Query psy10221
Match_columns 67
No_of_seqs 126 out of 1034
Neff 10.4
Searched_HMMs 46136
Date Fri Aug 16 20:56:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10221.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10221hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00412 LIM: LIM domain; Int 99.8 3.5E-19 7.5E-24 79.1 3.9 55 12-67 1-56 (58)
2 KOG1701|consensus 99.5 2.2E-16 4.8E-21 91.0 -2.8 63 4-67 329-391 (468)
3 KOG4577|consensus 99.3 9.5E-15 2.1E-19 81.3 -4.3 58 8-67 32-89 (383)
4 smart00132 LIM Zinc-binding do 99.3 4.6E-12 1E-16 51.7 2.7 37 11-47 1-38 (39)
5 KOG1701|consensus 99.3 3.6E-13 7.9E-18 78.0 -1.0 58 8-66 273-331 (468)
6 KOG1044|consensus 99.3 2.2E-12 4.7E-17 77.1 2.1 58 7-66 131-188 (670)
7 KOG1703|consensus 99.3 1.6E-12 3.4E-17 77.2 1.0 59 6-66 360-418 (479)
8 KOG2272|consensus 99.1 1E-11 2.2E-16 68.4 -1.1 58 7-66 193-250 (332)
9 KOG4577|consensus 98.9 1.4E-10 3.1E-15 65.0 0.1 61 6-66 89-151 (383)
10 KOG2272|consensus 98.8 8.5E-10 1.8E-14 61.0 0.2 58 9-67 254-311 (332)
11 KOG1700|consensus 98.6 5.4E-09 1.2E-13 56.4 -0.5 59 6-65 105-163 (200)
12 KOG1700|consensus 98.5 2.7E-08 5.8E-13 53.7 0.2 57 8-65 6-62 (200)
13 KOG1702|consensus 98.4 1.4E-08 3.1E-13 54.8 -1.6 57 10-67 5-61 (264)
14 KOG1703|consensus 98.2 1.1E-06 2.4E-11 52.7 2.4 57 9-66 303-359 (479)
15 KOG1044|consensus 98.1 2.5E-06 5.4E-11 52.0 2.7 53 9-62 16-68 (670)
16 KOG0490|consensus 97.0 9.8E-05 2.1E-09 40.3 -0.8 53 14-66 1-53 (235)
17 PF08394 Arc_trans_TRASH: Arch 95.0 0.029 6.3E-07 22.6 1.9 31 12-45 1-32 (37)
18 PF10367 Vps39_2: Vacuolar sor 94.7 0.04 8.8E-07 26.6 2.4 11 10-20 79-89 (109)
19 COG1645 Uncharacterized Zn-fin 94.5 0.024 5.2E-07 29.1 1.4 21 38-64 30-50 (131)
20 PF10367 Vps39_2: Vacuolar sor 94.1 0.048 1E-06 26.4 1.9 32 36-67 78-109 (109)
21 PF09943 DUF2175: Uncharacteri 92.9 0.046 9.9E-07 26.8 0.6 34 11-44 4-38 (101)
22 PF14471 DUF4428: Domain of un 92.2 0.08 1.7E-06 22.8 0.9 9 12-20 2-10 (51)
23 PF13240 zinc_ribbon_2: zinc-r 90.7 0.16 3.5E-06 18.2 1.0 10 12-21 2-11 (23)
24 PF12674 Zn_ribbon_2: Putative 88.9 0.24 5.3E-06 23.3 1.0 28 39-66 3-34 (81)
25 PF14446 Prok-RING_1: Prokaryo 88.9 0.34 7.4E-06 21.2 1.4 31 7-37 3-36 (54)
26 PF06677 Auto_anti-p27: Sjogre 88.4 0.36 7.8E-06 19.9 1.2 23 37-64 18-40 (41)
27 COG2191 Formylmethanofuran deh 87.8 0.26 5.6E-06 27.2 0.8 30 37-67 173-202 (206)
28 PF04570 DUF581: Protein of un 87.8 0.41 8.8E-06 21.2 1.3 25 38-62 18-43 (58)
29 PRK14890 putative Zn-ribbon RN 87.5 0.29 6.3E-06 21.8 0.7 17 7-23 5-21 (59)
30 PF10886 DUF2685: Protein of u 87.4 0.63 1.4E-05 20.3 1.7 26 10-35 2-27 (54)
31 PF06689 zf-C4_ClpX: ClpX C4-t 87.3 1.1 2.4E-05 18.3 2.4 27 38-64 3-30 (41)
32 PF04810 zf-Sec23_Sec24: Sec23 85.4 1 2.2E-05 18.2 1.8 31 9-44 2-32 (40)
33 COG2888 Predicted Zn-ribbon RN 84.8 0.43 9.3E-06 21.3 0.6 15 9-23 9-23 (61)
34 PF00645 zf-PARP: Poly(ADP-rib 84.6 0.58 1.2E-05 21.7 1.0 32 7-38 5-47 (82)
35 PF11781 RRN7: RNA polymerase 84.6 0.81 1.8E-05 18.2 1.3 22 38-64 10-31 (36)
36 KOG2893|consensus 84.5 0.43 9.2E-06 27.2 0.6 40 7-49 8-47 (341)
37 PF02069 Metallothio_Pro: Prok 84.4 0.91 2E-05 19.7 1.5 24 38-62 9-32 (52)
38 PF13834 DUF4193: Domain of un 84.1 0.34 7.4E-06 23.7 0.1 29 36-64 70-98 (99)
39 PRK00420 hypothetical protein; 81.7 0.95 2.1E-05 22.7 1.1 10 55-64 37-46 (112)
40 COG4847 Uncharacterized protei 81.1 0.53 1.2E-05 22.9 0.1 36 11-46 8-44 (103)
41 PF07503 zf-HYPF: HypF finger; 80.6 0.43 9.4E-06 18.9 -0.2 31 12-47 2-32 (35)
42 PF07754 DUF1610: Domain of un 80.5 1.4 3E-05 16.0 1.1 10 13-22 2-11 (24)
43 KOG3579|consensus 79.8 0.95 2E-05 26.5 0.9 32 10-41 269-300 (352)
44 COG4357 Zinc finger domain con 78.4 0.12 2.5E-06 25.2 -2.6 53 12-65 38-90 (105)
45 PF10764 Gin: Inhibitor of sig 77.8 2.4 5.2E-05 17.8 1.6 29 12-48 2-30 (46)
46 cd02249 ZZ Zinc finger, ZZ typ 77.7 1.1 2.5E-05 18.5 0.6 11 11-21 2-12 (46)
47 smart00291 ZnF_ZZ Zinc-binding 73.9 1.6 3.5E-05 17.9 0.6 9 11-19 6-14 (44)
48 cd02335 ZZ_ADA2 Zinc finger, Z 71.6 3.7 8E-05 17.3 1.4 11 11-21 2-12 (49)
49 cd02336 ZZ_RSC8 Zinc finger, Z 71.6 3.2 6.9E-05 17.4 1.2 26 39-66 3-31 (45)
50 PF14255 Cys_rich_CPXG: Cystei 71.0 2.2 4.8E-05 18.5 0.7 29 11-39 2-30 (52)
51 PRK00807 50S ribosomal protein 70.5 4.4 9.5E-05 17.4 1.6 32 10-44 2-36 (52)
52 PF13248 zf-ribbon_3: zinc-rib 69.7 2.6 5.6E-05 15.3 0.7 13 10-22 3-15 (26)
53 COG4332 Uncharacterized protei 68.3 4.9 0.00011 22.1 1.7 45 4-48 12-61 (203)
54 cd02340 ZZ_NBR1_like Zinc fing 67.4 3.2 6.9E-05 17.1 0.8 11 11-21 2-12 (43)
55 PHA02610 uvsY.-2 hypothetical 67.3 5.2 0.00011 17.3 1.4 25 10-34 2-26 (53)
56 PF12773 DZR: Double zinc ribb 66.4 8 0.00017 16.0 2.0 16 5-20 8-23 (50)
57 TIGR02098 MJ0042_CXXC MJ0042 f 66.1 2.1 4.5E-05 16.8 0.1 31 11-46 4-35 (38)
58 PF10080 DUF2318: Predicted me 63.4 7.2 0.00016 19.3 1.7 30 30-64 29-58 (102)
59 cd02341 ZZ_ZZZ3 Zinc finger, Z 63.1 4.2 9E-05 17.2 0.7 6 12-17 3-8 (48)
60 COG4068 Uncharacterized protei 62.5 4 8.7E-05 18.2 0.6 17 8-24 7-23 (64)
61 cd00162 RING RING-finger (Real 62.3 5.7 0.00012 15.3 1.1 26 12-37 2-27 (45)
62 COG0266 Nei Formamidopyrimidin 61.6 6.3 0.00014 22.9 1.5 13 9-21 245-257 (273)
63 PF13639 zf-RING_2: Ring finge 61.5 3.4 7.3E-05 16.6 0.3 28 11-38 2-31 (44)
64 cd02342 ZZ_UBA_plant Zinc fing 61.3 5.3 0.00011 16.6 0.9 6 12-17 3-8 (43)
65 PF09723 Zn-ribbon_8: Zinc rib 61.2 1.7 3.8E-05 17.7 -0.6 10 11-20 7-16 (42)
66 PF00096 zf-C2H2: Zinc finger, 61.2 3.4 7.5E-05 13.9 0.3 12 37-48 1-12 (23)
67 PF12874 zf-met: Zinc-finger o 60.5 3.6 7.8E-05 14.2 0.3 12 37-48 1-12 (25)
68 PF09889 DUF2116: Uncharacteri 60.2 4.5 9.7E-05 18.0 0.6 13 10-22 4-16 (59)
69 PRK12775 putative trifunctiona 59.9 13 0.00029 25.4 2.9 53 5-62 792-845 (1006)
70 PRK12495 hypothetical protein; 58.2 5.6 0.00012 22.5 0.9 12 9-20 42-53 (226)
71 PF13717 zinc_ribbon_4: zinc-r 58.0 4.2 9.2E-05 16.0 0.3 10 11-20 4-13 (36)
72 PF13894 zf-C2H2_4: C2H2-type 57.3 4.8 0.0001 13.3 0.4 12 37-48 1-12 (24)
73 PF12171 zf-C2H2_jaz: Zinc-fin 57.1 8.6 0.00019 13.7 1.1 13 37-49 2-14 (27)
74 PRK08359 transcription factor; 56.4 9.7 0.00021 20.7 1.6 21 11-31 8-29 (176)
75 PF00628 PHD: PHD-finger; Int 56.0 15 0.00033 15.0 2.3 27 12-38 2-30 (51)
76 PF00130 C1_1: Phorbol esters/ 55.0 12 0.00026 15.5 1.5 14 7-20 9-22 (53)
77 PF08746 zf-RING-like: RING-li 53.8 6.1 0.00013 16.2 0.5 27 12-38 1-29 (43)
78 cd02338 ZZ_PCMF_like Zinc fing 53.7 5.8 0.00013 16.7 0.4 10 11-20 2-12 (49)
79 COG1656 Uncharacterized conser 53.3 5.4 0.00012 21.5 0.3 40 6-45 94-139 (165)
80 TIGR02420 dksA RNA polymerase- 52.9 2.6 5.7E-05 20.8 -0.8 14 9-22 80-93 (110)
81 PRK00398 rpoP DNA-directed RNA 52.2 6.3 0.00014 16.2 0.4 27 11-46 5-31 (46)
82 cd02337 ZZ_CBP Zinc finger, ZZ 52.2 7.4 0.00016 15.8 0.6 6 12-17 3-8 (41)
83 PF02591 DUF164: Putative zinc 51.3 2.4 5.3E-05 18.3 -1.0 11 38-48 24-34 (56)
84 cd02334 ZZ_dystrophin Zinc fin 51.1 7.1 0.00015 16.6 0.5 7 11-17 2-8 (49)
85 TIGR00270 conserved hypothetic 50.8 20 0.00044 19.0 2.2 21 11-31 2-23 (154)
86 COG2075 RPL24A Ribosomal prote 49.8 14 0.0003 16.9 1.3 25 9-33 3-30 (66)
87 PF01927 Mut7-C: Mut7-C RNAse 49.7 12 0.00025 19.5 1.2 37 9-45 91-133 (147)
88 PRK00085 recO DNA repair prote 49.6 9.4 0.0002 21.2 0.9 11 9-19 149-159 (247)
89 PRK14891 50S ribosomal protein 49.4 15 0.00033 19.0 1.5 25 9-33 4-31 (131)
90 COG1381 RecO Recombinational D 48.8 11 0.00023 21.5 1.1 28 36-64 154-181 (251)
91 PLN03123 poly [ADP-ribose] pol 48.5 19 0.0004 24.9 2.2 32 7-38 15-57 (981)
92 PF14354 Lar_restr_allev: Rest 48.3 17 0.00037 15.6 1.5 13 8-20 2-14 (61)
93 PF13719 zinc_ribbon_5: zinc-r 48.0 8.3 0.00018 15.2 0.4 10 11-20 4-13 (37)
94 smart00531 TFIIE Transcription 47.9 4.6 9.9E-05 21.0 -0.5 35 10-47 100-134 (147)
95 smart00504 Ubox Modified RING 47.9 15 0.00032 15.7 1.2 27 11-38 3-29 (63)
96 PRK09710 lar restriction allev 47.8 29 0.00062 15.8 2.2 31 8-44 5-35 (64)
97 PF11331 DUF3133: Protein of u 47.7 5.7 0.00012 16.8 -0.1 35 10-46 7-41 (46)
98 PF07649 C1_3: C1-like domain; 47.3 11 0.00023 13.9 0.7 11 38-48 2-12 (30)
99 cd02344 ZZ_HERC2 Zinc finger, 46.3 21 0.00045 14.9 1.5 7 11-17 2-8 (45)
100 TIGR00613 reco DNA repair prot 46.2 18 0.00038 20.1 1.7 10 8-17 146-155 (241)
101 PRK14810 formamidopyrimidine-D 45.6 16 0.00036 21.0 1.5 9 38-46 246-254 (272)
102 cd02345 ZZ_dah Zinc finger, ZZ 45.5 7.6 0.00016 16.4 0.1 10 11-20 2-12 (49)
103 PF13912 zf-C2H2_6: C2H2-type 45.2 8.9 0.00019 13.4 0.3 12 37-48 2-13 (27)
104 PHA02768 hypothetical protein; 44.9 4.8 0.0001 17.6 -0.5 40 11-51 7-46 (55)
105 smart00834 CxxC_CXXC_SSSS Puta 44.7 5.4 0.00012 15.6 -0.4 10 11-20 7-16 (41)
106 PF05502 Dynactin_p62: Dynacti 43.7 16 0.00036 22.9 1.4 38 10-48 27-64 (483)
107 PF01286 XPA_N: XPA protein N- 43.7 8.9 0.00019 15.1 0.2 15 9-23 3-17 (34)
108 TIGR00577 fpg formamidopyrimid 43.0 20 0.00042 20.7 1.5 9 38-46 247-255 (272)
109 TIGR02605 CxxC_CxxC_SSSS putat 42.3 6.9 0.00015 16.4 -0.3 11 11-21 7-17 (52)
110 PRK01103 formamidopyrimidine/5 42.2 21 0.00045 20.6 1.6 9 38-46 247-255 (274)
111 TIGR01053 LSD1 zinc finger dom 42.1 16 0.00034 14.0 0.8 10 11-20 3-12 (31)
112 PF06750 DiS_P_DiS: Bacterial 41.7 15 0.00032 17.7 0.8 41 6-48 30-70 (92)
113 smart00355 ZnF_C2H2 zinc finge 41.5 15 0.00033 12.0 0.7 11 38-48 2-12 (26)
114 PRK14811 formamidopyrimidine-D 41.3 21 0.00046 20.5 1.5 11 10-20 236-246 (269)
115 smart00659 RPOLCX RNA polymera 41.2 15 0.00033 15.2 0.7 10 11-20 4-13 (44)
116 PF01258 zf-dskA_traR: Prokary 41.1 14 0.00031 14.3 0.6 12 11-22 5-16 (36)
117 KOG0978|consensus 41.1 7.5 0.00016 25.6 -0.3 28 8-39 642-669 (698)
118 PF14149 YhfH: YhfH-like prote 41.0 6.7 0.00014 15.8 -0.4 15 7-21 11-25 (37)
119 PF06170 DUF983: Protein of un 41.0 19 0.00042 17.2 1.1 19 2-20 1-19 (86)
120 PF03966 Trm112p: Trm112p-like 40.4 9.4 0.0002 17.1 0.0 12 53-64 48-59 (68)
121 PRK13945 formamidopyrimidine-D 40.3 23 0.00049 20.6 1.5 10 37-46 255-264 (282)
122 PF03107 C1_2: C1 domain; Int 40.3 25 0.00055 13.0 1.2 12 37-48 1-12 (30)
123 PF04216 FdhE: Protein involve 40.1 12 0.00026 21.6 0.4 38 10-47 173-222 (290)
124 PF00569 ZZ: Zinc finger, ZZ t 39.7 7.4 0.00016 16.1 -0.4 6 60-65 30-35 (46)
125 COG1998 RPS31 Ribosomal protei 39.6 17 0.00036 15.7 0.7 10 55-64 34-43 (51)
126 PF14803 Nudix_N_2: Nudix N-te 39.6 9.8 0.00021 14.9 0.0 10 11-20 2-11 (34)
127 PF12855 Ecl1: Life-span regul 39.0 12 0.00026 15.5 0.2 8 55-62 20-27 (43)
128 PF06827 zf-FPG_IleRS: Zinc fi 38.7 10 0.00023 14.0 0.0 12 10-21 2-13 (30)
129 TIGR00373 conserved hypothetic 38.1 7 0.00015 20.7 -0.7 29 11-47 111-139 (158)
130 PF10235 Cript: Microtubule-as 37.8 15 0.00033 17.8 0.5 13 10-22 70-82 (90)
131 PF12760 Zn_Tnp_IS1595: Transp 37.7 34 0.00073 14.0 1.5 8 10-17 19-26 (46)
132 PRK04016 DNA-directed RNA poly 37.5 12 0.00025 16.9 0.1 12 37-48 5-16 (62)
133 PF06467 zf-FCS: MYM-type Zinc 37.0 21 0.00046 14.1 0.8 14 9-22 6-19 (43)
134 PF03226 Yippee-Mis18: Yippee 36.9 19 0.00042 17.1 0.8 14 37-50 3-16 (96)
135 PRK10445 endonuclease VIII; Pr 36.7 28 0.00061 20.0 1.5 9 38-46 237-245 (263)
136 PF08792 A2L_zn_ribbon: A2L zi 36.5 33 0.00072 13.2 1.4 10 55-64 18-27 (33)
137 KOG2186|consensus 36.3 8 0.00017 22.4 -0.7 37 11-48 5-41 (276)
138 PF10083 DUF2321: Uncharacteri 36.0 28 0.00061 18.7 1.3 38 10-48 40-80 (158)
139 smart00249 PHD PHD zinc finger 34.9 35 0.00076 13.1 1.4 26 12-37 2-29 (47)
140 COG1885 Uncharacterized protei 34.5 32 0.00069 17.3 1.3 19 6-24 46-64 (115)
141 PRK06266 transcription initiat 34.5 10 0.00022 20.5 -0.4 30 11-48 119-148 (178)
142 PRK05978 hypothetical protein; 34.2 26 0.00055 18.6 1.0 31 10-48 34-64 (148)
143 PHA03082 DNA-dependent RNA pol 33.9 13 0.00029 16.5 -0.0 13 37-49 5-17 (63)
144 PHA02929 N1R/p28-like protein; 33.6 31 0.00066 19.8 1.3 14 9-22 174-187 (238)
145 KOG1723|consensus 33.3 22 0.00047 19.2 0.7 16 9-24 3-18 (162)
146 PF05864 Chordopox_RPO7: Chord 33.2 14 0.00031 16.4 0.0 13 37-49 5-17 (63)
147 TIGR00622 ssl1 transcription f 33.2 51 0.0011 16.7 2.0 11 11-21 57-67 (112)
148 TIGR03831 YgiT_finger YgiT-typ 33.2 21 0.00045 14.1 0.5 13 10-22 33-45 (46)
149 smart00746 TRASH metallochaper 33.1 32 0.00069 12.0 1.5 9 12-20 1-9 (39)
150 PF04475 DUF555: Protein of un 33.1 40 0.00086 16.7 1.5 19 6-24 44-62 (102)
151 smart00451 ZnF_U1 U1-like zinc 33.0 24 0.00052 13.1 0.7 12 37-48 4-15 (35)
152 PF10170 C6_DPF: Cysteine-rich 32.7 28 0.00061 17.1 1.0 30 35-64 48-77 (97)
153 KOG2879|consensus 32.1 39 0.00084 20.0 1.6 34 4-40 234-267 (298)
154 TIGR01384 TFS_arch transcripti 31.8 28 0.00061 16.8 0.9 11 11-21 2-12 (104)
155 COG1096 Predicted RNA-binding 31.7 34 0.00074 18.9 1.3 22 37-64 150-171 (188)
156 COG4306 Uncharacterized protei 31.4 50 0.0011 17.2 1.8 37 10-47 40-79 (160)
157 PF08271 TF_Zn_Ribbon: TFIIB z 31.2 18 0.00039 14.5 0.2 10 11-20 21-30 (43)
158 COG2174 RPL34A Ribosomal prote 31.2 31 0.00067 16.8 1.0 16 6-21 31-46 (93)
159 PRK03922 hypothetical protein; 31.2 43 0.00094 16.9 1.5 19 6-24 46-64 (113)
160 PF13790 DUF4182: Domain of un 30.9 27 0.00058 14.1 0.6 13 8-20 2-14 (38)
161 PF01194 RNA_pol_N: RNA polyme 30.3 24 0.00053 15.8 0.5 11 38-48 6-16 (60)
162 cd00472 Ribosomal_L24e_L24 Rib 30.3 43 0.00092 14.6 1.3 25 9-33 3-30 (54)
163 PF11494 Ta0938: Ta0938; Inte 29.8 31 0.00067 17.1 0.8 12 10-21 15-26 (105)
164 PF10892 DUF2688: Protein of u 29.8 16 0.00035 16.1 -0.1 11 10-20 11-21 (60)
165 PRK00432 30S ribosomal protein 29.5 39 0.00084 14.3 1.1 10 55-64 34-43 (50)
166 PF01412 ArfGap: Putative GTPa 29.3 32 0.00069 17.1 0.9 12 7-18 11-22 (116)
167 PF10122 Mu-like_Com: Mu-like 29.2 12 0.00026 16.2 -0.6 13 9-21 4-16 (51)
168 cd02343 ZZ_EF Zinc finger, ZZ 28.9 30 0.00065 14.7 0.6 9 11-19 2-10 (48)
169 PF13465 zf-H2C2_2: Zinc-finge 28.8 24 0.00053 12.5 0.3 9 37-45 15-23 (26)
170 PF02207 zf-UBR: Putative zinc 28.6 60 0.0013 14.6 1.7 7 59-65 26-32 (71)
171 cd02339 ZZ_Mind_bomb Zinc fing 28.2 32 0.00069 14.3 0.7 7 11-17 2-8 (45)
172 PF12677 DUF3797: Domain of un 27.7 64 0.0014 13.8 1.6 27 10-36 14-42 (49)
173 PRK10778 dksA RNA polymerase-b 27.7 11 0.00024 19.9 -1.0 15 8-22 110-124 (151)
174 PRK13796 GTPase YqeH; Provisio 27.0 43 0.00094 20.2 1.3 10 11-20 2-11 (365)
175 PRK14559 putative protein seri 26.9 82 0.0018 20.9 2.5 12 8-19 14-25 (645)
176 KOG1829|consensus 26.7 27 0.00059 22.7 0.4 13 35-47 339-351 (580)
177 PF12156 ATPase-cat_bd: Putati 26.3 70 0.0015 15.2 1.7 31 11-44 2-34 (88)
178 PRK06424 transcription factor; 26.2 49 0.0011 17.4 1.3 20 12-31 3-22 (144)
179 smart00714 LITAF Possible memb 26.1 35 0.00075 15.1 0.6 16 4-19 47-62 (67)
180 PF10571 UPF0547: Uncharacteri 25.9 37 0.00081 12.3 0.6 10 11-20 2-11 (26)
181 KOG1734|consensus 25.7 34 0.00075 20.2 0.7 31 8-38 223-262 (328)
182 smart00109 C1 Protein kinase C 25.1 29 0.00063 13.7 0.3 14 8-21 10-23 (49)
183 PF13842 Tnp_zf-ribbon_2: DDE_ 24.7 36 0.00077 13.0 0.5 10 37-46 17-26 (32)
184 PF00020 TNFR_c6: TNFR/NGFR cy 24.2 29 0.00063 13.5 0.2 11 34-44 13-23 (39)
185 PF01246 Ribosomal_L24e: Ribos 24.2 39 0.00085 15.6 0.6 25 9-33 3-30 (71)
186 COG1571 Predicted DNA-binding 24.1 72 0.0016 20.0 1.8 35 5-49 346-380 (421)
187 TIGR02419 C4_traR_proteo phage 23.8 45 0.00098 14.8 0.8 16 7-22 29-44 (63)
188 COG5347 GTPase-activating prot 23.8 54 0.0012 19.7 1.3 39 6-48 17-55 (319)
189 PF07282 OrfB_Zn_ribbon: Putat 23.7 63 0.0014 14.2 1.2 13 9-21 28-40 (69)
190 PF04502 DUF572: Family of unk 23.2 79 0.0017 18.9 1.9 38 9-46 40-87 (324)
191 PHA00080 DksA-like zinc finger 23.1 48 0.001 15.2 0.8 33 7-45 29-61 (72)
192 PF05810 NinF: NinF protein; 23.1 31 0.00067 15.2 0.2 13 11-23 19-31 (58)
193 KOG2462|consensus 23.0 34 0.00075 20.1 0.4 38 9-47 161-198 (279)
194 COG1644 RPB10 DNA-directed RNA 22.9 23 0.00051 16.0 -0.2 11 38-48 6-16 (63)
195 PLN00032 DNA-directed RNA poly 22.8 29 0.00064 16.1 0.1 11 38-48 6-16 (71)
196 smart00105 ArfGap Putative GTP 22.7 93 0.002 15.3 1.8 36 8-47 2-37 (112)
197 COG1813 Predicted transcriptio 22.5 81 0.0018 17.2 1.7 20 12-31 6-25 (165)
198 TIGR00143 hypF [NiFe] hydrogen 22.4 43 0.00093 22.3 0.7 35 7-46 116-150 (711)
199 PF09888 DUF2115: Uncharacteri 22.4 92 0.002 16.7 1.9 20 43-62 122-141 (163)
200 TIGR02890 spore_yteA sporulati 22.4 12 0.00026 19.9 -1.4 14 9-22 86-99 (159)
201 PRK01022 hypothetical protein; 22.4 94 0.002 16.8 1.9 20 43-62 124-143 (167)
202 PF13695 zf-3CxxC: Zinc-bindin 22.1 93 0.002 15.0 1.7 29 11-39 7-44 (98)
203 PF10071 DUF2310: Zn-ribbon-co 21.7 52 0.0011 19.2 0.9 31 8-44 219-249 (258)
204 PF09855 DUF2082: Nucleic-acid 21.6 92 0.002 14.0 1.5 17 11-27 2-18 (64)
205 PF15269 zf-C2H2_7: Zinc-finge 21.5 52 0.0011 13.9 0.7 17 24-40 11-27 (54)
206 PF11571 Med27: Mediator compl 21.3 21 0.00046 17.0 -0.6 10 10-19 55-64 (90)
207 PF08790 zf-LYAR: LYAR-type C2 21.3 33 0.00071 12.9 0.0 11 37-47 1-11 (28)
208 PF13909 zf-H2C2_5: C2H2-type 21.2 41 0.00088 11.3 0.3 6 38-43 2-7 (24)
No 1
>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=99.78 E-value=3.5e-19 Score=79.10 Aligned_cols=55 Identities=33% Similarity=0.796 Sum_probs=49.1
Q ss_pred ccccCccccCceee-eecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221 12 CVACGESITDKYLL-QVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67 (67)
Q Consensus 12 C~~C~~~i~~~~~~-~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k 67 (67)
|.+|+++|.+.+.+ .+.++.||++||+|..|+++|.+.. ++..++++||+.||.+
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD-FYEKDGKPYCKDCYQK 56 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSS-EEEETTEEEEHHHHHH
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCe-eEeECCEEECHHHHhh
Confidence 78999999977665 6999999999999999999998876 6889999999999863
No 2
>KOG1701|consensus
Probab=99.53 E-value=2.2e-16 Score=90.99 Aligned_cols=63 Identities=33% Similarity=0.734 Sum_probs=57.0
Q ss_pred ccccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221 4 TIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67 (67)
Q Consensus 4 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k 67 (67)
.|+....+|..|++.|.++ ++++.++.||+.||+|..|.+.|++..+....++++||..||+|
T Consensus 329 cyq~tlekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~ 391 (468)
T KOG1701|consen 329 CYQDTLEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHK 391 (468)
T ss_pred HHHHHHHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhh
Confidence 3566678999999999997 78999999999999999999999998877778999999999975
No 3
>KOG4577|consensus
Probab=99.35 E-value=9.5e-15 Score=81.30 Aligned_cols=58 Identities=40% Similarity=1.041 Sum_probs=53.8
Q ss_pred CCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221 8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67 (67)
Q Consensus 8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k 67 (67)
+.+.|++|.+.|.++.++.++++.||..|++|+.|..+|.+. +|.+++.+||+.+|+|
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr--CFsR~~s~yCkedFfK 89 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADR--CFSREGSVYCKEDFFK 89 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH--HhhcCCceeehHHHHH
Confidence 678999999999999999999999999999999999999875 6789999999999875
No 4
>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=99.27 E-value=4.6e-12 Score=51.69 Aligned_cols=37 Identities=32% Similarity=0.889 Sum_probs=32.8
Q ss_pred cccccCccccCc-eeeeecCceeccccccccccccccC
Q psy10221 11 YCVACGESITDK-YLLQVSDKSWHAQCLRCCICQLVLD 47 (67)
Q Consensus 11 ~C~~C~~~i~~~-~~~~~~~~~~h~~cf~C~~C~~~l~ 47 (67)
+|.+|+++|.+. ..+.+.++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 488999999975 5678889999999999999999885
No 5
>KOG1701|consensus
Probab=99.27 E-value=3.6e-13 Score=77.99 Aligned_cols=58 Identities=22% Similarity=0.583 Sum_probs=50.4
Q ss_pred CCccccccCccccCce-eeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221 8 ELRYCVACGESITDKY-LLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66 (67)
Q Consensus 8 ~~~~C~~C~~~i~~~~-~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~ 66 (67)
.+.+|.+|+|.|.... .+.++++.||..||+|..|++.|.+.. +|..|+++||+.||.
T Consensus 273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~-FY~v~~k~~CE~cyq 331 (468)
T KOG1701|consen 273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQS-FYQVDGKPYCEGCYQ 331 (468)
T ss_pred hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhcccc-ccccCCcccchHHHH
Confidence 3458999999999543 478999999999999999999998765 578999999999985
No 6
>KOG1044|consensus
Probab=99.27 E-value=2.2e-12 Score=77.12 Aligned_cols=58 Identities=34% Similarity=0.796 Sum_probs=52.8
Q ss_pred cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221 7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66 (67)
Q Consensus 7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~ 66 (67)
.+...|++|++.|...+.+.++++.||..||+|..|+..|.+. +..++|.+||+.||+
T Consensus 131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge--y~skdg~pyce~dy~ 188 (670)
T KOG1044|consen 131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE--YMSKDGVPYCEKDYQ 188 (670)
T ss_pred cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce--eeccCCCcchhhhhh
Confidence 4567899999999998889999999999999999999999875 578999999999986
No 7
>KOG1703|consensus
Probab=99.25 E-value=1.6e-12 Score=77.17 Aligned_cols=59 Identities=24% Similarity=0.529 Sum_probs=51.8
Q ss_pred ccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221 6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66 (67)
Q Consensus 6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~ 66 (67)
....+.|.+|+.+|.+. .+.+.+..||+.||.|..|++++.+.. ++.+++.+||+.||.
T Consensus 360 ~~~~p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~~~~-~~~~~~~pyce~~~~ 418 (479)
T KOG1703|consen 360 APFRPNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLKNSS-FFESDGEPYCEDHYK 418 (479)
T ss_pred HhhCccccccCCchHHh-HhhhccCeechhceeeecccCCCCCCc-ccccCCccchhhhHh
Confidence 34568999999999986 677889999999999999999998865 578999999999985
No 8
>KOG2272|consensus
Probab=99.07 E-value=1e-11 Score=68.40 Aligned_cols=58 Identities=24% Similarity=0.619 Sum_probs=50.4
Q ss_pred cCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221 7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66 (67)
Q Consensus 7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~ 66 (67)
-+.++|..|.++|.+. ++.++++.||.+.|+|+.|.+|.-+-. -|++.|..||+.+|.
T Consensus 193 mgipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPFlGHr-HYEkkGlaYCe~h~~ 250 (332)
T KOG2272|consen 193 MGIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPFLGHR-HYEKKGLAYCETHYH 250 (332)
T ss_pred cCCcccccccCchHHH-HHHHhccccchhheeehhcCCcccchh-hhhhcCchhHHHHHH
Confidence 3568999999999975 678999999999999999999986644 378999999999985
No 9
>KOG4577|consensus
Probab=98.94 E-value=1.4e-10 Score=64.96 Aligned_cols=61 Identities=28% Similarity=0.593 Sum_probs=50.2
Q ss_pred ccCCccccccCccccCceee-eecCceeccccccccccccccCCCCce-eeeCCeecchhhhc
Q psy10221 6 ITELRYCVACGESITDKYLL-QVSDKSWHAQCLRCCICQLVLDRHPSC-FIKDEAVYCKQDYA 66 (67)
Q Consensus 6 ~~~~~~C~~C~~~i~~~~~~-~~~~~~~h~~cf~C~~C~~~l~~~~~~-~~~~~~~~C~~~y~ 66 (67)
+.-...|..|.+.|.+..++ .+.+..||..||.|..|++.|..++.+ ++.|+++.|+.+|.
T Consensus 89 KrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE 151 (383)
T KOG4577|consen 89 KRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYE 151 (383)
T ss_pred HHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHH
Confidence 33456899999999987665 477889999999999999999765544 55889999999984
No 10
>KOG2272|consensus
Probab=98.81 E-value=8.5e-10 Score=60.98 Aligned_cols=58 Identities=22% Similarity=0.596 Sum_probs=52.5
Q ss_pred CccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221 9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k 67 (67)
...|-.|+.+|... +++++++.|-++||+|+.|.+-|...+.+++-|-+|.|+.||.|
T Consensus 254 G~~CF~C~~~i~G~-vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 254 GNLCFICNRVIGGD-VVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred hhhheecCCccCcc-HHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 35788999999875 78999999999999999999999998888999999999999974
No 11
>KOG1700|consensus
Probab=98.60 E-value=5.4e-09 Score=56.41 Aligned_cols=59 Identities=20% Similarity=0.492 Sum_probs=49.6
Q ss_pred ccCCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhh
Q psy10221 6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65 (67)
Q Consensus 6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y 65 (67)
......|..|.+.+++.+.+...+..||..||+|+.|+..|.... +...++.++|...+
T Consensus 105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~-~~~~~g~l~~~~~~ 163 (200)
T KOG1700|consen 105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKN-YAALEGVLYCKHHF 163 (200)
T ss_pred hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcc-hhhcCCccccchhh
Confidence 344578999999999988899999999999999999999998865 45678888886543
No 12
>KOG1700|consensus
Probab=98.49 E-value=2.7e-08 Score=53.74 Aligned_cols=57 Identities=23% Similarity=0.458 Sum_probs=48.7
Q ss_pred CCccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhh
Q psy10221 8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65 (67)
Q Consensus 8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y 65 (67)
....|..|++.++-.+.+...+..||..||.|..|.+.|.... +..+++.+||+.+|
T Consensus 6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~-~~~~e~~~yc~~~~ 62 (200)
T KOG1700|consen 6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSG-YSEHEGVPYCKNCH 62 (200)
T ss_pred ccchhhhccCcchHHHHHhccCcchhhhHHhcccccccccccc-ccccccccccccch
Confidence 3458999999999777777889999999999999999998755 46699999999854
No 13
>KOG1702|consensus
Probab=98.44 E-value=1.4e-08 Score=54.78 Aligned_cols=57 Identities=28% Similarity=0.626 Sum_probs=47.8
Q ss_pred ccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221 10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k 67 (67)
..|..|++.+++.+.+.-+++.||..||.|..|+.+|.-.. +-.-+.++||..+|.|
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKn-yKgy~kkpycn~hYpk 61 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKN-YKGYDKKPYCNPHYPK 61 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhh-ccccccCCCcCccccc
Confidence 45788999999888888999999999999999999997643 3346788999999864
No 14
>KOG1703|consensus
Probab=98.20 E-value=1.1e-06 Score=52.72 Aligned_cols=57 Identities=19% Similarity=0.535 Sum_probs=49.9
Q ss_pred CccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221 9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~ 66 (67)
.+.|..|...|.....+.++++.||+.+|.|..|...+..... ...+|.+||..||.
T Consensus 303 ~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~-~~~~g~~~c~~~~~ 359 (479)
T KOG1703|consen 303 RPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGP-RELDGKILCHECFH 359 (479)
T ss_pred cccccccccCcccceeEeeccccccccceeeccccccccCCCc-cccCCCccHHHHHH
Confidence 4889999999998557889999999999999999999987654 67889999998874
No 15
>KOG1044|consensus
Probab=98.11 E-value=2.5e-06 Score=52.01 Aligned_cols=53 Identities=21% Similarity=0.442 Sum_probs=43.9
Q ss_pred CccccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecch
Q psy10221 9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCK 62 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~ 62 (67)
...|..|.+.-... ++++.++.||..||.|..|+..|..+.++.-.+.++|+.
T Consensus 16 ~i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt 68 (670)
T KOG1044|consen 16 GIKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGT 68 (670)
T ss_pred ceehhhhCCccccc-eeEeeccccceeeeeccccCCCcccccceecccceeecc
Confidence 35799999888874 889999999999999999999999887654455667764
No 16
>KOG0490|consensus
Probab=97.02 E-value=9.8e-05 Score=40.28 Aligned_cols=53 Identities=49% Similarity=1.113 Sum_probs=42.3
Q ss_pred ccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhhc
Q psy10221 14 ACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDYA 66 (67)
Q Consensus 14 ~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~ 66 (67)
+|+..|.+...+...+..||..|..|..|...+......+.++|..+|..+|.
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~ 53 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQ 53 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccch
Confidence 36677777777777799999999999999999973333455699999998875
No 17
>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=95.00 E-value=0.029 Score=22.62 Aligned_cols=31 Identities=26% Similarity=0.628 Sum_probs=20.8
Q ss_pred ccccCccccCcee-eeecCceeccccccccccccc
Q psy10221 12 CVACGESITDKYL-LQVSDKSWHAQCLRCCICQLV 45 (67)
Q Consensus 12 C~~C~~~i~~~~~-~~~~~~~~h~~cf~C~~C~~~ 45 (67)
|..|+.+|.+..+ +...++.|+ |.|..|...
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHH
Confidence 6779999985544 567788887 444555443
No 18
>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=94.68 E-value=0.04 Score=26.62 Aligned_cols=11 Identities=27% Similarity=0.900 Sum_probs=5.5
Q ss_pred ccccccCcccc
Q psy10221 10 RYCVACGESIT 20 (67)
Q Consensus 10 ~~C~~C~~~i~ 20 (67)
..|..|++++.
T Consensus 79 ~~C~vC~k~l~ 89 (109)
T PF10367_consen 79 TKCSVCGKPLG 89 (109)
T ss_pred CCccCcCCcCC
Confidence 34555555554
No 19
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=94.55 E-value=0.024 Score=29.06 Aligned_cols=21 Identities=38% Similarity=0.709 Sum_probs=16.4
Q ss_pred cccccccccCCCCceeeeCCeecchhh
Q psy10221 38 RCCICQLVLDRHPSCFIKDEAVYCKQD 64 (67)
Q Consensus 38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~ 64 (67)
.|..|+.|| |.++|.+||..|
T Consensus 30 hCp~Cg~PL------F~KdG~v~CPvC 50 (131)
T COG1645 30 HCPKCGTPL------FRKDGEVFCPVC 50 (131)
T ss_pred hCcccCCcc------eeeCCeEECCCC
Confidence 467788777 458999999887
No 20
>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=94.10 E-value=0.048 Score=26.35 Aligned_cols=32 Identities=13% Similarity=0.164 Sum_probs=24.2
Q ss_pred cccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221 36 CLRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67 (67)
Q Consensus 36 cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k 67 (67)
--.|..|+++|....+....+|.++...|..|
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIKR 109 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccccC
Confidence 35799999999886655557788887777654
No 21
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=92.87 E-value=0.046 Score=26.84 Aligned_cols=34 Identities=24% Similarity=0.497 Sum_probs=25.5
Q ss_pred cccccCccccCceeeeecC-ceecccccccccccc
Q psy10221 11 YCVACGESITDKYLLQVSD-KSWHAQCLRCCICQL 44 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~~~-~~~h~~cf~C~~C~~ 44 (67)
.|..|+++|..++.+++.. ..-|..||.-..-.+
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~~k 38 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKASKK 38 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHHhhh
Confidence 5899999999888877544 557999987554433
No 22
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=92.16 E-value=0.08 Score=22.79 Aligned_cols=9 Identities=44% Similarity=1.224 Sum_probs=4.2
Q ss_pred ccccCcccc
Q psy10221 12 CVACGESIT 20 (67)
Q Consensus 12 C~~C~~~i~ 20 (67)
|+.|++.+.
T Consensus 2 C~iCg~kig 10 (51)
T PF14471_consen 2 CAICGKKIG 10 (51)
T ss_pred CCccccccc
Confidence 444544443
No 23
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.74 E-value=0.16 Score=18.17 Aligned_cols=10 Identities=50% Similarity=1.208 Sum_probs=5.3
Q ss_pred ccccCccccC
Q psy10221 12 CVACGESITD 21 (67)
Q Consensus 12 C~~C~~~i~~ 21 (67)
|..|+..|.+
T Consensus 2 Cp~CG~~~~~ 11 (23)
T PF13240_consen 2 CPNCGAEIED 11 (23)
T ss_pred CcccCCCCCC
Confidence 4555555543
No 24
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=88.94 E-value=0.24 Score=23.34 Aligned_cols=28 Identities=25% Similarity=0.515 Sum_probs=15.2
Q ss_pred ccccccccCCCCc-eeeeC---Ceecchhhhc
Q psy10221 39 CCICQLVLDRHPS-CFIKD---EAVYCKQDYA 66 (67)
Q Consensus 39 C~~C~~~l~~~~~-~~~~~---~~~~C~~~y~ 66 (67)
|..|+.||..... .-..| +.-||.-||.
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~ 34 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQ 34 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhc
Confidence 6777777765331 11122 3457777774
No 25
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.90 E-value=0.34 Score=21.17 Aligned_cols=31 Identities=19% Similarity=0.471 Sum_probs=20.9
Q ss_pred cCCccccccCcccc-Cceeee--ecCceeccccc
Q psy10221 7 TELRYCVACGESIT-DKYLLQ--VSDKSWHAQCL 37 (67)
Q Consensus 7 ~~~~~C~~C~~~i~-~~~~~~--~~~~~~h~~cf 37 (67)
.....|..|++.|. ...++. .=+..+|.+|.
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 34578999999995 222333 23677888886
No 26
>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=88.42 E-value=0.36 Score=19.86 Aligned_cols=23 Identities=35% Similarity=0.524 Sum_probs=14.3
Q ss_pred ccccccccccCCCCceeeeCCeecchhh
Q psy10221 37 LRCCICQLVLDRHPSCFIKDEAVYCKQD 64 (67)
Q Consensus 37 f~C~~C~~~l~~~~~~~~~~~~~~C~~~ 64 (67)
-.|..|+.||-. .++|+.+|..|
T Consensus 18 ~~Cp~C~~PL~~-----~k~g~~~Cv~C 40 (41)
T PF06677_consen 18 EHCPDCGTPLMR-----DKDGKIYCVSC 40 (41)
T ss_pred CccCCCCCeeEE-----ecCCCEECCCC
Confidence 345567766631 36778888765
No 27
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=87.84 E-value=0.26 Score=27.19 Aligned_cols=30 Identities=20% Similarity=0.389 Sum_probs=22.6
Q ss_pred ccccccccccCCCCceeeeCCeecchhhhcC
Q psy10221 37 LRCCICQLVLDRHPSCFIKDEAVYCKQDYAK 67 (67)
Q Consensus 37 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~k 67 (67)
-+|+.|+-...... ....+|++.|..||.+
T Consensus 173 v~C~kCGE~~~e~~-~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFMEPR-AVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccccch-hhhcCCceeccccccc
Confidence 58888988776543 2457899999999863
No 28
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=87.80 E-value=0.41 Score=21.24 Aligned_cols=25 Identities=20% Similarity=0.640 Sum_probs=18.0
Q ss_pred cccccccccCC-CCceeeeCCeecch
Q psy10221 38 RCCICQLVLDR-HPSCFIKDEAVYCK 62 (67)
Q Consensus 38 ~C~~C~~~l~~-~~~~~~~~~~~~C~ 62 (67)
.|..|++.|.. .++|.-++...+|.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS 43 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCS 43 (58)
T ss_pred HHHccCCCCCCCCCeeeecccccccc
Confidence 56788999984 45544577888885
No 29
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.52 E-value=0.29 Score=21.76 Aligned_cols=17 Identities=29% Similarity=0.585 Sum_probs=13.2
Q ss_pred cCCccccccCccccCce
Q psy10221 7 TELRYCVACGESITDKY 23 (67)
Q Consensus 7 ~~~~~C~~C~~~i~~~~ 23 (67)
...+.|..|+..|.+.+
T Consensus 5 ~~~~~CtSCg~~i~~~~ 21 (59)
T PRK14890 5 MEPPKCTSCGIEIAPRE 21 (59)
T ss_pred ccCccccCCCCcccCCC
Confidence 45568999999998654
No 30
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=87.37 E-value=0.63 Score=20.32 Aligned_cols=26 Identities=23% Similarity=0.558 Sum_probs=19.2
Q ss_pred ccccccCccccCceeeeecCceeccc
Q psy10221 10 RYCVACGESITDKYLLQVSDKSWHAQ 35 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~~~~~~~~h~~ 35 (67)
.+|..|+++|.++..+...+..-|+.
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~g 27 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHPG 27 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCcH
Confidence 47899999999876666666666653
No 31
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=87.32 E-value=1.1 Score=18.27 Aligned_cols=27 Identities=19% Similarity=0.301 Sum_probs=11.8
Q ss_pred cccccccccCCCCceeeeC-Ceecchhh
Q psy10221 38 RCCICQLVLDRHPSCFIKD-EAVYCKQD 64 (67)
Q Consensus 38 ~C~~C~~~l~~~~~~~~~~-~~~~C~~~ 64 (67)
+|+.|+++.......+... +...|..|
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~C 30 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDEC 30 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHH
Confidence 4566666665544333322 44456554
No 32
>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=85.41 E-value=1 Score=18.20 Aligned_cols=31 Identities=19% Similarity=0.490 Sum_probs=14.0
Q ss_pred CccccccCccccCceeeeecCceecccccccccccc
Q psy10221 9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQL 44 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~ 44 (67)
..+|..|+.-|-+--.+...++.| +|..|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 457788877776543344445555 6666664
No 33
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=84.85 E-value=0.43 Score=21.27 Aligned_cols=15 Identities=27% Similarity=0.603 Sum_probs=12.0
Q ss_pred CccccccCccccCce
Q psy10221 9 LRYCVACGESITDKY 23 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~ 23 (67)
.+.|..|+..|...+
T Consensus 9 ~~~CtSCg~~i~p~e 23 (61)
T COG2888 9 PPVCTSCGREIAPGE 23 (61)
T ss_pred CceeccCCCEeccCC
Confidence 678999999996554
No 34
>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=84.57 E-value=0.58 Score=21.73 Aligned_cols=32 Identities=22% Similarity=0.436 Sum_probs=19.6
Q ss_pred cCCccccccCccccCcee-ee----e-cC-----ceecccccc
Q psy10221 7 TELRYCVACGESITDKYL-LQ----V-SD-----KSWHAQCLR 38 (67)
Q Consensus 7 ~~~~~C~~C~~~i~~~~~-~~----~-~~-----~~~h~~cf~ 38 (67)
.+-..|..|++.|...++ +. . .+ ..+|..||.
T Consensus 5 s~Ra~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~ 47 (82)
T PF00645_consen 5 SGRAKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFF 47 (82)
T ss_dssp SSTEBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHH
T ss_pred CCCccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccc
Confidence 455689999999985433 21 1 12 346888876
No 35
>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=84.55 E-value=0.81 Score=18.20 Aligned_cols=22 Identities=23% Similarity=0.535 Sum_probs=14.3
Q ss_pred cccccccccCCCCceeeeCCeecchhh
Q psy10221 38 RCCICQLVLDRHPSCFIKDEAVYCKQD 64 (67)
Q Consensus 38 ~C~~C~~~l~~~~~~~~~~~~~~C~~~ 64 (67)
.|..|+.. .+...+|..||..|
T Consensus 10 ~C~~C~~~-----~~~~~dG~~yC~~c 31 (36)
T PF11781_consen 10 PCPVCGSR-----WFYSDDGFYYCDRC 31 (36)
T ss_pred cCCCCCCe-----EeEccCCEEEhhhC
Confidence 46666654 23567888888665
No 36
>KOG2893|consensus
Probab=84.51 E-value=0.43 Score=27.22 Aligned_cols=40 Identities=25% Similarity=0.537 Sum_probs=28.6
Q ss_pred cCCccccccCccccCceeeeecCceeccccccccccccccCCC
Q psy10221 7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRH 49 (67)
Q Consensus 7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~ 49 (67)
+..+-|..|+..+.+..++..-.+.=| |+|.+|.+-|-++
T Consensus 8 ~~kpwcwycnrefddekiliqhqkakh---fkchichkkl~sg 47 (341)
T KOG2893|consen 8 VDKPWCWYCNREFDDEKILIQHQKAKH---FKCHICHKKLFSG 47 (341)
T ss_pred cCCceeeecccccchhhhhhhhhhhcc---ceeeeehhhhccC
Confidence 345679999999988766655444434 8889999888554
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=84.42 E-value=0.91 Score=19.69 Aligned_cols=24 Identities=29% Similarity=0.650 Sum_probs=11.7
Q ss_pred cccccccccCCCCceeeeCCeecch
Q psy10221 38 RCCICQLVLDRHPSCFIKDEAVYCK 62 (67)
Q Consensus 38 ~C~~C~~~l~~~~~~~~~~~~~~C~ 62 (67)
.|..|...++... .+.++|+.||.
T Consensus 9 aC~~C~C~V~~~~-Ai~~dGk~YCS 32 (52)
T PF02069_consen 9 ACPSCSCVVSEEE-AIQKDGKYYCS 32 (52)
T ss_dssp SSTT----B-TTT-SEESSS-EESS
T ss_pred cCCCCEeEECchH-hHHhCCEeeec
Confidence 4566666666433 46788888884
No 38
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=84.11 E-value=0.34 Score=23.75 Aligned_cols=29 Identities=28% Similarity=0.421 Sum_probs=18.4
Q ss_pred cccccccccccCCCCceeeeCCeecchhh
Q psy10221 36 CLRCCICQLVLDRHPSCFIKDEAVYCKQD 64 (67)
Q Consensus 36 cf~C~~C~~~l~~~~~~~~~~~~~~C~~~ 64 (67)
=|+|+.|-.--.........+|.++|..|
T Consensus 70 EFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEechhhhccccCCCEecccc
Confidence 37888776543322233457899999877
No 39
>PRK00420 hypothetical protein; Validated
Probab=81.69 E-value=0.95 Score=22.74 Aligned_cols=10 Identities=40% Similarity=0.640 Sum_probs=5.2
Q ss_pred eCCeecchhh
Q psy10221 55 KDEAVYCKQD 64 (67)
Q Consensus 55 ~~~~~~C~~~ 64 (67)
++|+.+|..|
T Consensus 37 k~g~~~Cp~C 46 (112)
T PRK00420 37 KDGEVVCPVH 46 (112)
T ss_pred CCCceECCCC
Confidence 4555555544
No 40
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=81.08 E-value=0.53 Score=22.94 Aligned_cols=36 Identities=22% Similarity=0.348 Sum_probs=25.9
Q ss_pred cccccCccccCceeeeecC-ceecccccccccccccc
Q psy10221 11 YCVACGESITDKYLLQVSD-KSWHAQCLRCCICQLVL 46 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~~~-~~~h~~cf~C~~C~~~l 46 (67)
.|..|+.+|..++..+... .+-|-+|+.-+.-+++-
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~~ 44 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKPG 44 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCcC
Confidence 6899999999777766543 45788888766655543
No 41
>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=80.61 E-value=0.43 Score=18.92 Aligned_cols=31 Identities=26% Similarity=0.544 Sum_probs=17.1
Q ss_pred ccccCccccCceeeeecCceeccccccccccccccC
Q psy10221 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLD 47 (67)
Q Consensus 12 C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~ 47 (67)
|..|.+.+.+ ..++.||-.-..|..|+..+.
T Consensus 2 C~~C~~Ey~~-----p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFD-----PSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCS-----TTSTTTT-TT--BTTCC-SCC
T ss_pred CHHHHHHHcC-----CCCCcccCcCccCCCCCCCEE
Confidence 4455544433 346788988899999997764
No 42
>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=80.51 E-value=1.4 Score=16.02 Aligned_cols=10 Identities=30% Similarity=0.886 Sum_probs=4.4
Q ss_pred cccCccccCc
Q psy10221 13 VACGESITDK 22 (67)
Q Consensus 13 ~~C~~~i~~~ 22 (67)
..|+..|.+.
T Consensus 2 ~sC~~~i~~r 11 (24)
T PF07754_consen 2 TSCGRPIAPR 11 (24)
T ss_pred ccCCCcccCc
Confidence 3444444433
No 43
>KOG3579|consensus
Probab=79.81 E-value=0.95 Score=26.47 Aligned_cols=32 Identities=25% Similarity=0.563 Sum_probs=25.9
Q ss_pred ccccccCccccCceeeeecCceeccccccccc
Q psy10221 10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCI 41 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~ 41 (67)
..|.-|.+.++|...+.--...-|+.||-|+.
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR 300 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR 300 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCH
Confidence 45789999999887777667778999998864
No 44
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=78.44 E-value=0.12 Score=25.24 Aligned_cols=53 Identities=17% Similarity=0.508 Sum_probs=29.2
Q ss_pred ccccCccccCceeeeecCceeccccccccccccccCCCCceeeeCCeecchhhh
Q psy10221 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQDY 65 (67)
Q Consensus 12 C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y 65 (67)
|..|...+.+-......-..+++.+.-|..|...|+-.+ +...+.-++|...|
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~E-Y~~~~~Cp~C~spF 90 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAE-YGMCGSCPYCQSPF 90 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHH-HhhcCCCCCcCCCC
Confidence 444555555433333444557777788888888876422 33344445554433
No 45
>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=77.77 E-value=2.4 Score=17.82 Aligned_cols=29 Identities=17% Similarity=0.499 Sum_probs=15.2
Q ss_pred ccccCccccCceeeeecCceeccccccccccccccCC
Q psy10221 12 CVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR 48 (67)
Q Consensus 12 C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~ 48 (67)
|..|+++..++ + +-..-|-|..|.+.|..
T Consensus 2 CiiC~~~~~~G--I------~I~~~fIC~~CE~~iv~ 30 (46)
T PF10764_consen 2 CIICGKEKEEG--I------HIYGKFICSDCEKEIVN 30 (46)
T ss_pred eEeCCCcCCCC--E------EEECeEehHHHHHHhcc
Confidence 55566655543 1 12233667777766643
No 46
>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=77.74 E-value=1.1 Score=18.52 Aligned_cols=11 Identities=27% Similarity=0.606 Sum_probs=6.0
Q ss_pred cccccCccccC
Q psy10221 11 YCVACGESITD 21 (67)
Q Consensus 11 ~C~~C~~~i~~ 21 (67)
.|..|+++|.+
T Consensus 2 ~C~~C~~~i~g 12 (46)
T cd02249 2 SCDGCLKPIVG 12 (46)
T ss_pred CCcCCCCCCcC
Confidence 35666665443
No 47
>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=73.94 E-value=1.6 Score=17.92 Aligned_cols=9 Identities=44% Similarity=1.147 Sum_probs=4.6
Q ss_pred cccccCccc
Q psy10221 11 YCVACGESI 19 (67)
Q Consensus 11 ~C~~C~~~i 19 (67)
.|..|+.+|
T Consensus 6 ~C~~C~~~i 14 (44)
T smart00291 6 SCDTCGKPI 14 (44)
T ss_pred CCCCCCCCC
Confidence 455555543
No 48
>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=71.57 E-value=3.7 Score=17.26 Aligned_cols=11 Identities=36% Similarity=0.739 Sum_probs=6.7
Q ss_pred cccccCccccC
Q psy10221 11 YCVACGESITD 21 (67)
Q Consensus 11 ~C~~C~~~i~~ 21 (67)
.|..|.+.+..
T Consensus 2 ~Cd~C~~~~~~ 12 (49)
T cd02335 2 HCDYCSKDITG 12 (49)
T ss_pred CCCCcCCCCCC
Confidence 46667666654
No 49
>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=71.56 E-value=3.2 Score=17.35 Aligned_cols=26 Identities=19% Similarity=0.364 Sum_probs=12.9
Q ss_pred ccccccccCCCCceee---eCCeecchhhhc
Q psy10221 39 CCICQLVLDRHPSCFI---KDEAVYCKQDYA 66 (67)
Q Consensus 39 C~~C~~~l~~~~~~~~---~~~~~~C~~~y~ 66 (67)
|..|+..+... .+. ..+..+|..||.
T Consensus 3 C~~Cg~D~t~v--ryh~~~~~~~dLC~~CF~ 31 (45)
T cd02336 3 CFTCGNDCTRV--RYHNLKAKKYDLCPSCYQ 31 (45)
T ss_pred ccCCCCccCce--EEEecCCCccccChHHHh
Confidence 55555555431 121 123456777774
No 50
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=70.98 E-value=2.2 Score=18.45 Aligned_cols=29 Identities=28% Similarity=0.555 Sum_probs=18.0
Q ss_pred cccccCccccCceeeeecCceeccccccc
Q psy10221 11 YCVACGESITDKYLLQVSDKSWHAQCLRC 39 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~~~~~~h~~cf~C 39 (67)
.|+.|+..+.-.-=.+..++.|-.+|-.|
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vC 30 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVC 30 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhc
Confidence 58889988863211344566777776544
No 51
>PRK00807 50S ribosomal protein L24e; Validated
Probab=70.45 E-value=4.4 Score=17.44 Aligned_cols=32 Identities=19% Similarity=0.344 Sum_probs=19.6
Q ss_pred ccccccCccccCcee---eeecCceecccccccccccc
Q psy10221 10 RYCVACGESITDKYL---LQVSDKSWHAQCLRCCICQL 44 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~---~~~~~~~~h~~cf~C~~C~~ 44 (67)
..|..|+..|.+... +...++.+. |.+..|.+
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~---Fcs~KC~~ 36 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY---FCSSKCEK 36 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE---EeCHHHHH
Confidence 468999999984433 345566665 44444544
No 52
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=69.66 E-value=2.6 Score=15.28 Aligned_cols=13 Identities=31% Similarity=0.894 Sum_probs=9.1
Q ss_pred ccccccCccccCc
Q psy10221 10 RYCVACGESITDK 22 (67)
Q Consensus 10 ~~C~~C~~~i~~~ 22 (67)
..|..|+..+.+.
T Consensus 3 ~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 3 MFCPNCGAEIDPD 15 (26)
T ss_pred CCCcccCCcCCcc
Confidence 4688888877644
No 53
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.33 E-value=4.9 Score=22.07 Aligned_cols=45 Identities=16% Similarity=0.368 Sum_probs=30.2
Q ss_pred ccccCCccccccCcccc----CceeeeecCceecccc-ccccccccccCC
Q psy10221 4 TIITELRYCVACGESIT----DKYLLQVSDKSWHAQC-LRCCICQLVLDR 48 (67)
Q Consensus 4 ~~~~~~~~C~~C~~~i~----~~~~~~~~~~~~h~~c-f~C~~C~~~l~~ 48 (67)
++.+....|.+|+..-. ++..+.+.++..-.+- ++|..|.....-
T Consensus 12 ~~pq~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~tWN~ 61 (203)
T COG4332 12 GAPQPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYTWNI 61 (203)
T ss_pred cCChhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCCccch
Confidence 45566678999987654 4545667777533332 689999988753
No 54
>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=67.44 E-value=3.2 Score=17.07 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=6.7
Q ss_pred cccccCccccC
Q psy10221 11 YCVACGESITD 21 (67)
Q Consensus 11 ~C~~C~~~i~~ 21 (67)
.|.+|+++|..
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 46777775543
No 55
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=67.27 E-value=5.2 Score=17.32 Aligned_cols=25 Identities=20% Similarity=0.567 Sum_probs=16.5
Q ss_pred ccccccCccccCceeeeecCceecc
Q psy10221 10 RYCVACGESITDKYLLQVSDKSWHA 34 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~~~~~~~~h~ 34 (67)
..|..|+.+|..+-.+......-|+
T Consensus 2 ~iCvvCK~Pi~~al~v~T~~Gpvh~ 26 (53)
T PHA02610 2 KICVVCKQPIEKALVVETEKGPVHP 26 (53)
T ss_pred ceeeeeCCchhhceEEecCCCCCCC
Confidence 4688899999766555555555554
No 56
>PF12773 DZR: Double zinc ribbon
Probab=66.38 E-value=8 Score=15.97 Aligned_cols=16 Identities=19% Similarity=0.711 Sum_probs=10.9
Q ss_pred cccCCccccccCcccc
Q psy10221 5 IITELRYCVACGESIT 20 (67)
Q Consensus 5 ~~~~~~~C~~C~~~i~ 20 (67)
+..+...|..|+..+.
T Consensus 8 ~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCccccCChhhcCChh
Confidence 4455677777777776
No 57
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=66.14 E-value=2.1 Score=16.79 Aligned_cols=31 Identities=26% Similarity=0.437 Sum_probs=15.7
Q ss_pred cccccCccccC-ceeeeecCceecccccccccccccc
Q psy10221 11 YCVACGESITD-KYLLQVSDKSWHAQCLRCCICQLVL 46 (67)
Q Consensus 11 ~C~~C~~~i~~-~~~~~~~~~~~h~~cf~C~~C~~~l 46 (67)
.|..|+..+.- ...+...+. -++|..|+..+
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence 57778776652 212222221 25677776654
No 58
>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=63.37 E-value=7.2 Score=19.28 Aligned_cols=30 Identities=20% Similarity=0.463 Sum_probs=19.4
Q ss_pred ceeccccccccccccccCCCCceeeeCCeecchhh
Q psy10221 30 KSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCKQD 64 (67)
Q Consensus 30 ~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~ 64 (67)
..+...--.|..|+ + .-|++.++.+.|..|
T Consensus 29 g~~~va~daCeiC~----~-~GY~q~g~~lvC~~C 58 (102)
T PF10080_consen 29 GSYRVAFDACEICG----P-KGYYQEGDQLVCKNC 58 (102)
T ss_pred CCEEEEEEeccccC----C-CceEEECCEEEEecC
Confidence 34444445677772 2 336788889999887
No 59
>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=63.15 E-value=4.2 Score=17.22 Aligned_cols=6 Identities=50% Similarity=1.392 Sum_probs=3.4
Q ss_pred ccccCc
Q psy10221 12 CVACGE 17 (67)
Q Consensus 12 C~~C~~ 17 (67)
|..|+.
T Consensus 3 Cd~C~~ 8 (48)
T cd02341 3 CDSCGI 8 (48)
T ss_pred CCCCCC
Confidence 555655
No 60
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=62.49 E-value=4 Score=18.19 Aligned_cols=17 Identities=35% Similarity=0.688 Sum_probs=12.9
Q ss_pred CCccccccCccccCcee
Q psy10221 8 ELRYCVACGESITDKYL 24 (67)
Q Consensus 8 ~~~~C~~C~~~i~~~~~ 24 (67)
....|..|+++|...+.
T Consensus 7 PH~HC~VCg~aIp~de~ 23 (64)
T COG4068 7 PHRHCVVCGKAIPPDEQ 23 (64)
T ss_pred CCccccccCCcCCCccc
Confidence 34679999999987654
No 61
>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=62.29 E-value=5.7 Score=15.27 Aligned_cols=26 Identities=19% Similarity=0.514 Sum_probs=11.4
Q ss_pred ccccCccccCceeeeecCceeccccc
Q psy10221 12 CVACGESITDKYLLQVSDKSWHAQCL 37 (67)
Q Consensus 12 C~~C~~~i~~~~~~~~~~~~~h~~cf 37 (67)
|..|...+.....+..-+..||..|+
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~ 27 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCI 27 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHH
Confidence 55566655332222223444554443
No 62
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=61.58 E-value=6.3 Score=22.91 Aligned_cols=13 Identities=31% Similarity=0.631 Sum_probs=7.7
Q ss_pred CccccccCccccC
Q psy10221 9 LRYCVACGESITD 21 (67)
Q Consensus 9 ~~~C~~C~~~i~~ 21 (67)
...|..|+.+|..
T Consensus 245 GepC~~CGt~I~k 257 (273)
T COG0266 245 GEPCRRCGTPIEK 257 (273)
T ss_pred CCCCCccCCEeEE
Confidence 4456666666654
No 63
>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=61.53 E-value=3.4 Score=16.65 Aligned_cols=28 Identities=21% Similarity=0.494 Sum_probs=15.6
Q ss_pred cccccCccccCceeeee--cCceecccccc
Q psy10221 11 YCVACGESITDKYLLQV--SDKSWHAQCLR 38 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~--~~~~~h~~cf~ 38 (67)
.|.-|.+.+.+.+.+.. =+..||.+|+.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~ 31 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIK 31 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHH
Confidence 46777777753333322 35567766653
No 64
>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=61.28 E-value=5.3 Score=16.64 Aligned_cols=6 Identities=50% Similarity=1.403 Sum_probs=3.1
Q ss_pred ccccCc
Q psy10221 12 CVACGE 17 (67)
Q Consensus 12 C~~C~~ 17 (67)
|.+|+.
T Consensus 3 CDgCg~ 8 (43)
T cd02342 3 CDGCGV 8 (43)
T ss_pred CCCCCC
Confidence 555553
No 65
>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=61.19 E-value=1.7 Score=17.68 Aligned_cols=10 Identities=30% Similarity=0.913 Sum_probs=5.2
Q ss_pred cccccCcccc
Q psy10221 11 YCVACGESIT 20 (67)
Q Consensus 11 ~C~~C~~~i~ 20 (67)
.|..|+..+.
T Consensus 7 ~C~~Cg~~fe 16 (42)
T PF09723_consen 7 RCEECGHEFE 16 (42)
T ss_pred EeCCCCCEEE
Confidence 3555655544
No 66
>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=61.18 E-value=3.4 Score=13.95 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=7.4
Q ss_pred ccccccccccCC
Q psy10221 37 LRCCICQLVLDR 48 (67)
Q Consensus 37 f~C~~C~~~l~~ 48 (67)
|.|..|++....
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 456777766543
No 67
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=60.49 E-value=3.6 Score=14.24 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=8.4
Q ss_pred ccccccccccCC
Q psy10221 37 LRCCICQLVLDR 48 (67)
Q Consensus 37 f~C~~C~~~l~~ 48 (67)
|.|..|++.+.+
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 467788877654
No 68
>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=60.17 E-value=4.5 Score=18.00 Aligned_cols=13 Identities=31% Similarity=0.869 Sum_probs=9.3
Q ss_pred ccccccCccccCc
Q psy10221 10 RYCVACGESITDK 22 (67)
Q Consensus 10 ~~C~~C~~~i~~~ 22 (67)
..|..||++|.+.
T Consensus 4 kHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 4 KHCPVCGKPIPPD 16 (59)
T ss_pred CcCCcCCCcCCcc
Confidence 4677888887754
No 69
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=59.88 E-value=13 Score=25.42 Aligned_cols=53 Identities=17% Similarity=0.279 Sum_probs=32.2
Q ss_pred cccCCccccccCccccC-ceeeeecCceeccccccccccccccCCCCceeeeCCeecch
Q psy10221 5 IITELRYCVACGESITD-KYLLQVSDKSWHAQCLRCCICQLVLDRHPSCFIKDEAVYCK 62 (67)
Q Consensus 5 ~~~~~~~C~~C~~~i~~-~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~~~~~~~~~~C~ 62 (67)
+.++...|.+|..++.. .+.+--.+... -++|.+|++.-.+.. +..+.-++|.
T Consensus 792 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~--~~~~~~~~~~ 845 (1006)
T PRK12775 792 AETGVATCPKCHRPLEGDEEYVCCATSEL---QWRCDDCGKVSEGFA--FPYGMCPACG 845 (1006)
T ss_pred ccCCCccCcccCCCCCCCceeEEecCcce---eeehhhhcccccccc--CCcCcCcccc
Confidence 35667899999999984 33343333222 258999998765433 3334455553
No 70
>PRK12495 hypothetical protein; Provisional
Probab=58.20 E-value=5.6 Score=22.46 Aligned_cols=12 Identities=33% Similarity=0.717 Sum_probs=7.7
Q ss_pred CccccccCcccc
Q psy10221 9 LRYCVACGESIT 20 (67)
Q Consensus 9 ~~~C~~C~~~i~ 20 (67)
...|..|+.+|.
T Consensus 42 a~hC~~CG~PIp 53 (226)
T PRK12495 42 NAHCDECGDPIF 53 (226)
T ss_pred hhhcccccCccc
Confidence 346777777765
No 71
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=57.95 E-value=4.2 Score=16.01 Aligned_cols=10 Identities=20% Similarity=0.577 Sum_probs=5.9
Q ss_pred cccccCcccc
Q psy10221 11 YCVACGESIT 20 (67)
Q Consensus 11 ~C~~C~~~i~ 20 (67)
.|..|+....
T Consensus 4 ~Cp~C~~~y~ 13 (36)
T PF13717_consen 4 TCPNCQAKYE 13 (36)
T ss_pred ECCCCCCEEe
Confidence 4666666554
No 72
>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=57.27 E-value=4.8 Score=13.29 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=5.7
Q ss_pred ccccccccccCC
Q psy10221 37 LRCCICQLVLDR 48 (67)
Q Consensus 37 f~C~~C~~~l~~ 48 (67)
|.|..|+.....
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 456667665543
No 73
>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=57.12 E-value=8.6 Score=13.70 Aligned_cols=13 Identities=15% Similarity=0.503 Sum_probs=9.6
Q ss_pred ccccccccccCCC
Q psy10221 37 LRCCICQLVLDRH 49 (67)
Q Consensus 37 f~C~~C~~~l~~~ 49 (67)
|.|..|++.+.+.
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 5788888877653
No 74
>PRK08359 transcription factor; Validated
Probab=56.44 E-value=9.7 Score=20.72 Aligned_cols=21 Identities=24% Similarity=0.656 Sum_probs=12.8
Q ss_pred cccccCccccCc-eeeeecCce
Q psy10221 11 YCVACGESITDK-YLLQVSDKS 31 (67)
Q Consensus 11 ~C~~C~~~i~~~-~~~~~~~~~ 31 (67)
.|.-||..|... ..+...|..
T Consensus 8 ~CEiCG~~i~g~~~~v~ieGae 29 (176)
T PRK08359 8 YCEICGAEIRGPGHRIRIEGAE 29 (176)
T ss_pred eeecCCCccCCCCeEEEEcCeE
Confidence 477888888754 344454443
No 75
>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=55.98 E-value=15 Score=15.03 Aligned_cols=27 Identities=30% Similarity=0.779 Sum_probs=15.6
Q ss_pred ccccCccccCceeeeec--Cceecccccc
Q psy10221 12 CVACGESITDKYLLQVS--DKSWHAQCLR 38 (67)
Q Consensus 12 C~~C~~~i~~~~~~~~~--~~~~h~~cf~ 38 (67)
|..|++.-.+..++.=. +..+|..|..
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~ 30 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVG 30 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTST
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCC
Confidence 66677744444444322 4668888864
No 76
>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=54.97 E-value=12 Score=15.53 Aligned_cols=14 Identities=36% Similarity=0.802 Sum_probs=10.1
Q ss_pred cCCccccccCcccc
Q psy10221 7 TELRYCVACGESIT 20 (67)
Q Consensus 7 ~~~~~C~~C~~~i~ 20 (67)
.....|..|++.|.
T Consensus 9 ~~~~~C~~C~~~i~ 22 (53)
T PF00130_consen 9 SKPTYCDVCGKFIW 22 (53)
T ss_dssp SSTEB-TTSSSBEC
T ss_pred CCCCCCcccCcccC
Confidence 45678999999883
No 77
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=53.77 E-value=6.1 Score=16.20 Aligned_cols=27 Identities=26% Similarity=0.544 Sum_probs=11.1
Q ss_pred ccccCccccCceeee--ecCceecccccc
Q psy10221 12 CVACGESITDKYLLQ--VSDKSWHAQCLR 38 (67)
Q Consensus 12 C~~C~~~i~~~~~~~--~~~~~~h~~cf~ 38 (67)
|..|.+.+.-+..=. .=+..||..|+.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~ 29 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFK 29 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHH
Confidence 456666666543322 123458888864
No 78
>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=53.69 E-value=5.8 Score=16.70 Aligned_cols=10 Identities=40% Similarity=0.996 Sum_probs=5.8
Q ss_pred cccccC-cccc
Q psy10221 11 YCVACG-ESIT 20 (67)
Q Consensus 11 ~C~~C~-~~i~ 20 (67)
.|.+|+ .+|.
T Consensus 2 ~C~~C~~~~i~ 12 (49)
T cd02338 2 SCDGCGKSNFT 12 (49)
T ss_pred CCCCCcCCCcE
Confidence 466777 4444
No 79
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=53.29 E-value=5.4 Score=21.46 Aligned_cols=40 Identities=18% Similarity=0.364 Sum_probs=23.7
Q ss_pred ccCCccccccCccccCceeeeecC------ceeccccccccccccc
Q psy10221 6 ITELRYCVACGESITDKYLLQVSD------KSWHAQCLRCCICQLV 45 (67)
Q Consensus 6 ~~~~~~C~~C~~~i~~~~~~~~~~------~~~h~~cf~C~~C~~~ 45 (67)
......|..|+.++.....-.+.+ -..+.....|..|++-
T Consensus 94 ~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 94 FPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred ccccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 455788999999887321111111 1235556778888864
No 80
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=52.85 E-value=2.6 Score=20.82 Aligned_cols=14 Identities=43% Similarity=0.949 Sum_probs=10.4
Q ss_pred CccccccCccccCc
Q psy10221 9 LRYCVACGESITDK 22 (67)
Q Consensus 9 ~~~C~~C~~~i~~~ 22 (67)
-..|..|+++|...
T Consensus 80 yG~C~~Cge~I~~~ 93 (110)
T TIGR02420 80 YGYCEECGEEIGLR 93 (110)
T ss_pred CCchhccCCcccHH
Confidence 36788888888754
No 81
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=52.24 E-value=6.3 Score=16.20 Aligned_cols=27 Identities=22% Similarity=0.539 Sum_probs=15.4
Q ss_pred cccccCccccCceeeeecCceecccccccccccccc
Q psy10221 11 YCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL 46 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l 46 (67)
.|..|+..+...... . -++|..|+.++
T Consensus 5 ~C~~CG~~~~~~~~~----~-----~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYG----T-----GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCC----C-----ceECCCCCCeE
Confidence 577888776532111 1 25677777654
No 82
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=52.21 E-value=7.4 Score=15.82 Aligned_cols=6 Identities=33% Similarity=1.115 Sum_probs=3.2
Q ss_pred ccccCc
Q psy10221 12 CVACGE 17 (67)
Q Consensus 12 C~~C~~ 17 (67)
|..|..
T Consensus 3 C~~C~~ 8 (41)
T cd02337 3 CNECKH 8 (41)
T ss_pred CCCCCC
Confidence 555644
No 83
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=51.29 E-value=2.4 Score=18.25 Aligned_cols=11 Identities=27% Similarity=0.694 Sum_probs=6.2
Q ss_pred cccccccccCC
Q psy10221 38 RCCICQLVLDR 48 (67)
Q Consensus 38 ~C~~C~~~l~~ 48 (67)
+|+.|...|+.
T Consensus 24 ~C~gC~~~l~~ 34 (56)
T PF02591_consen 24 TCSGCHMELPP 34 (56)
T ss_pred ccCCCCEEcCH
Confidence 55566666544
No 84
>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=51.13 E-value=7.1 Score=16.59 Aligned_cols=7 Identities=43% Similarity=0.971 Sum_probs=4.1
Q ss_pred cccccCc
Q psy10221 11 YCVACGE 17 (67)
Q Consensus 11 ~C~~C~~ 17 (67)
.|..|++
T Consensus 2 ~Cd~C~~ 8 (49)
T cd02334 2 KCNICKE 8 (49)
T ss_pred CCCCCCC
Confidence 4666664
No 85
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=50.76 E-value=20 Score=18.96 Aligned_cols=21 Identities=24% Similarity=0.657 Sum_probs=13.3
Q ss_pred cccccCccccCc-eeeeecCce
Q psy10221 11 YCVACGESITDK-YLLQVSDKS 31 (67)
Q Consensus 11 ~C~~C~~~i~~~-~~~~~~~~~ 31 (67)
.|.-||..|... ..+...|..
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~ 23 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSE 23 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeE
Confidence 377888888755 445555544
No 86
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=49.81 E-value=14 Score=16.86 Aligned_cols=25 Identities=24% Similarity=0.436 Sum_probs=16.2
Q ss_pred CccccccCccccCcee---eeecCceec
Q psy10221 9 LRYCVACGESITDKYL---LQVSDKSWH 33 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~---~~~~~~~~h 33 (67)
...|..|+..|+++.. +...++.++
T Consensus 3 ~~~CsFcG~~I~PGtG~m~Vr~Dg~v~~ 30 (66)
T COG2075 3 VRVCSFCGKKIEPGTGIMYVRNDGKVLR 30 (66)
T ss_pred eeEecCcCCccCCCceEEEEecCCeEEE
Confidence 4578899999985433 334555554
No 87
>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=49.68 E-value=12 Score=19.48 Aligned_cols=37 Identities=16% Similarity=0.262 Sum_probs=20.6
Q ss_pred CccccccCccccCceeeeec------Cceeccccccccccccc
Q psy10221 9 LRYCVACGESITDKYLLQVS------DKSWHAQCLRCCICQLV 45 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~~~~~------~~~~h~~cf~C~~C~~~ 45 (67)
...|..|+..+.....-.+. -...+..-+.|..|++-
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCE
Confidence 57899999887632111111 11123445788888864
No 88
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=49.58 E-value=9.4 Score=21.24 Aligned_cols=11 Identities=36% Similarity=0.824 Sum_probs=5.2
Q ss_pred CccccccCccc
Q psy10221 9 LRYCVACGESI 19 (67)
Q Consensus 9 ~~~C~~C~~~i 19 (67)
...|..|++++
T Consensus 149 l~~C~~Cg~~~ 159 (247)
T PRK00085 149 LDHCAVCGAPG 159 (247)
T ss_pred hhhHhcCCCCC
Confidence 34455555443
No 89
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=49.35 E-value=15 Score=19.02 Aligned_cols=25 Identities=24% Similarity=0.271 Sum_probs=17.6
Q ss_pred CccccccCccccCcee---eeecCceec
Q psy10221 9 LRYCVACGESITDKYL---LQVSDKSWH 33 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~---~~~~~~~~h 33 (67)
...|..|+..|+++.. +...++.|+
T Consensus 4 ~e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 4 TRTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred eeeecCcCCcccCCCCcEEEecCCCEEE
Confidence 4579999999996543 445566665
No 90
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=48.76 E-value=11 Score=21.45 Aligned_cols=28 Identities=18% Similarity=0.260 Sum_probs=14.2
Q ss_pred cccccccccccCCCCceeeeCCeecchhh
Q psy10221 36 CLRCCICQLVLDRHPSCFIKDEAVYCKQD 64 (67)
Q Consensus 36 cf~C~~C~~~l~~~~~~~~~~~~~~C~~~ 64 (67)
=..|+.|+.+..... ++...+...|..|
T Consensus 154 l~~Ca~cg~~~~~~~-~s~~~~~~~C~~~ 181 (251)
T COG1381 154 LTSCARCGTPVDPVY-FSPKSGGFLCSKC 181 (251)
T ss_pred hHHHhCcCCcCCCcc-eeeccCcccchhc
Confidence 345566666655432 2445555555544
No 91
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=48.48 E-value=19 Score=24.87 Aligned_cols=32 Identities=25% Similarity=0.411 Sum_probs=20.6
Q ss_pred cCCccccccCccccCcee-eee-------cC---ceecccccc
Q psy10221 7 TELRYCVACGESITDKYL-LQV-------SD---KSWHAQCLR 38 (67)
Q Consensus 7 ~~~~~C~~C~~~i~~~~~-~~~-------~~---~~~h~~cf~ 38 (67)
++-..|.+|.+.|.-.++ +.. .+ ..+|..||.
T Consensus 15 S~Rs~Ck~C~~~I~K~~lRi~~~v~~~~~dg~~~~W~H~~Cf~ 57 (981)
T PLN03123 15 SSRSSCKTCKSPIDKDELRLGKMVQSTQFDGFMPMWNHASCIL 57 (981)
T ss_pred CCCccccccCCcccCCCeEEEEeecccccCCCCCeeecccccc
Confidence 445789999999985433 211 12 356888885
No 92
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=48.31 E-value=17 Score=15.62 Aligned_cols=13 Identities=38% Similarity=0.774 Sum_probs=8.9
Q ss_pred CCccccccCcccc
Q psy10221 8 ELRYCVACGESIT 20 (67)
Q Consensus 8 ~~~~C~~C~~~i~ 20 (67)
....|..||....
T Consensus 2 ~LkPCPFCG~~~~ 14 (61)
T PF14354_consen 2 ELKPCPFCGSADV 14 (61)
T ss_pred CCcCCCCCCCcce
Confidence 3567888976654
No 93
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=47.99 E-value=8.3 Score=15.18 Aligned_cols=10 Identities=20% Similarity=0.617 Sum_probs=6.1
Q ss_pred cccccCcccc
Q psy10221 11 YCVACGESIT 20 (67)
Q Consensus 11 ~C~~C~~~i~ 20 (67)
.|..|+....
T Consensus 4 ~CP~C~~~f~ 13 (37)
T PF13719_consen 4 TCPNCQTRFR 13 (37)
T ss_pred ECCCCCceEE
Confidence 4666666654
No 94
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=47.88 E-value=4.6 Score=21.00 Aligned_cols=35 Identities=23% Similarity=0.276 Sum_probs=21.8
Q ss_pred ccccccCccccCceeeeecCceeccccccccccccccC
Q psy10221 10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLD 47 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~ 47 (67)
=.|+.|+..+...+.+...+. ..-|.|..|+..|.
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 368889877764333322221 22389999998874
No 95
>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=47.85 E-value=15 Score=15.70 Aligned_cols=27 Identities=15% Similarity=0.365 Sum_probs=16.2
Q ss_pred cccccCccccCceeeeecCceecccccc
Q psy10221 11 YCVACGESITDKYLLQVSDKSWHAQCLR 38 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~~~~~~h~~cf~ 38 (67)
.|+-|++.+.+. ++...|..|-..|+.
T Consensus 3 ~Cpi~~~~~~~P-v~~~~G~v~~~~~i~ 29 (63)
T smart00504 3 LCPISLEVMKDP-VILPSGQTYERRAIE 29 (63)
T ss_pred CCcCCCCcCCCC-EECCCCCEEeHHHHH
Confidence 467777777664 444556556555553
No 96
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=47.79 E-value=29 Score=15.76 Aligned_cols=31 Identities=16% Similarity=0.447 Sum_probs=19.4
Q ss_pred CCccccccCccccCceeeeecCceecccccccccccc
Q psy10221 8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQL 44 (67)
Q Consensus 8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~ 44 (67)
....|..|+..+... .+.+..|- +.|..|+.
T Consensus 5 ~lKPCPFCG~~~~~v---~~~~g~~~---v~C~~CgA 35 (64)
T PRK09710 5 NVKPCPFCGCPSVTV---KAISGYYR---AKCNGCES 35 (64)
T ss_pred cccCCCCCCCceeEE---EecCceEE---EEcCCCCc
Confidence 457899999887643 34456564 44555554
No 97
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=47.73 E-value=5.7 Score=16.77 Aligned_cols=35 Identities=31% Similarity=0.481 Sum_probs=18.1
Q ss_pred ccccccCccccCceeeeecCceecccccccccccccc
Q psy10221 10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL 46 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l 46 (67)
..|..|.+.+.-........+..+ =++|..|+..|
T Consensus 7 v~C~~C~~lLqlP~~~~~~~k~~~--klrCGaCs~vl 41 (46)
T PF11331_consen 7 VVCSSCFELLQLPAKFSLSKKNQQ--KLRCGACSEVL 41 (46)
T ss_pred eECccHHHHHcCCCccCCCcccee--EEeCCCCceeE
Confidence 467778777762222222222222 26677777655
No 98
>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=47.30 E-value=11 Score=13.95 Aligned_cols=11 Identities=36% Similarity=0.766 Sum_probs=2.8
Q ss_pred cccccccccCC
Q psy10221 38 RCCICQLVLDR 48 (67)
Q Consensus 38 ~C~~C~~~l~~ 48 (67)
.|..|+.++.+
T Consensus 2 ~C~~C~~~~~~ 12 (30)
T PF07649_consen 2 RCDACGKPIDG 12 (30)
T ss_dssp --TTTS----S
T ss_pred cCCcCCCcCCC
Confidence 45566655543
No 99
>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=46.31 E-value=21 Score=14.91 Aligned_cols=7 Identities=29% Similarity=0.748 Sum_probs=3.6
Q ss_pred cccccCc
Q psy10221 11 YCVACGE 17 (67)
Q Consensus 11 ~C~~C~~ 17 (67)
.|.+|+.
T Consensus 2 ~Cd~C~~ 8 (45)
T cd02344 2 TCDGCQM 8 (45)
T ss_pred CCCCCCC
Confidence 3555653
No 100
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=46.18 E-value=18 Score=20.08 Aligned_cols=10 Identities=40% Similarity=1.142 Sum_probs=4.4
Q ss_pred CCccccccCc
Q psy10221 8 ELRYCVACGE 17 (67)
Q Consensus 8 ~~~~C~~C~~ 17 (67)
....|..|++
T Consensus 146 ~l~~C~~cg~ 155 (241)
T TIGR00613 146 DLDKCAVCGS 155 (241)
T ss_pred ccCccCCCCC
Confidence 3344444443
No 101
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=45.64 E-value=16 Score=21.00 Aligned_cols=9 Identities=22% Similarity=0.704 Sum_probs=3.8
Q ss_pred ccccccccc
Q psy10221 38 RCCICQLVL 46 (67)
Q Consensus 38 ~C~~C~~~l 46 (67)
.|-.|+.++
T Consensus 246 pCprCG~~I 254 (272)
T PRK14810 246 PCLNCKTPI 254 (272)
T ss_pred cCCCCCCee
Confidence 344444444
No 102
>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=45.46 E-value=7.6 Score=16.37 Aligned_cols=10 Identities=40% Similarity=0.956 Sum_probs=6.4
Q ss_pred cccccCc-ccc
Q psy10221 11 YCVACGE-SIT 20 (67)
Q Consensus 11 ~C~~C~~-~i~ 20 (67)
.|..|.+ +|.
T Consensus 2 ~C~~C~~~~i~ 12 (49)
T cd02345 2 SCSACRKQDIS 12 (49)
T ss_pred cCCCCCCCCce
Confidence 4677776 555
No 103
>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=45.20 E-value=8.9 Score=13.45 Aligned_cols=12 Identities=17% Similarity=0.520 Sum_probs=8.3
Q ss_pred ccccccccccCC
Q psy10221 37 LRCCICQLVLDR 48 (67)
Q Consensus 37 f~C~~C~~~l~~ 48 (67)
|.|..|++....
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 567778777654
No 104
>PHA02768 hypothetical protein; Provisional
Probab=44.89 E-value=4.8 Score=17.65 Aligned_cols=40 Identities=20% Similarity=0.360 Sum_probs=24.4
Q ss_pred cccccCccccCceeeeecCceeccccccccccccccCCCCc
Q psy10221 11 YCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRHPS 51 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~~~ 51 (67)
.|..|++.......+ .....-|..-++|..|++.....+.
T Consensus 7 ~C~~CGK~Fs~~~~L-~~H~r~H~k~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 7 ECPICGEIYIKRKSM-ITHLRKHNTNLKLSNCKRISLRTGE 46 (55)
T ss_pred CcchhCCeeccHHHH-HHHHHhcCCcccCCcccceecccce
Confidence 688899988754322 1122235556788888887654443
No 105
>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=44.74 E-value=5.4 Score=15.64 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=6.2
Q ss_pred cccccCcccc
Q psy10221 11 YCVACGESIT 20 (67)
Q Consensus 11 ~C~~C~~~i~ 20 (67)
.|..|++.+.
T Consensus 7 ~C~~Cg~~fe 16 (41)
T smart00834 7 RCEDCGHTFE 16 (41)
T ss_pred EcCCCCCEEE
Confidence 4666766554
No 106
>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=43.75 E-value=16 Score=22.92 Aligned_cols=38 Identities=21% Similarity=0.461 Sum_probs=25.6
Q ss_pred ccccccCccccCceeeeecCceeccccccccccccccCC
Q psy10221 10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR 48 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~ 48 (67)
-.|..|-..+...+ +...+......||.|-.|..+|..
T Consensus 27 ~yCp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 27 YYCPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred eECccccccCChhh-heeccceeccccccCCCCCCccee
Confidence 45667766665443 334445556689999999999864
No 107
>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=43.74 E-value=8.9 Score=15.09 Aligned_cols=15 Identities=33% Similarity=0.851 Sum_probs=6.4
Q ss_pred CccccccCccccCce
Q psy10221 9 LRYCVACGESITDKY 23 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~ 23 (67)
.+.|..|++++.+..
T Consensus 3 ~~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 3 YPKCDECGKPFMDSY 17 (34)
T ss_dssp -EE-TTT--EES-SS
T ss_pred CchHhHhCCHHHHHH
Confidence 356777777776654
No 108
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.97 E-value=20 Score=20.69 Aligned_cols=9 Identities=22% Similarity=0.600 Sum_probs=4.1
Q ss_pred ccccccccc
Q psy10221 38 RCCICQLVL 46 (67)
Q Consensus 38 ~C~~C~~~l 46 (67)
.|-.|+.++
T Consensus 247 pC~~Cg~~I 255 (272)
T TIGR00577 247 PCRRCGTPI 255 (272)
T ss_pred CCCCCCCee
Confidence 344455444
No 109
>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=42.27 E-value=6.9 Score=16.37 Aligned_cols=11 Identities=36% Similarity=0.860 Sum_probs=7.2
Q ss_pred cccccCccccC
Q psy10221 11 YCVACGESITD 21 (67)
Q Consensus 11 ~C~~C~~~i~~ 21 (67)
.|..|+.....
T Consensus 7 ~C~~Cg~~fe~ 17 (52)
T TIGR02605 7 RCTACGHRFEV 17 (52)
T ss_pred EeCCCCCEeEE
Confidence 57778766653
No 110
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=42.23 E-value=21 Score=20.58 Aligned_cols=9 Identities=22% Similarity=0.600 Sum_probs=4.4
Q ss_pred ccccccccc
Q psy10221 38 RCCICQLVL 46 (67)
Q Consensus 38 ~C~~C~~~l 46 (67)
.|-.|+..+
T Consensus 247 pC~~Cg~~I 255 (274)
T PRK01103 247 PCRRCGTPI 255 (274)
T ss_pred CCCCCCCee
Confidence 344455554
No 111
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=42.09 E-value=16 Score=13.98 Aligned_cols=10 Identities=20% Similarity=0.604 Sum_probs=6.0
Q ss_pred cccccCcccc
Q psy10221 11 YCVACGESIT 20 (67)
Q Consensus 11 ~C~~C~~~i~ 20 (67)
.|..|+..+.
T Consensus 3 ~C~~C~t~L~ 12 (31)
T TIGR01053 3 VCGGCRTLLM 12 (31)
T ss_pred CcCCCCcEee
Confidence 4666666554
No 112
>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=41.70 E-value=15 Score=17.69 Aligned_cols=41 Identities=22% Similarity=0.342 Sum_probs=23.5
Q ss_pred ccCCccccccCccccCceeeeecCceeccccccccccccccCC
Q psy10221 6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR 48 (67)
Q Consensus 6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~ 48 (67)
......|..|++++.-.+.+-.. +|-..--+|..|+.+++.
T Consensus 30 ~~~rS~C~~C~~~L~~~~lIPi~--S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 30 IFPRSHCPHCGHPLSWWDLIPIL--SYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred cCCCCcCcCCCCcCcccccchHH--HHHHhCCCCcccCCCCCh
Confidence 34457788888888744333221 233333467777777754
No 113
>smart00355 ZnF_C2H2 zinc finger.
Probab=41.46 E-value=15 Score=12.02 Aligned_cols=11 Identities=36% Similarity=0.742 Sum_probs=6.5
Q ss_pred cccccccccCC
Q psy10221 38 RCCICQLVLDR 48 (67)
Q Consensus 38 ~C~~C~~~l~~ 48 (67)
.|..|+..+..
T Consensus 2 ~C~~C~~~f~~ 12 (26)
T smart00355 2 RCPECGKVFKS 12 (26)
T ss_pred CCCCCcchhCC
Confidence 56667666543
No 114
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=41.32 E-value=21 Score=20.53 Aligned_cols=11 Identities=36% Similarity=0.902 Sum_probs=5.5
Q ss_pred ccccccCcccc
Q psy10221 10 RYCVACGESIT 20 (67)
Q Consensus 10 ~~C~~C~~~i~ 20 (67)
..|..|+.+|.
T Consensus 236 ~pC~~Cg~~I~ 246 (269)
T PRK14811 236 QPCPRCGTPIE 246 (269)
T ss_pred CCCCcCCCeeE
Confidence 34555555553
No 115
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=41.19 E-value=15 Score=15.17 Aligned_cols=10 Identities=30% Similarity=0.777 Sum_probs=5.4
Q ss_pred cccccCcccc
Q psy10221 11 YCVACGESIT 20 (67)
Q Consensus 11 ~C~~C~~~i~ 20 (67)
.|..|+..+.
T Consensus 4 ~C~~Cg~~~~ 13 (44)
T smart00659 4 ICGECGRENE 13 (44)
T ss_pred ECCCCCCEee
Confidence 3556665544
No 116
>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=41.14 E-value=14 Score=14.26 Aligned_cols=12 Identities=42% Similarity=1.074 Sum_probs=7.1
Q ss_pred cccccCccccCc
Q psy10221 11 YCVACGESITDK 22 (67)
Q Consensus 11 ~C~~C~~~i~~~ 22 (67)
.|..|+++|...
T Consensus 5 ~C~~CGe~I~~~ 16 (36)
T PF01258_consen 5 ICEDCGEPIPEE 16 (36)
T ss_dssp B-TTTSSBEEHH
T ss_pred CccccCChHHHH
Confidence 477777777643
No 117
>KOG0978|consensus
Probab=41.14 E-value=7.5 Score=25.59 Aligned_cols=28 Identities=36% Similarity=0.633 Sum_probs=20.2
Q ss_pred CCccccccCccccCceeeeecCceeccccccc
Q psy10221 8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRC 39 (67)
Q Consensus 8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C 39 (67)
+.-.|+.|+...-+. +..+.+|..|+.|
T Consensus 642 ~~LkCs~Cn~R~Kd~----vI~kC~H~FC~~C 669 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKDA----VITKCGHVFCEEC 669 (698)
T ss_pred hceeCCCccCchhhH----HHHhcchHHHHHH
Confidence 346799998666664 2357899999866
No 118
>PF14149 YhfH: YhfH-like protein
Probab=40.99 E-value=6.7 Score=15.79 Aligned_cols=15 Identities=27% Similarity=0.758 Sum_probs=11.4
Q ss_pred cCCccccccCccccC
Q psy10221 7 TELRYCVACGESITD 21 (67)
Q Consensus 7 ~~~~~C~~C~~~i~~ 21 (67)
.....|..||+.|.+
T Consensus 11 Lp~K~C~~CG~~i~E 25 (37)
T PF14149_consen 11 LPPKKCTECGKEIEE 25 (37)
T ss_pred CCCcccHHHHHHHHH
Confidence 456789999998864
No 119
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=40.95 E-value=19 Score=17.16 Aligned_cols=19 Identities=21% Similarity=0.536 Sum_probs=11.5
Q ss_pred ccccccCCccccccCcccc
Q psy10221 2 FKTIITELRYCVACGESIT 20 (67)
Q Consensus 2 ~~~~~~~~~~C~~C~~~i~ 20 (67)
|.+|-.-.+.|..|+....
T Consensus 1 F~g~Lk~~~~C~~CG~d~~ 19 (86)
T PF06170_consen 1 FRGYLKVAPRCPHCGLDYS 19 (86)
T ss_pred CCccccCCCcccccCCccc
Confidence 3445555667777776654
No 120
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=40.36 E-value=9.4 Score=17.09 Aligned_cols=12 Identities=17% Similarity=0.301 Sum_probs=8.5
Q ss_pred eeeCCeecchhh
Q psy10221 53 FIKDEAVYCKQD 64 (67)
Q Consensus 53 ~~~~~~~~C~~~ 64 (67)
...+|.+.|..|
T Consensus 48 ~i~eg~L~Cp~c 59 (68)
T PF03966_consen 48 EIVEGELICPEC 59 (68)
T ss_dssp ETTTTEEEETTT
T ss_pred cccCCEEEcCCC
Confidence 346788888776
No 121
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.30 E-value=23 Score=20.56 Aligned_cols=10 Identities=20% Similarity=0.481 Sum_probs=4.9
Q ss_pred cccccccccc
Q psy10221 37 LRCCICQLVL 46 (67)
Q Consensus 37 f~C~~C~~~l 46 (67)
-.|-.|+.++
T Consensus 255 ~pC~~Cg~~I 264 (282)
T PRK13945 255 KPCRKCGTPI 264 (282)
T ss_pred CCCCcCCCee
Confidence 3444555554
No 122
>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=40.27 E-value=25 Score=12.99 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=6.7
Q ss_pred ccccccccccCC
Q psy10221 37 LRCCICQLVLDR 48 (67)
Q Consensus 37 f~C~~C~~~l~~ 48 (67)
|.|..|.+.+.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF03107_consen 1 FWCDVCRRKIDG 12 (30)
T ss_pred CCCCCCCCCcCC
Confidence 346666665554
No 123
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=40.08 E-value=12 Score=21.62 Aligned_cols=38 Identities=21% Similarity=0.454 Sum_probs=13.7
Q ss_pred ccccccCccccCceeeeec------------CceeccccccccccccccC
Q psy10221 10 RYCVACGESITDKYLLQVS------------DKSWHAQCLRCCICQLVLD 47 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~~~~------------~~~~h~~cf~C~~C~~~l~ 47 (67)
..|..||..-.-..+.... +..||..-..|..|+..-.
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~ 222 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDH 222 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCC
Confidence 6899999876533222221 2236655666777776543
No 124
>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=39.69 E-value=7.4 Score=16.07 Aligned_cols=6 Identities=17% Similarity=0.860 Sum_probs=3.7
Q ss_pred cchhhh
Q psy10221 60 YCKQDY 65 (67)
Q Consensus 60 ~C~~~y 65 (67)
+|..||
T Consensus 30 LC~~C~ 35 (46)
T PF00569_consen 30 LCEDCF 35 (46)
T ss_dssp EEHHHH
T ss_pred hhhHHH
Confidence 466665
No 125
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=39.65 E-value=17 Score=15.67 Aligned_cols=10 Identities=10% Similarity=0.238 Sum_probs=4.1
Q ss_pred eCCeecchhh
Q psy10221 55 KDEAVYCKQD 64 (67)
Q Consensus 55 ~~~~~~C~~~ 64 (67)
+.++.+|..|
T Consensus 34 H~dR~~CGkC 43 (51)
T COG1998 34 HKDRWACGKC 43 (51)
T ss_pred cCceeEeccc
Confidence 3334444433
No 126
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=39.56 E-value=9.8 Score=14.89 Aligned_cols=10 Identities=30% Similarity=1.165 Sum_probs=3.8
Q ss_pred cccccCcccc
Q psy10221 11 YCVACGESIT 20 (67)
Q Consensus 11 ~C~~C~~~i~ 20 (67)
.|..|+.++.
T Consensus 2 fC~~CG~~l~ 11 (34)
T PF14803_consen 2 FCPQCGGPLE 11 (34)
T ss_dssp B-TTT--B-E
T ss_pred ccccccChhh
Confidence 4677777764
No 127
>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=39.00 E-value=12 Score=15.53 Aligned_cols=8 Identities=38% Similarity=1.111 Sum_probs=5.2
Q ss_pred eCCeecch
Q psy10221 55 KDEAVYCK 62 (67)
Q Consensus 55 ~~~~~~C~ 62 (67)
.++.+||.
T Consensus 20 ~~~~lYCS 27 (43)
T PF12855_consen 20 DDGSLYCS 27 (43)
T ss_pred CCCccccC
Confidence 46677774
No 128
>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=38.66 E-value=10 Score=13.95 Aligned_cols=12 Identities=33% Similarity=0.625 Sum_probs=5.7
Q ss_pred ccccccCccccC
Q psy10221 10 RYCVACGESITD 21 (67)
Q Consensus 10 ~~C~~C~~~i~~ 21 (67)
..|..|+..|.+
T Consensus 2 ~~C~rC~~~~~~ 13 (30)
T PF06827_consen 2 EKCPRCWNYIED 13 (30)
T ss_dssp SB-TTT--BBEE
T ss_pred CcCccCCCcceE
Confidence 357777777654
No 129
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=38.13 E-value=7 Score=20.68 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=19.5
Q ss_pred cccccCccccCceeeeecCceeccccccccccccccC
Q psy10221 11 YCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLD 47 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~ 47 (67)
.|..|+..+.-.+.+. .-|.|..|+..|.
T Consensus 111 ~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 111 ICPNMCVRFTFNEAME--------LNFTCPRCGAMLD 139 (158)
T ss_pred ECCCCCcEeeHHHHHH--------cCCcCCCCCCEee
Confidence 5888886665333332 2489999998875
No 130
>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=37.79 E-value=15 Score=17.78 Aligned_cols=13 Identities=38% Similarity=0.925 Sum_probs=9.0
Q ss_pred ccccccCccccCc
Q psy10221 10 RYCVACGESITDK 22 (67)
Q Consensus 10 ~~C~~C~~~i~~~ 22 (67)
..|+.||+.|.+.
T Consensus 70 GiCamCGKki~dt 82 (90)
T PF10235_consen 70 GICAMCGKKILDT 82 (90)
T ss_pred CcccccCCeeccc
Confidence 4677788877653
No 131
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=37.70 E-value=34 Score=13.98 Aligned_cols=8 Identities=38% Similarity=0.953 Sum_probs=3.9
Q ss_pred ccccccCc
Q psy10221 10 RYCVACGE 17 (67)
Q Consensus 10 ~~C~~C~~ 17 (67)
..|..|+.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 34555554
No 132
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=37.45 E-value=12 Score=16.90 Aligned_cols=12 Identities=33% Similarity=0.869 Sum_probs=8.5
Q ss_pred ccccccccccCC
Q psy10221 37 LRCCICQLVLDR 48 (67)
Q Consensus 37 f~C~~C~~~l~~ 48 (67)
.+|.+|++.+++
T Consensus 5 vRCFTCGkvi~~ 16 (62)
T PRK04016 5 VRCFTCGKVIAE 16 (62)
T ss_pred eEecCCCCChHH
Confidence 367778888765
No 133
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=36.99 E-value=21 Score=14.07 Aligned_cols=14 Identities=29% Similarity=0.740 Sum_probs=6.0
Q ss_pred CccccccCccccCc
Q psy10221 9 LRYCVACGESITDK 22 (67)
Q Consensus 9 ~~~C~~C~~~i~~~ 22 (67)
...|..|++.+...
T Consensus 6 ~~~C~~C~~~~~~~ 19 (43)
T PF06467_consen 6 MKTCSYCKKYIPNK 19 (43)
T ss_dssp CEE-TTT--EEECC
T ss_pred CCcCcccCCcccCC
Confidence 34566666666543
No 134
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=36.89 E-value=19 Score=17.10 Aligned_cols=14 Identities=21% Similarity=0.631 Sum_probs=11.2
Q ss_pred ccccccccccCCCC
Q psy10221 37 LRCCICQLVLDRHP 50 (67)
Q Consensus 37 f~C~~C~~~l~~~~ 50 (67)
|.|..|+.+|.+..
T Consensus 3 f~C~~C~t~l~ds~ 16 (96)
T PF03226_consen 3 FQCKNCKTILADSN 16 (96)
T ss_pred EECCCCCCCcCCHH
Confidence 78899999987644
No 135
>PRK10445 endonuclease VIII; Provisional
Probab=36.66 E-value=28 Score=19.97 Aligned_cols=9 Identities=22% Similarity=0.648 Sum_probs=4.4
Q ss_pred ccccccccc
Q psy10221 38 RCCICQLVL 46 (67)
Q Consensus 38 ~C~~C~~~l 46 (67)
.|-.|+.++
T Consensus 237 ~Cp~Cg~~I 245 (263)
T PRK10445 237 ACERCGGII 245 (263)
T ss_pred CCCCCCCEe
Confidence 344455554
No 136
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=36.54 E-value=33 Score=13.22 Aligned_cols=10 Identities=20% Similarity=0.235 Sum_probs=4.5
Q ss_pred eCCeecchhh
Q psy10221 55 KDEAVYCKQD 64 (67)
Q Consensus 55 ~~~~~~C~~~ 64 (67)
.++..+|..|
T Consensus 18 ~~~~~~C~~C 27 (33)
T PF08792_consen 18 EDDYEVCIFC 27 (33)
T ss_pred cCCeEEcccC
Confidence 3444445443
No 137
>KOG2186|consensus
Probab=36.32 E-value=8 Score=22.40 Aligned_cols=37 Identities=22% Similarity=0.496 Sum_probs=24.1
Q ss_pred cccccCccccCceeeeecCceeccccccccccccccCC
Q psy10221 11 YCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR 48 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~ 48 (67)
.|..|+..|--..+-.... ..|-.+|+|.+|++.+..
T Consensus 5 tCnvCgEsvKKp~vekH~s-rCrn~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 5 TCNVCGESVKKPQVEKHMS-RCRNAYFSCIDCGKTFER 41 (276)
T ss_pred ehhhhhhhccccchHHHHH-hccCCeeEEeeccccccc
Confidence 5788888886432221111 135578999999998765
No 138
>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=36.04 E-value=28 Score=18.69 Aligned_cols=38 Identities=18% Similarity=0.325 Sum_probs=21.8
Q ss_pred ccccccCccccCceee---eecCceeccccccccccccccCC
Q psy10221 10 RYCVACGESITDKYLL---QVSDKSWHAQCLRCCICQLVLDR 48 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~---~~~~~~~h~~cf~C~~C~~~l~~ 48 (67)
..|..|+.+|...+.+ ...+..|+.- --|..|+++...
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~P-sYC~~CGkpyPW 80 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAP-SYCHNCGKPYPW 80 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCC-hhHHhCCCCCch
Confidence 4577788888754332 2334445432 356777777653
No 139
>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 COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.55 E-value=32 Score=17.27 Aligned_cols=19 Identities=21% Similarity=0.555 Sum_probs=14.0
Q ss_pred ccCCccccccCccccCcee
Q psy10221 6 ITELRYCVACGESITDKYL 24 (67)
Q Consensus 6 ~~~~~~C~~C~~~i~~~~~ 24 (67)
..|...|+.|+.++....+
T Consensus 46 e~G~t~CP~Cg~~~e~~fv 64 (115)
T COG1885 46 EVGSTSCPKCGEPFESAFV 64 (115)
T ss_pred ecccccCCCCCCccceeEE
Confidence 3456789999999887543
No 141
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=34.47 E-value=10 Score=20.50 Aligned_cols=30 Identities=23% Similarity=0.531 Sum_probs=19.7
Q ss_pred cccccCccccCceeeeecCceeccccccccccccccCC
Q psy10221 11 YCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR 48 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~ 48 (67)
.|..|+....-.+.+. .-|.|..|+..|..
T Consensus 119 ~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHIRFTFDEAME--------YGFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCcEEeHHHHhh--------cCCcCCCCCCCCee
Confidence 5777876665333321 24899999988853
No 142
>PRK05978 hypothetical protein; Provisional
Probab=34.24 E-value=26 Score=18.60 Aligned_cols=31 Identities=23% Similarity=0.417 Sum_probs=17.9
Q ss_pred ccccccCccccCceeeeecCceeccccccccccccccCC
Q psy10221 10 RYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR 48 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~ 48 (67)
.+|..|++.=.-... ..---+|..|+..+..
T Consensus 34 grCP~CG~G~LF~g~--------Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGKLFRAF--------LKPVDHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCcccccc--------cccCCCccccCCcccc
Confidence 578888887663211 1122456777777653
No 143
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=33.92 E-value=13 Score=16.48 Aligned_cols=13 Identities=31% Similarity=0.608 Sum_probs=10.1
Q ss_pred ccccccccccCCC
Q psy10221 37 LRCCICQLVLDRH 49 (67)
Q Consensus 37 f~C~~C~~~l~~~ 49 (67)
..|+.|++.|+..
T Consensus 5 lVCsTCGrDlSee 17 (63)
T PHA03082 5 LVCSTCGRDLSEE 17 (63)
T ss_pred eeecccCcchhHH
Confidence 5788999888753
No 144
>PHA02929 N1R/p28-like protein; Provisional
Probab=33.60 E-value=31 Score=19.77 Aligned_cols=14 Identities=36% Similarity=0.657 Sum_probs=10.8
Q ss_pred CccccccCccccCc
Q psy10221 9 LRYCVACGESITDK 22 (67)
Q Consensus 9 ~~~C~~C~~~i~~~ 22 (67)
...|+-|...+.+.
T Consensus 174 ~~eC~ICle~~~~~ 187 (238)
T PHA02929 174 DKECAICMEKVYDK 187 (238)
T ss_pred CCCCccCCcccccC
Confidence 46799999887754
No 145
>KOG1723|consensus
Probab=33.27 E-value=22 Score=19.20 Aligned_cols=16 Identities=19% Similarity=0.322 Sum_probs=12.3
Q ss_pred CccccccCccccCcee
Q psy10221 9 LRYCVACGESITDKYL 24 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~ 24 (67)
...|..|+.+|++...
T Consensus 3 i~kc~fcss~IyPgHg 18 (162)
T KOG1723|consen 3 IEKCYFCSSPIYPGHG 18 (162)
T ss_pred eeeeeeecCcccCCCc
Confidence 4578999999997633
No 146
>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=33.21 E-value=14 Score=16.38 Aligned_cols=13 Identities=31% Similarity=0.608 Sum_probs=10.1
Q ss_pred ccccccccccCCC
Q psy10221 37 LRCCICQLVLDRH 49 (67)
Q Consensus 37 f~C~~C~~~l~~~ 49 (67)
..|+.|++.|+..
T Consensus 5 lvCSTCGrDlSee 17 (63)
T PF05864_consen 5 LVCSTCGRDLSEE 17 (63)
T ss_pred eeecccCCcchHH
Confidence 5788999888753
No 147
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.19 E-value=51 Score=16.68 Aligned_cols=11 Identities=18% Similarity=0.875 Sum_probs=6.1
Q ss_pred cccccCccccC
Q psy10221 11 YCVACGESITD 21 (67)
Q Consensus 11 ~C~~C~~~i~~ 21 (67)
.|.+|.+++.+
T Consensus 57 ~C~~C~~~f~~ 67 (112)
T TIGR00622 57 FCFGCQGPFPK 67 (112)
T ss_pred cccCcCCCCCC
Confidence 46666665543
No 148
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=33.19 E-value=21 Score=14.13 Aligned_cols=13 Identities=38% Similarity=0.779 Sum_probs=9.4
Q ss_pred ccccccCccccCc
Q psy10221 10 RYCVACGESITDK 22 (67)
Q Consensus 10 ~~C~~C~~~i~~~ 22 (67)
..|..|++.+.+.
T Consensus 33 ~~C~~CGE~~~~~ 45 (46)
T TIGR03831 33 LVCPQCGEEYLDA 45 (46)
T ss_pred cccccCCCEeeCC
Confidence 4688888877653
No 149
>smart00746 TRASH metallochaperone-like domain.
Probab=33.10 E-value=32 Score=11.97 Aligned_cols=9 Identities=44% Similarity=1.113 Sum_probs=5.7
Q ss_pred ccccCcccc
Q psy10221 12 CVACGESIT 20 (67)
Q Consensus 12 C~~C~~~i~ 20 (67)
|..|+..|.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 556777665
No 150
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=33.08 E-value=40 Score=16.74 Aligned_cols=19 Identities=21% Similarity=0.572 Sum_probs=13.8
Q ss_pred ccCCccccccCccccCcee
Q psy10221 6 ITELRYCVACGESITDKYL 24 (67)
Q Consensus 6 ~~~~~~C~~C~~~i~~~~~ 24 (67)
..+...|..|++++.....
T Consensus 44 evG~~~cP~Cge~~~~a~v 62 (102)
T PF04475_consen 44 EVGDTICPKCGEELDSAFV 62 (102)
T ss_pred ecCcccCCCCCCccCceEE
Confidence 4456789999988877543
No 151
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=33.01 E-value=24 Score=13.06 Aligned_cols=12 Identities=17% Similarity=0.761 Sum_probs=8.9
Q ss_pred ccccccccccCC
Q psy10221 37 LRCCICQLVLDR 48 (67)
Q Consensus 37 f~C~~C~~~l~~ 48 (67)
+.|..|++.+.+
T Consensus 4 ~~C~~C~~~~~~ 15 (35)
T smart00451 4 FYCKLCNVTFTD 15 (35)
T ss_pred eEccccCCccCC
Confidence 568888887764
No 152
>PF10170 C6_DPF: Cysteine-rich domain; InterPro: IPR018785 This entry represents the N-terminal approximately 100 amino acids of a family of proteins found in a range of organisms, including human, chicken and Drosophila [, , ]. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Probab=32.72 E-value=28 Score=17.14 Aligned_cols=30 Identities=17% Similarity=0.290 Sum_probs=16.4
Q ss_pred ccccccccccccCCCCceeeeCCeecchhh
Q psy10221 35 QCLRCCICQLVLDRHPSCFIKDEAVYCKQD 64 (67)
Q Consensus 35 ~cf~C~~C~~~l~~~~~~~~~~~~~~C~~~ 64 (67)
---.|+.|+++.-.+..+-.-..+-+|..|
T Consensus 48 LGa~CS~C~~~VC~~~~CSlFYtkrFC~pC 77 (97)
T PF10170_consen 48 LGAPCSICGKPVCVGQDCSLFYTKRFCLPC 77 (97)
T ss_pred ECccccccCCceEcCCCccEEeeCceeHHH
Confidence 345788888886433223233334566655
No 153
>KOG2879|consensus
Probab=32.09 E-value=39 Score=20.00 Aligned_cols=34 Identities=29% Similarity=0.397 Sum_probs=21.5
Q ss_pred ccccCCccccccCccccCceeeeecCceecccccccc
Q psy10221 4 TIITELRYCVACGESITDKYLLQVSDKSWHAQCLRCC 40 (67)
Q Consensus 4 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~ 40 (67)
+..+....|..|++.-..... .++.-|..|..|.
T Consensus 234 s~~t~~~~C~~Cg~~PtiP~~---~~~C~HiyCY~Ci 267 (298)
T KOG2879|consen 234 STGTSDTECPVCGEPPTIPHV---IGKCGHIYCYYCI 267 (298)
T ss_pred ccccCCceeeccCCCCCCCee---eccccceeehhhh
Confidence 334456789999988875433 3445566666553
No 154
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=31.79 E-value=28 Score=16.77 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=8.0
Q ss_pred cccccCccccC
Q psy10221 11 YCVACGESITD 21 (67)
Q Consensus 11 ~C~~C~~~i~~ 21 (67)
.|..|+..+..
T Consensus 2 fC~~Cg~~l~~ 12 (104)
T TIGR01384 2 FCPKCGSLMTP 12 (104)
T ss_pred CCcccCccccc
Confidence 58888877754
No 155
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=31.69 E-value=34 Score=18.95 Aligned_cols=22 Identities=27% Similarity=0.505 Sum_probs=14.7
Q ss_pred ccccccccccCCCCceeeeCCeecchhh
Q psy10221 37 LRCCICQLVLDRHPSCFIKDEAVYCKQD 64 (67)
Q Consensus 37 f~C~~C~~~l~~~~~~~~~~~~~~C~~~ 64 (67)
-.|+.|+.+|- .++..++|+.|
T Consensus 150 A~CsrC~~~L~------~~~~~l~Cp~C 171 (188)
T COG1096 150 ARCSRCRAPLV------KKGNMLKCPNC 171 (188)
T ss_pred EEccCCCcceE------EcCcEEECCCC
Confidence 46777776662 25667788876
No 156
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.43 E-value=50 Score=17.20 Aligned_cols=37 Identities=19% Similarity=0.429 Sum_probs=20.2
Q ss_pred ccccccCccccCceeee---ecCceeccccccccccccccC
Q psy10221 10 RYCVACGESITDKYLLQ---VSDKSWHAQCLRCCICQLVLD 47 (67)
Q Consensus 10 ~~C~~C~~~i~~~~~~~---~~~~~~h~~cf~C~~C~~~l~ 47 (67)
..|..|+.+|.....+. .++..|-+-- -|..|+++..
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~ps-fchncgs~fp 79 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPS-FCHNCGSRFP 79 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcc-hhhcCCCCCC
Confidence 45777777777544432 3444454443 3566666554
No 157
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=31.24 E-value=18 Score=14.55 Aligned_cols=10 Identities=30% Similarity=0.843 Sum_probs=4.2
Q ss_pred cccccCcccc
Q psy10221 11 YCVACGESIT 20 (67)
Q Consensus 11 ~C~~C~~~i~ 20 (67)
.|..||..|.
T Consensus 21 vC~~CG~Vl~ 30 (43)
T PF08271_consen 21 VCPNCGLVLE 30 (43)
T ss_dssp EETTT-BBEE
T ss_pred ECCCCCCEee
Confidence 4444544443
No 158
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=31.17 E-value=31 Score=16.81 Aligned_cols=16 Identities=19% Similarity=0.609 Sum_probs=10.8
Q ss_pred ccCCccccccCccccC
Q psy10221 6 ITELRYCVACGESITD 21 (67)
Q Consensus 6 ~~~~~~C~~C~~~i~~ 21 (67)
..+.+.|+.|+.++..
T Consensus 31 ~~~~p~C~~cg~pL~G 46 (93)
T COG2174 31 KPTIPKCAICGRPLGG 46 (93)
T ss_pred cCCCCcccccCCccCC
Confidence 4456777777777764
No 159
>PRK03922 hypothetical protein; Provisional
Probab=31.17 E-value=43 Score=16.92 Aligned_cols=19 Identities=26% Similarity=0.684 Sum_probs=14.1
Q ss_pred ccCCccccccCccccCcee
Q psy10221 6 ITELRYCVACGESITDKYL 24 (67)
Q Consensus 6 ~~~~~~C~~C~~~i~~~~~ 24 (67)
..|...|+.|++++.....
T Consensus 46 evG~~~cP~cge~~~~afv 64 (113)
T PRK03922 46 EVGLTICPKCGEPFDSAFV 64 (113)
T ss_pred ecCcccCCCCCCcCCcEEE
Confidence 4466789999999887643
No 160
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=30.93 E-value=27 Score=14.13 Aligned_cols=13 Identities=31% Similarity=0.631 Sum_probs=9.4
Q ss_pred CCccccccCcccc
Q psy10221 8 ELRYCVACGESIT 20 (67)
Q Consensus 8 ~~~~C~~C~~~i~ 20 (67)
+...|..|++.|.
T Consensus 2 GtIvCq~C~~~Id 14 (38)
T PF13790_consen 2 GTIVCQHCNETID 14 (38)
T ss_pred CEEEeccccceee
Confidence 3457888888876
No 161
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=30.31 E-value=24 Score=15.76 Aligned_cols=11 Identities=36% Similarity=0.902 Sum_probs=6.5
Q ss_pred cccccccccCC
Q psy10221 38 RCCICQLVLDR 48 (67)
Q Consensus 38 ~C~~C~~~l~~ 48 (67)
+|-+|++.+++
T Consensus 6 RCFTCGkvi~~ 16 (60)
T PF01194_consen 6 RCFTCGKVIGN 16 (60)
T ss_dssp S-STTTSBTCG
T ss_pred ecCCCCCChhH
Confidence 56667777754
No 162
>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=30.26 E-value=43 Score=14.57 Aligned_cols=25 Identities=20% Similarity=0.301 Sum_probs=16.0
Q ss_pred CccccccCccccCcee---eeecCceec
Q psy10221 9 LRYCVACGESITDKYL---LQVSDKSWH 33 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~---~~~~~~~~h 33 (67)
...|..|+..|+++.. +...++.++
T Consensus 3 ~~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 3 TEKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEEecCcCCeecCCCccEEEecCCCEEE
Confidence 4578889999985432 344555554
No 163
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=29.82 E-value=31 Score=17.07 Aligned_cols=12 Identities=33% Similarity=0.725 Sum_probs=2.7
Q ss_pred ccccccCccccC
Q psy10221 10 RYCVACGESITD 21 (67)
Q Consensus 10 ~~C~~C~~~i~~ 21 (67)
..|+.|+.+..+
T Consensus 15 ~~CalCG~tWg~ 26 (105)
T PF11494_consen 15 MGCALCGATWGD 26 (105)
T ss_dssp GS-SS---S---
T ss_pred ccccccCCcHHH
Confidence 346666666554
No 164
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=29.82 E-value=16 Score=16.13 Aligned_cols=11 Identities=45% Similarity=0.936 Sum_probs=9.4
Q ss_pred ccccccCcccc
Q psy10221 10 RYCVACGESIT 20 (67)
Q Consensus 10 ~~C~~C~~~i~ 20 (67)
..|.+|+++|.
T Consensus 11 t~CrRCGk~i~ 21 (60)
T PF10892_consen 11 TPCRRCGKSIR 21 (60)
T ss_pred ehhhhhCccHH
Confidence 46899999997
No 165
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=29.54 E-value=39 Score=14.34 Aligned_cols=10 Identities=10% Similarity=0.089 Sum_probs=5.2
Q ss_pred eCCeecchhh
Q psy10221 55 KDEAVYCKQD 64 (67)
Q Consensus 55 ~~~~~~C~~~ 64 (67)
+.+...|..|
T Consensus 34 ~~~r~~C~~C 43 (50)
T PRK00432 34 HLDRWHCGKC 43 (50)
T ss_pred cCCcEECCCc
Confidence 3445556554
No 166
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=29.30 E-value=32 Score=17.11 Aligned_cols=12 Identities=25% Similarity=0.769 Sum_probs=5.7
Q ss_pred cCCccccccCcc
Q psy10221 7 TELRYCVACGES 18 (67)
Q Consensus 7 ~~~~~C~~C~~~ 18 (67)
++-..|.-|+.+
T Consensus 11 ~~N~~CaDCg~~ 22 (116)
T PF01412_consen 11 PGNKVCADCGAP 22 (116)
T ss_dssp TTCTB-TTT-SB
T ss_pred cCcCcCCCCCCC
Confidence 444667777633
No 167
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=29.20 E-value=12 Score=16.19 Aligned_cols=13 Identities=15% Similarity=0.393 Sum_probs=8.9
Q ss_pred CccccccCccccC
Q psy10221 9 LRYCVACGESITD 21 (67)
Q Consensus 9 ~~~C~~C~~~i~~ 21 (67)
..+|..|++.+..
T Consensus 4 eiRC~~CnklLa~ 16 (51)
T PF10122_consen 4 EIRCGHCNKLLAK 16 (51)
T ss_pred ceeccchhHHHhh
Confidence 3467888877764
No 168
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=28.85 E-value=30 Score=14.70 Aligned_cols=9 Identities=33% Similarity=0.733 Sum_probs=5.2
Q ss_pred cccccCccc
Q psy10221 11 YCVACGESI 19 (67)
Q Consensus 11 ~C~~C~~~i 19 (67)
.|.+|.+.+
T Consensus 2 ~CdgC~~~~ 10 (48)
T cd02343 2 SCDGCDEIA 10 (48)
T ss_pred CCCCCCCcC
Confidence 366676643
No 169
>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=28.84 E-value=24 Score=12.47 Aligned_cols=9 Identities=22% Similarity=0.659 Sum_probs=5.4
Q ss_pred ccccccccc
Q psy10221 37 LRCCICQLV 45 (67)
Q Consensus 37 f~C~~C~~~ 45 (67)
|.|..|++.
T Consensus 15 ~~C~~C~k~ 23 (26)
T PF13465_consen 15 YKCPYCGKS 23 (26)
T ss_dssp EEESSSSEE
T ss_pred CCCCCCcCe
Confidence 566666654
No 170
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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 N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=28.56 E-value=60 Score=14.60 Aligned_cols=7 Identities=14% Similarity=0.586 Sum_probs=3.7
Q ss_pred ecchhhh
Q psy10221 59 VYCKQDY 65 (67)
Q Consensus 59 ~~C~~~y 65 (67)
.+|..||
T Consensus 26 ~iC~~CF 32 (71)
T PF02207_consen 26 GICEECF 32 (71)
T ss_dssp BBEHHHH
T ss_pred EEchhhC
Confidence 3455554
No 171
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=28.21 E-value=32 Score=14.26 Aligned_cols=7 Identities=29% Similarity=0.961 Sum_probs=4.3
Q ss_pred cccccCc
Q psy10221 11 YCVACGE 17 (67)
Q Consensus 11 ~C~~C~~ 17 (67)
.|.+|++
T Consensus 2 ~Cd~C~~ 8 (45)
T cd02339 2 ICDTCRK 8 (45)
T ss_pred CCCCCCC
Confidence 4667773
No 172
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=27.73 E-value=64 Score=13.82 Aligned_cols=27 Identities=22% Similarity=0.556 Sum_probs=16.0
Q ss_pred ccccccCcccc-Cce-eeeecCceecccc
Q psy10221 10 RYCVACGESIT-DKY-LLQVSDKSWHAQC 36 (67)
Q Consensus 10 ~~C~~C~~~i~-~~~-~~~~~~~~~h~~c 36 (67)
..|+.|+.... +.+ .+...+..|+..|
T Consensus 14 ~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 14 CKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred ccCcccCCcEeecCcceEEEeccceeeee
Confidence 56888877665 222 3555566666555
No 173
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=27.68 E-value=11 Score=19.92 Aligned_cols=15 Identities=33% Similarity=0.897 Sum_probs=11.3
Q ss_pred CCccccccCccccCc
Q psy10221 8 ELRYCVACGESITDK 22 (67)
Q Consensus 8 ~~~~C~~C~~~i~~~ 22 (67)
.-..|..|+++|...
T Consensus 110 tYG~Ce~CGe~I~~~ 124 (151)
T PRK10778 110 DFGYCESCGVEIGIR 124 (151)
T ss_pred CCceeccCCCcccHH
Confidence 346788999998754
No 174
>PRK13796 GTPase YqeH; Provisional
Probab=27.03 E-value=43 Score=20.16 Aligned_cols=10 Identities=40% Similarity=1.215 Sum_probs=7.4
Q ss_pred cccccCcccc
Q psy10221 11 YCVACGESIT 20 (67)
Q Consensus 11 ~C~~C~~~i~ 20 (67)
.|.+||..+.
T Consensus 2 ~C~GCG~~lq 11 (365)
T PRK13796 2 RCIGCGAAIQ 11 (365)
T ss_pred cccCCCceeE
Confidence 5888887774
No 175
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.93 E-value=82 Score=20.88 Aligned_cols=12 Identities=42% Similarity=1.118 Sum_probs=6.0
Q ss_pred CCccccccCccc
Q psy10221 8 ELRYCVACGESI 19 (67)
Q Consensus 8 ~~~~C~~C~~~i 19 (67)
++..|..||.++
T Consensus 14 ~akFC~~CG~~l 25 (645)
T PRK14559 14 NNRFCQKCGTSL 25 (645)
T ss_pred CCccccccCCCC
Confidence 344555555544
No 176
>KOG1829|consensus
Probab=26.68 E-value=27 Score=22.70 Aligned_cols=13 Identities=31% Similarity=0.682 Sum_probs=8.5
Q ss_pred ccccccccccccC
Q psy10221 35 QCLRCCICQLVLD 47 (67)
Q Consensus 35 ~cf~C~~C~~~l~ 47 (67)
.-|.|+.|+.++.
T Consensus 339 Q~~~CAgC~~~i~ 351 (580)
T KOG1829|consen 339 QNFRCAGCGHTIG 351 (580)
T ss_pred cCceecccCCCcc
Confidence 3466777777765
No 177
>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=26.30 E-value=70 Score=15.17 Aligned_cols=31 Identities=19% Similarity=0.499 Sum_probs=16.8
Q ss_pred cccccCccccCcee--eeecCceecccccccccccc
Q psy10221 11 YCVACGESITDKYL--LQVSDKSWHAQCLRCCICQL 44 (67)
Q Consensus 11 ~C~~C~~~i~~~~~--~~~~~~~~h~~cf~C~~C~~ 44 (67)
.|..|+.+|..... +...+..-+ |.|..|..
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~---FCC~GC~~ 34 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERP---FCCPGCQA 34 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccc---cccHHHHH
Confidence 58899999963222 333343322 55555543
No 178
>PRK06424 transcription factor; Provisional
Probab=26.23 E-value=49 Score=17.40 Aligned_cols=20 Identities=15% Similarity=0.514 Sum_probs=14.8
Q ss_pred ccccCccccCceeeeecCce
Q psy10221 12 CVACGESITDKYLLQVSDKS 31 (67)
Q Consensus 12 C~~C~~~i~~~~~~~~~~~~ 31 (67)
|.-||+.|.....+...|.-
T Consensus 3 CE~CG~~~~~~~~v~ieg~~ 22 (144)
T PRK06424 3 CEMCGKKVPQTTKVMIDGAI 22 (144)
T ss_pred ccccCcccCCceEEEEcCee
Confidence 88899999876666666654
No 179
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=26.12 E-value=35 Score=15.12 Aligned_cols=16 Identities=25% Similarity=0.654 Sum_probs=8.1
Q ss_pred ccccCCccccccCccc
Q psy10221 4 TIITELRYCVACGESI 19 (67)
Q Consensus 4 ~~~~~~~~C~~C~~~i 19 (67)
..+.....|+.|+..|
T Consensus 47 ~~kd~~H~Cp~C~~~l 62 (67)
T smart00714 47 SFKDVNHYCPNCGAFL 62 (67)
T ss_pred cccCccEECCCCCCEe
Confidence 3444455555555544
No 180
>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=25.95 E-value=37 Score=12.31 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=5.7
Q ss_pred cccccCcccc
Q psy10221 11 YCVACGESIT 20 (67)
Q Consensus 11 ~C~~C~~~i~ 20 (67)
.|..|++.|.
T Consensus 2 ~CP~C~~~V~ 11 (26)
T PF10571_consen 2 TCPECGAEVP 11 (26)
T ss_pred cCCCCcCCch
Confidence 4566666554
No 181
>KOG1734|consensus
Probab=25.68 E-value=34 Score=20.23 Aligned_cols=31 Identities=23% Similarity=0.532 Sum_probs=19.4
Q ss_pred CCccccccCccccCce---ee------eecCceecccccc
Q psy10221 8 ELRYCVACGESITDKY---LL------QVSDKSWHAQCLR 38 (67)
Q Consensus 8 ~~~~C~~C~~~i~~~~---~~------~~~~~~~h~~cf~ 38 (67)
+...|+.|++.+.... .+ ..-+..||..|.+
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIr 262 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIR 262 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhh
Confidence 3468999999986322 11 1235678887754
No 182
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=25.11 E-value=29 Score=13.70 Aligned_cols=14 Identities=29% Similarity=0.541 Sum_probs=9.5
Q ss_pred CCccccccCccccC
Q psy10221 8 ELRYCVACGESITD 21 (67)
Q Consensus 8 ~~~~C~~C~~~i~~ 21 (67)
....|..|.+.|..
T Consensus 10 ~~~~C~~C~~~i~~ 23 (49)
T smart00109 10 KPTKCCVCRKSIWG 23 (49)
T ss_pred CCCCccccccccCc
Confidence 34568888877754
No 183
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=24.75 E-value=36 Score=12.97 Aligned_cols=10 Identities=30% Similarity=0.806 Sum_probs=6.8
Q ss_pred cccccccccc
Q psy10221 37 LRCCICQLVL 46 (67)
Q Consensus 37 f~C~~C~~~l 46 (67)
|.|..|+..|
T Consensus 17 ~~C~~C~v~l 26 (32)
T PF13842_consen 17 YMCSKCDVPL 26 (32)
T ss_pred EEccCCCCcc
Confidence 6777777555
No 184
>PF00020 TNFR_c6: TNFR/NGFR cysteine-rich region; InterPro: IPR001368 A number of proteins, some of which are known to be receptors for growth factors have been found to contain a cysteine-rich domain at the N-terminal region that can be subdivided into four (or in some cases, three) repeats containing six conserved cysteines all of which are involved in intrachain disulphide bonds []. CD27 (also called S152 or T14) mediates a co-stimulatory signal for T and B cell activation and is involved in murine T cell development. Tyrosine-phosphorylation of ZAP-70 following CD27 ligation of T cells has been reported [], but not confirmed independently. CD30 was originally identified as Ki-1, an antigen expressed on Reed-Sternberg cells in Hodgkin's lymphomas and other non-Hodgkin's lymphomas, particularly diffuse large-cell lymphoma and immunoblastic lymphoma. CD30 has pleiotropic effects on CD30-positive lymphoma cell lines ranging from cell proliferation to cell death. It is thought to be involved in negative selection of T-cells in the thymus and is involved in TCR-mediated cell death. CD30 is a member of the TNFR family of molecules, activate NFkB through interaction with TRAF2 and TRAF5. CD40 (Bp50) plays a central role in the regulation of cell-mediated immunity as well as antibody mediated immunity. It is central to T cell dependent (TD)-responses and may influence survival of B cell lymphomas. CD95 (also called APO-1, fas antigen, Fas tumour necrosis factor receptor superfamily, member 6, TNFRSF6 or apoptosis antigen 1, APT1) is expressed, typically at high levels, on activated T and B cells. It is involved in the mediation of apoptosis-inducing signals. Other proteins known to belong to this family [, , , ] are, tumour Necrosis Factor type I and type II receptors (TNFR), Rabbit fibroma virus soluble TNF receptor (protein T2), lymphotoxin alpha/beta receptor, low-affinity nerve growth factor receptor (LA-NGFR) (p75), T-cell antigen OX40, Wsl-1, a receptor (for a yet undefined ligand) that mediates apoptosis and Vaccinia virus protein A53 (SalF19R). CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/).; GO: 0005488 binding; PDB: 3TJE_F 3QD6_S 3ALQ_U 3IJ2_Y 3BUK_D 1SG1_X 1NCF_B 1EXT_A 1FT4_B 1TNR_R ....
Probab=24.19 E-value=29 Score=13.50 Aligned_cols=11 Identities=45% Similarity=1.084 Sum_probs=9.1
Q ss_pred ccccccccccc
Q psy10221 34 AQCLRCCICQL 44 (67)
Q Consensus 34 ~~cf~C~~C~~ 44 (67)
..|+.|..|..
T Consensus 13 ~~C~~C~~C~~ 23 (39)
T PF00020_consen 13 PQCLPCSRCPP 23 (39)
T ss_dssp SSEEEEESBTT
T ss_pred CcCCccCCcCc
Confidence 67888888886
No 185
>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=24.16 E-value=39 Score=15.58 Aligned_cols=25 Identities=16% Similarity=0.113 Sum_probs=12.7
Q ss_pred CccccccCccccCcee---eeecCceec
Q psy10221 9 LRYCVACGESITDKYL---LQVSDKSWH 33 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~---~~~~~~~~h 33 (67)
...|..|+..|+++.. +...++.++
T Consensus 3 ~~~C~Fsg~~I~PG~G~~~Vr~DG~v~~ 30 (71)
T PF01246_consen 3 TEKCSFSGYKIYPGHGKMYVRNDGKVFY 30 (71)
T ss_dssp SEE-TTT-SEE-SSSSEEEE-TTS-EEE
T ss_pred eEEecccCCccCCCCCeEEEecCCCeEE
Confidence 4679999999986543 334455554
No 186
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.14 E-value=72 Score=20.03 Aligned_cols=35 Identities=17% Similarity=0.375 Sum_probs=23.8
Q ss_pred cccCCccccccCccccCceeeeecCceeccccccccccccccCCC
Q psy10221 5 IITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDRH 49 (67)
Q Consensus 5 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~~ 49 (67)
+....+.|..|+.....+ |+. -|+|..|+..+...
T Consensus 346 ~~~~~p~Cp~Cg~~m~S~------G~~----g~rC~kCg~~~~~~ 380 (421)
T COG1571 346 YERVNPVCPRCGGRMKSA------GRN----GFRCKKCGTRARET 380 (421)
T ss_pred eEEcCCCCCccCCchhhc------CCC----CcccccccccCCcc
Confidence 455678899998766543 222 37888888887653
No 187
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=23.79 E-value=45 Score=14.82 Aligned_cols=16 Identities=44% Similarity=0.918 Sum_probs=12.3
Q ss_pred cCCccccccCccccCc
Q psy10221 7 TELRYCVACGESITDK 22 (67)
Q Consensus 7 ~~~~~C~~C~~~i~~~ 22 (67)
.+...|..|+.+|...
T Consensus 29 ~s~g~C~~Cg~~Ip~~ 44 (63)
T TIGR02419 29 PSLRECEDCGEPIPEA 44 (63)
T ss_pred CCCCeeccCCCcChHH
Confidence 3456899999999864
No 188
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=23.75 E-value=54 Score=19.67 Aligned_cols=39 Identities=18% Similarity=0.401 Sum_probs=22.0
Q ss_pred ccCCccccccCccccCceeeeecCceeccccccccccccccCC
Q psy10221 6 ITELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLDR 48 (67)
Q Consensus 6 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~~ 48 (67)
..+-.+|.-|+.+- +.. ....-..| -|+.|+.-.+.|+.
T Consensus 17 ~~~Nk~CaDCga~~-P~W-~S~nlGvf--iCi~CagvHRsLGv 55 (319)
T COG5347 17 DSSNKKCADCGAPN-PTW-ASVNLGVF--LCIDCAGVHRSLGV 55 (319)
T ss_pred ccccCccccCCCCC-Cce-EecccCeE--EEeecchhhhcccc
Confidence 34557888888776 332 22221222 36777776777764
No 189
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=23.67 E-value=63 Score=14.17 Aligned_cols=13 Identities=23% Similarity=0.583 Sum_probs=6.5
Q ss_pred CccccccCccccC
Q psy10221 9 LRYCVACGESITD 21 (67)
Q Consensus 9 ~~~C~~C~~~i~~ 21 (67)
...|+.|+.....
T Consensus 28 Sq~C~~CG~~~~~ 40 (69)
T PF07282_consen 28 SQTCPRCGHRNKK 40 (69)
T ss_pred ccCccCccccccc
Confidence 3455555555443
No 190
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=23.23 E-value=79 Score=18.86 Aligned_cols=38 Identities=18% Similarity=0.398 Sum_probs=22.8
Q ss_pred CccccccCccccCceeeeec-----C-----ceecccccccccccccc
Q psy10221 9 LRYCVACGESITDKYLLQVS-----D-----KSWHAQCLRCCICQLVL 46 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~~~~~-----~-----~~~h~~cf~C~~C~~~l 46 (67)
...|..|+..|+-+....+. + ......-++|..|+..+
T Consensus 40 ~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i 87 (324)
T PF04502_consen 40 NIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEI 87 (324)
T ss_pred cCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEE
Confidence 46799999999854333321 2 22233446777777665
No 191
>PHA00080 DksA-like zinc finger domain containing protein
Probab=23.11 E-value=48 Score=15.22 Aligned_cols=33 Identities=24% Similarity=0.626 Sum_probs=19.9
Q ss_pred cCCccccccCccccCceeeeecCceeccccccccccccc
Q psy10221 7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLV 45 (67)
Q Consensus 7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~ 45 (67)
.+...|..|+++|... .+.+ -|.+..|..|...
T Consensus 29 ~~~~~C~~Cg~~Ip~~-Rl~a-----~P~~~~Cv~Cq~~ 61 (72)
T PHA00080 29 PSATHCEECGDPIPEA-RREA-----VPGCRTCVSCQEI 61 (72)
T ss_pred CCCCEecCCCCcCcHH-HHHh-----CCCccCcHHHHHH
Confidence 3456899999999854 2222 3344556666543
No 192
>PF05810 NinF: NinF protein; InterPro: IPR008712 This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
Probab=23.08 E-value=31 Score=15.23 Aligned_cols=13 Identities=23% Similarity=0.790 Sum_probs=10.2
Q ss_pred cccccCccccCce
Q psy10221 11 YCVACGESITDKY 23 (67)
Q Consensus 11 ~C~~C~~~i~~~~ 23 (67)
.|+.|++.+...+
T Consensus 19 lCa~C~~~L~~~E 31 (58)
T PF05810_consen 19 LCANCGQKLHPDE 31 (58)
T ss_pred HHhccCcccccch
Confidence 4999999887654
No 193
>KOG2462|consensus
Probab=23.02 E-value=34 Score=20.10 Aligned_cols=38 Identities=18% Similarity=0.255 Sum_probs=15.8
Q ss_pred CccccccCccccCceeeeecCceeccccccccccccccC
Q psy10221 9 LRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLD 47 (67)
Q Consensus 9 ~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~ 47 (67)
+..|..|++.-..... ..+-..-|.--+.|.+|++.++
T Consensus 161 a~~C~~C~K~YvSmpA-LkMHirTH~l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 161 AFSCKYCGKVYVSMPA-LKMHIRTHTLPCECGICGKAFS 198 (279)
T ss_pred cccCCCCCceeeehHH-HhhHhhccCCCccccccccccc
Confidence 3455555554442211 1111222433445555555543
No 194
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=22.89 E-value=23 Score=15.95 Aligned_cols=11 Identities=36% Similarity=0.875 Sum_probs=7.0
Q ss_pred cccccccccCC
Q psy10221 38 RCCICQLVLDR 48 (67)
Q Consensus 38 ~C~~C~~~l~~ 48 (67)
+|-.|++++++
T Consensus 6 RCFsCGkvi~~ 16 (63)
T COG1644 6 RCFSCGKVIGH 16 (63)
T ss_pred EeecCCCCHHH
Confidence 45667777654
No 195
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=22.78 E-value=29 Score=16.06 Aligned_cols=11 Identities=36% Similarity=0.902 Sum_probs=7.2
Q ss_pred cccccccccCC
Q psy10221 38 RCCICQLVLDR 48 (67)
Q Consensus 38 ~C~~C~~~l~~ 48 (67)
+|.+|++.+++
T Consensus 6 RCFTCGkvig~ 16 (71)
T PLN00032 6 RCFTCGKVIGN 16 (71)
T ss_pred eecCCCCCcHH
Confidence 56667777754
No 196
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=22.74 E-value=93 Score=15.34 Aligned_cols=36 Identities=19% Similarity=0.403 Sum_probs=17.3
Q ss_pred CCccccccCccccCceeeeecCceeccccccccccccccC
Q psy10221 8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVLD 47 (67)
Q Consensus 8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l~ 47 (67)
+-..|+-|+..- +.. +...-.. .-|..|+.-.+.|+
T Consensus 2 ~N~~CaDC~~~~-p~w-~s~~~Gi--fvC~~CsgiHR~lg 37 (112)
T smart00105 2 GNKKCFDCGAPN-PTW-ASVNLGV--FLCIECSGIHRSLG 37 (112)
T ss_pred CCCcccCCCCCC-CCc-EEeccce--eEhHHhHHHHHhcC
Confidence 346788887633 222 2221111 13566666566664
No 197
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=22.53 E-value=81 Score=17.15 Aligned_cols=20 Identities=25% Similarity=0.584 Sum_probs=12.1
Q ss_pred ccccCccccCceeeeecCce
Q psy10221 12 CVACGESITDKYLLQVSDKS 31 (67)
Q Consensus 12 C~~C~~~i~~~~~~~~~~~~ 31 (67)
|.-|+..|.....+...+.-
T Consensus 6 CEiCG~~i~~~~~v~vegse 25 (165)
T COG1813 6 CELCGREIDKPIKVKVEGAE 25 (165)
T ss_pred eeccccccCCCeeEEeecce
Confidence 77888888744344444443
No 198
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=22.44 E-value=43 Score=22.30 Aligned_cols=35 Identities=29% Similarity=0.632 Sum_probs=24.6
Q ss_pred cCCccccccCccccCceeeeecCceecccccccccccccc
Q psy10221 7 TELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQLVL 46 (67)
Q Consensus 7 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~~l 46 (67)
...+.|..|.+...+. .++.||-+-..|..|+..|
T Consensus 116 ~~f~~C~~C~~ey~~p-----~~rr~h~~~~~C~~Cgp~l 150 (711)
T TIGR00143 116 ADFPLCPDCAKEYKDP-----LDRRFHAQPIACPRCGPQL 150 (711)
T ss_pred CCCcCCHHHHHHhcCC-----ccccCCCCCccCCCCCcEE
Confidence 3445677776655432 4677888888999999887
No 199
>PF09888 DUF2115: Uncharacterized protein conserved in archaea (DUF2115); InterPro: IPR019215 This entry represents various hypothetical archaeal proteins, has no known function.
Probab=22.44 E-value=92 Score=16.74 Aligned_cols=20 Identities=15% Similarity=0.177 Sum_probs=13.3
Q ss_pred ccccCCCCceeeeCCeecch
Q psy10221 43 QLVLDRHPSCFIKDEAVYCK 62 (67)
Q Consensus 43 ~~~l~~~~~~~~~~~~~~C~ 62 (67)
+++..++.....++|..||+
T Consensus 122 G~~FPGG~~V~~~~g~YYCP 141 (163)
T PF09888_consen 122 GMPFPGGFKVEEKNGNYYCP 141 (163)
T ss_pred CCCCCCCeEEEEECCEEeCc
Confidence 44555655545678888995
No 200
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=22.38 E-value=12 Score=19.94 Aligned_cols=14 Identities=29% Similarity=0.719 Sum_probs=11.5
Q ss_pred CccccccCccccCc
Q psy10221 9 LRYCVACGESITDK 22 (67)
Q Consensus 9 ~~~C~~C~~~i~~~ 22 (67)
-..|..|+.+|...
T Consensus 86 YG~Ce~CGe~I~~~ 99 (159)
T TIGR02890 86 YGICEVCGKPIPYE 99 (159)
T ss_pred CCeecccCCcccHH
Confidence 46899999999864
No 201
>PRK01022 hypothetical protein; Provisional
Probab=22.36 E-value=94 Score=16.82 Aligned_cols=20 Identities=15% Similarity=0.115 Sum_probs=13.3
Q ss_pred ccccCCCCceeeeCCeecch
Q psy10221 43 QLVLDRHPSCFIKDEAVYCK 62 (67)
Q Consensus 43 ~~~l~~~~~~~~~~~~~~C~ 62 (67)
++++.++.....++|..||+
T Consensus 124 G~~FPGG~~V~~~~g~yYCP 143 (167)
T PRK01022 124 GTPFPGGFKVEEKNGVYYCP 143 (167)
T ss_pred CCCCCCCeEEEeECCEEeCc
Confidence 45566655545678888985
No 202
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=22.12 E-value=93 Score=15.00 Aligned_cols=29 Identities=17% Similarity=0.547 Sum_probs=17.1
Q ss_pred cccccCccccCceeeee---------cCceeccccccc
Q psy10221 11 YCVACGESITDKYLLQV---------SDKSWHAQCLRC 39 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~---------~~~~~h~~cf~C 39 (67)
.|..|+.....+.+... .-+.|+..|-.|
T Consensus 7 ~C~~C~~~W~S~~v~i~f~~~~~g~v~~rv~~Q~C~~C 44 (98)
T PF13695_consen 7 QCSKCSRGWTSAKVWILFHMYRGGQVNMRVFGQRCKKC 44 (98)
T ss_pred ECCCCCCCCccCEEEEEEEEcCCCeEEEEEECCCCCCC
Confidence 57778777776654332 123466666665
No 203
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=21.67 E-value=52 Score=19.17 Aligned_cols=31 Identities=26% Similarity=0.468 Sum_probs=19.3
Q ss_pred CCccccccCccccCceeeeecCceecccccccccccc
Q psy10221 8 ELRYCVACGESITDKYLLQVSDKSWHAQCLRCCICQL 44 (67)
Q Consensus 8 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~cf~C~~C~~ 44 (67)
....|+.|++...-.+- .- +..-|+|..|.-
T Consensus 219 ~~r~CP~Cg~~W~L~~p---lh---~iFdFKCD~CRL 249 (258)
T PF10071_consen 219 QARKCPSCGGDWRLKEP---LH---DIFDFKCDPCRL 249 (258)
T ss_pred hCCCCCCCCCccccCCc---hh---hceeccCCccee
Confidence 35789999987764322 22 333477777763
No 204
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=21.57 E-value=92 Score=14.04 Aligned_cols=17 Identities=18% Similarity=0.417 Sum_probs=9.3
Q ss_pred cccccCccccCceeeee
Q psy10221 11 YCVACGESITDKYLLQV 27 (67)
Q Consensus 11 ~C~~C~~~i~~~~~~~~ 27 (67)
.|.+|+..-.+...+++
T Consensus 2 ~C~KCg~~~~e~~~v~~ 18 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRA 18 (64)
T ss_pred CCCCCCCcceecceEEc
Confidence 47777776654333333
No 205
>PF15269 zf-C2H2_7: Zinc-finger
Probab=21.48 E-value=52 Score=13.87 Aligned_cols=17 Identities=18% Similarity=0.612 Sum_probs=11.9
Q ss_pred eeeecCceecccccccc
Q psy10221 24 LLQVSDKSWHAQCLRCC 40 (67)
Q Consensus 24 ~~~~~~~~~h~~cf~C~ 40 (67)
+.+.-++.|.-.||.|-
T Consensus 11 iprp~gkp~~ykcfqcp 27 (54)
T PF15269_consen 11 IPRPPGKPFKYKCFQCP 27 (54)
T ss_pred CCCCCCCCccceeecCC
Confidence 34456778888888874
No 206
>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=21.34 E-value=21 Score=17.00 Aligned_cols=10 Identities=30% Similarity=0.869 Sum_probs=6.4
Q ss_pred ccccccCccc
Q psy10221 10 RYCVACGESI 19 (67)
Q Consensus 10 ~~C~~C~~~i 19 (67)
..|.+|++.+
T Consensus 55 ~pC~~C~klL 64 (90)
T PF11571_consen 55 TPCKKCGKLL 64 (90)
T ss_pred chhhHHHhHh
Confidence 4566666666
No 207
>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=21.29 E-value=33 Score=12.88 Aligned_cols=11 Identities=27% Similarity=0.661 Sum_probs=7.8
Q ss_pred ccccccccccC
Q psy10221 37 LRCCICQLVLD 47 (67)
Q Consensus 37 f~C~~C~~~l~ 47 (67)
|.|.+|++.+.
T Consensus 1 ~sCiDC~~~F~ 11 (28)
T PF08790_consen 1 FSCIDCSKDFD 11 (28)
T ss_dssp EEETTTTEEEE
T ss_pred CeeecCCCCcC
Confidence 46778887764
No 208
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=21.24 E-value=41 Score=11.29 Aligned_cols=6 Identities=33% Similarity=1.143 Sum_probs=2.2
Q ss_pred cccccc
Q psy10221 38 RCCICQ 43 (67)
Q Consensus 38 ~C~~C~ 43 (67)
+|..|+
T Consensus 2 ~C~~C~ 7 (24)
T PF13909_consen 2 KCPHCS 7 (24)
T ss_dssp E-SSSS
T ss_pred CCCCCC
Confidence 344443
Done!