Query psy10674
Match_columns 138
No_of_seqs 206 out of 1342
Neff 9.3
Searched_HMMs 46136
Date Fri Aug 16 15:46:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10674.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10674hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.9 1.2E-26 2.6E-31 172.7 3.9 131 2-134 291-457 (468)
2 KOG1701|consensus 99.9 4.6E-27 1E-31 174.9 -2.3 111 15-133 276-386 (468)
3 KOG2272|consensus 99.9 2.8E-26 6E-31 160.9 -2.9 128 2-133 88-246 (332)
4 KOG4577|consensus 99.9 1.2E-24 2.5E-29 155.3 -3.7 114 12-133 32-147 (383)
5 KOG2272|consensus 99.9 9.9E-24 2.1E-28 148.1 0.0 130 2-134 152-307 (332)
6 KOG1044|consensus 99.9 1.9E-22 4.1E-27 155.0 4.7 127 2-132 80-243 (670)
7 KOG1703|consensus 99.8 1.1E-21 2.5E-26 152.9 3.9 132 1-134 318-476 (479)
8 KOG1044|consensus 99.7 1.1E-18 2.4E-23 134.5 4.9 131 2-134 31-185 (670)
9 KOG1703|consensus 99.7 1.5E-18 3.2E-23 135.5 3.7 112 14-134 304-415 (479)
10 PF00412 LIM: LIM domain; Int 99.6 7.2E-15 1.6E-19 83.4 5.4 58 16-78 1-58 (58)
11 PF00412 LIM: LIM domain; Int 99.5 1.4E-14 3.1E-19 82.2 3.1 51 83-134 1-52 (58)
12 KOG1700|consensus 99.3 2.3E-13 5E-18 95.2 -1.0 115 14-135 8-162 (200)
13 smart00132 LIM Zinc-binding do 99.0 1.8E-10 3.9E-15 59.7 2.9 37 82-118 1-38 (39)
14 KOG4577|consensus 99.0 5.7E-11 1.2E-15 85.6 -1.3 77 2-78 49-154 (383)
15 smart00132 LIM Zinc-binding do 98.6 3.2E-08 6.9E-13 51.0 3.1 38 15-57 1-38 (39)
16 KOG1700|consensus 97.8 3.5E-06 7.7E-11 59.1 0.0 54 81-135 8-61 (200)
17 KOG0490|consensus 97.7 2.7E-06 5.9E-11 60.6 -2.8 92 39-133 16-113 (235)
18 KOG1702|consensus 97.2 1.7E-05 3.6E-10 55.2 -3.5 57 15-77 6-62 (264)
19 KOG1702|consensus 97.2 4E-05 8.6E-10 53.4 -1.9 53 81-134 5-57 (264)
20 PF08394 Arc_trans_TRASH: Arch 95.2 0.0074 1.6E-07 30.7 0.5 32 83-117 1-33 (37)
21 PF14446 Prok-RING_1: Prokaryo 94.2 0.036 7.8E-07 30.6 1.7 36 81-116 6-50 (54)
22 PF10367 Vps39_2: Vacuolar sor 90.8 0.19 4.1E-06 31.2 2.0 28 81-108 79-107 (109)
23 PF10083 DUF2321: Uncharacteri 90.4 0.17 3.7E-06 34.0 1.6 50 66-118 27-79 (158)
24 COG4357 Zinc finger domain con 89.4 0.045 9.8E-07 33.7 -1.6 53 82-135 37-89 (105)
25 PF13240 zinc_ribbon_2: zinc-r 88.8 0.26 5.7E-06 22.2 1.1 9 83-91 2-10 (23)
26 PF09943 DUF2175: Uncharacteri 88.0 0.18 3.8E-06 31.5 0.3 30 82-111 4-34 (101)
27 PRK14890 putative Zn-ribbon RN 87.7 0.67 1.4E-05 26.0 2.4 50 13-88 7-56 (59)
28 KOG0490|consensus 86.7 0.13 2.9E-06 36.4 -1.0 47 86-134 2-50 (235)
29 PF10235 Cript: Microtubule-as 85.6 0.49 1.1E-05 29.0 1.3 44 41-93 39-82 (90)
30 COG2888 Predicted Zn-ribbon RN 84.4 1.8 3.9E-05 24.3 3.1 20 10-29 6-25 (61)
31 PF13248 zf-ribbon_3: zinc-rib 84.4 0.59 1.3E-05 21.6 1.0 9 82-90 4-12 (26)
32 PF07191 zinc-ribbons_6: zinc- 84.3 0.32 6.9E-06 28.3 0.1 59 48-118 3-61 (70)
33 smart00504 Ubox Modified RING 84.2 2 4.4E-05 23.7 3.4 49 47-96 2-51 (63)
34 PF11781 RRN7: RNA polymerase 83.9 0.44 9.6E-06 24.0 0.5 24 109-137 10-33 (36)
35 PF14835 zf-RING_6: zf-RING of 83.4 0.9 2E-05 26.0 1.7 49 47-96 8-56 (65)
36 PF10886 DUF2685: Protein of u 81.3 1.4 3E-05 24.2 1.8 26 81-106 2-27 (54)
37 PF02069 Metallothio_Pro: Prok 81.2 0.93 2E-05 24.8 1.1 24 110-134 10-33 (52)
38 PF14569 zf-UDP: Zinc-binding 80.2 2.1 4.6E-05 25.4 2.5 43 48-90 11-61 (80)
39 PF10367 Vps39_2: Vacuolar sor 79.0 1.3 2.8E-05 27.3 1.5 13 49-61 81-93 (109)
40 PF13920 zf-C3HC4_3: Zinc fing 78.6 3.8 8.3E-05 21.7 3.1 43 48-91 4-48 (50)
41 PF00645 zf-PARP: Poly(ADP-rib 78.4 0.67 1.4E-05 27.6 -0.0 35 14-48 8-47 (82)
42 PF14471 DUF4428: Domain of un 78.1 2.2 4.9E-05 23.1 2.0 29 48-77 1-30 (51)
43 PF07754 DUF1610: Domain of un 77.5 1.7 3.6E-05 19.8 1.2 11 16-26 1-11 (24)
44 COG1645 Uncharacterized Zn-fin 74.9 1.6 3.5E-05 28.6 1.1 22 48-74 30-51 (131)
45 PF06677 Auto_anti-p27: Sjogre 74.6 1.6 3.5E-05 22.6 0.8 22 48-73 19-40 (41)
46 PF01258 zf-dskA_traR: Prokary 72.9 0.83 1.8E-05 22.8 -0.5 28 49-76 6-33 (36)
47 COG4847 Uncharacterized protei 72.9 1.4 3E-05 27.2 0.3 32 81-112 7-39 (103)
48 PLN03208 E3 ubiquitin-protein 72.9 6.6 0.00014 27.5 3.8 51 46-97 18-85 (193)
49 KOG0320|consensus 71.3 2.7 5.9E-05 29.0 1.5 53 43-95 128-182 (187)
50 PF12674 Zn_ribbon_2: Putative 70.7 1.9 4.2E-05 25.8 0.6 29 48-76 2-35 (81)
51 PF06906 DUF1272: Protein of u 70.4 8.3 0.00018 21.4 3.0 45 48-93 7-54 (57)
52 PRK00807 50S ribosomal protein 67.7 2.6 5.5E-05 23.0 0.7 33 81-116 2-37 (52)
53 PF12773 DZR: Double zinc ribb 67.3 4.8 0.0001 21.3 1.7 11 81-91 13-23 (50)
54 PRK14559 putative protein seri 66.7 3.9 8.5E-05 34.0 1.8 10 15-24 3-12 (645)
55 cd02336 ZZ_RSC8 Zinc finger, Z 65.4 7.6 0.00016 20.5 2.2 29 48-76 2-32 (45)
56 COG4306 Uncharacterized protei 64.5 6.4 0.00014 25.7 2.1 49 67-118 28-79 (160)
57 cd00162 RING RING-finger (Real 62.7 8.3 0.00018 19.0 2.1 25 65-89 18-44 (45)
58 smart00291 ZnF_ZZ Zinc-binding 62.3 9.2 0.0002 19.8 2.2 29 48-76 6-36 (44)
59 PRK00420 hypothetical protein; 60.0 4.1 8.9E-05 26.0 0.7 23 47-73 24-46 (112)
60 KOG1813|consensus 59.6 6 0.00013 29.6 1.5 45 47-92 242-287 (313)
61 PF04570 DUF581: Protein of un 59.4 6.4 0.00014 22.0 1.3 9 110-118 19-27 (58)
62 TIGR03826 YvyF flagellar opero 58.6 6.4 0.00014 26.1 1.4 22 48-75 5-26 (137)
63 smart00704 ZnF_CDGSH CDGSH-typ 57.3 6.3 0.00014 20.0 1.0 7 128-134 24-30 (38)
64 COG2191 Formylmethanofuran deh 57.3 3.7 8E-05 29.0 0.1 31 47-77 173-203 (206)
65 KOG3002|consensus 56.4 11 0.00024 28.3 2.5 44 46-91 48-91 (299)
66 PF13923 zf-C3HC4_2: Zinc fing 56.2 23 0.00049 17.5 3.0 30 49-78 1-30 (39)
67 PF11571 Med27: Mediator compl 55.5 6.5 0.00014 23.9 1.0 16 74-90 49-64 (90)
68 PF14634 zf-RING_5: zinc-RING 55.4 16 0.00035 18.7 2.4 40 49-88 2-44 (44)
69 smart00249 PHD PHD zinc finger 55.3 11 0.00024 18.8 1.8 26 83-108 2-29 (47)
70 PF04564 U-box: U-box domain; 54.3 30 0.00066 19.9 3.7 51 45-96 3-55 (73)
71 PF00569 ZZ: Zinc finger, ZZ t 53.5 19 0.00041 18.8 2.5 11 66-76 27-37 (46)
72 PF06827 zf-FPG_IleRS: Zinc fi 53.3 3.4 7.4E-05 19.5 -0.4 11 81-91 2-12 (30)
73 PF12855 Ecl1: Life-span regul 53.2 7 0.00015 20.5 0.7 20 110-134 9-28 (43)
74 PF00628 PHD: PHD-finger; Int 52.6 14 0.00031 19.3 2.0 26 83-108 2-29 (51)
75 COG5152 Uncharacterized conser 51.2 5.8 0.00012 28.0 0.3 46 47-93 197-243 (259)
76 PLN02638 cellulose synthase A 50.5 13 0.00028 32.7 2.3 25 66-90 43-69 (1079)
77 cd02335 ZZ_ADA2 Zinc finger, Z 47.6 22 0.00048 18.8 2.2 9 68-76 25-33 (49)
78 PF14570 zf-RING_4: RING/Ubox 47.1 26 0.00057 18.8 2.4 24 66-89 21-46 (48)
79 PF04641 Rtf2: Rtf2 RING-finge 46.1 52 0.0011 24.1 4.6 56 43-98 110-168 (260)
80 KOG3476|consensus 46.0 2.9 6.4E-05 25.3 -1.5 38 47-93 55-92 (100)
81 PLN02195 cellulose synthase A 44.9 19 0.00041 31.5 2.4 25 67-91 33-59 (977)
82 KOG3579|consensus 44.8 12 0.00026 28.0 1.1 48 81-134 269-316 (352)
83 PF00096 zf-C2H2: Zinc finger, 44.4 7 0.00015 16.7 -0.1 12 108-119 1-12 (23)
84 KOG0978|consensus 44.2 6.6 0.00014 32.9 -0.3 49 47-96 644-694 (698)
85 PF07649 C1_3: C1-like domain; 42.9 14 0.00031 17.3 0.9 11 82-92 2-12 (30)
86 PF13834 DUF4193: Domain of un 42.8 8.3 0.00018 24.0 0.1 29 106-134 69-97 (99)
87 PLN02400 cellulose synthase 42.2 17 0.00038 32.0 1.8 44 47-90 37-88 (1085)
88 PF08209 Sgf11: Sgf11 (transcr 41.7 5.4 0.00012 19.6 -0.7 17 108-124 5-21 (33)
89 PF01286 XPA_N: XPA protein N- 41.4 7.1 0.00015 19.4 -0.3 11 14-24 4-14 (34)
90 cd02249 ZZ Zinc finger, ZZ typ 40.6 17 0.00036 19.0 1.0 10 82-91 2-11 (46)
91 KOG2893|consensus 40.5 7.3 0.00016 28.3 -0.5 11 107-117 34-44 (341)
92 KOG3579|consensus 40.3 14 0.0003 27.6 0.9 48 13-71 268-315 (352)
93 KOG3896|consensus 39.1 13 0.00028 28.5 0.5 37 80-118 45-81 (449)
94 PHA02610 uvsY.-2 hypothetical 38.9 27 0.00058 19.0 1.6 25 81-105 2-26 (53)
95 PF12156 ATPase-cat_bd: Putati 38.7 12 0.00027 22.6 0.4 33 82-117 2-36 (88)
96 PF10571 UPF0547: Uncharacteri 38.6 21 0.00046 16.4 1.1 9 82-90 2-10 (26)
97 cd02342 ZZ_UBA_plant Zinc fing 37.9 35 0.00076 17.8 1.9 29 48-76 2-33 (43)
98 PLN02436 cellulose synthase A 37.6 26 0.00055 31.1 2.1 44 47-90 37-88 (1094)
99 PF05502 Dynactin_p62: Dynacti 37.5 20 0.00043 28.9 1.4 36 82-118 28-63 (483)
100 KOG2462|consensus 37.5 12 0.00026 27.7 0.2 33 81-119 188-227 (279)
101 PF10080 DUF2318: Predicted me 37.0 23 0.0005 22.2 1.4 32 41-76 30-61 (102)
102 PLN02189 cellulose synthase 36.8 27 0.00059 30.8 2.2 45 47-91 35-87 (1040)
103 PHA02929 N1R/p28-like protein; 36.5 21 0.00045 26.0 1.3 38 81-118 175-227 (238)
104 PF00130 C1_1: Phorbol esters/ 36.4 34 0.00074 18.0 1.9 10 81-90 12-21 (53)
105 PF13894 zf-C2H2_4: C2H2-type 36.0 14 0.00031 15.4 0.3 11 108-118 1-11 (24)
106 PF13639 zf-RING_2: Ring finge 35.7 7.7 0.00017 19.8 -0.8 27 82-108 2-30 (44)
107 PF12171 zf-C2H2_jaz: Zinc-fin 35.1 24 0.00053 15.9 1.0 13 108-120 2-14 (27)
108 PLN02915 cellulose synthase A 34.7 31 0.00066 30.5 2.2 24 67-90 42-67 (1044)
109 COG0266 Nei Formamidopyrimidin 34.5 23 0.00049 26.4 1.2 11 81-91 246-256 (273)
110 cd02341 ZZ_ZZZ3 Zinc finger, Z 34.5 23 0.00049 18.9 0.9 10 82-91 2-12 (48)
111 KOG4443|consensus 34.3 23 0.0005 29.5 1.3 22 98-119 106-127 (694)
112 PF12874 zf-met: Zinc-finger o 33.3 14 0.00031 16.1 0.0 12 108-119 1-12 (25)
113 PF14149 YhfH: YhfH-like prote 32.7 14 0.0003 18.7 -0.1 19 74-92 7-25 (37)
114 PLN03123 poly [ADP-ribose] pol 32.1 34 0.00074 30.1 2.1 30 80-109 17-57 (981)
115 TIGR00595 priA primosomal prot 31.4 29 0.00064 28.0 1.5 39 48-89 224-262 (505)
116 COG1996 RPC10 DNA-directed RNA 31.0 22 0.00047 19.2 0.5 10 81-90 7-16 (49)
117 PF01927 Mut7-C: Mut7-C RNAse 31.0 26 0.00056 23.2 1.0 14 43-56 121-134 (147)
118 PRK11595 DNA utilization prote 31.0 50 0.0011 23.5 2.5 37 48-90 7-44 (227)
119 PF09723 Zn-ribbon_8: Zinc rib 30.9 9.7 0.00021 19.6 -0.9 10 47-56 6-15 (42)
120 PHA02768 hypothetical protein; 30.5 10 0.00022 21.0 -0.8 12 107-118 31-42 (55)
121 PF14255 Cys_rich_CPXG: Cystei 30.4 16 0.00036 19.9 -0.0 28 82-110 2-30 (52)
122 KOG2186|consensus 30.1 11 0.00024 27.6 -1.0 42 14-62 4-45 (276)
123 PRK01343 zinc-binding protein; 29.9 36 0.00079 19.0 1.3 10 81-90 10-19 (57)
124 PRK14873 primosome assembly pr 29.8 28 0.00061 29.2 1.2 39 47-89 393-431 (665)
125 PRK14891 50S ribosomal protein 29.7 38 0.00082 22.2 1.5 33 81-116 5-40 (131)
126 PF03107 C1_2: C1 domain; Int 29.6 41 0.00089 15.7 1.3 11 109-119 2-12 (30)
127 COG2075 RPL24A Ribosomal prote 29.3 45 0.00098 19.1 1.6 9 48-56 5-13 (66)
128 PF04810 zf-Sec23_Sec24: Sec23 29.2 48 0.001 16.7 1.6 30 81-115 3-32 (40)
129 cd00472 Ribosomal_L24e_L24 Rib 29.0 39 0.00084 18.6 1.3 24 81-104 4-30 (54)
130 COG0068 HypF Hydrogenase matur 29.0 22 0.00048 30.0 0.5 85 10-117 98-183 (750)
131 smart00834 CxxC_CXXC_SSSS Puta 29.0 11 0.00025 18.7 -0.8 10 47-56 6-15 (41)
132 PF07503 zf-HYPF: HypF finger; 28.9 27 0.00058 17.3 0.6 18 39-56 14-31 (35)
133 smart00531 TFIIE Transcription 28.8 13 0.00028 24.7 -0.8 35 81-118 100-134 (147)
134 PF13912 zf-C2H2_6: C2H2-type 28.7 19 0.00041 16.0 0.0 12 108-119 2-13 (27)
135 cd02344 ZZ_HERC2 Zinc finger, 28.4 54 0.0012 17.2 1.7 10 67-76 24-33 (45)
136 PF06750 DiS_P_DiS: Bacterial 27.8 17 0.00038 22.2 -0.3 37 47-92 34-70 (92)
137 COG3813 Uncharacterized protei 27.8 92 0.002 18.3 2.7 45 48-93 7-54 (84)
138 PF10764 Gin: Inhibitor of sig 27.7 82 0.0018 16.6 2.4 7 50-56 3-9 (46)
139 PF08790 zf-LYAR: LYAR-type C2 26.9 11 0.00024 17.8 -1.0 16 108-123 1-16 (28)
140 cd02340 ZZ_NBR1_like Zinc fing 26.9 39 0.00085 17.4 1.0 20 82-114 2-21 (43)
141 TIGR00570 cdk7 CDK-activating 26.8 80 0.0017 24.0 3.0 29 66-94 27-57 (309)
142 PF09360 zf-CDGSH: Iron-bindin 26.6 31 0.00068 17.4 0.6 7 128-134 29-35 (38)
143 cd02338 ZZ_PCMF_like Zinc fing 26.5 54 0.0012 17.4 1.6 9 68-76 25-33 (49)
144 PF02591 DUF164: Putative zinc 26.4 8.4 0.00018 21.1 -1.7 11 82-92 24-34 (56)
145 KOG2114|consensus 25.8 29 0.00064 29.9 0.6 36 81-117 841-882 (933)
146 PRK06266 transcription initiat 25.7 16 0.00035 25.2 -0.7 32 12-57 116-147 (178)
147 PF13901 DUF4206: Domain of un 25.6 49 0.0011 23.3 1.6 29 81-109 153-188 (202)
148 COG4068 Uncharacterized protei 24.8 32 0.00069 19.3 0.5 16 81-96 9-24 (64)
149 PRK00398 rpoP DNA-directed RNA 24.5 29 0.00063 18.0 0.3 29 81-118 4-32 (46)
150 COG1997 RPL43A Ribosomal prote 24.5 77 0.0017 19.3 2.1 37 80-125 35-71 (89)
151 cd02334 ZZ_dystrophin Zinc fin 24.0 74 0.0016 17.0 1.8 10 67-76 24-33 (49)
152 KOG1244|consensus 23.9 66 0.0014 24.1 2.0 10 65-74 294-303 (336)
153 COG1198 PriA Primosomal protei 23.9 45 0.00097 28.4 1.3 40 47-89 445-484 (730)
154 PF09889 DUF2116: Uncharacteri 23.6 41 0.00089 18.9 0.8 13 81-93 4-16 (59)
155 smart00659 RPOLCX RNA polymera 23.6 30 0.00064 18.1 0.2 10 47-56 3-12 (44)
156 PRK12495 hypothetical protein; 23.1 33 0.00072 24.6 0.4 11 47-57 43-53 (226)
157 KOG1734|consensus 23.1 21 0.00046 26.5 -0.6 14 43-56 221-234 (328)
158 PRK14714 DNA polymerase II lar 23.0 68 0.0015 29.2 2.3 54 47-119 668-721 (1337)
159 smart00355 ZnF_C2H2 zinc finge 23.0 43 0.00094 13.9 0.7 12 108-119 1-12 (26)
160 PF01246 Ribosomal_L24e: Ribos 22.9 39 0.00084 19.7 0.6 24 81-104 4-30 (71)
161 COG3369 Zinc finger domain con 22.9 41 0.00088 19.9 0.7 7 128-134 41-47 (78)
162 TIGR00270 conserved hypothetic 22.7 1E+02 0.0022 20.8 2.7 26 49-74 3-31 (154)
163 PF07975 C1_4: TFIIH C1-like d 22.6 34 0.00074 18.6 0.3 8 83-90 2-9 (51)
164 PF13465 zf-H2C2_2: Zinc-finge 22.1 29 0.00063 15.6 -0.0 10 108-117 15-24 (26)
165 KOG4739|consensus 22.0 60 0.0013 23.6 1.5 34 58-92 15-49 (233)
166 PF09862 DUF2089: Protein of u 21.8 38 0.00082 21.7 0.4 9 110-118 15-23 (113)
167 cd02345 ZZ_dah Zinc finger, ZZ 21.7 73 0.0016 16.9 1.5 9 68-76 25-33 (49)
168 PF00320 GATA: GATA zinc finge 21.6 1.2E+02 0.0026 14.8 2.6 13 64-76 16-29 (36)
169 PF08189 Meleagrin: Meleagrin/ 21.5 39 0.00084 17.0 0.4 7 131-137 11-17 (39)
170 PRK05580 primosome assembly pr 21.3 60 0.0013 27.3 1.6 39 48-89 392-430 (679)
171 PF13926 DUF4211: Domain of un 21.1 72 0.0016 21.2 1.7 23 109-131 118-140 (153)
172 TIGR02605 CxxC_CxxC_SSSS putat 20.8 54 0.0012 17.2 0.9 10 81-90 6-15 (52)
173 PF05864 Chordopox_RPO7: Chord 20.8 20 0.00043 20.0 -0.9 16 109-124 6-21 (63)
174 PF08792 A2L_zn_ribbon: A2L zi 20.8 75 0.0016 15.4 1.3 10 63-72 17-26 (33)
175 PF04981 NMD3: NMD3 family ; 20.7 1E+02 0.0022 22.2 2.5 24 49-78 1-24 (236)
176 PHA03082 DNA-dependent RNA pol 20.3 20 0.00043 20.0 -0.9 15 109-123 6-20 (63)
177 KOG3039|consensus 20.2 1.8E+02 0.004 21.5 3.7 84 14-97 184-276 (303)
No 1
>KOG1701|consensus
Probab=99.93 E-value=1.2e-26 Score=172.71 Aligned_cols=131 Identities=25% Similarity=0.573 Sum_probs=113.5
Q ss_pred eeecCCCcCcCCcccccccccccCCCeEEEecc-------------------------ccCCCCCCcccCcccccCCccc
Q psy10674 2 TLAENKTFHVKHFCCYECDKKVQFENYTGKITQ-------------------------SQESEVLWHPQCFVCSTCDELL 56 (138)
Q Consensus 2 ~~a~g~~~h~~~~~C~~C~~~i~~~~~~~~~~~-------------------------~~~~~~~~H~~Cf~C~~C~~~l 56 (138)
++||++.||.+||+|..|++.|....|+...++ +-++|+.||+.||+|.+|.+.|
T Consensus 291 c~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~l 370 (468)
T KOG1701|consen 291 VEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCL 370 (468)
T ss_pred HHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHHHHHHHHhcccccCCCceEEEEecccc
Confidence 479999999999999999999997777665443 1278899999999999999999
Q ss_pred cCCceee-eCCeeecHHHHHhhcCCCcccccCcccccCc------EEEeCCCccccCCccccccccccC----CCCeeec
Q psy10674 57 VDLMYFH-YKGNVYCLRDYATMLDIPRCHACDELIFVNE------YTLAENKTFHVKHFCCYECDKELC----NQSYIPV 125 (138)
Q Consensus 57 ~~~~~~~-~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~~------~~~~~~~~~H~~CF~C~~C~~~l~----~~~f~~~ 125 (138)
.+..|.+ .++++||-.||.+.| +++|+.|+++|++.+ .|+++++.||.+|++|..|+..|+ ++..|..
T Consensus 371 dgipFtvd~~n~v~Cv~dfh~kf-APrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPl 449 (468)
T KOG1701|consen 371 DGIPFTVDSQNNVYCVPDFHKKF-APRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPL 449 (468)
T ss_pred CCccccccCCCceeeehhhhhhc-CcchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceec
Confidence 9988866 789999999999999 799999999999642 344999999999999999999998 5667878
Q ss_pred CCCCCccCC
Q psy10674 126 TESRPGQDS 134 (138)
Q Consensus 126 ~~~~~y~~~ 134 (138)
| |.+.|..
T Consensus 450 d-~HllCk~ 457 (468)
T KOG1701|consen 450 D-GHLLCKT 457 (468)
T ss_pred c-Cceeech
Confidence 8 8887765
No 2
>KOG1701|consensus
Probab=99.92 E-value=4.6e-27 Score=174.91 Aligned_cols=111 Identities=26% Similarity=0.518 Sum_probs=101.4
Q ss_pred ccccccccccCCCeEEEeccccCCCCCCcccCcccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccccCc
Q psy10674 15 CCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNE 94 (138)
Q Consensus 15 ~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~~ 94 (138)
+|.+|++.|..+..-+ .|+++.||..||+|..|++.|.++.||..++++||+.||.+.+ ++|..|+++|++.
T Consensus 276 iC~~C~K~V~g~~~ac-----~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl--ekC~~Cg~~I~d~- 347 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAV-----EAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL--EKCNKCGEPIMDR- 347 (468)
T ss_pred hhhhcCCcccCcchHH-----HHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH--HHHhhhhhHHHHH-
Confidence 7999999999655443 2378899999999999999999999999999999999999986 7999999999764
Q ss_pred EEEeCCCccccCCccccccccccCCCCeeecCCCCCccC
Q psy10674 95 YTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRPGQD 133 (138)
Q Consensus 95 ~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~y~~ 133 (138)
|+.|.|+.||+.||+|..|++.|+|..|++..++++||.
T Consensus 348 iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv 386 (468)
T KOG1701|consen 348 ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCV 386 (468)
T ss_pred HHHhcccccCCCceEEEEeccccCCccccccCCCceeee
Confidence 667999999999999999999999999999999999995
No 3
>KOG2272|consensus
Probab=99.90 E-value=2.8e-26 Score=160.94 Aligned_cols=128 Identities=28% Similarity=0.475 Sum_probs=107.9
Q ss_pred eeecCCCcCcCCcccccccccccCCCeEEEecc-------------------------------ccCCCCCCcccCcccc
Q psy10674 2 TLAENKTFHVKHFCCYECDKKVQFENYTGKITQ-------------------------------SQESEVLWHPQCFVCS 50 (138)
Q Consensus 2 ~~a~g~~~h~~~~~C~~C~~~i~~~~~~~~~~~-------------------------------~~~~~~~~H~~Cf~C~ 50 (138)
|.||+.+|||.||.|..|++.|.+..++-..++ ...++.+||+.+|+|.
T Consensus 88 ikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt 167 (332)
T KOG2272|consen 88 IKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCT 167 (332)
T ss_pred HHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecc
Confidence 579999999999999999999986444322111 2356779999999999
Q ss_pred cCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccccCcEEEeCCCccccCCccccccccccCCCCeeecCCCCC
Q psy10674 51 TCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRP 130 (138)
Q Consensus 51 ~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~ 130 (138)
.|++.|.. ...+..+.+||.+|+.++- .|.|..|.+||.+ .+|.++|+.||.++|+|+.|.+|+-|-+.|+++ |.+
T Consensus 168 ~C~keL~s-daRevk~eLyClrChD~mg-ipiCgaC~rpIee-rvi~amgKhWHveHFvCa~CekPFlGHrHYEkk-Gla 243 (332)
T KOG2272|consen 168 TCGKELTS-DAREVKGELYCLRCHDKMG-IPICGACRRPIEE-RVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKK-GLA 243 (332)
T ss_pred cccccccc-hhhhhccceeccccccccC-CcccccccCchHH-HHHHHhccccchhheeehhcCCcccchhhhhhc-Cch
Confidence 99999954 3556788999999998764 8999999999964 455599999999999999999999999999999 999
Q ss_pred ccC
Q psy10674 131 GQD 133 (138)
Q Consensus 131 y~~ 133 (138)
||.
T Consensus 244 YCe 246 (332)
T KOG2272|consen 244 YCE 246 (332)
T ss_pred hHH
Confidence 985
No 4
>KOG4577|consensus
Probab=99.87 E-value=1.2e-24 Score=155.27 Aligned_cols=114 Identities=26% Similarity=0.661 Sum_probs=102.1
Q ss_pred CCcccccccccccCCCeEEEeccccCCCCCCcccCcccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccc
Q psy10674 12 KHFCCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIF 91 (138)
Q Consensus 12 ~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~ 91 (138)
+-++|+.|.+.|. ++++..+ +++.||..|++|+.|..+|.+ ..|.+++.+||+.+|.++|| .+|..|...|.
T Consensus 32 eip~CagC~q~Il-DrFilKv-----l~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfG-TKCsaC~~GIp 103 (383)
T KOG4577|consen 32 EIPICAGCDQHIL-DRFILKV-----LDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFG-TKCSACQEGIP 103 (383)
T ss_pred ccccccchHHHHH-HHHHHHH-----HhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhC-CcchhhcCCCC
Confidence 5688999999998 6676654 466999999999999999966 58999999999999999998 69999999999
Q ss_pred cCcEEE-eCCCccccCCccccccccccC-CCCeeecCCCCCccC
Q psy10674 92 VNEYTL-AENKTFHVKHFCCYECDKELC-NQSYIPVTESRPGQD 133 (138)
Q Consensus 92 ~~~~~~-~~~~~~H~~CF~C~~C~~~l~-~~~f~~~~~~~~y~~ 133 (138)
+..+|. |.+.+||.+||.|..|++.|. |+.||+.+|++.-|.
T Consensus 104 PtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK 147 (383)
T KOG4577|consen 104 PTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCK 147 (383)
T ss_pred hHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehh
Confidence 877766 999999999999999999998 999999998888764
No 5
>KOG2272|consensus
Probab=99.87 E-value=9.9e-24 Score=148.15 Aligned_cols=130 Identities=25% Similarity=0.525 Sum_probs=109.9
Q ss_pred eeecCCCcCcCCcccccccccccCCCeEEEe------------------------cc-ccCCCCCCcccCcccccCCccc
Q psy10674 2 TLAENKTFHVKHFCCYECDKKVQFENYTGKI------------------------TQ-SQESEVLWHPQCFVCSTCDELL 56 (138)
Q Consensus 2 ~~a~g~~~h~~~~~C~~C~~~i~~~~~~~~~------------------------~~-~~~~~~~~H~~Cf~C~~C~~~l 56 (138)
|...|..|||-+|+|..|++.|..+...+.. ++ +.++|..||.++|+|+.|.+|+
T Consensus 152 l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPF 231 (332)
T KOG2272|consen 152 LTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPF 231 (332)
T ss_pred ccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcc
Confidence 3456889999999999999998753222111 11 3478899999999999999999
Q ss_pred cCCceeeeCCeeecHHHHHhhcCCCcccccCcccccCcEEEeCCCccccCCccccccccccC-CCCeeecCCCCCccCC
Q psy10674 57 VDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELC-NQSYIPVTESRPGQDS 134 (138)
Q Consensus 57 ~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~-~~~f~~~~~~~~y~~~ 134 (138)
-+-..|++.|.+||+++|.+++| ..|..|+.+| +++++.|.++.|-++||.|+.|++.|. ...|++.| -+|-|..
T Consensus 232 lGHrHYEkkGlaYCe~h~~qLfG-~~CF~C~~~i-~G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~D-mkP~CKk 307 (332)
T KOG2272|consen 232 LGHRHYEKKGLAYCETHYHQLFG-NLCFICNRVI-GGDVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFD-MKPVCKK 307 (332)
T ss_pred cchhhhhhcCchhHHHHHHHHhh-hhheecCCcc-CccHHHHhhhhhccccccccccccccccccceeeec-cchHHHH
Confidence 88889999999999999999998 7999999999 566777999999999999999999998 67788888 8887753
No 6
>KOG1044|consensus
Probab=99.86 E-value=1.9e-22 Score=155.02 Aligned_cols=127 Identities=24% Similarity=0.484 Sum_probs=109.8
Q ss_pred eeecCCCcCcCCcccccccccccCCCeEEEecc------------------------------------ccCCCCCCccc
Q psy10674 2 TLAENKTFHVKHFCCYECDKKVQFENYTGKITQ------------------------------------SQESEVLWHPQ 45 (138)
Q Consensus 2 ~~a~g~~~h~~~~~C~~C~~~i~~~~~~~~~~~------------------------------------~~~~~~~~H~~ 45 (138)
+.|+|++||+.||+|..|..+...+..+...++ +++++..||..
T Consensus 80 vsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~ 159 (670)
T KOG1044|consen 80 VSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVS 159 (670)
T ss_pred EecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeee
Confidence 579999999999999999999987766543211 34788899999
Q ss_pred CcccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccccCcEEEeCCCccccCCccccccccccC-CCCeee
Q psy10674 46 CFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELC-NQSYIP 124 (138)
Q Consensus 46 Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~-~~~f~~ 124 (138)
||+|..|+..|.+ .|...+|.+||+.+|.+.|| -+|..|.+.|.+. ++.|.|++|||.|-+|++|+.+++ |+..|+
T Consensus 160 cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fg-vkc~~c~~fisgk-vLqag~kh~HPtCARCsRCgqmF~eGEEMYl 236 (670)
T KOG1044|consen 160 CFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFG-VKCEECEKFISGK-VLQAGDKHFHPTCARCSRCGQMFGEGEEMYL 236 (670)
T ss_pred eeehhhhcccccc-eeeccCCCcchhhhhhhhcC-eehHHhhhhhhhh-hhhccCcccCcchhhhhhhccccccchheee
Confidence 9999999999966 59999999999999999998 5999999999665 566999999999999999999998 888888
Q ss_pred cCCCCCcc
Q psy10674 125 VTESRPGQ 132 (138)
Q Consensus 125 ~~~~~~y~ 132 (138)
+. ..++.
T Consensus 237 QG-s~iWH 243 (670)
T KOG1044|consen 237 QG-SEIWH 243 (670)
T ss_pred cc-ccccC
Confidence 86 55554
No 7
>KOG1703|consensus
Probab=99.84 E-value=1.1e-21 Score=152.94 Aligned_cols=132 Identities=25% Similarity=0.559 Sum_probs=114.7
Q ss_pred CeeecCCCcCcCCcccccccccccCCCeEEEecc--------------------------ccCCCCCCcccCcccccCCc
Q psy10674 1 YTLAENKTFHVKHFCCYECDKKVQFENYTGKITQ--------------------------SQESEVLWHPQCFVCSTCDE 54 (138)
Q Consensus 1 ~~~a~g~~~h~~~~~C~~C~~~i~~~~~~~~~~~--------------------------~~~~~~~~H~~Cf~C~~C~~ 54 (138)
.+.|+++.||+.++.|..|...|..+.+....++ +.+++..||++||.|..|++
T Consensus 318 ~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~~ 397 (479)
T KOG1703|consen 318 VIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALGRLWHPECFVCADCGK 397 (479)
T ss_pred eEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhccCeechhceeeecccC
Confidence 3689999999999999999999886655332111 23568899999999999999
Q ss_pred cccCCceeeeCCeeecHHHHHhhcCCCcccccCcccccC-cEEEeCCCccccCCccccccccccCCCCeeecCCCCCccC
Q psy10674 55 LLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVN-EYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRPGQD 133 (138)
Q Consensus 55 ~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~y~~ 133 (138)
+|....|+..++.+||+.||.++++ .+|..|.++|... ..+.+++..||..||+|..|.+.|.++.|+... ++|+|-
T Consensus 398 ~~~~~~~~~~~~~pyce~~~~~~~~-~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~-~~p~c~ 475 (479)
T KOG1703|consen 398 PLKNSSFFESDGEPYCEDHYKKLFT-TKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETL-DKPLCQ 475 (479)
T ss_pred CCCCCcccccCCccchhhhHhhhcc-ccchhccchhHhhhhHhhccCccccccceehhhhhccccCCceeecC-Cccccc
Confidence 9999999999999999999999995 6999999998633 356699999999999999999999999999999 999997
Q ss_pred C
Q psy10674 134 S 134 (138)
Q Consensus 134 ~ 134 (138)
+
T Consensus 476 ~ 476 (479)
T KOG1703|consen 476 K 476 (479)
T ss_pred c
Confidence 6
No 8
>KOG1044|consensus
Probab=99.75 E-value=1.1e-18 Score=134.52 Aligned_cols=131 Identities=23% Similarity=0.445 Sum_probs=105.5
Q ss_pred eeecCCCcCcCCcccccccccccCCCeEEEec----------------cccCCCCCCcccCcccccCCccccCC-ceeee
Q psy10674 2 TLAENKTFHVKHFCCYECDKKVQFENYTGKIT----------------QSQESEVLWHPQCFVCSTCDELLVDL-MYFHY 64 (138)
Q Consensus 2 ~~a~g~~~h~~~~~C~~C~~~i~~~~~~~~~~----------------~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~ 64 (138)
+.+.++.+|..||+|..|+..|..+.+....+ -+.++++.||+.||.|..|+.++... ..-..
T Consensus 31 lrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~ 110 (670)
T KOG1044|consen 31 LRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFS 110 (670)
T ss_pred eEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceecccCCCCCCCCeeeec
Confidence 46778999999999999999998776654321 13468899999999999999999443 33445
Q ss_pred CCeeecHHHHHhh-------cCCCcccccCcccccCcEEEeCCCccccCCccccccccccCCCCeeecCCCCCccCC
Q psy10674 65 KGNVYCLRDYATM-------LDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRPGQDS 134 (138)
Q Consensus 65 ~~~~yC~~c~~~~-------~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~y~~~ 134 (138)
.....|+.|-.-. .+...|++|++.|..+..+.|+++.||..||+|..|..+|.++ |+.++ |.|||-+
T Consensus 111 gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge-y~skd-g~pyce~ 185 (670)
T KOG1044|consen 111 GKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE-YMSKD-GVPYCEK 185 (670)
T ss_pred chhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce-eeccC-CCcchhh
Confidence 5567788776322 2235899999999988888899999999999999999999875 88888 9999965
No 9
>KOG1703|consensus
Probab=99.73 E-value=1.5e-18 Score=135.53 Aligned_cols=112 Identities=23% Similarity=0.492 Sum_probs=99.4
Q ss_pred cccccccccccCCCeEEEeccccCCCCCCcccCcccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccccC
Q psy10674 14 FCCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVN 93 (138)
Q Consensus 14 ~~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~ 93 (138)
+.|..|++.|....++.. ++..||+++|.|..|+..+....+...+|.+||..|+.+.+ ++.|.+|+++|.++
T Consensus 304 p~c~~c~~~i~~~~~i~~------~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~-~p~C~~C~~~i~~~ 376 (479)
T KOG1703|consen 304 PLCLSCNQKIRSVKVIVA------LGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPF-RPNCKRCLLPILEE 376 (479)
T ss_pred ccccccccCcccceeEee------ccccccccceeeccccccccCCCccccCCCccHHHHHHHhh-CccccccCCchHHh
Confidence 678999999984355554 46699999999999999998877888999999999999998 79999999999764
Q ss_pred cEEEeCCCccccCCccccccccccCCCCeeecCCCCCccCC
Q psy10674 94 EYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRPGQDS 134 (138)
Q Consensus 94 ~~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~y~~~ 134 (138)
+|.|.++.||++||.|..|+++|.+..|++.+ |.|||..
T Consensus 377 -~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~-~~pyce~ 415 (479)
T KOG1703|consen 377 -GVCALGRLWHPECFVCADCGKPLKNSSFFESD-GEPYCED 415 (479)
T ss_pred -HhhhccCeechhceeeecccCCCCCCcccccC-Cccchhh
Confidence 56688999999999999999999999999999 9999975
No 10
>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=99.56 E-value=7.2e-15 Score=83.39 Aligned_cols=58 Identities=31% Similarity=0.702 Sum_probs=50.6
Q ss_pred cccccccccCCCeEEEeccccCCCCCCcccCcccccCCccccCCceeeeCCeeecHHHHHhhc
Q psy10674 16 CYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATML 78 (138)
Q Consensus 16 C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~ 78 (138)
|..|+++|.+++.++.. .+..||++||+|..|+++|.+..++..++++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~-----~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKA-----MGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEE-----TTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEe-----CCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 78999999977776433 46699999999999999998888999999999999998864
No 11
>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=99.50 E-value=1.4e-14 Score=82.17 Aligned_cols=51 Identities=25% Similarity=0.510 Sum_probs=46.4
Q ss_pred ccccCcccccCcEE-EeCCCccccCCccccccccccCCCCeeecCCCCCccCC
Q psy10674 83 CHACDELIFVNEYT-LAENKTFHVKHFCCYECDKELCNQSYIPVTESRPGQDS 134 (138)
Q Consensus 83 C~~C~~~I~~~~~~-~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~y~~~ 134 (138)
|++|+++|.+++++ .+.|+.||++||+|..|+++|.+..|++.+ |+|||.+
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~~~~C~~ 52 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKD-GKPYCKD 52 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEET-TEEEEHH
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeEC-CEEECHH
Confidence 78999999988776 499999999999999999999988899999 9999964
No 12
>KOG1700|consensus
Probab=99.30 E-value=2.3e-13 Score=95.25 Aligned_cols=115 Identities=24% Similarity=0.468 Sum_probs=94.5
Q ss_pred cccccccccccCCCeEEEeccccCCCCCCcccCcccccCCccccCCceeeeCCeeecHHHHHhhcC--------------
Q psy10674 14 FCCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLD-------------- 79 (138)
Q Consensus 14 ~~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~-------------- 79 (138)
..|..|++.+...+.+.. .+..||+.||+|..|.+.|....+...++.+||+.++...++
T Consensus 8 ~kc~~c~k~vy~~e~~~~------~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~ 81 (200)
T KOG1700|consen 8 DKCNACGKTVYFVEKVQK------DGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAG 81 (200)
T ss_pred chhhhccCcchHHHHHhc------cCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccC
Confidence 468888888875554442 466999999999999999988889999999999985433310
Q ss_pred --------------------------CCcccccCcccccCcEEEeCCCccccCCccccccccccCCCCeeecCCCCCccC
Q psy10674 80 --------------------------IPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRPGQD 133 (138)
Q Consensus 80 --------------------------~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~y~~ 133 (138)
...|..|++.+.+.+-+...+..||..||+|+.|+..|+...+...+ |.+||+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~-g~l~~~ 160 (200)
T KOG1700|consen 82 GLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALE-GVLYCK 160 (200)
T ss_pred CCCcccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcC-Cccccc
Confidence 15899999999876666688999999999999999999999999888 999987
Q ss_pred CC
Q psy10674 134 SP 135 (138)
Q Consensus 134 ~~ 135 (138)
-.
T Consensus 161 ~~ 162 (200)
T KOG1700|consen 161 HH 162 (200)
T ss_pred hh
Confidence 64
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=99.04 E-value=1.8e-10 Score=59.69 Aligned_cols=37 Identities=30% Similarity=0.515 Sum_probs=33.0
Q ss_pred cccccCcccccC-cEEEeCCCccccCCccccccccccC
Q psy10674 82 RCHACDELIFVN-EYTLAENKTFHVKHFCCYECDKELC 118 (138)
Q Consensus 82 ~C~~C~~~I~~~-~~~~~~~~~~H~~CF~C~~C~~~l~ 118 (138)
+|.+|+++|.+. .++.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999886 5666899999999999999999986
No 14
>KOG4577|consensus
Probab=98.96 E-value=5.7e-11 Score=85.61 Aligned_cols=77 Identities=18% Similarity=0.493 Sum_probs=58.5
Q ss_pred eeecCCCcCcCCcccccccccccCCCeE------EEec-------c--------------ccCCCCCCcccCcccccCCc
Q psy10674 2 TLAENKTFHVKHFCCYECDKKVQFENYT------GKIT-------Q--------------SQESEVLWHPQCFVCSTCDE 54 (138)
Q Consensus 2 ~~a~g~~~h~~~~~C~~C~~~i~~~~~~------~~~~-------~--------------~~~~~~~~H~~Cf~C~~C~~ 54 (138)
+.++++.||..|++|..|..+|.+.-+. ...+ + -.+.+.+||.+||.|.+|++
T Consensus 49 lKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R 128 (383)
T KOG4577|consen 49 LKVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKR 128 (383)
T ss_pred HHHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhc
Confidence 4688999999999999999998743221 1100 0 01567899999999999999
Q ss_pred cc-cCCcee-eeCCeeecHHHHHhhc
Q psy10674 55 LL-VDLMYF-HYKGNVYCLRDYATML 78 (138)
Q Consensus 55 ~l-~~~~~~-~~~~~~yC~~c~~~~~ 78 (138)
+| .+..|| .+|+++.|+++|++..
T Consensus 129 ~L~TGdEFYLmeD~rLvCK~DYE~Ak 154 (383)
T KOG4577|consen 129 QLATGDEFYLMEDARLVCKDDYETAK 154 (383)
T ss_pred ccccCCeeEEeccceeehhhhHHHHH
Confidence 99 444555 5899999999998753
No 15
>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=98.64 E-value=3.2e-08 Score=51.04 Aligned_cols=38 Identities=32% Similarity=0.749 Sum_probs=30.0
Q ss_pred ccccccccccCCCeEEEeccccCCCCCCcccCcccccCCcccc
Q psy10674 15 CCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLV 57 (138)
Q Consensus 15 ~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 57 (138)
+|..|+++|.+++..+.. .+..||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~-----~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRA-----LGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEe-----CCccccccCCCCcccCCcCc
Confidence 488999999866343332 46699999999999999885
No 16
>KOG1700|consensus
Probab=97.84 E-value=3.5e-06 Score=59.15 Aligned_cols=54 Identities=24% Similarity=0.485 Sum_probs=48.3
Q ss_pred CcccccCcccccCcEEEeCCCccccCCccccccccccCCCCeeecCCCCCccCCC
Q psy10674 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRPGQDSP 135 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~y~~~~ 135 (138)
.+|.+|++.+...+.+...|..||..||+|..|.+.|....+..++ +.|||+.+
T Consensus 8 ~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e-~~~yc~~~ 61 (200)
T KOG1700|consen 8 DKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHE-GVPYCKNC 61 (200)
T ss_pred chhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccc-cccccccc
Confidence 5899999999876666688999999999999999999988899888 99999874
No 17
>KOG0490|consensus
Probab=97.67 E-value=2.7e-06 Score=60.63 Aligned_cols=92 Identities=28% Similarity=0.570 Sum_probs=72.9
Q ss_pred CCCCcccCcccccCCcccc--CCceeeeCCeeecHHHHHh--hcCCCcccccCcccccCcEEE-eCCCccccCCcccccc
Q psy10674 39 EVLWHPQCFVCSTCDELLV--DLMYFHYKGNVYCLRDYAT--MLDIPRCHACDELIFVNEYTL-AENKTFHVKHFCCYEC 113 (138)
Q Consensus 39 ~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~yC~~c~~~--~~~~~~C~~C~~~I~~~~~~~-~~~~~~H~~CF~C~~C 113 (138)
+..||..|..|..|...|. ...+.. ++..||..++.. .++ .+|.+|...|...+.++ +..+. |..||.|..|
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~-~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~ 92 (235)
T KOG0490|consen 16 DRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS-KRCARCKFTISQLDELERAFEKV-HLPCFACREC 92 (235)
T ss_pred cHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc-ccccCCCCCcCHHHHHHHhhcCC-CcCccchHHH
Confidence 4589999999999999996 444445 999999999987 554 69999999996555444 66676 9999999999
Q ss_pred ccccC-CCCeeecCCCCCccC
Q psy10674 114 DKELC-NQSYIPVTESRPGQD 133 (138)
Q Consensus 114 ~~~l~-~~~f~~~~~~~~y~~ 133 (138)
...+. +..+.++++.+.++.
T Consensus 93 la~~~~~~e~rVqvwFqnrra 113 (235)
T KOG0490|consen 93 LALLLTGDEFRVQVWFQNRRA 113 (235)
T ss_pred HhhcCCCCeeeeehhhhhhcH
Confidence 88654 778888875566654
No 18
>KOG1702|consensus
Probab=97.18 E-value=1.7e-05 Score=55.20 Aligned_cols=57 Identities=28% Similarity=0.514 Sum_probs=45.6
Q ss_pred ccccccccccCCCeEEEeccccCCCCCCcccCcccccCCccccCCceeeeCCeeecHHHHHhh
Q psy10674 15 CCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATM 77 (138)
Q Consensus 15 ~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~ 77 (138)
.|..|++.+.+-+.+.. ++..||..||+|..|+.+|....+...+.++||..+|.+.
T Consensus 6 n~~~cgk~vYPvE~v~c------ldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq 62 (264)
T KOG1702|consen 6 NREDCGKTVYPVEEVKC------LDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQ 62 (264)
T ss_pred hhhhhccccccHHHHhh------HHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccc
Confidence 35677777765544433 4559999999999999999888888899999999998654
No 19
>KOG1702|consensus
Probab=97.15 E-value=4e-05 Score=53.39 Aligned_cols=53 Identities=19% Similarity=0.341 Sum_probs=44.6
Q ss_pred CcccccCcccccCcEEEeCCCccccCCccccccccccCCCCeeecCCCCCccCC
Q psy10674 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRPGQDS 134 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~y~~~ 134 (138)
+.|..|++.+.+-+-+.-+++.||.-||+|..|+.+|.-.+|--.+ .+|||+.
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~-kkpycn~ 57 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYD-KKPYCNP 57 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccc-cCCCcCc
Confidence 4567888888776666688999999999999999999877776666 8999986
No 20
>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=95.17 E-value=0.0074 Score=30.66 Aligned_cols=32 Identities=28% Similarity=0.668 Sum_probs=23.5
Q ss_pred ccccCcccccCcEEE-eCCCccccCCcccccccccc
Q psy10674 83 CHACDELIFVNEYTL-AENKTFHVKHFCCYECDKEL 117 (138)
Q Consensus 83 C~~C~~~I~~~~~~~-~~~~~~H~~CF~C~~C~~~l 117 (138)
|.-|+++|.+..++. ..++.|+ |.|..|.+.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence 677999998776554 7888888 6667776554
No 21
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=94.20 E-value=0.036 Score=30.56 Aligned_cols=36 Identities=14% Similarity=0.471 Sum_probs=26.6
Q ss_pred CcccccCcccc-cCcEEE--eCCCccccCCc----cccc--cccc
Q psy10674 81 PRCHACDELIF-VNEYTL--AENKTFHVKHF----CCYE--CDKE 116 (138)
Q Consensus 81 ~~C~~C~~~I~-~~~~~~--~~~~~~H~~CF----~C~~--C~~~ 116 (138)
.+|..|+++|. ++++++ .=+..||.+|+ .|.. |+..
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~ 50 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTG 50 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCC
Confidence 59999999997 345665 56889999988 3665 5544
No 22
>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=90.79 E-value=0.19 Score=31.24 Aligned_cols=28 Identities=11% Similarity=0.348 Sum_probs=20.6
Q ss_pred CcccccCcccccCcEEE-eCCCccccCCc
Q psy10674 81 PRCHACDELIFVNEYTL-AENKTFHVKHF 108 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~~-~~~~~~H~~CF 108 (138)
..|+.|+++|....++. ..|..+|..|+
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 58999999997665555 45666787775
No 23
>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=90.44 E-value=0.17 Score=33.99 Aligned_cols=50 Identities=16% Similarity=0.383 Sum_probs=36.2
Q ss_pred CeeecHHHHHhhcCCCcccccCcccccCcEE---EeCCCccccCCccccccccccC
Q psy10674 66 GNVYCLRDYATMLDIPRCHACDELIFVNEYT---LAENKTFHVKHFCCYECDKELC 118 (138)
Q Consensus 66 ~~~yC~~c~~~~~~~~~C~~C~~~I~~~~~~---~~~~~~~H~~CF~C~~C~~~l~ 118 (138)
..-||..|-.+.. ..|+.|+.+|.+..++ ...+..|++--| |..|+++++
T Consensus 27 ~~~fC~kCG~~tI--~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsY-C~~CGkpyP 79 (158)
T PF10083_consen 27 REKFCSKCGAKTI--TSCPNCSTPIRGDYHVEGVFGLGGHYEAPSY-CHNCGKPYP 79 (158)
T ss_pred HHHHHHHhhHHHH--HHCcCCCCCCCCceecCCeeeeCCCCCCChh-HHhCCCCCc
Confidence 4569999998887 6999999999765332 144566665432 888888875
No 24
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=89.39 E-value=0.045 Score=33.66 Aligned_cols=53 Identities=25% Similarity=0.344 Sum_probs=39.5
Q ss_pred cccccCcccccCcEEEeCCCccccCCccccccccccCCCCeeecCCCCCccCCC
Q psy10674 82 RCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRPGQDSP 135 (138)
Q Consensus 82 ~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~y~~~~ 135 (138)
.|..|...+..-.+....-..+++.+-.|..|.+.|+-..|.+.. .=|||.||
T Consensus 37 aCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~-~Cp~C~sp 89 (105)
T COG4357 37 ACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCG-SCPYCQSP 89 (105)
T ss_pred hHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcC-CCCCcCCC
Confidence 566777666554455455567888888899999888877788777 78888885
No 25
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=88.76 E-value=0.26 Score=22.19 Aligned_cols=9 Identities=33% Similarity=0.704 Sum_probs=4.7
Q ss_pred ccccCcccc
Q psy10674 83 CHACDELIF 91 (138)
Q Consensus 83 C~~C~~~I~ 91 (138)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 455555553
No 26
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=88.01 E-value=0.18 Score=31.50 Aligned_cols=30 Identities=17% Similarity=0.376 Sum_probs=23.2
Q ss_pred cccccCcccccCcEEE-eCCCccccCCcccc
Q psy10674 82 RCHACDELIFVNEYTL-AENKTFHVKHFCCY 111 (138)
Q Consensus 82 ~C~~C~~~I~~~~~~~-~~~~~~H~~CF~C~ 111 (138)
+|..|+++|..++... ..+..-|.+||+=.
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 7999999999877443 56678898888643
No 27
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.68 E-value=0.67 Score=26.01 Aligned_cols=50 Identities=20% Similarity=0.431 Sum_probs=27.1
Q ss_pred CcccccccccccCCCeEEEeccccCCCCCCcccCcccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCc
Q psy10674 13 HFCCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDE 88 (138)
Q Consensus 13 ~~~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~ 88 (138)
-.+|..|+.+|.+.+..+. |.|-.|+..+.. -|..|-.+.. .-+|..|+.
T Consensus 7 ~~~CtSCg~~i~~~~~~~~---------------F~CPnCG~~~I~----------RC~~CRk~~~-~Y~CP~CGF 56 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVK---------------FLCPNCGEVIIY----------RCEKCRKQSN-PYTCPKCGF 56 (59)
T ss_pred CccccCCCCcccCCCccCE---------------eeCCCCCCeeEe----------echhHHhcCC-ceECCCCCC
Confidence 3567788877775442211 677777765322 1555543333 246666653
No 28
>KOG0490|consensus
Probab=86.69 E-value=0.13 Score=36.43 Aligned_cols=47 Identities=17% Similarity=0.310 Sum_probs=37.2
Q ss_pred cCcccccCcEEEeCCCccccCCccccccccccC--CCCeeecCCCCCccCC
Q psy10674 86 CDELIFVNEYTLAENKTFHVKHFCCYECDKELC--NQSYIPVTESRPGQDS 134 (138)
Q Consensus 86 C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~--~~~f~~~~~~~~y~~~ 134 (138)
|+..|.+.....+.+..||..|..|..|...|. ...|.. + |..||..
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-g~~~~~~ 50 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-D-GSIYCKR 50 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-C-Ccccccc
Confidence 667777665555679999999999999999997 555555 6 9999875
No 29
>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=85.62 E-value=0.49 Score=28.95 Aligned_cols=44 Identities=20% Similarity=0.432 Sum_probs=32.3
Q ss_pred CCcccCcccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccccC
Q psy10674 41 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVN 93 (138)
Q Consensus 41 ~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~ 93 (138)
.|-+.--.|..|+..+.. .|.-||..|..+. -.|+.|++.|.+.
T Consensus 39 Py~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk---GiCamCGKki~dt 82 (90)
T PF10235_consen 39 PYAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK---GICAMCGKKILDT 82 (90)
T ss_pred cccccCcccccccccccc------CCCccChhhhccc---CcccccCCeeccc
Confidence 565555578888877643 2467999998764 4899999999764
No 30
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=84.39 E-value=1.8 Score=24.29 Aligned_cols=20 Identities=10% Similarity=0.265 Sum_probs=12.4
Q ss_pred CcCCcccccccccccCCCeE
Q psy10674 10 HVKHFCCYECDKKVQFENYT 29 (138)
Q Consensus 10 h~~~~~C~~C~~~i~~~~~~ 29 (138)
+..-.+|..|+..|.+++..
T Consensus 6 ~~~~~~CtSCg~~i~p~e~~ 25 (61)
T COG2888 6 MKDPPVCTSCGREIAPGETA 25 (61)
T ss_pred ccCCceeccCCCEeccCCce
Confidence 33456778888777555443
No 31
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=84.35 E-value=0.59 Score=21.58 Aligned_cols=9 Identities=33% Similarity=0.730 Sum_probs=5.0
Q ss_pred cccccCccc
Q psy10674 82 RCHACDELI 90 (138)
Q Consensus 82 ~C~~C~~~I 90 (138)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 455566554
No 32
>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=84.26 E-value=0.32 Score=28.31 Aligned_cols=59 Identities=19% Similarity=0.373 Sum_probs=24.5
Q ss_pred ccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccccCcEEEeCCCccccCCccccccccccC
Q psy10674 48 VCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELC 118 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~ 118 (138)
.|..|..+|.. .++..+|..|.........|+-|++++ +++.|-|.. =|.|..|+..++
T Consensus 3 ~CP~C~~~L~~-----~~~~~~C~~C~~~~~~~a~CPdC~~~L---e~LkACGAv----dYFC~~c~gLiS 61 (70)
T PF07191_consen 3 TCPKCQQELEW-----QGGHYHCEACQKDYKKEAFCPDCGQPL---EVLKACGAV----DYFCNHCHGLIS 61 (70)
T ss_dssp B-SSS-SBEEE-----ETTEEEETTT--EEEEEEE-TTT-SB----EEEEETTEE----EEE-TTTT-EE-
T ss_pred cCCCCCCccEE-----eCCEEECccccccceecccCCCcccHH---HHHHHhccc----ceeeccCCceee
Confidence 35555555422 235556655543322224777777777 344454421 134666666655
No 33
>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=84.24 E-value=2 Score=23.74 Aligned_cols=49 Identities=16% Similarity=0.173 Sum_probs=35.2
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhhcC-CCcccccCcccccCcEE
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLD-IPRCHACDELIFVNEYT 96 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~-~~~C~~C~~~I~~~~~~ 96 (138)
|.|..|+..+.+ ......|..||+.+..+.+. ...|+.|++++...+++
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~ 51 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLI 51 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhce
Confidence 578888888865 45557789999988865431 24799999888655544
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=83.94 E-value=0.44 Score=23.98 Aligned_cols=24 Identities=17% Similarity=0.135 Sum_probs=15.2
Q ss_pred cccccccccCCCCeeecCCCCCccCCCCC
Q psy10674 109 CCYECDKELCNQSYIPVTESRPGQDSPGS 137 (138)
Q Consensus 109 ~C~~C~~~l~~~~f~~~~~~~~y~~~~~~ 137 (138)
.|..|+.. .|...+ |+.||++.++
T Consensus 10 ~C~~C~~~----~~~~~d-G~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDD-GFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe----EeEccC-CEEEhhhCce
Confidence 37777643 344444 9999987653
No 35
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=83.44 E-value=0.9 Score=26.00 Aligned_cols=49 Identities=14% Similarity=0.463 Sum_probs=22.2
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccccCcEE
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEYT 96 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~~~~ 96 (138)
.+|+.|...|........=.-++|..|-.+.+| ..|+.|+.|--..++.
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~-~~CPvC~~Paw~qD~~ 56 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG-SECPVCHTPAWIQDIQ 56 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTT-TB-SSS--B-S-SS--
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcC-CCCCCcCChHHHHHHH
Confidence 567888777754323344556788888877776 5799999887655543
No 36
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=81.33 E-value=1.4 Score=24.24 Aligned_cols=26 Identities=19% Similarity=0.194 Sum_probs=19.4
Q ss_pred CcccccCcccccCcEEEeCCCccccC
Q psy10674 81 PRCHACDELIFVNEYTLAENKTFHVK 106 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~~~~~~~~H~~ 106 (138)
.+|..|++||.+...+...+..-|+.
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~g 27 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHPG 27 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCcH
Confidence 48999999998766665666677763
No 37
>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=81.24 E-value=0.93 Score=24.79 Aligned_cols=24 Identities=13% Similarity=0.207 Sum_probs=9.7
Q ss_pred ccccccccCCCCeeecCCCCCccCC
Q psy10674 110 CYECDKELCNQSYIPVTESRPGQDS 134 (138)
Q Consensus 110 C~~C~~~l~~~~f~~~~~~~~y~~~ 134 (138)
|..|...++...=+.++ ||.||+.
T Consensus 10 C~~C~C~V~~~~Ai~~d-Gk~YCS~ 33 (52)
T PF02069_consen 10 CPSCSCVVSEEEAIQKD-GKYYCSE 33 (52)
T ss_dssp STT----B-TTTSEESS-S-EESSH
T ss_pred CCCCEeEECchHhHHhC-CEeeecH
Confidence 44555555544445555 6666653
No 38
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=80.19 E-value=2.1 Score=25.37 Aligned_cols=43 Identities=14% Similarity=0.306 Sum_probs=15.4
Q ss_pred ccccCCccc----cCCceee--eCCeeecHHHHH--hhcCCCcccccCccc
Q psy10674 48 VCSTCDELL----VDLMYFH--YKGNVYCLRDYA--TMLDIPRCHACDELI 90 (138)
Q Consensus 48 ~C~~C~~~l----~~~~~~~--~~~~~yC~~c~~--~~~~~~~C~~C~~~I 90 (138)
.|.+|+..+ .+..|.. .=+.+.|+.||. ..-|...|.+|+.+-
T Consensus 11 iCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 11 ICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred ccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 456665554 1222222 345678898884 344567899998543
No 39
>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=79.04 E-value=1.3 Score=27.34 Aligned_cols=13 Identities=31% Similarity=0.813 Sum_probs=6.0
Q ss_pred cccCCccccCCce
Q psy10674 49 CSTCDELLVDLMY 61 (138)
Q Consensus 49 C~~C~~~l~~~~~ 61 (138)
|..|+++|..+.|
T Consensus 81 C~vC~k~l~~~~f 93 (109)
T PF10367_consen 81 CSVCGKPLGNSVF 93 (109)
T ss_pred ccCcCCcCCCceE
Confidence 4455555544333
No 40
>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=78.59 E-value=3.8 Score=21.72 Aligned_cols=43 Identities=23% Similarity=0.444 Sum_probs=27.6
Q ss_pred ccccCCccccCCceeeeCCee-ecHHHHHhhc-CCCcccccCcccc
Q psy10674 48 VCSTCDELLVDLMYFHYKGNV-YCLRDYATML-DIPRCHACDELIF 91 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~~~~~~-yC~~c~~~~~-~~~~C~~C~~~I~ 91 (138)
.|..|...... ..+..=|-. +|..|..+.. ...+|+.|..+|.
T Consensus 4 ~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 46666666543 233445566 9999997763 2369999999984
No 41
>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=78.37 E-value=0.67 Score=27.56 Aligned_cols=35 Identities=20% Similarity=0.321 Sum_probs=19.9
Q ss_pred cccccccccccCCCeEEEeccccCC-----CCCCcccCcc
Q psy10674 14 FCCYECDKKVQFENYTGKITQSQES-----EVLWHPQCFV 48 (138)
Q Consensus 14 ~~C~~C~~~i~~~~~~~~~~~~~~~-----~~~~H~~Cf~ 48 (138)
-+|..|++.|..+++.+-....... ...||..||.
T Consensus 8 a~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~ 47 (82)
T PF00645_consen 8 AKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFF 47 (82)
T ss_dssp EBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHH
T ss_pred ccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccc
Confidence 4688999999977765432110001 1356777775
No 42
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=78.07 E-value=2.2 Score=23.15 Aligned_cols=29 Identities=14% Similarity=0.323 Sum_probs=20.8
Q ss_pred ccccCCccccCC-ceeeeCCeeecHHHHHhh
Q psy10674 48 VCSTCDELLVDL-MYFHYKGNVYCLRDYATM 77 (138)
Q Consensus 48 ~C~~C~~~l~~~-~~~~~~~~~yC~~c~~~~ 77 (138)
.|..|+..++-- .+...|| ..|.+|+.+.
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 478888888442 3556777 6899998775
No 43
>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=77.47 E-value=1.7 Score=19.85 Aligned_cols=11 Identities=18% Similarity=0.697 Sum_probs=6.1
Q ss_pred cccccccccCC
Q psy10674 16 CYECDKKVQFE 26 (138)
Q Consensus 16 C~~C~~~i~~~ 26 (138)
|..|+.+|.+.
T Consensus 1 C~sC~~~i~~r 11 (24)
T PF07754_consen 1 CTSCGRPIAPR 11 (24)
T ss_pred CccCCCcccCc
Confidence 45566666543
No 44
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=74.94 E-value=1.6 Score=28.59 Aligned_cols=22 Identities=27% Similarity=0.656 Sum_probs=16.8
Q ss_pred ccccCCccccCCceeeeCCeeecHHHH
Q psy10674 48 VCSTCDELLVDLMYFHYKGNVYCLRDY 74 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~~~~~~yC~~c~ 74 (138)
.|..|+.|| | .++|.+||+.|-
T Consensus 30 hCp~Cg~PL----F-~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL----F-RKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc----e-eeCCeEECCCCC
Confidence 478898887 3 389999887764
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=74.57 E-value=1.6 Score=22.62 Aligned_cols=22 Identities=27% Similarity=0.735 Sum_probs=13.1
Q ss_pred ccccCCccccCCceeeeCCeeecHHH
Q psy10674 48 VCSTCDELLVDLMYFHYKGNVYCLRD 73 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~~~~~~yC~~c 73 (138)
.|..|+.||- ..++++.||..|
T Consensus 19 ~Cp~C~~PL~----~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLM----RDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeE----EecCCCEECCCC
Confidence 4566777662 245677777543
No 46
>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=72.94 E-value=0.83 Score=22.77 Aligned_cols=28 Identities=18% Similarity=0.433 Sum_probs=17.5
Q ss_pred cccCCccccCCceeeeCCeeecHHHHHh
Q psy10674 49 CSTCDELLVDLMYFHYKGNVYCLRDYAT 76 (138)
Q Consensus 49 C~~C~~~l~~~~~~~~~~~~yC~~c~~~ 76 (138)
|..|+.++.........+..+|..|...
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 7777777765555556777777777654
No 47
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=72.92 E-value=1.4 Score=27.18 Aligned_cols=32 Identities=16% Similarity=0.323 Sum_probs=22.3
Q ss_pred CcccccCcccccCcE-EEeCCCccccCCccccc
Q psy10674 81 PRCHACDELIFVNEY-TLAENKTFHVKHFCCYE 112 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~-~~~~~~~~H~~CF~C~~ 112 (138)
-+|..|+++|..++. +......-|-+||.=+.
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~ 39 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESK 39 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHH
Confidence 389999999987763 33455667878776444
No 48
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=72.89 E-value=6.6 Score=27.54 Aligned_cols=51 Identities=18% Similarity=0.405 Sum_probs=33.3
Q ss_pred CcccccCCccccCCceeeeCCeeecHHHHHhhc-----------------CCCcccccCcccccCcEEE
Q psy10674 46 CFVCSTCDELLVDLMYFHYKGNVYCLRDYATML-----------------DIPRCHACDELIFVNEYTL 97 (138)
Q Consensus 46 Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~-----------------~~~~C~~C~~~I~~~~~~~ 97 (138)
-|.|.+|...+.+ .....=|-.||..|..+.. +..+|+.|..+|....++.
T Consensus 18 ~~~CpICld~~~d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvP 85 (193)
T PLN03208 18 DFDCNICLDQVRD-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVP 85 (193)
T ss_pred ccCCccCCCcCCC-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEE
Confidence 4777777766643 2344566778887775421 1258999999998766554
No 49
>KOG0320|consensus
Probab=71.28 E-value=2.7 Score=29.02 Aligned_cols=53 Identities=17% Similarity=0.453 Sum_probs=37.6
Q ss_pred cccCcccccCCccccCCc-eeeeCCeeecHHHHHhhcC-CCcccccCcccccCcE
Q psy10674 43 HPQCFVCSTCDELLVDLM-YFHYKGNVYCLRDYATMLD-IPRCHACDELIFVNEY 95 (138)
Q Consensus 43 H~~Cf~C~~C~~~l~~~~-~~~~~~~~yC~~c~~~~~~-~~~C~~C~~~I~~~~~ 95 (138)
-..+++|-+|=....... +..+=|.++|+.|..+.+. +.+|+.|++.|...++
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~ 182 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQF 182 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhh
Confidence 345788888866664433 4457789999999876542 3599999998865444
No 50
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=70.69 E-value=1.9 Score=25.82 Aligned_cols=29 Identities=28% Similarity=0.471 Sum_probs=19.2
Q ss_pred ccccCCccccCCceee-----eCCeeecHHHHHh
Q psy10674 48 VCSTCDELLVDLMYFH-----YKGNVYCLRDYAT 76 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~-----~~~~~yC~~c~~~ 76 (138)
.|+.|+.||.....+. ..+.-||..||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 4888999996554332 2335689888864
No 51
>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=70.45 E-value=8.3 Score=21.39 Aligned_cols=45 Identities=24% Similarity=0.425 Sum_probs=29.5
Q ss_pred ccccCCccccCC---ceeeeCCeeecHHHHHhhcCCCcccccCcccccC
Q psy10674 48 VCSTCDELLVDL---MYFHYKGNVYCLRDYATMLDIPRCHACDELIFVN 93 (138)
Q Consensus 48 ~C~~C~~~l~~~---~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~ 93 (138)
.|..|++.|... .+.=.-.=-||.+|...++. ..|+-|+..+..+
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~-~~CPNCgGelv~R 54 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLN-GVCPNCGGELVRR 54 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc-CcCcCCCCccccC
Confidence 467777777332 22223345588899888873 6999998776543
No 52
>PRK00807 50S ribosomal protein L24e; Validated
Probab=67.67 E-value=2.6 Score=23.04 Aligned_cols=33 Identities=24% Similarity=0.610 Sum_probs=20.7
Q ss_pred CcccccCcccccCc---EEEeCCCccccCCccccccccc
Q psy10674 81 PRCHACDELIFVNE---YTLAENKTFHVKHFCCYECDKE 116 (138)
Q Consensus 81 ~~C~~C~~~I~~~~---~~~~~~~~~H~~CF~C~~C~~~ 116 (138)
..|.-|+..|.++. ++...|+.|. |.+..|.+.
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~---Fcs~KC~~~ 37 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY---FCSSKCEKN 37 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE---EeCHHHHHH
Confidence 36788888887554 2446677776 555566543
No 53
>PF12773 DZR: Double zinc ribbon
Probab=67.26 E-value=4.8 Score=21.29 Aligned_cols=11 Identities=18% Similarity=0.425 Sum_probs=8.2
Q ss_pred CcccccCcccc
Q psy10674 81 PRCHACDELIF 91 (138)
Q Consensus 81 ~~C~~C~~~I~ 91 (138)
..|..|+.++.
T Consensus 13 ~fC~~CG~~l~ 23 (50)
T PF12773_consen 13 KFCPHCGTPLP 23 (50)
T ss_pred cCChhhcCChh
Confidence 57888887775
No 54
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=66.69 E-value=3.9 Score=33.99 Aligned_cols=10 Identities=20% Similarity=0.564 Sum_probs=5.2
Q ss_pred cccccccccc
Q psy10674 15 CCYECDKKVQ 24 (138)
Q Consensus 15 ~C~~C~~~i~ 24 (138)
+|..|+..+.
T Consensus 3 ~Cp~Cg~~n~ 12 (645)
T PRK14559 3 ICPQCQFENP 12 (645)
T ss_pred cCCCCCCcCC
Confidence 4555555544
No 55
>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=65.37 E-value=7.6 Score=20.50 Aligned_cols=29 Identities=24% Similarity=0.390 Sum_probs=17.5
Q ss_pred ccccCCccccCCceee--eCCeeecHHHHHh
Q psy10674 48 VCSTCDELLVDLMYFH--YKGNVYCLRDYAT 76 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~--~~~~~yC~~c~~~ 76 (138)
.|..|+..+....|.- ..+..+|.+||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 4667777775432321 2346688888876
No 56
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.53 E-value=6.4 Score=25.68 Aligned_cols=49 Identities=16% Similarity=0.443 Sum_probs=33.1
Q ss_pred eeecHHHHHhhcCCCcccccCcccccCcEEE---eCCCccccCCccccccccccC
Q psy10674 67 NVYCLRDYATMLDIPRCHACDELIFVNEYTL---AENKTFHVKHFCCYECDKELC 118 (138)
Q Consensus 67 ~~yC~~c~~~~~~~~~C~~C~~~I~~~~~~~---~~~~~~H~~CF~C~~C~~~l~ 118 (138)
..+|..|-.... ..|+.|+-+|.+..++. -.|.-|-+-=| |..|+++++
T Consensus 28 eafcskcgeati--~qcp~csasirgd~~vegvlglg~dye~psf-chncgs~fp 79 (160)
T COG4306 28 EAFCSKCGEATI--TQCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGSRFP 79 (160)
T ss_pred HHHHhhhchHHH--hcCCccCCcccccceeeeeeccCCCCCCcch-hhcCCCCCC
Confidence 346777766655 58999999998765554 45566665533 777877765
No 57
>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=62.67 E-value=8.3 Score=18.99 Aligned_cols=25 Identities=24% Similarity=0.491 Sum_probs=12.7
Q ss_pred CCeeecHHHHHhhcC--CCcccccCcc
Q psy10674 65 KGNVYCLRDYATMLD--IPRCHACDEL 89 (138)
Q Consensus 65 ~~~~yC~~c~~~~~~--~~~C~~C~~~ 89 (138)
=+-.+|..|..+.+. ..+|+.|+..
T Consensus 18 C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 18 CGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 345566666543321 2357666654
No 58
>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=62.28 E-value=9.2 Score=19.82 Aligned_cols=29 Identities=24% Similarity=0.525 Sum_probs=14.1
Q ss_pred ccccCCccccCCceee--eCCeeecHHHHHh
Q psy10674 48 VCSTCDELLVDLMYFH--YKGNVYCLRDYAT 76 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~--~~~~~yC~~c~~~ 76 (138)
.|..|++++.+..|.= =.+--+|..||.+
T Consensus 6 ~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~ 36 (44)
T smart00291 6 SCDTCGKPIVGVRYHCLVCPDYDLCQSCFAK 36 (44)
T ss_pred CCCCCCCCCcCCEEECCCCCCccchHHHHhC
Confidence 4555555554433311 1234467777754
No 59
>PRK00420 hypothetical protein; Validated
Probab=59.96 E-value=4.1 Score=26.01 Aligned_cols=23 Identities=26% Similarity=0.468 Sum_probs=12.4
Q ss_pred cccccCCccccCCceeeeCCeeecHHH
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRD 73 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c 73 (138)
-.|..|+.+| |-.++|+.||..|
T Consensus 24 ~~CP~Cg~pL----f~lk~g~~~Cp~C 46 (112)
T PRK00420 24 KHCPVCGLPL----FELKDGEVVCPVH 46 (112)
T ss_pred CCCCCCCCcc----eecCCCceECCCC
Confidence 3466777665 2225555555444
No 60
>KOG1813|consensus
Probab=59.61 E-value=6 Score=29.57 Aligned_cols=45 Identities=16% Similarity=0.323 Sum_probs=33.5
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhhcC-CCcccccCccccc
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLD-IPRCHACDELIFV 92 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~-~~~C~~C~~~I~~ 92 (138)
|.|.+|.+.+.. +....-+..+|+.|..+.+- .++|..|++.+.+
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhccccccCCcceeccccccc
Confidence 788888887743 34456678899999876552 2799999999865
No 61
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=59.36 E-value=6.4 Score=22.04 Aligned_cols=9 Identities=56% Similarity=1.246 Sum_probs=4.5
Q ss_pred ccccccccC
Q psy10674 110 CYECDKELC 118 (138)
Q Consensus 110 C~~C~~~l~ 118 (138)
|..|++.|.
T Consensus 19 C~~C~k~L~ 27 (58)
T PF04570_consen 19 CYLCKKKLD 27 (58)
T ss_pred HHccCCCCC
Confidence 444555554
No 62
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=58.61 E-value=6.4 Score=26.08 Aligned_cols=22 Identities=32% Similarity=0.732 Sum_probs=11.1
Q ss_pred ccccCCccccCCceeeeCCeeecHHHHH
Q psy10674 48 VCSTCDELLVDLMYFHYKGNVYCLRDYA 75 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~ 75 (138)
.|..|++.+.. .++.+|..|+.
T Consensus 5 nC~~CgklF~~------~~~~iCp~C~~ 26 (137)
T TIGR03826 5 NCPKCGRLFVK------TGRDVCPSCYE 26 (137)
T ss_pred cccccchhhhh------cCCccCHHHhH
Confidence 45556554321 24456666663
No 63
>smart00704 ZnF_CDGSH CDGSH-type zinc finger. Function unknown.
Probab=57.32 E-value=6.3 Score=20.01 Aligned_cols=7 Identities=29% Similarity=0.192 Sum_probs=5.4
Q ss_pred CCCccCC
Q psy10674 128 SRPGQDS 134 (138)
Q Consensus 128 ~~~y~~~ 134 (138)
++||||-
T Consensus 24 ~~PfCDG 30 (38)
T smart00704 24 NFPYCDG 30 (38)
T ss_pred CCCccCC
Confidence 7888883
No 64
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=57.31 E-value=3.7 Score=28.98 Aligned_cols=31 Identities=23% Similarity=0.393 Sum_probs=24.9
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhh
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATM 77 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~ 77 (138)
-+|+.|+..+....-...+|++.|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5799999988666666789999999998643
No 65
>KOG3002|consensus
Probab=56.37 E-value=11 Score=28.34 Aligned_cols=44 Identities=18% Similarity=0.352 Sum_probs=36.3
Q ss_pred CcccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccc
Q psy10674 46 CFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIF 91 (138)
Q Consensus 46 Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~ 91 (138)
=+-|.+|...|....+.-.+|-+.|..|-.++. .+|+.|..+|.
T Consensus 48 lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~--~~CP~Cr~~~g 91 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS--NKCPTCRLPIG 91 (299)
T ss_pred hccCchhhccCcccceecCCCcEehhhhhhhhc--ccCCccccccc
Confidence 366788888887666777899999999987765 69999999995
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=56.18 E-value=23 Score=17.52 Aligned_cols=30 Identities=23% Similarity=0.436 Sum_probs=17.8
Q ss_pred cccCCccccCCceeeeCCeeecHHHHHhhc
Q psy10674 49 CSTCDELLVDLMYFHYKGNVYCLRDYATML 78 (138)
Q Consensus 49 C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~ 78 (138)
|..|...+.+......=|-.||..|..+.+
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~ 30 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYL 30 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHH
Confidence 455656554422345667888888876543
No 67
>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=55.55 E-value=6.5 Score=23.90 Aligned_cols=16 Identities=25% Similarity=0.858 Sum_probs=13.0
Q ss_pred HHhhcCCCcccccCccc
Q psy10674 74 YATMLDIPRCHACDELI 90 (138)
Q Consensus 74 ~~~~~~~~~C~~C~~~I 90 (138)
|..++ +..|.+|++.+
T Consensus 49 Y~~lf-s~pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLF-STPCKKCGKLL 64 (90)
T ss_pred Hhhhc-cchhhHHHhHh
Confidence 45667 57999999988
No 68
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=55.38 E-value=16 Score=18.71 Aligned_cols=40 Identities=18% Similarity=0.491 Sum_probs=20.8
Q ss_pred cccCCcccc-C-CceeeeCCeeecHHHHHhhc-CCCcccccCc
Q psy10674 49 CSTCDELLV-D-LMYFHYKGNVYCLRDYATML-DIPRCHACDE 88 (138)
Q Consensus 49 C~~C~~~l~-~-~~~~~~~~~~yC~~c~~~~~-~~~~C~~C~~ 88 (138)
|..|...+. . ..+...=|-++|..|..+.. ....|+.|++
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 445555541 1 22223445667777776654 1247777753
No 69
>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 PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=54.31 E-value=30 Score=19.89 Aligned_cols=51 Identities=16% Similarity=0.164 Sum_probs=32.3
Q ss_pred cCcccccCCccccCCceeeeCCeeecHHHHHhhcC--CCcccccCcccccCcEE
Q psy10674 45 QCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLD--IPRCHACDELIFVNEYT 96 (138)
Q Consensus 45 ~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~--~~~C~~C~~~I~~~~~~ 96 (138)
+=|.|..++..+.+ ......|..|.+....+.+. ...|..++.+|...+++
T Consensus 3 ~~f~CpIt~~lM~d-PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~ 55 (73)
T PF04564_consen 3 DEFLCPITGELMRD-PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLI 55 (73)
T ss_dssp GGGB-TTTSSB-SS-EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSE
T ss_pred cccCCcCcCcHhhC-ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccce
Confidence 44788888887755 46667889999887755442 25799998888765544
No 71
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=53.50 E-value=19 Score=18.83 Aligned_cols=11 Identities=9% Similarity=0.223 Sum_probs=7.5
Q ss_pred CeeecHHHHHh
Q psy10674 66 GNVYCLRDYAT 76 (138)
Q Consensus 66 ~~~yC~~c~~~ 76 (138)
+--+|..||.+
T Consensus 27 d~dLC~~C~~~ 37 (46)
T PF00569_consen 27 DYDLCEDCFSK 37 (46)
T ss_dssp S-EEEHHHHHH
T ss_pred CCchhhHHHhC
Confidence 45588888876
No 72
>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=53.34 E-value=3.4 Score=19.50 Aligned_cols=11 Identities=27% Similarity=0.585 Sum_probs=6.0
Q ss_pred CcccccCcccc
Q psy10674 81 PRCHACDELIF 91 (138)
Q Consensus 81 ~~C~~C~~~I~ 91 (138)
.+|..|...|.
T Consensus 2 ~~C~rC~~~~~ 12 (30)
T PF06827_consen 2 EKCPRCWNYIE 12 (30)
T ss_dssp SB-TTT--BBE
T ss_pred CcCccCCCcce
Confidence 57888888874
No 73
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=53.25 E-value=7 Score=20.47 Aligned_cols=20 Identities=20% Similarity=0.365 Sum_probs=12.1
Q ss_pred ccccccccCCCCeeecCCCCCccCC
Q psy10674 110 CYECDKELCNQSYIPVTESRPGQDS 134 (138)
Q Consensus 110 C~~C~~~l~~~~f~~~~~~~~y~~~ 134 (138)
|..|.+.+.. ..++.+|||.
T Consensus 9 C~~Cdk~~~~-----~~~~~lYCSe 28 (43)
T PF12855_consen 9 CIVCDKQIDP-----PDDGSLYCSE 28 (43)
T ss_pred HHHhhccccC-----CCCCccccCH
Confidence 5556666543 3347888874
No 74
>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=52.62 E-value=14 Score=19.33 Aligned_cols=26 Identities=15% Similarity=0.282 Sum_probs=11.8
Q ss_pred ccccCcccccCcEEE--eCCCccccCCc
Q psy10674 83 CHACDELIFVNEYTL--AENKTFHVKHF 108 (138)
Q Consensus 83 C~~C~~~I~~~~~~~--~~~~~~H~~CF 108 (138)
|..|++.-.++.++. .=++.||..|.
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~ 29 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECV 29 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTS
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccC
Confidence 445555333334443 22455565543
No 75
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=51.21 E-value=5.8 Score=28.02 Aligned_cols=46 Identities=15% Similarity=0.356 Sum_probs=33.7
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhhc-CCCcccccCcccccC
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATML-DIPRCHACDELIFVN 93 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~-~~~~C~~C~~~I~~~ 93 (138)
|.|..|++.... +....=|..+|..|+.+.+ ..+.|..|++...+.
T Consensus 197 F~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~ 243 (259)
T COG5152 197 FLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGR 243 (259)
T ss_pred eeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhccc
Confidence 788999887643 3445667889999997654 237999999887654
No 76
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=50.45 E-value=13 Score=32.74 Aligned_cols=25 Identities=16% Similarity=0.243 Sum_probs=14.7
Q ss_pred CeeecHHHHH--hhcCCCcccccCccc
Q psy10674 66 GNVYCLRDYA--TMLDIPRCHACDELI 90 (138)
Q Consensus 66 ~~~yC~~c~~--~~~~~~~C~~C~~~I 90 (138)
+-+.|+.||+ +.-|...|++|+..-
T Consensus 43 ~FPVCrpCYEYEr~eG~q~CPqCktrY 69 (1079)
T PLN02638 43 AFPVCRPCYEYERKDGNQSCPQCKTKY 69 (1079)
T ss_pred CCccccchhhhhhhcCCccCCccCCch
Confidence 3456666662 344556777777643
No 77
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=47.56 E-value=22 Score=18.83 Aligned_cols=9 Identities=22% Similarity=0.615 Sum_probs=4.9
Q ss_pred eecHHHHHh
Q psy10674 68 VYCLRDYAT 76 (138)
Q Consensus 68 ~yC~~c~~~ 76 (138)
-+|..||..
T Consensus 25 dLC~~Cf~~ 33 (49)
T cd02335 25 DLCLECFSA 33 (49)
T ss_pred chhHHhhhC
Confidence 356666543
No 78
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=47.06 E-value=26 Score=18.76 Aligned_cols=24 Identities=33% Similarity=0.589 Sum_probs=11.5
Q ss_pred CeeecHHHHHhhcC--CCcccccCcc
Q psy10674 66 GNVYCLRDYATMLD--IPRCHACDEL 89 (138)
Q Consensus 66 ~~~yC~~c~~~~~~--~~~C~~C~~~ 89 (138)
+--+|..||.+... .-+|++|.++
T Consensus 21 gf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 21 GFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp S----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 34578888876652 3589999875
No 79
>PF04641 Rtf2: Rtf2 RING-finger
Probab=46.06 E-value=52 Score=24.05 Aligned_cols=56 Identities=11% Similarity=0.258 Sum_probs=41.5
Q ss_pred cccCcccccCCccccCC-cee--eeCCeeecHHHHHhhcCCCcccccCcccccCcEEEe
Q psy10674 43 HPQCFVCSTCDELLVDL-MYF--HYKGNVYCLRDYATMLDIPRCHACDELIFVNEYTLA 98 (138)
Q Consensus 43 H~~Cf~C~~C~~~l~~~-~~~--~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~~~~~~ 98 (138)
...-|.|.+.++.|.+. .|. ..-|-++......++-....|..|+++....++|..
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~~~DiI~L 168 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFTEEDIIPL 168 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCccccCCEEEe
Confidence 45568899999999653 232 267889999888776413589999999987777753
No 80
>KOG3476|consensus
Probab=46.04 E-value=2.9 Score=25.29 Aligned_cols=38 Identities=24% Similarity=0.501 Sum_probs=27.4
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccccC
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVN 93 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~ 93 (138)
-+|..|...+. ..|.-||..|..+. -.|+-|++.|.+.
T Consensus 55 ~kC~iCk~~vH------Q~GshYC~tCAY~K---giCAMCGKki~nT 92 (100)
T KOG3476|consen 55 AKCRICKQLVH------QPGSHYCQTCAYKK---GICAMCGKKILNT 92 (100)
T ss_pred chhHHHHHHhc------CCcchhHhHhhhhh---hHHHHhhhHhhcc
Confidence 45777766552 24567999998775 3899999999654
No 81
>PLN02195 cellulose synthase A
Probab=44.87 E-value=19 Score=31.49 Aligned_cols=25 Identities=12% Similarity=0.069 Sum_probs=17.9
Q ss_pred eeecHHHH--HhhcCCCcccccCcccc
Q psy10674 67 NVYCLRDY--ATMLDIPRCHACDELIF 91 (138)
Q Consensus 67 ~~yC~~c~--~~~~~~~~C~~C~~~I~ 91 (138)
-+.|+.|| ++.-|...|++|+..-.
T Consensus 33 ~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 33 YPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CccccchhhhhhhcCCccCCccCCccc
Confidence 45677777 34556789999998776
No 82
>KOG3579|consensus
Probab=44.83 E-value=12 Score=27.98 Aligned_cols=48 Identities=17% Similarity=0.180 Sum_probs=34.1
Q ss_pred CcccccCcccccCcEEEeCCCccccCCccccccccccCCCCeeecCCCCCccCC
Q psy10674 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRPGQDS 134 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~~~~~~y~~~ 134 (138)
-.|.-|++.+.+..+|.--...-|.-||-|++ ..|..+ -..|..||-|
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR--esIK~Q----g~sgevYCPS 316 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR--ESIKQQ----GASGEVYCPS 316 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCH--HHHHhh----cCCCceeCCC
Confidence 37888999998888888778888999999975 223221 1126777766
No 83
>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=44.45 E-value=7 Score=16.75 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=8.6
Q ss_pred ccccccccccCC
Q psy10674 108 FCCYECDKELCN 119 (138)
Q Consensus 108 F~C~~C~~~l~~ 119 (138)
|.|..|++.+..
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 568888877653
No 84
>KOG0978|consensus
Probab=44.17 E-value=6.6 Score=32.89 Aligned_cols=49 Identities=22% Similarity=0.482 Sum_probs=28.5
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhhcCC--CcccccCcccccCcEE
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDI--PRCHACDELIFVNEYT 96 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~--~~C~~C~~~I~~~~~~ 96 (138)
.+|..|+....+ .....=+-+||..|-..++.+ -+|+.|+.+..+.++.
T Consensus 644 LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 644 LKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVH 694 (698)
T ss_pred eeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccc
Confidence 456666654432 122244556777776554421 4888888888766654
No 85
>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=42.93 E-value=14 Score=17.27 Aligned_cols=11 Identities=45% Similarity=0.779 Sum_probs=3.2
Q ss_pred cccccCccccc
Q psy10674 82 RCHACDELIFV 92 (138)
Q Consensus 82 ~C~~C~~~I~~ 92 (138)
.|..|++++.+
T Consensus 2 ~C~~C~~~~~~ 12 (30)
T PF07649_consen 2 RCDACGKPIDG 12 (30)
T ss_dssp --TTTS----S
T ss_pred cCCcCCCcCCC
Confidence 46667776643
No 86
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=42.83 E-value=8.3 Score=24.00 Aligned_cols=29 Identities=14% Similarity=0.228 Sum_probs=19.5
Q ss_pred CCccccccccccCCCCeeecCCCCCccCC
Q psy10674 106 KHFCCYECDKELCNQSYIPVTESRPGQDS 134 (138)
Q Consensus 106 ~CF~C~~C~~~l~~~~f~~~~~~~~y~~~ 134 (138)
+=|+|+.|--+-...+-....+|++||.-
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~D 97 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRD 97 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEeccc
Confidence 45889998666554444555559999863
No 87
>PLN02400 cellulose synthase
Probab=42.21 E-value=17 Score=32.04 Aligned_cols=44 Identities=14% Similarity=0.293 Sum_probs=26.9
Q ss_pred cccccCCccc----cCCceee--eCCeeecHHHHH--hhcCCCcccccCccc
Q psy10674 47 FVCSTCDELL----VDLMYFH--YKGNVYCLRDYA--TMLDIPRCHACDELI 90 (138)
Q Consensus 47 f~C~~C~~~l----~~~~~~~--~~~~~yC~~c~~--~~~~~~~C~~C~~~I 90 (138)
-.|++|+..+ .+..|.. .=+-|.|+.||+ ++-|...|++|+..-
T Consensus 37 qiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrY 88 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRY 88 (1085)
T ss_pred ceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCcc
Confidence 3677787765 2223332 445678888873 344567888887643
No 88
>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=41.68 E-value=5.4 Score=19.62 Aligned_cols=17 Identities=18% Similarity=0.669 Sum_probs=10.9
Q ss_pred ccccccccccCCCCeee
Q psy10674 108 FCCYECDKELCNQSYIP 124 (138)
Q Consensus 108 F~C~~C~~~l~~~~f~~ 124 (138)
|.|..|++++...+|..
T Consensus 5 ~~C~nC~R~v~a~RfA~ 21 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAP 21 (33)
T ss_dssp EE-TTTSSEEEGGGHHH
T ss_pred EECCCCcCCcchhhhHH
Confidence 45777777777666654
No 89
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=41.41 E-value=7.1 Score=19.36 Aligned_cols=11 Identities=36% Similarity=0.576 Sum_probs=4.9
Q ss_pred ccccccccccc
Q psy10674 14 FCCYECDKKVQ 24 (138)
Q Consensus 14 ~~C~~C~~~i~ 24 (138)
+.|..|++++.
T Consensus 4 ~~C~eC~~~f~ 14 (34)
T PF01286_consen 4 PKCDECGKPFM 14 (34)
T ss_dssp EE-TTT--EES
T ss_pred chHhHhCCHHH
Confidence 45666666665
No 90
>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=40.62 E-value=17 Score=18.98 Aligned_cols=10 Identities=30% Similarity=0.757 Sum_probs=6.6
Q ss_pred cccccCcccc
Q psy10674 82 RCHACDELIF 91 (138)
Q Consensus 82 ~C~~C~~~I~ 91 (138)
.|..|+++|.
T Consensus 2 ~C~~C~~~i~ 11 (46)
T cd02249 2 SCDGCLKPIV 11 (46)
T ss_pred CCcCCCCCCc
Confidence 4777777664
No 91
>KOG2893|consensus
Probab=40.47 E-value=7.3 Score=28.35 Aligned_cols=11 Identities=55% Similarity=1.123 Sum_probs=5.3
Q ss_pred Ccccccccccc
Q psy10674 107 HFCCYECDKEL 117 (138)
Q Consensus 107 CF~C~~C~~~l 117 (138)
+|+|.+|.+.|
T Consensus 34 hfkchichkkl 44 (341)
T KOG2893|consen 34 HFKCHICHKKL 44 (341)
T ss_pred cceeeeehhhh
Confidence 45555554443
No 92
>KOG3579|consensus
Probab=40.31 E-value=14 Score=27.62 Aligned_cols=48 Identities=27% Similarity=0.580 Sum_probs=31.5
Q ss_pred CcccccccccccCCCeEEEeccccCCCCCCcccCcccccCCccccCCceeeeCCeeecH
Q psy10674 13 HFCCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCL 71 (138)
Q Consensus 13 ~~~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~ 71 (138)
.+.|..|++.|++.-|+..- ...-|+-||-|+.= .|.. ....+.+||.
T Consensus 268 pLcCTLC~ERLEDTHFVQCP------SVp~HKFCFPCSRe--sIK~---Qg~sgevYCP 315 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTHFVQCP------SVPSHKFCFPCSRE--SIKQ---QGASGEVYCP 315 (352)
T ss_pred ceeehhhhhhhccCceeecC------CCcccceecccCHH--HHHh---hcCCCceeCC
Confidence 36799999999988777543 22678889987632 2211 1234578885
No 93
>KOG3896|consensus
Probab=39.14 E-value=13 Score=28.54 Aligned_cols=37 Identities=24% Similarity=0.284 Sum_probs=27.8
Q ss_pred CCcccccCcccccCcEEEeCCCccccCCccccccccccC
Q psy10674 80 IPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELC 118 (138)
Q Consensus 80 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~ 118 (138)
+..|..|-+.+...+.. ..+.-..+||.|..|...|+
T Consensus 45 shfCp~CLEn~ps~EAr--lKKn~CAnCfDCP~C~htLS 81 (449)
T KOG3896|consen 45 SHFCPRCLENSPSPEAR--LKKNKCANCFDCPKCAHTLS 81 (449)
T ss_pred cccchhhccCCCchHHH--hhhccccccccCcchhhhhh
Confidence 35888898888654432 34556789999999998887
No 94
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=38.90 E-value=27 Score=19.02 Aligned_cols=25 Identities=20% Similarity=0.238 Sum_probs=15.6
Q ss_pred CcccccCcccccCcEEEeCCCcccc
Q psy10674 81 PRCHACDELIFVNEYTLAENKTFHV 105 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~~~~~~~~H~ 105 (138)
.+|..|++||.....+......-|+
T Consensus 2 ~iCvvCK~Pi~~al~v~T~~Gpvh~ 26 (53)
T PHA02610 2 KICVVCKQPIEKALVVETEKGPVHP 26 (53)
T ss_pred ceeeeeCCchhhceEEecCCCCCCC
Confidence 3788999999554444344455554
No 95
>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=38.74 E-value=12 Score=22.61 Aligned_cols=33 Identities=21% Similarity=0.609 Sum_probs=20.6
Q ss_pred cccccCcccccCc-EEE-eCCCccccCCcccccccccc
Q psy10674 82 RCHACDELIFVNE-YTL-AENKTFHVKHFCCYECDKEL 117 (138)
Q Consensus 82 ~C~~C~~~I~~~~-~~~-~~~~~~H~~CF~C~~C~~~l 117 (138)
.|..|+.+|..+. +.. ..|.. .=|.|..|..+.
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~---~~FCC~GC~~V~ 36 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEE---RPFCCPGCQAVY 36 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCc---cccccHHHHHHH
Confidence 6889999996433 322 44543 336788887653
No 96
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=38.58 E-value=21 Score=16.40 Aligned_cols=9 Identities=22% Similarity=0.818 Sum_probs=5.0
Q ss_pred cccccCccc
Q psy10674 82 RCHACDELI 90 (138)
Q Consensus 82 ~C~~C~~~I 90 (138)
.|+.|+..|
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 455555555
No 97
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=37.86 E-value=35 Score=17.84 Aligned_cols=29 Identities=14% Similarity=0.295 Sum_probs=13.4
Q ss_pred ccccCCc-cccCCceee--eCCeeecHHHHHh
Q psy10674 48 VCSTCDE-LLVDLMYFH--YKGNVYCLRDYAT 76 (138)
Q Consensus 48 ~C~~C~~-~l~~~~~~~--~~~~~yC~~c~~~ 76 (138)
.|..|+. |+.+..|.- -.+--+|+.||.+
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~ 33 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSR 33 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhh
Confidence 3555654 454443321 2233356666544
No 98
>PLN02436 cellulose synthase A
Probab=37.61 E-value=26 Score=31.07 Aligned_cols=44 Identities=14% Similarity=0.246 Sum_probs=26.8
Q ss_pred cccccCCccc----cCCceee--eCCeeecHHHHH--hhcCCCcccccCccc
Q psy10674 47 FVCSTCDELL----VDLMYFH--YKGNVYCLRDYA--TMLDIPRCHACDELI 90 (138)
Q Consensus 47 f~C~~C~~~l----~~~~~~~--~~~~~yC~~c~~--~~~~~~~C~~C~~~I 90 (138)
-.|++|+..+ .+..|.. .=+-+.|+.||+ +.-|...|++|+..-
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y 88 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRY 88 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCch
Confidence 3677777765 2222322 345677888873 334567888888754
No 99
>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=37.49 E-value=20 Score=28.86 Aligned_cols=36 Identities=22% Similarity=0.300 Sum_probs=19.7
Q ss_pred cccccCcccccCcEEEeCCCccccCCccccccccccC
Q psy10674 82 RCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELC 118 (138)
Q Consensus 82 ~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~ 118 (138)
.|+.|-..+...++. +.+..=-.+||.|..|..+|.
T Consensus 28 yCp~CL~~~p~~e~~-~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 28 YCPNCLFEVPSSEAR-SEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred ECccccccCChhhhe-eccceeccccccCCCCCCcce
Confidence 555555555433322 222222337888888888776
No 100
>KOG2462|consensus
Probab=37.47 E-value=12 Score=27.72 Aligned_cols=33 Identities=21% Similarity=0.577 Sum_probs=18.5
Q ss_pred CcccccCcccccCcEE------E-eCCCccccCCccccccccccCC
Q psy10674 81 PRCHACDELIFVNEYT------L-AENKTFHVKHFCCYECDKELCN 119 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~------~-~~~~~~H~~CF~C~~C~~~l~~ 119 (138)
-.|..|++... +.++ . ...+. |.|..|++.|.+
T Consensus 188 c~C~iCGKaFS-RPWLLQGHiRTHTGEKP-----F~C~hC~kAFAD 227 (279)
T KOG2462|consen 188 CECGICGKAFS-RPWLLQGHIRTHTGEKP-----FSCPHCGKAFAD 227 (279)
T ss_pred ccccccccccc-chHHhhcccccccCCCC-----ccCCcccchhcc
Confidence 36777777663 2221 1 22233 668888877764
No 101
>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=36.98 E-value=23 Score=22.21 Aligned_cols=32 Identities=13% Similarity=0.237 Sum_probs=22.9
Q ss_pred CCcccCcccccCCccccCCceeeeCCeeecHHHHHh
Q psy10674 41 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYAT 76 (138)
Q Consensus 41 ~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~ 76 (138)
.+...==.|..| .+..|+.+++.+.|..|-.+
T Consensus 30 ~~~va~daCeiC----~~~GY~q~g~~lvC~~C~~~ 61 (102)
T PF10080_consen 30 SYRVAFDACEIC----GPKGYYQEGDQLVCKNCGVR 61 (102)
T ss_pred CEEEEEEecccc----CCCceEEECCEEEEecCCCE
Confidence 444444468888 35679999999999888643
No 102
>PLN02189 cellulose synthase
Probab=36.83 E-value=27 Score=30.79 Aligned_cols=45 Identities=18% Similarity=0.335 Sum_probs=27.8
Q ss_pred cccccCCcccc----CCceee--eCCeeecHHHHH--hhcCCCcccccCcccc
Q psy10674 47 FVCSTCDELLV----DLMYFH--YKGNVYCLRDYA--TMLDIPRCHACDELIF 91 (138)
Q Consensus 47 f~C~~C~~~l~----~~~~~~--~~~~~yC~~c~~--~~~~~~~C~~C~~~I~ 91 (138)
-.|.+|+..++ +..|.. .=+-+.|+.||+ +.-|...|++|+..-.
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 36778877762 223332 345678888874 3345678888887543
No 103
>PHA02929 N1R/p28-like protein; Provisional
Probab=36.47 E-value=21 Score=25.97 Aligned_cols=38 Identities=21% Similarity=0.473 Sum_probs=22.6
Q ss_pred CcccccCcccccCc-------EEEeCCCccccCCc--------cccccccccC
Q psy10674 81 PRCHACDELIFVNE-------YTLAENKTFHVKHF--------CCYECDKELC 118 (138)
Q Consensus 81 ~~C~~C~~~I~~~~-------~~~~~~~~~H~~CF--------~C~~C~~~l~ 118 (138)
..|+.|...+.+.+ ++..-+..||.+|. .|..|..++.
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 46777777765432 11133566777776 4777776654
No 104
>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=36.36 E-value=34 Score=18.02 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=6.8
Q ss_pred CcccccCccc
Q psy10674 81 PRCHACDELI 90 (138)
Q Consensus 81 ~~C~~C~~~I 90 (138)
..|..|++.|
T Consensus 12 ~~C~~C~~~i 21 (53)
T PF00130_consen 12 TYCDVCGKFI 21 (53)
T ss_dssp EB-TTSSSBE
T ss_pred CCCcccCccc
Confidence 4777888777
No 105
>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=36.02 E-value=14 Score=15.44 Aligned_cols=11 Identities=36% Similarity=0.760 Sum_probs=5.9
Q ss_pred ccccccccccC
Q psy10674 108 FCCYECDKELC 118 (138)
Q Consensus 108 F~C~~C~~~l~ 118 (138)
|.|..|+..+.
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 56777777655
No 106
>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=35.72 E-value=7.7 Score=19.83 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=15.9
Q ss_pred cccccCcccccCc-EEE-eCCCccccCCc
Q psy10674 82 RCHACDELIFVNE-YTL-AENKTFHVKHF 108 (138)
Q Consensus 82 ~C~~C~~~I~~~~-~~~-~~~~~~H~~CF 108 (138)
.|+.|.+.+.+++ ++. .=+..||.+|.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci 30 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCI 30 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHH
Confidence 5778888885433 332 33566666654
No 107
>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=35.12 E-value=24 Score=15.85 Aligned_cols=13 Identities=38% Similarity=0.938 Sum_probs=9.7
Q ss_pred ccccccccccCCC
Q psy10674 108 FCCYECDKELCNQ 120 (138)
Q Consensus 108 F~C~~C~~~l~~~ 120 (138)
|.|..|++.+.+.
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 6688888887743
No 108
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=34.66 E-value=31 Score=30.50 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=12.6
Q ss_pred eeecHHHHH--hhcCCCcccccCccc
Q psy10674 67 NVYCLRDYA--TMLDIPRCHACDELI 90 (138)
Q Consensus 67 ~~yC~~c~~--~~~~~~~C~~C~~~I 90 (138)
-+.|+.||+ +.-|...|++|+.+-
T Consensus 42 fpvCr~cyeye~~~g~~~cp~c~t~y 67 (1044)
T PLN02915 42 FPVCKPCYEYERSEGNQCCPQCNTRY 67 (1044)
T ss_pred CccccchhhhhhhcCCccCCccCCch
Confidence 345555552 333455677776543
No 109
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.51 E-value=23 Score=26.35 Aligned_cols=11 Identities=27% Similarity=0.588 Sum_probs=9.7
Q ss_pred CcccccCcccc
Q psy10674 81 PRCHACDELIF 91 (138)
Q Consensus 81 ~~C~~C~~~I~ 91 (138)
+.|..|+.+|.
T Consensus 246 epC~~CGt~I~ 256 (273)
T COG0266 246 EPCRRCGTPIE 256 (273)
T ss_pred CCCCccCCEeE
Confidence 68999999994
No 110
>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=34.46 E-value=23 Score=18.93 Aligned_cols=10 Identities=30% Similarity=0.750 Sum_probs=6.2
Q ss_pred cccccCc-ccc
Q psy10674 82 RCHACDE-LIF 91 (138)
Q Consensus 82 ~C~~C~~-~I~ 91 (138)
.|..|+. +|.
T Consensus 2 ~Cd~C~~~pI~ 12 (48)
T cd02341 2 KCDSCGIEPIP 12 (48)
T ss_pred CCCCCCCCccc
Confidence 4667776 664
No 111
>KOG4443|consensus
Probab=34.32 E-value=23 Score=29.51 Aligned_cols=22 Identities=23% Similarity=0.338 Sum_probs=17.9
Q ss_pred eCCCccccCCccccccccccCC
Q psy10674 98 AENKTFHVKHFCCYECDKELCN 119 (138)
Q Consensus 98 ~~~~~~H~~CF~C~~C~~~l~~ 119 (138)
..+..+-++|++|..|+..|.|
T Consensus 106 ~sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 106 PSGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred cCcccccHHHHhhhhccccccc
Confidence 4677778888999999888876
No 112
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=33.29 E-value=14 Score=16.08 Aligned_cols=12 Identities=33% Similarity=0.905 Sum_probs=8.6
Q ss_pred ccccccccccCC
Q psy10674 108 FCCYECDKELCN 119 (138)
Q Consensus 108 F~C~~C~~~l~~ 119 (138)
|.|..|++.+.+
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 568888877764
No 113
>PF14149 YhfH: YhfH-like protein
Probab=32.71 E-value=14 Score=18.68 Aligned_cols=19 Identities=21% Similarity=0.398 Sum_probs=13.6
Q ss_pred HHhhcCCCcccccCccccc
Q psy10674 74 YATMLDIPRCHACDELIFV 92 (138)
Q Consensus 74 ~~~~~~~~~C~~C~~~I~~ 92 (138)
|.+.+....|..|++.|..
T Consensus 7 FfrnLp~K~C~~CG~~i~E 25 (37)
T PF14149_consen 7 FFRNLPPKKCTECGKEIEE 25 (37)
T ss_pred HHHhCCCcccHHHHHHHHH
Confidence 4444556799999999853
No 114
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=32.11 E-value=34 Score=30.12 Aligned_cols=30 Identities=20% Similarity=0.310 Sum_probs=20.6
Q ss_pred CCcccccCcccccCcEEEe--------CC---CccccCCcc
Q psy10674 80 IPRCHACDELIFVNEYTLA--------EN---KTFHVKHFC 109 (138)
Q Consensus 80 ~~~C~~C~~~I~~~~~~~~--------~~---~~~H~~CF~ 109 (138)
...|.+|++.|.-+++-.+ .| ..||..||.
T Consensus 17 Rs~Ck~C~~~I~K~~lRi~~~v~~~~~dg~~~~W~H~~Cf~ 57 (981)
T PLN03123 17 RSSCKTCKSPIDKDELRLGKMVQSTQFDGFMPMWNHASCIL 57 (981)
T ss_pred CccccccCCcccCCCeEEEEeecccccCCCCCeeecccccc
Confidence 4589999999976653321 13 467889986
No 115
>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=31.35 E-value=29 Score=27.99 Aligned_cols=39 Identities=23% Similarity=0.419 Sum_probs=26.5
Q ss_pred ccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcc
Q psy10674 48 VCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDEL 89 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~ 89 (138)
+|..|+.+| .|....+.+.|..|-.+..-...|+.|+..
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 456666666 355567788898887554323689999874
No 116
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.03 E-value=22 Score=19.20 Aligned_cols=10 Identities=20% Similarity=0.733 Sum_probs=7.2
Q ss_pred CcccccCccc
Q psy10674 81 PRCHACDELI 90 (138)
Q Consensus 81 ~~C~~C~~~I 90 (138)
-+|..|+..+
T Consensus 7 Y~C~~Cg~~~ 16 (49)
T COG1996 7 YKCARCGREV 16 (49)
T ss_pred EEhhhcCCee
Confidence 3677777777
No 117
>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=31.01 E-value=26 Score=23.24 Aligned_cols=14 Identities=14% Similarity=0.619 Sum_probs=7.6
Q ss_pred cccCcccccCCccc
Q psy10674 43 HPQCFVCSTCDELL 56 (138)
Q Consensus 43 H~~Cf~C~~C~~~l 56 (138)
+.+-+.|..|++..
T Consensus 121 ~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 121 YDEFWRCPGCGKIY 134 (147)
T ss_pred CCeEEECCCCCCEe
Confidence 33445666666544
No 118
>PRK11595 DNA utilization protein GntX; Provisional
Probab=30.95 E-value=50 Score=23.53 Aligned_cols=37 Identities=16% Similarity=0.175 Sum_probs=21.7
Q ss_pred ccccCCccccCCceeeeCCeeecHHHHHhhcC-CCcccccCccc
Q psy10674 48 VCSTCDELLVDLMYFHYKGNVYCLRDYATMLD-IPRCHACDELI 90 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~-~~~C~~C~~~I 90 (138)
.|..|+.++... ...+|..|..++.. .+.|..|+.++
T Consensus 7 ~C~~C~~~~~~~------~~~lC~~C~~~l~~~~~~C~~Cg~~~ 44 (227)
T PRK11595 7 LCWLCRMPLALS------HWGICSVCSRALRTLKTCCPQCGLPA 44 (227)
T ss_pred cCccCCCccCCC------CCcccHHHHhhCCcccCcCccCCCcC
Confidence 356676666321 12378888765421 24688888775
No 119
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=30.90 E-value=9.7 Score=19.57 Aligned_cols=10 Identities=20% Similarity=0.863 Sum_probs=5.9
Q ss_pred cccccCCccc
Q psy10674 47 FVCSTCDELL 56 (138)
Q Consensus 47 f~C~~C~~~l 56 (138)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 5566666544
No 120
>PHA02768 hypothetical protein; Provisional
Probab=30.47 E-value=10 Score=20.97 Aligned_cols=12 Identities=8% Similarity=0.177 Sum_probs=5.8
Q ss_pred CccccccccccC
Q psy10674 107 HFCCYECDKELC 118 (138)
Q Consensus 107 CF~C~~C~~~l~ 118 (138)
=++|..|++.+.
T Consensus 31 ~~kc~~C~k~f~ 42 (55)
T PHA02768 31 NLKLSNCKRISL 42 (55)
T ss_pred cccCCcccceec
Confidence 345555555433
No 121
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=30.44 E-value=16 Score=19.88 Aligned_cols=28 Identities=21% Similarity=0.412 Sum_probs=13.1
Q ss_pred cccccCcccccCcEE-EeCCCccccCCccc
Q psy10674 82 RCHACDELIFVNEYT-LAENKTFHVKHFCC 110 (138)
Q Consensus 82 ~C~~C~~~I~~~~~~-~~~~~~~H~~CF~C 110 (138)
.|+.|+.+|.- .+- ...++.|-.+|-.|
T Consensus 2 ~CPyCge~~~~-~iD~s~~~Q~yiEDC~vC 30 (52)
T PF14255_consen 2 QCPYCGEPIEI-LIDPSAGDQEYIEDCQVC 30 (52)
T ss_pred CCCCCCCeeEE-EEecCCCCeeEEeehhhc
Confidence 36666666631 111 13345566565444
No 122
>KOG2186|consensus
Probab=30.11 E-value=11 Score=27.63 Aligned_cols=42 Identities=19% Similarity=0.472 Sum_probs=27.3
Q ss_pred cccccccccccCCCeEEEeccccCCCCCCcccCcccccCCccccCCcee
Q psy10674 14 FCCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYF 62 (138)
Q Consensus 14 ~~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~ 62 (138)
|+|..|+..+.-..+--... ..|..+|.|..|++.+.+..|.
T Consensus 4 FtCnvCgEsvKKp~vekH~s-------rCrn~~fSCIDC~k~F~~~sYk 45 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHMS-------RCRNAYFSCIDCGKTFERVSYK 45 (276)
T ss_pred EehhhhhhhccccchHHHHH-------hccCCeeEEeecccccccchhh
Confidence 78888988876322211111 3466789999999988665443
No 123
>PRK01343 zinc-binding protein; Provisional
Probab=29.88 E-value=36 Score=18.96 Aligned_cols=10 Identities=20% Similarity=0.577 Sum_probs=7.2
Q ss_pred CcccccCccc
Q psy10674 81 PRCHACDELI 90 (138)
Q Consensus 81 ~~C~~C~~~I 90 (138)
.+|..|+++.
T Consensus 10 ~~CP~C~k~~ 19 (57)
T PRK01343 10 RPCPECGKPS 19 (57)
T ss_pred CcCCCCCCcC
Confidence 4677787765
No 124
>PRK14873 primosome assembly protein PriA; Provisional
Probab=29.75 E-value=28 Score=29.22 Aligned_cols=39 Identities=21% Similarity=0.198 Sum_probs=26.1
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcc
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDEL 89 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~ 89 (138)
++|..|+.+|. |....+.+.|..|-.... ...|..|+..
T Consensus 393 ~~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~-p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLG---LPSAGGTPRCRWCGRAAP-DWRCPRCGSD 431 (665)
T ss_pred eECCCCCCcee---EecCCCeeECCCCcCCCc-CccCCCCcCC
Confidence 34666766663 444566788888866554 4689999875
No 125
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=29.74 E-value=38 Score=22.18 Aligned_cols=33 Identities=21% Similarity=0.432 Sum_probs=22.1
Q ss_pred CcccccCcccccCc---EEEeCCCccccCCccccccccc
Q psy10674 81 PRCHACDELIFVNE---YTLAENKTFHVKHFCCYECDKE 116 (138)
Q Consensus 81 ~~C~~C~~~I~~~~---~~~~~~~~~H~~CF~C~~C~~~ 116 (138)
..|.-|+.+|.++. +|...|+.|+ |.=++|.+.
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~---FcssKC~k~ 40 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLH---FVDSKCEKN 40 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEE---EecHHHHHH
Confidence 57999999998875 4546678777 333345433
No 126
>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=29.62 E-value=41 Score=15.74 Aligned_cols=11 Identities=18% Similarity=0.633 Sum_probs=4.8
Q ss_pred cccccccccCC
Q psy10674 109 CCYECDKELCN 119 (138)
Q Consensus 109 ~C~~C~~~l~~ 119 (138)
.|..|.+.+.+
T Consensus 2 ~C~~C~~~~~~ 12 (30)
T PF03107_consen 2 WCDVCRRKIDG 12 (30)
T ss_pred CCCCCCCCcCC
Confidence 34444444443
No 127
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=29.28 E-value=45 Score=19.14 Aligned_cols=9 Identities=44% Similarity=1.051 Sum_probs=5.6
Q ss_pred ccccCCccc
Q psy10674 48 VCSTCDELL 56 (138)
Q Consensus 48 ~C~~C~~~l 56 (138)
+|+-|+..+
T Consensus 5 ~CsFcG~~I 13 (66)
T COG2075 5 VCSFCGKKI 13 (66)
T ss_pred EecCcCCcc
Confidence 456666666
No 128
>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=29.16 E-value=48 Score=16.72 Aligned_cols=30 Identities=23% Similarity=0.389 Sum_probs=12.9
Q ss_pred CcccccCcccccCcEEEeCCCccccCCcccccccc
Q psy10674 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDK 115 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~ 115 (138)
.+|..|+--|-+-..+...++.| +|..|+.
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 47777777775543333444554 4666654
No 129
>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=29.04 E-value=39 Score=18.57 Aligned_cols=24 Identities=25% Similarity=0.629 Sum_probs=16.8
Q ss_pred CcccccCcccccCc---EEEeCCCccc
Q psy10674 81 PRCHACDELIFVNE---YTLAENKTFH 104 (138)
Q Consensus 81 ~~C~~C~~~I~~~~---~~~~~~~~~H 104 (138)
..|.-|+..|.++. ++...|+.++
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEE
Confidence 57888888888764 4446666665
No 130
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=29.02 E-value=22 Score=29.97 Aligned_cols=85 Identities=20% Similarity=0.425 Sum_probs=52.9
Q ss_pred CcCCcccccccccccCCCeEEEeccccCCCCCCcccCcccccCCccccCCceeeeCCeeecHHHH-HhhcCCCcccccCc
Q psy10674 10 HVKHFCCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY-ATMLDIPRCHACDE 88 (138)
Q Consensus 10 h~~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~-~~~~~~~~C~~C~~ 88 (138)
-|+-.+|..|-+.|.+. .++.|+=---.|..|+-. |...+..||=+..- ...| +.|..|.+
T Consensus 98 ~pD~a~C~~Cl~Ei~dp-----------~~rrY~YPF~~CT~CGPR-----fTIi~alPYDR~nTsM~~F--~lC~~C~~ 159 (750)
T COG0068 98 PPDAATCEDCLEEIFDP-----------NSRRYLYPFINCTNCGPR-----FTIIEALPYDRENTSMADF--PLCPFCDK 159 (750)
T ss_pred CCchhhhHHHHHHhcCC-----------CCcceeccccccCCCCcc-----eeeeccCCCCcccCccccC--cCCHHHHH
Confidence 45667788887777532 233566665678999654 33333344322211 1223 67887775
Q ss_pred ccccCcEEEeCCCccccCCcccccccccc
Q psy10674 89 LIFVNEYTLAENKTFHVKHFCCYECDKEL 117 (138)
Q Consensus 89 ~I~~~~~~~~~~~~~H~~CF~C~~C~~~l 117 (138)
++....++.||..=..|..|+-.+
T Consensus 160 -----EY~dP~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 160 -----EYKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred -----HhcCccccccccccccCcccCCCe
Confidence 234478899999999999998754
No 131
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=29.00 E-value=11 Score=18.73 Aligned_cols=10 Identities=20% Similarity=0.916 Sum_probs=5.8
Q ss_pred cccccCCccc
Q psy10674 47 FVCSTCDELL 56 (138)
Q Consensus 47 f~C~~C~~~l 56 (138)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (41)
T smart00834 6 YRCEDCGHTF 15 (41)
T ss_pred EEcCCCCCEE
Confidence 4566666544
No 132
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=28.88 E-value=27 Score=17.33 Aligned_cols=18 Identities=22% Similarity=0.510 Sum_probs=9.1
Q ss_pred CCCCcccCcccccCCccc
Q psy10674 39 EVLWHPQCFVCSTCDELL 56 (138)
Q Consensus 39 ~~~~H~~Cf~C~~C~~~l 56 (138)
++.||-.=..|..|+=.+
T Consensus 14 ~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 14 NRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp STTTT-TT--BTTCC-SC
T ss_pred CCcccCcCccCCCCCCCE
Confidence 446777777777776544
No 133
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=28.77 E-value=13 Score=24.74 Aligned_cols=35 Identities=23% Similarity=0.381 Sum_probs=23.1
Q ss_pred CcccccCcccccCcEEEeCCCccccCCccccccccccC
Q psy10674 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELC 118 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~ 118 (138)
-.|+.|+......+.+...+. ..=|.|..|+.+|.
T Consensus 100 Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 100 YKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred EECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 379999987765544322221 33499999998875
No 134
>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=28.70 E-value=19 Score=16.00 Aligned_cols=12 Identities=42% Similarity=0.944 Sum_probs=8.4
Q ss_pred ccccccccccCC
Q psy10674 108 FCCYECDKELCN 119 (138)
Q Consensus 108 F~C~~C~~~l~~ 119 (138)
|.|..|++.+..
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 568888877663
No 135
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=28.40 E-value=54 Score=17.24 Aligned_cols=10 Identities=20% Similarity=0.404 Sum_probs=5.9
Q ss_pred eeecHHHHHh
Q psy10674 67 NVYCLRDYAT 76 (138)
Q Consensus 67 ~~yC~~c~~~ 76 (138)
--+|+.||..
T Consensus 24 yDLC~~Cf~~ 33 (45)
T cd02344 24 FDFCENCFKT 33 (45)
T ss_pred ccchHHhhCC
Confidence 4466666654
No 136
>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=27.85 E-value=17 Score=22.19 Aligned_cols=37 Identities=22% Similarity=0.297 Sum_probs=19.6
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCccccc
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFV 92 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~ 92 (138)
-.|..|+++|.-..-.. .=. |.-.. -+|..|+++|..
T Consensus 34 S~C~~C~~~L~~~~lIP-----i~S--~l~lr--GrCr~C~~~I~~ 70 (92)
T PF06750_consen 34 SHCPHCGHPLSWWDLIP-----ILS--YLLLR--GRCRYCGAPIPP 70 (92)
T ss_pred CcCcCCCCcCcccccch-----HHH--HHHhC--CCCcccCCCCCh
Confidence 45777777774322111 111 33333 378888888753
No 137
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.84 E-value=92 Score=18.28 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=27.7
Q ss_pred ccccCCccccCCc---eeeeCCeeecHHHHHhhcCCCcccccCcccccC
Q psy10674 48 VCSTCDELLVDLM---YFHYKGNVYCLRDYATMLDIPRCHACDELIFVN 93 (138)
Q Consensus 48 ~C~~C~~~l~~~~---~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~ 93 (138)
.|.-|.+.|.... ..-.-.--+|.+|...+++ ..|.-|+..+...
T Consensus 7 nCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~-g~CPnCGGelv~R 54 (84)
T COG3813 7 NCECCDRDLPPDSTDARICTFECTFCADCAENRLH-GLCPNCGGELVAR 54 (84)
T ss_pred CCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc-CcCCCCCchhhcC
Confidence 3555667663321 1112334578889887775 6999999866543
No 138
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=27.71 E-value=82 Score=16.60 Aligned_cols=7 Identities=14% Similarity=0.264 Sum_probs=2.7
Q ss_pred ccCCccc
Q psy10674 50 STCDELL 56 (138)
Q Consensus 50 ~~C~~~l 56 (138)
..|+++.
T Consensus 3 iiC~~~~ 9 (46)
T PF10764_consen 3 IICGKEK 9 (46)
T ss_pred EeCCCcC
Confidence 3344433
No 139
>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=26.91 E-value=11 Score=17.83 Aligned_cols=16 Identities=38% Similarity=0.968 Sum_probs=11.3
Q ss_pred ccccccccccCCCCee
Q psy10674 108 FCCYECDKELCNQSYI 123 (138)
Q Consensus 108 F~C~~C~~~l~~~~f~ 123 (138)
|.|..|.+.+.+..|.
T Consensus 1 ~sCiDC~~~F~~~~y~ 16 (28)
T PF08790_consen 1 FSCIDCSKDFDGDSYK 16 (28)
T ss_dssp EEETTTTEEEEGGGTT
T ss_pred CeeecCCCCcCcCCcC
Confidence 5688888888765553
No 140
>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=26.87 E-value=39 Score=17.42 Aligned_cols=20 Identities=25% Similarity=0.687 Sum_probs=12.7
Q ss_pred cccccCcccccCcEEEeCCCccccCCccccccc
Q psy10674 82 RCHACDELIFVNEYTLAENKTFHVKHFCCYECD 114 (138)
Q Consensus 82 ~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~ 114 (138)
.|.+|+++|.+. -|+|..|.
T Consensus 2 ~Cd~C~~~i~G~-------------ry~C~~C~ 21 (43)
T cd02340 2 ICDGCQGPIVGV-------------RYKCLVCP 21 (43)
T ss_pred CCCCCCCcCcCC-------------eEECCCCC
Confidence 577777766431 26777774
No 141
>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=26.75 E-value=80 Score=23.97 Aligned_cols=29 Identities=21% Similarity=0.444 Sum_probs=19.4
Q ss_pred CeeecHHHHHhhc--CCCcccccCcccccCc
Q psy10674 66 GNVYCLRDYATML--DIPRCHACDELIFVNE 94 (138)
Q Consensus 66 ~~~yC~~c~~~~~--~~~~C~~C~~~I~~~~ 94 (138)
|-.+|..|....+ +...|+.|+.++....
T Consensus 27 GH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 27 GHTLCESCVDLLFVRGSGSCPECDTPLRKNN 57 (309)
T ss_pred CCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence 4557777776644 2347999998886543
No 142
>PF09360 zf-CDGSH: Iron-binding zinc finger CDGSH type; InterPro: IPR018967 This entry represents iron-sulphur domain containing proteins that have a CDGSH sequence motif (although the Ser residue can also be an Ala or Thr), and is found in proteins from a wide range of organisms with the exception of fungi. The CDGSH-type domain binds a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family []. CDGSH-type domains are found in mitoNEET, an iron-containing integral protein of the outer mitochondrian membrane (OMM). MitoNEET forms a dimeric structure with a NEET fold, and contains two domains: a beta-cap region and a cluster-binding domain that coordinated two acid-labile 2Fe-2S clusters (one bound to each protomer) []. The CDGSH iron-sulphur domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, (IPR019610 from INTERPRO) [, ]. The whole protein regulates oxidative capacity and may function in electron transfer, for instance in redox reactions with metabolic intermediates, cofactors and/or proteins localized at the OMM. ; GO: 0051537 2 iron, 2 sulfur cluster binding, 0043231 intracellular membrane-bounded organelle; PDB: 3TBO_A 3FNV_B 3TBM_B 3TBN_A 3S2R_A 3S2Q_A 3LPQ_A 2QH7_A 3EW0_A 2R13_A ....
Probab=26.64 E-value=31 Score=17.36 Aligned_cols=7 Identities=29% Similarity=0.415 Sum_probs=3.8
Q ss_pred CCCccCC
Q psy10674 128 SRPGQDS 134 (138)
Q Consensus 128 ~~~y~~~ 134 (138)
++||||-
T Consensus 29 ~~PfCDG 35 (38)
T PF09360_consen 29 NKPFCDG 35 (38)
T ss_dssp TTTB--S
T ss_pred CCCccCC
Confidence 7888874
No 143
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=26.47 E-value=54 Score=17.38 Aligned_cols=9 Identities=22% Similarity=0.478 Sum_probs=5.1
Q ss_pred eecHHHHHh
Q psy10674 68 VYCLRDYAT 76 (138)
Q Consensus 68 ~yC~~c~~~ 76 (138)
-+|..||..
T Consensus 25 dlC~~Cf~~ 33 (49)
T cd02338 25 DLCADCYDS 33 (49)
T ss_pred ccchhHHhC
Confidence 356666653
No 144
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=26.39 E-value=8.4 Score=21.05 Aligned_cols=11 Identities=18% Similarity=0.483 Sum_probs=4.9
Q ss_pred cccccCccccc
Q psy10674 82 RCHACDELIFV 92 (138)
Q Consensus 82 ~C~~C~~~I~~ 92 (138)
.|.+|+-.|.+
T Consensus 24 ~C~gC~~~l~~ 34 (56)
T PF02591_consen 24 TCSGCHMELPP 34 (56)
T ss_pred ccCCCCEEcCH
Confidence 44444444433
No 145
>KOG2114|consensus
Probab=25.77 E-value=29 Score=29.88 Aligned_cols=36 Identities=22% Similarity=0.545 Sum_probs=23.5
Q ss_pred CcccccCcccccCcEEE-eCCCccccCCcc-----cccccccc
Q psy10674 81 PRCHACDELIFVNEYTL-AENKTFHVKHFC-----CYECDKEL 117 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~~-~~~~~~H~~CF~-----C~~C~~~l 117 (138)
.+|..|..++ +-.+|. .-+..||.+||. |.+|...+
T Consensus 841 skCs~C~~~L-dlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 841 SKCSACEGTL-DLPFVHFLCGHSYHQHCLEDKEDKCPKCLPEL 882 (933)
T ss_pred eeecccCCcc-ccceeeeecccHHHHHhhccCcccCCccchhh
Confidence 3788888777 334444 347778888876 77776543
No 146
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=25.72 E-value=16 Score=25.20 Aligned_cols=32 Identities=31% Similarity=0.743 Sum_probs=20.2
Q ss_pred CCcccccccccccCCCeEEEeccccCCCCCCcccCcccccCCcccc
Q psy10674 12 KHFCCYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLV 57 (138)
Q Consensus 12 ~~~~C~~C~~~i~~~~~~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 57 (138)
.-+.|..|+..+...+.. + .-|.|..|+.+|.
T Consensus 116 ~~Y~Cp~C~~rytf~eA~---------~-----~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAM---------E-----YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHh---------h-----cCCcCCCCCCCCe
Confidence 346788887665533221 1 1389999999884
No 147
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=25.61 E-value=49 Score=23.26 Aligned_cols=29 Identities=24% Similarity=0.434 Sum_probs=16.2
Q ss_pred CcccccCc--ccccCc---EEE--eCCCccccCCcc
Q psy10674 81 PRCHACDE--LIFVNE---YTL--AENKTFHVKHFC 109 (138)
Q Consensus 81 ~~C~~C~~--~I~~~~---~~~--~~~~~~H~~CF~ 109 (138)
..|..|+. .|.+=+ .+. .=+..||.+||.
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~ 188 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR 188 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC
Confidence 47888874 343311 222 225667888776
No 148
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=24.79 E-value=32 Score=19.30 Aligned_cols=16 Identities=25% Similarity=0.488 Sum_probs=11.4
Q ss_pred CcccccCcccccCcEE
Q psy10674 81 PRCHACDELIFVNEYT 96 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~ 96 (138)
..|..|+++|..++.+
T Consensus 9 ~HC~VCg~aIp~de~~ 24 (64)
T COG4068 9 RHCVVCGKAIPPDEQV 24 (64)
T ss_pred ccccccCCcCCCccch
Confidence 4788888888766543
No 149
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=24.51 E-value=29 Score=18.00 Aligned_cols=29 Identities=21% Similarity=0.528 Sum_probs=17.8
Q ss_pred CcccccCcccccCcEEEeCCCccccCCccccccccccC
Q psy10674 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELC 118 (138)
Q Consensus 81 ~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~ 118 (138)
-+|..|+..+...+.. . =++|..|+.++.
T Consensus 4 y~C~~CG~~~~~~~~~----~-----~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYG----T-----GVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCC----C-----ceECCCCCCeEE
Confidence 3789999877432211 1 256888876543
No 150
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.50 E-value=77 Score=19.32 Aligned_cols=37 Identities=19% Similarity=0.496 Sum_probs=26.1
Q ss_pred CCcccccCcccccCcEEEeCCCccccCCccccccccccCCCCeeec
Q psy10674 80 IPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPV 125 (138)
Q Consensus 80 ~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~~~~f~~~ 125 (138)
...|+.|+++.... .....| .|..|+..+.|..|...
T Consensus 35 ~~~Cp~C~~~~VkR----~a~GIW-----~C~kCg~~fAGgay~P~ 71 (89)
T COG1997 35 KHVCPFCGRTTVKR----IATGIW-----KCRKCGAKFAGGAYTPV 71 (89)
T ss_pred CCcCCCCCCcceee----eccCeE-----EcCCCCCeecccccccc
Confidence 36999999986432 333444 48999999998877653
No 151
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=24.01 E-value=74 Score=16.98 Aligned_cols=10 Identities=10% Similarity=0.218 Sum_probs=5.9
Q ss_pred eeecHHHHHh
Q psy10674 67 NVYCLRDYAT 76 (138)
Q Consensus 67 ~~yC~~c~~~ 76 (138)
--+|..||..
T Consensus 24 ~DLC~~Cf~~ 33 (49)
T cd02334 24 YDLCQSCFFS 33 (49)
T ss_pred cCchHHHHhC
Confidence 3466667654
No 152
>KOG1244|consensus
Probab=23.86 E-value=66 Score=24.05 Aligned_cols=10 Identities=10% Similarity=0.155 Sum_probs=5.6
Q ss_pred CCeeecHHHH
Q psy10674 65 KGNVYCLRDY 74 (138)
Q Consensus 65 ~~~~yC~~c~ 74 (138)
|..++|.+|-
T Consensus 294 dqllfcddcd 303 (336)
T KOG1244|consen 294 DQLLFCDDCD 303 (336)
T ss_pred ceeEeecccC
Confidence 4455666653
No 153
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=23.86 E-value=45 Score=28.43 Aligned_cols=40 Identities=20% Similarity=0.319 Sum_probs=28.2
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcc
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDEL 89 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~ 89 (138)
++|..|+.+| .+....+.+.|..|-.+..-...|+.|+..
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 5677787776 355566888898887653324689999876
No 154
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=23.64 E-value=41 Score=18.85 Aligned_cols=13 Identities=23% Similarity=0.554 Sum_probs=9.5
Q ss_pred CcccccCcccccC
Q psy10674 81 PRCHACDELIFVN 93 (138)
Q Consensus 81 ~~C~~C~~~I~~~ 93 (138)
..|..|+++|.++
T Consensus 4 kHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 4 KHCPVCGKPIPPD 16 (59)
T ss_pred CcCCcCCCcCCcc
Confidence 4688888888654
No 155
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=23.59 E-value=30 Score=18.08 Aligned_cols=10 Identities=20% Similarity=0.873 Sum_probs=5.1
Q ss_pred cccccCCccc
Q psy10674 47 FVCSTCDELL 56 (138)
Q Consensus 47 f~C~~C~~~l 56 (138)
+.|..|+..+
T Consensus 3 Y~C~~Cg~~~ 12 (44)
T smart00659 3 YICGECGREN 12 (44)
T ss_pred EECCCCCCEe
Confidence 3455555543
No 156
>PRK12495 hypothetical protein; Provisional
Probab=23.12 E-value=33 Score=24.64 Aligned_cols=11 Identities=18% Similarity=0.682 Sum_probs=7.7
Q ss_pred cccccCCcccc
Q psy10674 47 FVCSTCDELLV 57 (138)
Q Consensus 47 f~C~~C~~~l~ 57 (138)
+.|..|+.+|.
T Consensus 43 ~hC~~CG~PIp 53 (226)
T PRK12495 43 AHCDECGDPIF 53 (226)
T ss_pred hhcccccCccc
Confidence 56777877774
No 157
>KOG1734|consensus
Probab=23.06 E-value=21 Score=26.53 Aligned_cols=14 Identities=29% Similarity=0.676 Sum_probs=8.3
Q ss_pred cccCcccccCCccc
Q psy10674 43 HPQCFVCSTCDELL 56 (138)
Q Consensus 43 H~~Cf~C~~C~~~l 56 (138)
|.+=-.|..|++++
T Consensus 221 hl~d~vCaVCg~~~ 234 (328)
T KOG1734|consen 221 HLSDSVCAVCGQQI 234 (328)
T ss_pred CCCcchhHhhcchh
Confidence 44445666666666
No 158
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.04 E-value=68 Score=29.17 Aligned_cols=54 Identities=20% Similarity=0.356 Sum_probs=27.7
Q ss_pred cccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcccccCcEEEeCCCccccCCccccccccccCC
Q psy10674 47 FVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCN 119 (138)
Q Consensus 47 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~CF~C~~C~~~l~~ 119 (138)
++|..|+..... .+|..|-........|..|+..+...+-. .. .|..|+.++..
T Consensus 668 rkCPkCG~~t~~---------~fCP~CGs~te~vy~CPsCGaev~~des~----a~------~CP~CGtplv~ 721 (1337)
T PRK14714 668 RRCPSCGTETYE---------NRCPDCGTHTEPVYVCPDCGAEVPPDESG----RV------ECPRCDVELTP 721 (1337)
T ss_pred EECCCCCCcccc---------ccCcccCCcCCCceeCccCCCccCCCccc----cc------cCCCCCCcccc
Confidence 667777664321 15666644332113577777766443211 11 26677777653
No 159
>smart00355 ZnF_C2H2 zinc finger.
Probab=23.01 E-value=43 Score=13.89 Aligned_cols=12 Identities=33% Similarity=0.775 Sum_probs=7.7
Q ss_pred ccccccccccCC
Q psy10674 108 FCCYECDKELCN 119 (138)
Q Consensus 108 F~C~~C~~~l~~ 119 (138)
|.|..|++.+..
T Consensus 1 ~~C~~C~~~f~~ 12 (26)
T smart00355 1 YRCPECGKVFKS 12 (26)
T ss_pred CCCCCCcchhCC
Confidence 457777776653
No 160
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=22.93 E-value=39 Score=19.71 Aligned_cols=24 Identities=21% Similarity=0.433 Sum_probs=13.3
Q ss_pred CcccccCcccccCc---EEEeCCCccc
Q psy10674 81 PRCHACDELIFVNE---YTLAENKTFH 104 (138)
Q Consensus 81 ~~C~~C~~~I~~~~---~~~~~~~~~H 104 (138)
..|.-|+..|.++. +|...|+.++
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr~DG~v~~ 30 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVRNDGKVFY 30 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE-TTS-EEE
T ss_pred EEecccCCccCCCCCeEEEecCCCeEE
Confidence 57888888888775 4445666665
No 161
>COG3369 Zinc finger domain containing protein (CDGSH-type) [Function unknown]
Probab=22.90 E-value=41 Score=19.94 Aligned_cols=7 Identities=29% Similarity=0.415 Sum_probs=6.0
Q ss_pred CCCccCC
Q psy10674 128 SRPGQDS 134 (138)
Q Consensus 128 ~~~y~~~ 134 (138)
++||||-
T Consensus 41 NKPfCDG 47 (78)
T COG3369 41 NKPFCDG 47 (78)
T ss_pred CCCccCC
Confidence 8999984
No 162
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=22.69 E-value=1e+02 Score=20.78 Aligned_cols=26 Identities=15% Similarity=0.290 Sum_probs=17.5
Q ss_pred cccCCccccCCceee-eCC--eeecHHHH
Q psy10674 49 CSTCDELLVDLMYFH-YKG--NVYCLRDY 74 (138)
Q Consensus 49 C~~C~~~l~~~~~~~-~~~--~~yC~~c~ 74 (138)
|..|++++.+..+.+ .+| ...|..|+
T Consensus 3 CEiCG~~i~~~~~~v~iega~l~vC~~C~ 31 (154)
T TIGR00270 3 CEICGRKIKGKGFKIVIEGSEMTVCGECR 31 (154)
T ss_pred cccCCCccCCCCeEEEEcCeEEehhhhHH
Confidence 788888887765543 344 34778887
No 163
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=22.61 E-value=34 Score=18.57 Aligned_cols=8 Identities=25% Similarity=1.007 Sum_probs=3.1
Q ss_pred ccccCccc
Q psy10674 83 CHACDELI 90 (138)
Q Consensus 83 C~~C~~~I 90 (138)
|.+|.+++
T Consensus 2 CfgC~~~~ 9 (51)
T PF07975_consen 2 CFGCQKPF 9 (51)
T ss_dssp ETTTTEE-
T ss_pred CccCCCCC
Confidence 34444444
No 164
>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=22.06 E-value=29 Score=15.60 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=5.3
Q ss_pred cccccccccc
Q psy10674 108 FCCYECDKEL 117 (138)
Q Consensus 108 F~C~~C~~~l 117 (138)
|.|..|++.+
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 4566665543
No 165
>KOG4739|consensus
Probab=21.98 E-value=60 Score=23.55 Aligned_cols=34 Identities=18% Similarity=0.300 Sum_probs=23.5
Q ss_pred CCceee-eCCeeecHHHHHhhcCCCcccccCccccc
Q psy10674 58 DLMYFH-YKGNVYCLRDYATMLDIPRCHACDELIFV 92 (138)
Q Consensus 58 ~~~~~~-~~~~~yC~~c~~~~~~~~~C~~C~~~I~~ 92 (138)
...|+. -=.-++|..|.....+ +.|..|+++|..
T Consensus 15 ~~~f~LTaC~HvfC~~C~k~~~~-~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 15 QDPFFLTACRHVFCEPCLKASSP-DVCPLCKKSIRI 49 (233)
T ss_pred CCceeeeechhhhhhhhcccCCc-cccccccceeee
Confidence 334544 4567888888766653 599999999754
No 166
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=21.79 E-value=38 Score=21.69 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=4.1
Q ss_pred ccccccccC
Q psy10674 110 CYECDKELC 118 (138)
Q Consensus 110 C~~C~~~l~ 118 (138)
|..|++.+.
T Consensus 15 C~~C~t~i~ 23 (113)
T PF09862_consen 15 CPSCGTEIE 23 (113)
T ss_pred cCCCCCEEE
Confidence 444444443
No 167
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=21.71 E-value=73 Score=16.88 Aligned_cols=9 Identities=33% Similarity=0.696 Sum_probs=5.1
Q ss_pred eecHHHHHh
Q psy10674 68 VYCLRDYAT 76 (138)
Q Consensus 68 ~yC~~c~~~ 76 (138)
-+|..||..
T Consensus 25 dLC~~Cf~~ 33 (49)
T cd02345 25 SLCLGCYTK 33 (49)
T ss_pred CchHHHHhC
Confidence 356666653
No 168
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=21.61 E-value=1.2e+02 Score=14.81 Aligned_cols=13 Identities=23% Similarity=0.097 Sum_probs=8.7
Q ss_pred eCCee-ecHHHHHh
Q psy10674 64 YKGNV-YCLRDYAT 76 (138)
Q Consensus 64 ~~~~~-yC~~c~~~ 76 (138)
.++.. +|..|...
T Consensus 16 ~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 16 PNGNRTLCNACGLY 29 (36)
T ss_dssp TTSEE-EEHHHHHH
T ss_pred CCCCCHHHHHHHHH
Confidence 35555 89888743
No 169
>PF08189 Meleagrin: Meleagrin/Cygnin family; InterPro: IPR012573 This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contain three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown [].
Probab=21.51 E-value=39 Score=16.97 Aligned_cols=7 Identities=29% Similarity=-0.192 Sum_probs=4.8
Q ss_pred ccCCCCC
Q psy10674 131 GQDSPGS 137 (138)
Q Consensus 131 y~~~~~~ 137 (138)
|||+.+|
T Consensus 11 YCS~~Cs 17 (39)
T PF08189_consen 11 YCSSKCS 17 (39)
T ss_pred eeccccc
Confidence 7777665
No 170
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.25 E-value=60 Score=27.32 Aligned_cols=39 Identities=18% Similarity=0.372 Sum_probs=24.7
Q ss_pred ccccCCccccCCceeeeCCeeecHHHHHhhcCCCcccccCcc
Q psy10674 48 VCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDEL 89 (138)
Q Consensus 48 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~~~~~C~~C~~~ 89 (138)
+|..|+.+| .|....+.+.|..|-....-...|+.|+..
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 455565555 244456778888886553223589999775
No 171
>PF13926 DUF4211: Domain of unknown function (DUF4211)
Probab=21.13 E-value=72 Score=21.20 Aligned_cols=23 Identities=13% Similarity=0.346 Sum_probs=13.6
Q ss_pred cccccccccCCCCeeecCCCCCc
Q psy10674 109 CCYECDKELCNQSYIPVTESRPG 131 (138)
Q Consensus 109 ~C~~C~~~l~~~~f~~~~~~~~y 131 (138)
.|..|++.-....+.+.-.|+||
T Consensus 118 ~C~AC~~~~~~a~~~i~l~G~~Y 140 (153)
T PF13926_consen 118 SCDACNRSGHPATFRIRLSGKPY 140 (153)
T ss_pred cCcccCCCCCCceEEEEeCCCCC
Confidence 46666665433356655557777
No 172
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=20.83 E-value=54 Score=17.25 Aligned_cols=10 Identities=40% Similarity=0.866 Sum_probs=7.2
Q ss_pred CcccccCccc
Q psy10674 81 PRCHACDELI 90 (138)
Q Consensus 81 ~~C~~C~~~I 90 (138)
-+|..|+...
T Consensus 6 y~C~~Cg~~f 15 (52)
T TIGR02605 6 YRCTACGHRF 15 (52)
T ss_pred EEeCCCCCEe
Confidence 3788888755
No 173
>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=20.82 E-value=20 Score=20.01 Aligned_cols=16 Identities=25% Similarity=0.752 Sum_probs=11.1
Q ss_pred cccccccccCCCCeee
Q psy10674 109 CCYECDKELCNQSYIP 124 (138)
Q Consensus 109 ~C~~C~~~l~~~~f~~ 124 (138)
.|+.|++.|+..+|.+
T Consensus 6 vCSTCGrDlSeeRy~L 21 (63)
T PF05864_consen 6 VCSTCGRDLSEERYRL 21 (63)
T ss_pred eecccCCcchHHHHHH
Confidence 4778888877666643
No 174
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=20.81 E-value=75 Score=15.43 Aligned_cols=10 Identities=10% Similarity=0.175 Sum_probs=4.3
Q ss_pred eeCCeeecHH
Q psy10674 63 HYKGNVYCLR 72 (138)
Q Consensus 63 ~~~~~~yC~~ 72 (138)
..++..+|..
T Consensus 17 ~~~~~~~C~~ 26 (33)
T PF08792_consen 17 KEDDYEVCIF 26 (33)
T ss_pred ecCCeEEccc
Confidence 3444444443
No 175
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=20.74 E-value=1e+02 Score=22.15 Aligned_cols=24 Identities=21% Similarity=0.501 Sum_probs=13.2
Q ss_pred cccCCccccCCceeeeCCeeecHHHHHhhc
Q psy10674 49 CSTCDELLVDLMYFHYKGNVYCLRDYATML 78 (138)
Q Consensus 49 C~~C~~~l~~~~~~~~~~~~yC~~c~~~~~ 78 (138)
|..||++.... . .-+|..||.+.+
T Consensus 1 C~~CG~~~~~~----~--~~lC~~C~~~~~ 24 (236)
T PF04981_consen 1 CPRCGREIEPL----I--DGLCPDCYLKRF 24 (236)
T ss_pred CCCCCCCCCCc----c--cccChHHhcccC
Confidence 55677654321 1 127888886654
No 176
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=20.34 E-value=20 Score=20.00 Aligned_cols=15 Identities=27% Similarity=0.853 Sum_probs=10.5
Q ss_pred cccccccccCCCCee
Q psy10674 109 CCYECDKELCNQSYI 123 (138)
Q Consensus 109 ~C~~C~~~l~~~~f~ 123 (138)
.|+.|++.|+..+|.
T Consensus 6 VCsTCGrDlSeeRy~ 20 (63)
T PHA03082 6 VCSTCGRDLSEERYR 20 (63)
T ss_pred eecccCcchhHHHHH
Confidence 477888877766653
No 177
>KOG3039|consensus
Probab=20.20 E-value=1.8e+02 Score=21.47 Aligned_cols=84 Identities=11% Similarity=0.129 Sum_probs=53.8
Q ss_pred cccccccccccCCCeEEEe---ccc--cCCCCCCcccCcccccCCccccCC-cee--eeCCeeecHHHHHhhcC-CCccc
Q psy10674 14 FCCYECDKKVQFENYTGKI---TQS--QESEVLWHPQCFVCSTCDELLVDL-MYF--HYKGNVYCLRDYATMLD-IPRCH 84 (138)
Q Consensus 14 ~~C~~C~~~i~~~~~~~~~---~~~--~~~~~~~H~~Cf~C~~C~~~l~~~-~~~--~~~~~~yC~~c~~~~~~-~~~C~ 84 (138)
.+|..=+++|.-.+++..- ... .-.+..-|..=|.|.++...|.+. ... ..-|.+++..|.+++.. -..|.
T Consensus 184 v~CP~s~kplklkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~p 263 (303)
T KOG3039|consen 184 VVCPVSGKPLKLKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDP 263 (303)
T ss_pred eeccCCCCccchhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccccccc
Confidence 4577777777654443210 000 000112355668899999999653 333 37789999999987652 14899
Q ss_pred ccCcccccCcEEE
Q psy10674 85 ACDELIFVNEYTL 97 (138)
Q Consensus 85 ~C~~~I~~~~~~~ 97 (138)
.|++++.+.++|.
T Consensus 264 v~d~plkdrdiI~ 276 (303)
T KOG3039|consen 264 VTDKPLKDRDIIG 276 (303)
T ss_pred CCCCcCcccceEe
Confidence 9999999988774
Done!