q Consensus 82 ~~~C~~C~~~i~-~~----~~~~~-------~~~~H~~Cf~C~~C~~~L~~~---~~~~~~g~~yC~~~~~~~~~--~~C 144 (185)
..+|..=+++|. -+ .+..+ +..-|..-|.|..|...|.+. .+...-|.++|.+|.+++.. .+|
T Consensus 183 ~v~CP~s~kplklkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~ 262 (303)
T KOG3039|consen 183 TVVCPVSGKPLKLKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVD 262 (303)
T ss_pred eeeccCCCCccchhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccc
Confidence 457888888882 21 22222 224566778999999999743 34478899999999887775 689
Q ss_pred CccCCcccCceE
Q psy3656 145 SYCNGPILDKCV 156 (185)
Q Consensus 145 ~~C~~~i~~~~~ 156 (185)
..|++++.++.|
T Consensus 263 pv~d~plkdrdi 274 (303)
T KOG3039|consen 263 PVTDKPLKDRDI 274 (303)
T ss_pred cCCCCcCcccce
Confidence 999999987544
No 120
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=28.51 E-value=48 Score=19.18 Aligned_cols=26 Identities=15% Similarity=0.346 Sum_probs=19.5
Q ss_pred CCCCccCCcccC---ceEEeCCCeecccC
Q psy3656 142 PRCSYCNGPILD---KCVTALEKTWHTEH 167 (185)
Q Consensus 142 ~~C~~C~~~i~~---~~~~~~~~~~H~~C 167 (185)
..|..|+.-..| -.|.+.+..|+..|
T Consensus 14 ~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 14 CKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred ccCcccCCcEeecCcceEEEeccceeeee
Confidence 568888877663 35678888888877
No 121
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.18 E-value=35 Score=24.01 Aligned_cols=11 Identities=27% Similarity=0.845 Sum_probs=5.7
Q ss_pred CCCccCCcccC
Q psy3656 143 RCSYCNGPILD 153 (185)
Q Consensus 143 ~C~~C~~~i~~ 153 (185)
.|..|+..|.|
T Consensus 41 qcp~csasirg 51 (160)
T COG4306 41 QCPICSASIRG 51 (160)
T ss_pred cCCccCCcccc
Confidence 45555555554
No 122
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=27.80 E-value=33 Score=20.68 Aligned_cols=9 Identities=33% Similarity=0.922 Sum_probs=5.5
Q ss_pred cccCCCccC
Q psy3656 170 CAQCGKQFG 178 (185)
Q Consensus 170 C~~C~~~l~ 178 (185)
|..|++.|+
T Consensus 19 C~~C~k~L~ 27 (58)
T PF04570_consen 19 CYLCKKKLD 27 (58)
T ss_pred HHccCCCCC
Confidence 666666664
No 123
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=27.78 E-value=43 Score=30.71 Aligned_cols=83 Identities=24% Similarity=0.582 Sum_probs=53.1
Q ss_pred CCCcccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccch-hhccCCCCCccCCcccCceEEeC
Q psy3656 81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY-HNLFSPRCSYCNGPILDKCVTAL 159 (185)
Q Consensus 81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~-~~~~~~~C~~C~~~i~~~~~~~~ 159 (185)
+..+|..|.+.+.+ -.++.|+=--..|..|+-.. .+....+|=.... ...| +.|..|.+...+. .
T Consensus 67 D~a~C~~Cl~E~~d----p~~Rry~YpF~nCt~CGPr~-----~i~~~lpydr~~t~m~~f-~~C~~C~~ey~~p----~ 132 (711)
T TIGR00143 67 DVATCSDCLEEMLD----KNDRRYLYPFISCTHCGPRF-----TIIEALPYDRENTSMADF-PLCPDCAKEYKDP----L 132 (711)
T ss_pred chhhHHHHHHHhcC----CCcccccCCcccccCCCCCe-----EEeecCCCCCCCcCCCCC-cCCHHHHHHhcCC----c
Confidence 35679999887753 34566776667888897654 3333344433211 1222 5677777765432 6
Q ss_pred CCeecccCcccccCCCcc
Q psy3656 160 EKTWHTEHFFCAQCGKQF 177 (185)
Q Consensus 160 ~~~~H~~Cf~C~~C~~~l 177 (185)
++.||-.=-.|..|+..|
T Consensus 133 ~rr~h~~~~~C~~Cgp~l 150 (711)
T TIGR00143 133 DRRFHAQPIACPRCGPQL 150 (711)
T ss_pred cccCCCCCccCCCCCcEE
Confidence 788888888888888877
No 124
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=27.44 E-value=22 Score=20.88 Aligned_cols=14 Identities=29% Similarity=0.757 Sum_probs=9.7
Q ss_pred CCCCcccccccccc
Q psy3656 80 TQKGCCSSCDKPIV 93 (185)
Q Consensus 80 ~~~~~C~~C~~~i~ 93 (185)
.....|.+|+-.|.
T Consensus 20 v~~~~C~gC~~~l~ 33 (56)
T PF02591_consen 20 VEGGTCSGCHMELP 33 (56)
T ss_pred eeCCccCCCCEEcC
Confidence 34567888887773
No 125
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=27.20 E-value=45 Score=23.53 Aligned_cols=30 Identities=20% Similarity=0.232 Sum_probs=21.2
Q ss_pred CCCCccCCcccC----ceEEeCCCeecccCcccc
Q psy3656 142 PRCSYCNGPILD----KCVTALEKTWHTEHFFCA 171 (185)
Q Consensus 142 ~~C~~C~~~i~~----~~~~~~~~~~H~~Cf~C~ 171 (185)
.+|.-|+..|.+ ++|...+++|+----+|.
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~ 38 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCE 38 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEEEecHHHH
Confidence 469999999974 456677888876544453
No 126
>smart00746 TRASH metallochaperone-like domain.
Probab=27.11 E-value=64 Score=15.60 Aligned_cols=21 Identities=29% Similarity=0.510 Sum_probs=12.5
Q ss_pred CCccCCccc-C---ceEEeCCCeec
Q psy3656 144 CSYCNGPIL-D---KCVTALEKTWH 164 (185)
Q Consensus 144 C~~C~~~i~-~---~~~~~~~~~~H 164 (185)
|..|+..|. . ......++.||
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~ 25 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFY 25 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEE
Confidence 667888775 2 22345566665
No 127
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=27.06 E-value=45 Score=15.90 Aligned_cols=19 Identities=26% Similarity=0.663 Sum_probs=8.9
Q ss_pred CccchhhccC--CCCCccCCc
Q psy3656 132 CEPDYHNLFS--PRCSYCNGP 150 (185)
Q Consensus 132 C~~~~~~~~~--~~C~~C~~~ 150 (185)
|..|....+. ..|..|+.+
T Consensus 5 C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 5 CPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred CCCCCCcChhhhccccccCCc
Confidence 4444333332 456666543
No 128
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=26.91 E-value=12 Score=20.96 Aligned_cols=8 Identities=25% Similarity=1.103 Sum_probs=2.8
Q ss_pred cccccccc
Q psy3656 85 CSSCDKPI 92 (185)
Q Consensus 85 C~~C~~~i 92 (185)
|..|.+.|
T Consensus 1 C~~C~~iv 8 (43)
T PF08746_consen 1 CEACKEIV 8 (43)
T ss_dssp -TTT-SB-
T ss_pred CcccchhH
Confidence 45565555
No 129
>PHA02768 hypothetical protein; Provisional
Probab=26.88 E-value=10 Score=22.64 Aligned_cols=11 Identities=18% Similarity=0.552 Sum_probs=5.5
Q ss_pred ccCCCCCCCCC
Q psy3656 109 FICTHCNQELG 119 (185)
Q Consensus 109 f~C~~C~~~L~ 119 (185)
|.|..|++.+.
T Consensus 6 y~C~~CGK~Fs 16 (55)
T PHA02768 6 YECPICGEIYI 16 (55)
T ss_pred cCcchhCCeec
Confidence 45555555443
No 130
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=26.56 E-value=42 Score=18.62 Aligned_cols=12 Identities=33% Similarity=0.863 Sum_probs=7.3
Q ss_pred CCCCccCCcccC
Q psy3656 142 PRCSYCNGPILD 153 (185)
Q Consensus 142 ~~C~~C~~~i~~ 153 (185)
..|..|+.+|.+
T Consensus 5 ~~C~~C~~~i~g 16 (44)
T smart00291 5 YSCDTCGKPIVG 16 (44)
T ss_pred cCCCCCCCCCcC
Confidence 457777765543
No 131
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=26.52 E-value=12 Score=25.47 Aligned_cols=28 Identities=21% Similarity=0.453 Sum_probs=16.0
Q ss_pred CCCCccCCcccCceEEeCCCeecccCcccccCC
Q psy3656 142 PRCSYCNGPILDKCVTALEKTWHTEHFFCAQCG 174 (185)
Q Consensus 142 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~ 174 (185)
..|-.|+++|....+.| .|+.-.|..|+
T Consensus 81 G~C~~Cge~I~~~RL~a-----~P~a~~Cv~Cq 108 (110)
T TIGR02420 81 GYCEECGEEIGLRRLEA-----RPTATLCIDCK 108 (110)
T ss_pred CchhccCCcccHHHHhh-----CCCccccHHhH
Confidence 46777777777555544 24444455543
No 132
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=26.32 E-value=43 Score=25.44 Aligned_cols=42 Identities=26% Similarity=0.568 Sum_probs=25.0
Q ss_pred CCccchhhccCCCCCccCC--cccC----ceEE--eCCCeecccCcc---cccCC
Q psy3656 131 YCEPDYHNLFSPRCSYCNG--PILD----KCVT--ALEKTWHTEHFF---CAQCG 174 (185)
Q Consensus 131 yC~~~~~~~~~~~C~~C~~--~i~~----~~~~--~~~~~~H~~Cf~---C~~C~ 174 (185)
.|+.|-.+ |-.|..|+. .|.+ ..+. .-+.+||.+||. |..|.
T Consensus 144 ~C~lC~~k--GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~~~CpkC~ 196 (202)
T PF13901_consen 144 SCELCQQK--GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRKKSCPKCA 196 (202)
T ss_pred HhHHHHhC--CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCCCCCCCcH
Confidence 35555443 457888874 4443 2232 236899999997 55554
No 133
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=26.18 E-value=31 Score=20.93 Aligned_cols=9 Identities=56% Similarity=1.353 Sum_probs=3.6
Q ss_pred cccCCCccC
Q psy3656 170 CAQCGKQFG 178 (185)
Q Consensus 170 C~~C~~~l~ 178 (185)
|.+|++.++
T Consensus 7 CFTCGkvi~ 15 (60)
T PF01194_consen 7 CFTCGKVIG 15 (60)
T ss_dssp -STTTSBTC
T ss_pred cCCCCCChh
Confidence 444444443
No 134
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=25.99 E-value=30 Score=25.55 Aligned_cols=36 Identities=28% Similarity=0.619 Sum_probs=25.1
Q ss_pred CCCCccCCcccC----ceE---EeCCCeecccCcccccCCCcc
Q psy3656 142 PRCSYCNGPILD----KCV---TALEKTWHTEHFFCAQCGKQF 177 (185)
Q Consensus 142 ~~C~~C~~~i~~----~~~---~~~~~~~H~~Cf~C~~C~~~l 177 (185)
.+|..|+..+.. +.. --.-...|-++++|..|++..
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 589999998862 222 112346778899999999865
No 135
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=25.87 E-value=56 Score=23.81 Aligned_cols=30 Identities=17% Similarity=0.368 Sum_probs=21.0
Q ss_pred CCccccccccc-ccceeeecCcccccCCccCCCCCCCCC
Q psy3656 82 KGCCSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELG 119 (185)
Q Consensus 82 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 119 (185)
.=.|..|+... +.+.+. .=|.|..|+..|.
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAME--------LNFTCPRCGAMLD 139 (158)
T ss_pred eEECCCCCcEeeHHHHHH--------cCCcCCCCCCEee
Confidence 34699999776 333332 2589999999884
No 136
>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=25.47 E-value=73 Score=17.84 Aligned_cols=10 Identities=20% Similarity=0.249 Sum_probs=5.5
Q ss_pred CCeecccCcc
Q psy3656 160 EKTWHTEHFF 169 (185)
Q Consensus 160 ~~~~H~~Cf~ 169 (185)
++.||..|..
T Consensus 21 ~~~~H~~C~~ 30 (51)
T PF00628_consen 21 NRWYHQECVG 30 (51)
T ss_dssp SCEEETTTST
T ss_pred ChhhCcccCC
Confidence 3566666543
No 137
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....
Probab=25.04 E-value=1.1e+02 Score=24.23 Aligned_cols=52 Identities=15% Similarity=0.202 Sum_probs=30.6
Q ss_pred eCCcCCCccchhhccCCCCCccCCcccC-----ceEEeCCCeecccCcc---------cccCCCcc
Q psy3656 126 RDSRPYCEPDYHNLFSPRCSYCNGPILD-----KCVTALEKTWHTEHFF---------CAQCGKQF 177 (185)
Q Consensus 126 ~~g~~yC~~~~~~~~~~~C~~C~~~i~~-----~~~~~~~~~~H~~Cf~---------C~~C~~~l 177 (185)
..|.+|+..-........|..|+..... .+|...-=+||++=|+ |..|.+.+
T Consensus 39 ~~~Gl~d~rlG~~~~~~~C~tC~~~~~~CpGHfGhI~L~~PV~h~~f~~~i~~iL~~~C~~C~~l~ 104 (337)
T PF04997_consen 39 IKGGLYDPRLGPIDKKQICSTCGLNYTECPGHFGHIELALPVYHPGFFKEIPKILRCICKKCSRLL 104 (337)
T ss_dssp BSSSSSSSSSS-SSSSSTSSSSSSSSSSCCCSEEEEEEEEEEETCCCHHHHHHHHTTSCTTTSCTS
T ss_pred ccccccChhhcCCCcccccccccccccccCCceeEEEeCHHHHhhcccccceeeeccccccccccc
Confidence 3445566554444444578888877653 2455555678876443 66666655
No 138
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=24.75 E-value=49 Score=23.21 Aligned_cols=28 Identities=18% Similarity=0.342 Sum_probs=19.4
Q ss_pred CCCCccCCcccCceEEeCCCeecccCcccc
Q psy3656 142 PRCSYCNGPILDKCVTALEKTWHTEHFFCA 171 (185)
Q Consensus 142 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~ 171 (185)
-.|..|+.+ +..|...++.|-..|-.|.
T Consensus 94 VlC~~C~sp--dT~l~k~~r~~~l~C~aCG 121 (125)
T PF01873_consen 94 VLCPECGSP--DTELIKEGRLIFLKCKACG 121 (125)
T ss_dssp SSCTSTSSS--SEEEEEETTCCEEEETTTS
T ss_pred EEcCCCCCC--ccEEEEcCCEEEEEecccC
Confidence 679999877 3444445888877776664
No 139
>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=24.58 E-value=63 Score=17.55 Aligned_cols=29 Identities=31% Similarity=0.637 Sum_probs=12.7
Q ss_pred Ccccccccccc-cceeeecCcccccCCccCCCCCC
Q psy3656 83 GCCSSCDKPIV-GQVITALGKTWHPEHFICTHCNQ 116 (185)
Q Consensus 83 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~ 116 (185)
.+|..|+--|. -..+...++.| +|..|+.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred cccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 45777777663 23344445555 6666654
No 140
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.53 E-value=83 Score=30.85 Aligned_cols=48 Identities=17% Similarity=0.398 Sum_probs=0.0
Q ss_pred cccccccccccceeeecCcccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhhccCC-----CCCccCCcccC
Q psy3656 84 CCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP-----RCSYCNGPILD 153 (185)
Q Consensus 84 ~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~~~~~-----~C~~C~~~i~~ 153 (185)
+|..|+..+.. +.|..|+..+ .-...|..|-...-.. .|..|+.++..
T Consensus 669 kCPkCG~~t~~--------------~fCP~CGs~t--------e~vy~CPsCGaev~~des~a~~CP~CGtplv~ 721 (1337)
T PRK14714 669 RCPSCGTETYE--------------NRCPDCGTHT--------EPVYVCPDCGAEVPPDESGRVECPRCDVELTP 721 (1337)
T ss_pred ECCCCCCcccc--------------ccCcccCCcC--------CCceeCccCCCccCCCccccccCCCCCCcccc
No 141
>KOG3576|consensus
Probab=24.48 E-value=4.2 Score=31.09 Aligned_cols=10 Identities=30% Similarity=0.660 Sum_probs=4.9
Q ss_pred Cccccccccc
Q psy3656 83 GCCSSCDKPI 92 (185)
Q Consensus 83 ~~C~~C~~~i 92 (185)
-.|..|+|..
T Consensus 118 ftCrvCgK~F 127 (267)
T KOG3576|consen 118 FTCRVCGKKF 127 (267)
T ss_pred eeeehhhhhh
Confidence 3455555543
No 142
>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=24.34 E-value=31 Score=16.72 Aligned_cols=10 Identities=50% Similarity=1.344 Sum_probs=6.1
Q ss_pred cccccCCCcc
Q psy3656 168 FFCAQCGKQF 177 (185)
Q Consensus 168 f~C~~C~~~l 177 (185)
|.|..|++.+
T Consensus 15 ~~C~~C~k~F 24 (26)
T PF13465_consen 15 YKCPYCGKSF 24 (26)
T ss_dssp EEESSSSEEE
T ss_pred CCCCCCcCee
Confidence 5666666654
No 143
>smart00355 ZnF_C2H2 zinc finger.
Probab=24.17 E-value=39 Score=15.24 Aligned_cols=12 Identities=42% Similarity=1.146 Sum_probs=8.1
Q ss_pred cccccCCCccCC
Q psy3656 168 FFCAQCGKQFGE 179 (185)
Q Consensus 168 f~C~~C~~~l~~ 179 (185)
|.|..|++.+..
T Consensus 1 ~~C~~C~~~f~~ 12 (26)
T smart00355 1 YRCPECGKVFKS 12 (26)
T ss_pred CCCCCCcchhCC
Confidence 467778777644
No 144
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=23.97 E-value=41 Score=22.16 Aligned_cols=19 Identities=26% Similarity=0.765 Sum_probs=13.6
Q ss_pred chhhccC--CCCCccCCcccC
Q psy3656 135 DYHNLFS--PRCSYCNGPILD 153 (185)
Q Consensus 135 ~~~~~~~--~~C~~C~~~i~~ 153 (185)
||.++.. ++|+.|+.++-|
T Consensus 26 h~~kK~~~~p~C~~cg~pL~G 46 (93)
T COG2174 26 HYEKKKPTIPKCAICGRPLGG 46 (93)
T ss_pred eeeeccCCCCcccccCCccCC
Confidence 3554444 789999998865
No 145
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=23.24 E-value=57 Score=27.86 Aligned_cols=33 Identities=27% Similarity=0.805 Sum_probs=23.7
Q ss_pred CCCCCccCCcccCceEEeCCCeecccCcccccCCCccCCCCe
Q psy3656 141 SPRCSYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEAMV 182 (185)
Q Consensus 141 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~ 182 (185)
.|+|..|+.. |...|+. -|+|..|+..+....+
T Consensus 350 ~p~Cp~Cg~~-----m~S~G~~----g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 350 NPVCPRCGGR-----MKSAGRN----GFRCKKCGTRARETLI 382 (421)
T ss_pred CCCCCccCCc-----hhhcCCC----CcccccccccCCcccc
Confidence 3789999876 3445554 6899999988766544
No 146
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=23.22 E-value=61 Score=19.64 Aligned_cols=11 Identities=36% Similarity=0.905 Sum_probs=7.2
Q ss_pred CCCCccCCccc
Q psy3656 142 PRCSYCNGPIL 152 (185)
Q Consensus 142 ~~C~~C~~~i~ 152 (185)
+.|.+|+..|.
T Consensus 10 ~~CtSCg~~i~ 20 (61)
T COG2888 10 PVCTSCGREIA 20 (61)
T ss_pred ceeccCCCEec
Confidence 56777777663
No 147
>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=22.64 E-value=23 Score=19.43 Aligned_cols=27 Identities=15% Similarity=0.310 Sum_probs=17.1
Q ss_pred CCCccCCccc-Cc-eE-EeCCCeecccCcc
Q psy3656 143 RCSYCNGPIL-DK-CV-TALEKTWHTEHFF 169 (185)
Q Consensus 143 ~C~~C~~~i~-~~-~~-~~~~~~~H~~Cf~ 169 (185)
.|..|.+.+. ++ .+ ..-++.||.+|+.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~ 31 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIK 31 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHH
Confidence 4777877775 22 22 2347888888764
No 148
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=22.17 E-value=55 Score=21.88 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=18.8
Q ss_pred ccCCCCCccCCcccCceEEeC----CCeecccCc
Q psy3656 139 LFSPRCSYCNGPILDKCVTAL----EKTWHTEHF 168 (185)
Q Consensus 139 ~~~~~C~~C~~~i~~~~~~~~----~~~~H~~Cf 168 (185)
++..+|..|++. .|-.+.-. ...||+.|-
T Consensus 53 ~~~~~C~iC~~~-~G~~i~C~~~~C~~~fH~~CA 85 (110)
T PF13832_consen 53 RFKLKCSICGKS-GGACIKCSHPGCSTAFHPTCA 85 (110)
T ss_pred hcCCcCcCCCCC-CceeEEcCCCCCCcCCCHHHH
Confidence 456788888887 44444422 477888774
No 149
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=21.98 E-value=73 Score=30.63 Aligned_cols=30 Identities=20% Similarity=0.506 Sum_probs=18.9
Q ss_pred CCcccccccccccceeeecCcccccCCccCCCCCCCC
Q psy3656 82 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL 118 (185)
Q Consensus 82 ~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L 118 (185)
..+|..|+..|- +.++|..| -.|..|+-++
T Consensus 17 ~qiCqICGD~vg---~~~~Ge~F----VAC~eC~FPV 46 (1079)
T PLN02638 17 GQVCQICGDNVG---KTVDGEPF----VACDVCAFPV 46 (1079)
T ss_pred CceeeecccccC---cCCCCCEE----EEeccCCCcc
Confidence 468999998872 23445545 3566666655
No 150
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=21.81 E-value=1.8e+02 Score=23.89 Aligned_cols=10 Identities=20% Similarity=0.703 Sum_probs=7.4
Q ss_pred CCcccccccc
Q psy3656 82 KGCCSSCDKP 91 (185)
Q Consensus 82 ~~~C~~C~~~ 91 (185)
...|..||..
T Consensus 187 ~~~CPvCGs~ 196 (309)
T PRK03564 187 RQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCc
Confidence 4678888864
No 151
>PLN02436 cellulose synthase A
Probab=21.63 E-value=79 Score=30.39 Aligned_cols=31 Identities=23% Similarity=0.599 Sum_probs=19.3
Q ss_pred CCCcccccccccccceeeecCcccccCCccCCCCCCCC
Q psy3656 81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL 118 (185)
Q Consensus 81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L 118 (185)
...+|..|+..|- +.++|..| -.|..|+-++
T Consensus 35 ~~~iCqICGD~Vg---~t~dGe~F----VACn~C~fpv 65 (1094)
T PLN02436 35 SGQTCQICGDEIE---LTVDGEPF----VACNECAFPV 65 (1094)
T ss_pred CCccccccccccC---cCCCCCEE----EeeccCCCcc
Confidence 3568999998872 23455545 3566666655
No 152
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=21.62 E-value=67 Score=18.99 Aligned_cols=25 Identities=24% Similarity=0.401 Sum_probs=17.5
Q ss_pred CCCCccCCcccC----ceEEeCCCeeccc
Q psy3656 142 PRCSYCNGPILD----KCVTALEKTWHTE 166 (185)
Q Consensus 142 ~~C~~C~~~i~~----~~~~~~~~~~H~~ 166 (185)
..|.-|+..|.+ ++|...+++|+=-
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~ 32 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFRFC 32 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEEEE
Confidence 468889998874 3566677777643
No 153
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=21.57 E-value=45 Score=21.72 Aligned_cols=10 Identities=30% Similarity=0.866 Sum_probs=6.6
Q ss_pred CCCccCCccc
Q psy3656 143 RCSYCNGPIL 152 (185)
Q Consensus 143 ~C~~C~~~i~ 152 (185)
.|..|+.+|.
T Consensus 2 ~C~HCg~~~p 11 (88)
T PF12156_consen 2 KCYHCGLPVP 11 (88)
T ss_pred CCCCCCCCCC
Confidence 4667777764
No 154
>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 COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=21.53 E-value=1.3e+02 Score=23.77 Aligned_cols=19 Identities=32% Similarity=0.538 Sum_probs=13.8
Q ss_pred CCCCCccCC-cccCceEEeC
Q psy3656 141 SPRCSYCNG-PILDKCVTAL 159 (185)
Q Consensus 141 ~~~C~~C~~-~i~~~~~~~~ 159 (185)
-++|..|+. .|.+.++-+.
T Consensus 146 ~p~C~~Cg~~~lrP~VV~fG 165 (250)
T COG0846 146 IPRCPKCGGPVLRPDVVWFG 165 (250)
T ss_pred CCcCccCCCccccCCEEEeC
Confidence 388999999 6667666543
No 156
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=21.46 E-value=52 Score=22.23 Aligned_cols=33 Identities=12% Similarity=0.428 Sum_probs=23.3
Q ss_pred cccccCCccCCCCCCCCCCCCeeeeCCcCCCccchhh
Q psy3656 102 KTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 138 (185)
Q Consensus 102 ~~~H~~Cf~C~~C~~~L~~~~~~~~~g~~yC~~~~~~ 138 (185)
..+...--.|..| ++..|++.++.+.|..|-.+
T Consensus 29 g~~~va~daCeiC----~~~GY~q~g~~lvC~~C~~~ 61 (102)
T PF10080_consen 29 GSYRVAFDACEIC----GPKGYYQEGDQLVCKNCGVR 61 (102)
T ss_pred CCEEEEEEecccc----CCCceEEECCEEEEecCCCE
Confidence 3444444467888 45678899999999988544
No 157
>PF14279 HNH_5: HNH endonuclease
Probab=21.34 E-value=32 Score=21.52 Aligned_cols=22 Identities=23% Similarity=0.688 Sum_probs=16.2
Q ss_pred EeCCCeecccCcccccCCCccCC
Q psy3656 157 TALEKTWHTEHFFCAQCGKQFGE 179 (185)
Q Consensus 157 ~~~~~~~H~~Cf~C~~C~~~l~~ 179 (185)
.+.|..++... .|..|+..||.
T Consensus 21 ~sLGG~~~~~~-vC~~CN~~~g~ 42 (71)
T PF14279_consen 21 ESLGGKLKINN-VCDKCNNKFGS 42 (71)
T ss_pred hhcCCcccccc-hhHHHhHHHhH
Confidence 56677777777 88888877753
No 158
>PRK11595 DNA utilization protein GntX; Provisional
Probab=21.16 E-value=68 Score=24.69 Aligned_cols=10 Identities=40% Similarity=1.045 Sum_probs=5.6
Q ss_pred Cccccccccc
Q psy3656 83 GCCSSCDKPI 92 (185)
Q Consensus 83 ~~C~~C~~~i 92 (185)
+.|..|++.+
T Consensus 6 ~~C~~C~~~~ 15 (227)
T PRK11595 6 GLCWLCRMPL 15 (227)
T ss_pred CcCccCCCcc
Confidence 3466666554
No 159
>PF11077 DUF2616: Protein of unknown function (DUF2616); InterPro: IPR020201 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Probab=21.15 E-value=66 Score=23.96 Aligned_cols=18 Identities=22% Similarity=0.371 Sum_probs=12.9
Q ss_pred eeeeCCcCCCccchhhcc
Q psy3656 123 FFERDSRPYCEPDYHNLF 140 (185)
Q Consensus 123 ~~~~~g~~yC~~~~~~~~ 140 (185)
++.-+-.++|..|..-+|
T Consensus 154 ~~~F~~~lFC~~ClFPLF 171 (173)
T PF11077_consen 154 FTYFNFNLFCKNCLFPLF 171 (173)
T ss_pred EEecChhhcccccCcccc
Confidence 557777888888866555
No 160
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=20.97 E-value=26 Score=23.55 Aligned_cols=11 Identities=36% Similarity=0.842 Sum_probs=8.5
Q ss_pred eeCCcCCCccc
Q psy3656 125 ERDSRPYCEPD 135 (185)
Q Consensus 125 ~~~g~~yC~~~ 135 (185)
..+|++||.+|
T Consensus 88 ~~~g~~iC~DC 98 (99)
T PF13834_consen 88 EKDGQPICRDC 98 (99)
T ss_pred ccCCCEecccc
Confidence 56788888877
No 161
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=20.90 E-value=1.8e+02 Score=19.31 Aligned_cols=34 Identities=26% Similarity=0.525 Sum_probs=16.0
Q ss_pred CCCCccCCcccCceEEeCC-CeecccCcccccCCCc
Q psy3656 142 PRCSYCNGPILDKCVTALE-KTWHTEHFFCAQCGKQ 176 (185)
Q Consensus 142 ~~C~~C~~~i~~~~~~~~~-~~~H~~Cf~C~~C~~~ 176 (185)
.+=+.|+..+.+..|.+.. +-|-.- -+|..|+..
T Consensus 42 DRas~C~g~M~Pi~v~~~~~g~w~ii-HrC~~Cg~l 76 (92)
T PF12647_consen 42 DRASDCGGRMEPIAVWVRRDGEWMII-HRCTRCGEL 76 (92)
T ss_pred CccccCCCeeeEEEEEEEcCCCEEEE-EecCCCCCc
Confidence 3444566665555454433 333221 145666553
No 162
>PLN02400 cellulose synthase
Probab=20.24 E-value=83 Score=30.27 Aligned_cols=31 Identities=19% Similarity=0.594 Sum_probs=18.7
Q ss_pred CCCcccccccccccceeeecCcccccCCccCCCCCCCC
Q psy3656 81 QKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQEL 118 (185)
Q Consensus 81 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~L 118 (185)
...+|..|+..|- +..+|..| -.|..|.-++
T Consensus 35 ~gqiCqICGD~VG---~t~dGe~F----VAC~eCaFPV 65 (1085)
T PLN02400 35 NGQICQICGDDVG---VTETGDVF----VACNECAFPV 65 (1085)
T ss_pred CCceeeecccccC---cCCCCCEE----EEEccCCCcc
Confidence 3568999998872 23444444 3556665555
No 163
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=20.24 E-value=58 Score=18.78 Aligned_cols=22 Identities=14% Similarity=0.304 Sum_probs=13.6
Q ss_pred CcCCCccchhhcc--CCCCCccCC
Q psy3656 128 SRPYCEPDYHNLF--SPRCSYCNG 149 (185)
Q Consensus 128 g~~yC~~~~~~~~--~~~C~~C~~ 149 (185)
.+..|..||.++- +..|..|+-
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 3456777776543 256777764
No 164
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.20 E-value=1e+02 Score=22.96 Aligned_cols=30 Identities=20% Similarity=0.503 Sum_probs=21.0
Q ss_pred CCccccccccc-ccceeeecCcccccCCccCCCCCCCCC
Q psy3656 82 KGCCSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELG 119 (185)
Q Consensus 82 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 119 (185)
.-.|..|+... +.+.+ . .-|.|..|+..|.
T Consensus 117 ~Y~Cp~C~~rytf~eA~---~-----~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAM---E-----YGFRCPQCGEMLE 147 (178)
T ss_pred EEECCCCCcEEeHHHHh---h-----cCCcCCCCCCCCe
Confidence 44799999777 33332 2 2589999999884
Done!