Query psy4437
Match_columns 131
No_of_seqs 202 out of 1226
Neff 9.4
Searched_HMMs 46136
Date Fri Aug 16 17:01:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4437.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4437hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.9 1.9E-27 4E-32 173.6 1.5 118 2-129 334-458 (468)
2 KOG4577|consensus 99.9 9.4E-29 2E-33 172.8 -5.3 115 2-130 33-150 (383)
3 KOG1701|consensus 99.9 1.3E-27 2.7E-32 174.5 -3.4 112 3-131 275-390 (468)
4 KOG2272|consensus 99.9 1.6E-26 3.4E-31 159.1 -3.7 127 2-130 73-249 (332)
5 KOG2272|consensus 99.9 2.2E-24 4.8E-29 148.6 -4.3 112 2-130 195-309 (332)
6 KOG1044|consensus 99.8 1.5E-22 3.3E-27 152.5 1.7 112 2-129 133-246 (670)
7 KOG1703|consensus 99.8 2.2E-21 4.8E-26 148.3 1.6 114 2-130 363-478 (479)
8 KOG1703|consensus 99.8 4.5E-21 9.9E-26 146.6 2.0 113 3-131 304-418 (479)
9 KOG1044|consensus 99.7 2.1E-18 4.5E-23 130.5 3.7 128 3-131 17-188 (670)
10 KOG1700|consensus 99.6 5E-17 1.1E-21 111.4 1.0 130 1-130 6-163 (200)
11 PF00412 LIM: LIM domain; Int 99.6 6.6E-17 1.4E-21 90.2 1.1 56 5-60 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.6 3.1E-16 6.8E-21 87.5 1.4 52 79-130 1-54 (58)
13 smart00132 LIM Zinc-binding do 99.1 1E-10 2.2E-15 59.6 3.1 37 4-40 1-38 (39)
14 smart00132 LIM Zinc-binding do 99.0 2.7E-10 5.8E-15 58.0 2.6 36 79-114 2-38 (39)
15 KOG4577|consensus 98.9 2.2E-11 4.8E-16 86.1 -4.1 57 75-131 32-88 (383)
16 KOG0490|consensus 98.2 1.3E-07 2.7E-12 66.2 -1.8 107 7-128 1-114 (235)
17 KOG1702|consensus 98.1 2.4E-07 5.1E-12 63.1 -1.8 60 2-61 4-64 (264)
18 KOG1700|consensus 98.1 7.8E-07 1.7E-11 61.3 0.3 59 2-60 108-167 (200)
19 KOG1702|consensus 97.6 5.4E-06 1.2E-10 56.6 -1.4 54 77-130 5-59 (264)
20 PF14446 Prok-RING_1: Prokaryo 95.5 0.012 2.7E-07 31.8 2.1 40 61-113 5-51 (54)
21 KOG0490|consensus 93.8 0.013 2.8E-07 40.8 -0.6 50 82-131 2-53 (235)
22 PF08394 Arc_trans_TRASH: Arch 92.0 0.098 2.1E-06 26.1 1.2 25 5-29 1-26 (37)
23 PF13248 zf-ribbon_3: zinc-rib 89.5 0.27 5.7E-06 22.4 1.4 14 1-14 1-14 (26)
24 PF14835 zf-RING_6: zf-RING of 88.8 0.62 1.4E-05 26.2 2.8 45 30-74 8-53 (65)
25 PF13240 zinc_ribbon_2: zinc-r 87.1 0.52 1.1E-05 20.8 1.5 9 64-72 2-10 (23)
26 PF10367 Vps39_2: Vacuolar sor 86.7 0.59 1.3E-05 28.4 2.1 29 77-105 79-108 (109)
27 PF09943 DUF2175: Uncharacteri 86.2 0.23 5.1E-06 30.4 0.1 29 78-106 4-33 (101)
28 PF10235 Cript: Microtubule-as 85.8 0.55 1.2E-05 28.2 1.5 44 24-89 39-82 (90)
29 PF12773 DZR: Double zinc ribb 85.1 1.4 2.9E-05 23.1 2.8 9 77-85 30-38 (50)
30 PF13717 zinc_ribbon_4: zinc-r 84.7 0.3 6.5E-06 24.1 0.0 33 1-38 1-34 (36)
31 KOG2462|consensus 84.5 0.68 1.5E-05 33.4 1.8 90 27-116 128-256 (279)
32 TIGR02098 MJ0042_CXXC MJ0042 f 83.8 0.34 7.4E-06 23.9 0.0 34 1-39 1-35 (38)
33 PF09943 DUF2175: Uncharacteri 83.2 0.39 8.4E-06 29.5 0.1 30 4-33 4-34 (101)
34 KOG1813|consensus 83.0 0.89 1.9E-05 33.2 1.9 46 30-75 242-289 (313)
35 PRK14559 putative protein seri 82.0 2.2 4.7E-05 34.8 3.9 37 51-88 17-53 (645)
36 PF13719 zinc_ribbon_5: zinc-r 81.1 0.55 1.2E-05 23.3 0.2 34 1-39 1-35 (37)
37 PRK14890 putative Zn-ribbon RN 80.0 1.4 3.1E-05 24.2 1.6 13 3-15 8-20 (59)
38 PF10886 DUF2685: Protein of u 79.3 1.8 3.9E-05 23.4 1.8 26 3-28 2-27 (54)
39 COG1645 Uncharacterized Zn-fin 79.1 1.4 3E-05 28.4 1.5 23 31-57 30-52 (131)
40 COG2191 Formylmethanofuran deh 78.3 1.4 3E-05 30.5 1.5 30 30-59 173-203 (206)
41 PF11781 RRN7: RNA polymerase 76.9 1.9 4.2E-05 21.2 1.4 22 105-129 10-31 (36)
42 PF06677 Auto_anti-p27: Sjogre 74.4 2 4.4E-05 21.9 1.1 21 106-129 20-40 (41)
43 PF02069 Metallothio_Pro: Prok 73.8 2.2 4.8E-05 22.9 1.2 22 106-127 10-32 (52)
44 PF05502 Dynactin_p62: Dynacti 73.5 3.9 8.5E-05 32.2 3.1 38 78-116 28-65 (483)
45 COG2191 Formylmethanofuran deh 69.1 2.5 5.3E-05 29.3 1.0 27 104-130 173-200 (206)
46 PF10367 Vps39_2: Vacuolar sor 69.0 4.5 9.7E-05 24.4 2.1 26 31-56 80-107 (109)
47 PF13834 DUF4193: Domain of un 68.3 2.5 5.4E-05 25.8 0.8 27 103-129 70-98 (99)
48 PF00645 zf-PARP: Poly(ADP-rib 67.6 1.6 3.5E-05 25.4 -0.1 9 97-105 39-47 (82)
49 PF07754 DUF1610: Domain of un 65.3 5.7 0.00012 17.7 1.4 8 81-88 3-10 (24)
50 PRK00420 hypothetical protein; 65.0 5 0.00011 25.2 1.7 10 120-129 37-46 (112)
51 PF13920 zf-C3HC4_3: Zinc fing 64.6 2.2 4.8E-05 22.3 0.0 29 31-59 4-33 (50)
52 KOG0978|consensus 63.7 0.88 1.9E-05 37.1 -2.3 47 30-76 644-693 (698)
53 PF01258 zf-dskA_traR: Prokary 63.6 0.69 1.5E-05 22.7 -1.9 25 32-56 6-31 (36)
54 COG4847 Uncharacterized protei 63.4 2.7 5.8E-05 25.5 0.3 36 77-112 7-43 (103)
55 cd02249 ZZ Zinc finger, ZZ typ 62.0 4.5 9.7E-05 20.8 0.9 8 50-57 24-31 (46)
56 PF07649 C1_3: C1-like domain; 61.4 4.1 8.8E-05 18.9 0.6 9 64-72 3-11 (30)
57 PF07503 zf-HYPF: HypF finger; 61.2 3 6.5E-05 20.4 0.2 31 5-40 2-32 (35)
58 cd00162 RING RING-finger (Real 60.4 5.4 0.00012 19.4 1.1 8 5-12 2-9 (45)
59 PF03604 DNA_RNApol_7kD: DNA d 59.7 9 0.00019 18.3 1.7 14 74-87 15-28 (32)
60 smart00504 Ubox Modified RING 59.1 4.3 9.3E-05 22.0 0.6 29 30-58 2-30 (63)
61 PF14471 DUF4428: Domain of un 57.8 2.5 5.5E-05 22.5 -0.5 28 31-59 1-30 (51)
62 PF04570 DUF581: Protein of un 57.6 5.3 0.00011 22.0 0.7 22 106-127 19-43 (58)
63 COG5152 Uncharacterized conser 56.8 1.9 4E-05 29.9 -1.4 44 30-73 197-242 (259)
64 smart00659 RPOLCX RNA polymera 55.7 7.1 0.00015 20.1 1.0 14 75-88 18-31 (44)
65 COG4357 Zinc finger domain con 55.0 1.7 3.6E-05 26.4 -1.6 35 7-41 40-74 (105)
66 PF06827 zf-FPG_IleRS: Zinc fi 54.4 4.5 9.8E-05 18.7 0.1 9 4-12 3-11 (30)
67 COG4357 Zinc finger domain con 53.9 2 4.3E-05 26.1 -1.4 22 95-116 54-75 (105)
68 PF07191 zinc-ribbons_6: zinc- 52.7 5.3 0.00012 22.8 0.3 37 31-71 3-40 (70)
69 PF00628 PHD: PHD-finger; Int 52.1 14 0.00031 19.0 1.9 6 5-10 2-7 (51)
70 KOG3476|consensus 51.9 0.68 1.5E-05 27.5 -3.5 14 77-90 80-93 (100)
71 smart00291 ZnF_ZZ Zinc-binding 51.6 8.5 0.00018 19.6 0.9 9 50-58 28-36 (44)
72 PF09723 Zn-ribbon_8: Zinc rib 51.0 7.1 0.00015 19.7 0.6 11 77-87 6-16 (42)
73 PF06750 DiS_P_DiS: Bacterial 50.9 5.4 0.00012 24.0 0.1 12 30-41 34-45 (92)
74 cd02340 ZZ_NBR1_like Zinc fing 50.2 13 0.00028 19.0 1.4 10 4-13 2-11 (43)
75 PRK00398 rpoP DNA-directed RNA 50.1 6.5 0.00014 20.2 0.3 29 3-40 4-32 (46)
76 COG2888 Predicted Zn-ribbon RN 49.3 12 0.00026 20.7 1.3 10 62-71 10-19 (61)
77 COG2075 RPL24A Ribosomal prote 48.7 15 0.00032 20.7 1.6 21 105-125 5-29 (66)
78 PF01286 XPA_N: XPA protein N- 46.4 13 0.00028 18.1 1.0 13 4-16 5-17 (34)
79 PF08271 TF_Zn_Ribbon: TFIIB z 45.9 20 0.00042 18.1 1.8 13 104-116 20-32 (43)
80 PHA02610 uvsY.-2 hypothetical 45.7 15 0.00032 19.7 1.2 24 78-101 3-26 (53)
81 PF00130 C1_1: Phorbol esters/ 45.0 13 0.00028 19.4 1.0 9 63-71 13-21 (53)
82 smart00834 CxxC_CXXC_SSSS Puta 44.6 11 0.00023 18.5 0.6 12 77-88 6-17 (41)
83 PF10083 DUF2321: Uncharacteri 44.4 22 0.00049 23.6 2.2 11 5-15 42-52 (158)
84 KOG3579|consensus 44.2 11 0.00024 27.7 0.8 29 5-33 271-299 (352)
85 COG1996 RPC10 DNA-directed RNA 44.1 10 0.00022 20.1 0.5 13 76-88 24-36 (49)
86 PF04810 zf-Sec23_Sec24: Sec23 43.4 18 0.00039 18.0 1.4 29 78-111 4-32 (40)
87 TIGR01206 lysW lysine biosynth 42.1 18 0.0004 19.5 1.3 33 1-40 1-33 (54)
88 KOG0320|consensus 41.9 4.5 9.8E-05 27.5 -1.3 52 26-90 128-181 (187)
89 PF10764 Gin: Inhibitor of sig 41.7 11 0.00023 19.7 0.3 30 4-41 1-30 (46)
90 PRK14714 DNA polymerase II lar 41.6 40 0.00087 30.0 3.8 37 50-88 668-704 (1337)
91 PF00096 zf-C2H2: Zinc finger, 41.4 9.4 0.0002 16.0 0.1 13 104-116 1-13 (23)
92 PRK00807 50S ribosomal protein 41.2 21 0.00045 19.1 1.5 9 79-87 4-12 (52)
93 TIGR02605 CxxC_CxxC_SSSS putat 40.0 14 0.00029 19.3 0.6 12 77-88 6-17 (52)
94 PF08772 NOB1_Zn_bind: Nin one 39.5 14 0.0003 21.4 0.6 32 60-91 8-39 (73)
95 PF06906 DUF1272: Protein of u 39.3 13 0.00028 20.3 0.5 22 50-71 30-51 (57)
96 cd02336 ZZ_RSC8 Zinc finger, Z 39.2 15 0.00032 19.0 0.6 28 31-58 2-32 (45)
97 PF01194 RNA_pol_N: RNA polyme 39.2 18 0.0004 20.0 1.0 12 2-13 4-15 (60)
98 PF11571 Med27: Mediator compl 39.0 10 0.00022 22.6 0.0 16 56-71 49-64 (90)
99 cd02335 ZZ_ADA2 Zinc finger, Z 38.4 28 0.00061 18.1 1.7 19 64-82 3-21 (49)
100 cd00729 rubredoxin_SM Rubredox 38.3 26 0.00055 16.8 1.4 7 78-84 20-26 (34)
101 PF14634 zf-RING_5: zinc-RING 38.1 13 0.00028 18.7 0.3 29 32-60 2-33 (44)
102 PF05864 Chordopox_RPO7: Chord 37.6 8.1 0.00018 21.1 -0.5 15 30-44 5-19 (63)
103 PF08746 zf-RING-like: RING-li 37.3 8.3 0.00018 19.7 -0.5 26 5-30 1-28 (43)
104 PF13639 zf-RING_2: Ring finge 36.6 6.7 0.00015 19.7 -0.9 27 4-30 2-30 (44)
105 PHA03082 DNA-dependent RNA pol 36.0 8.6 0.00019 21.0 -0.6 15 30-44 5-19 (63)
106 PF14255 Cys_rich_CPXG: Cystei 35.9 21 0.00046 19.1 0.9 28 79-106 3-30 (52)
107 cd02334 ZZ_dystrophin Zinc fin 35.7 27 0.00058 18.4 1.3 8 51-58 26-33 (49)
108 PF02591 DUF164: Putative zinc 34.8 18 0.0004 19.3 0.6 25 105-129 24-52 (56)
109 smart00109 C1 Protein kinase C 34.7 33 0.00071 17.1 1.6 8 64-71 14-21 (49)
110 smart00531 TFIIE Transcription 34.2 11 0.00024 24.6 -0.4 34 4-40 101-134 (147)
111 COG0068 HypF Hydrogenase matur 33.8 21 0.00045 29.6 1.0 82 3-113 102-183 (750)
112 cd02341 ZZ_ZZZ3 Zinc finger, Z 33.7 24 0.00052 18.5 0.9 8 51-58 28-35 (48)
113 PLN03208 E3 ubiquitin-protein 33.6 23 0.00051 24.4 1.1 29 29-57 18-46 (193)
114 PRK04016 DNA-directed RNA poly 33.5 17 0.00037 20.3 0.4 11 3-13 5-15 (62)
115 PLN00032 DNA-directed RNA poly 33.3 18 0.00038 20.8 0.4 12 2-13 4-15 (71)
116 PRK14559 putative protein seri 33.1 54 0.0012 27.0 3.2 40 61-116 15-54 (645)
117 PF12674 Zn_ribbon_2: Putative 32.8 18 0.0004 21.2 0.4 28 31-58 2-35 (81)
118 PF10571 UPF0547: Uncharacteri 32.3 42 0.00092 15.1 1.5 6 78-83 16-21 (26)
119 PF14803 Nudix_N_2: Nudix N-te 32.1 24 0.00052 17.1 0.7 8 79-86 3-10 (34)
120 TIGR00155 pqiA_fam integral me 31.5 26 0.00057 27.0 1.2 26 63-88 217-242 (403)
121 PF13894 zf-C2H2_4: C2H2-type 30.9 19 0.00041 14.7 0.2 13 104-116 1-13 (24)
122 PRK12496 hypothetical protein; 30.5 30 0.00064 23.1 1.2 26 62-87 128-154 (164)
123 PRK14714 DNA polymerase II lar 30.2 1.1E+02 0.0024 27.5 4.6 53 29-89 667-722 (1337)
124 PF15135 UPF0515: Uncharacteri 29.9 70 0.0015 23.1 3.0 36 2-41 132-167 (278)
125 smart00249 PHD PHD zinc finger 29.8 47 0.001 16.0 1.7 8 97-104 22-29 (47)
126 KOG3497|consensus 29.3 20 0.00043 19.9 0.2 13 2-14 4-16 (69)
127 PF11331 DUF3133: Protein of u 29.3 21 0.00046 18.6 0.3 10 104-113 32-41 (46)
128 PRK00085 recO DNA repair prote 28.9 31 0.00066 24.2 1.1 28 102-129 148-176 (247)
129 PF01927 Mut7-C: Mut7-C RNAse 28.8 37 0.00079 22.1 1.4 12 30-41 92-103 (147)
130 PF13912 zf-C2H2_6: C2H2-type 28.8 20 0.00043 15.6 0.1 13 104-116 2-14 (27)
131 PRK12495 hypothetical protein; 28.4 40 0.00087 23.8 1.5 27 77-114 43-69 (226)
132 cd00029 C1 Protein kinase C co 28.3 34 0.00073 17.2 1.0 6 64-69 14-19 (50)
133 PF05810 NinF: NinF protein; 28.2 13 0.00028 20.2 -0.7 19 64-82 20-38 (58)
134 cd02338 ZZ_PCMF_like Zinc fing 28.0 28 0.00062 18.1 0.6 8 51-58 26-33 (49)
135 PF07975 C1_4: TFIIH C1-like d 27.9 23 0.00051 18.9 0.3 6 105-110 23-28 (51)
136 PRK14873 primosome assembly pr 27.5 72 0.0016 26.4 3.1 55 16-70 370-431 (665)
137 COG0266 Nei Formamidopyrimidin 27.3 44 0.00094 24.4 1.6 26 77-103 246-271 (273)
138 KOG3579|consensus 27.2 41 0.00089 24.8 1.5 35 74-108 266-300 (352)
139 PF12171 zf-C2H2_jaz: Zinc-fin 27.2 35 0.00076 15.0 0.8 13 104-116 2-14 (27)
140 PF00569 ZZ: Zinc finger, ZZ t 27.1 21 0.00045 18.3 -0.0 8 50-57 29-36 (46)
141 COG1381 RecO Recombinational D 27.1 31 0.00067 24.7 0.9 29 101-129 152-181 (251)
142 PHA02929 N1R/p28-like protein; 27.1 32 0.00068 24.6 0.9 39 77-115 175-228 (238)
143 COG1644 RPB10 DNA-directed RNA 26.8 27 0.0006 19.4 0.4 12 2-13 4-15 (63)
144 PF12874 zf-met: Zinc-finger o 26.7 23 0.0005 15.1 0.1 13 104-116 1-13 (25)
145 TIGR00143 hypF [NiFe] hydrogen 26.7 28 0.0006 29.0 0.6 81 4-113 70-150 (711)
146 PRK04023 DNA polymerase II lar 26.6 98 0.0021 27.1 3.7 21 50-70 627-647 (1121)
147 PF03854 zf-P11: P-11 zinc fin 25.5 45 0.00098 17.6 1.1 12 45-56 11-22 (50)
148 COG1592 Rubrerythrin [Energy p 24.7 58 0.0013 22.0 1.8 23 63-85 136-158 (166)
149 TIGR00595 priA primosomal prot 24.4 98 0.0021 24.6 3.3 54 17-70 201-262 (505)
150 PF06221 zf-C2HC5: Putative zi 24.3 72 0.0016 17.4 1.8 28 61-88 18-47 (57)
151 cd02342 ZZ_UBA_plant Zinc fing 24.1 41 0.00089 17.3 0.8 7 51-57 26-32 (43)
152 PF12855 Ecl1: Life-span regul 23.9 26 0.00057 17.9 0.0 19 106-127 9-27 (43)
153 PF03107 C1_2: C1 domain; Int 23.9 53 0.0012 15.0 1.1 12 30-41 1-12 (30)
154 smart00214 VWC von Willebrand 23.6 50 0.0011 17.7 1.1 14 93-106 8-22 (59)
155 PF03966 Trm112p: Trm112p-like 23.3 60 0.0013 18.0 1.4 13 117-129 47-59 (68)
156 PRK06266 transcription initiat 22.9 25 0.00054 23.9 -0.3 11 30-40 137-147 (178)
157 PF11077 DUF2616: Protein of u 22.9 52 0.0011 22.4 1.3 31 101-131 137-168 (173)
158 PF08792 A2L_zn_ribbon: A2L zi 22.4 88 0.0019 14.9 1.7 11 119-129 17-27 (33)
159 PF10122 Mu-like_Com: Mu-like 22.3 31 0.00066 18.4 0.1 11 30-40 5-15 (51)
160 cd00472 Ribosomal_L24e_L24 Rib 22.3 60 0.0013 17.5 1.2 10 78-87 5-14 (54)
161 PF09862 DUF2089: Protein of u 22.2 39 0.00085 21.2 0.5 11 78-88 14-24 (113)
162 PF03884 DUF329: Domain of unk 22.1 40 0.00087 18.4 0.5 13 1-13 1-13 (57)
163 KOG2932|consensus 22.0 45 0.00097 25.0 0.9 41 31-71 92-133 (389)
164 PF13695 zf-3CxxC: Zinc-bindin 21.8 58 0.0013 19.6 1.3 12 30-41 6-17 (98)
165 smart00661 RPOL9 RNA polymeras 21.5 1.1E+02 0.0024 15.5 2.2 7 5-11 3-9 (52)
166 KOG2114|consensus 21.2 42 0.0009 28.5 0.6 36 3-39 841-882 (933)
167 PF10080 DUF2318: Predicted me 21.1 75 0.0016 19.6 1.6 13 117-129 46-58 (102)
168 COG4306 Uncharacterized protei 21.0 1.1E+02 0.0025 19.7 2.4 11 5-15 42-52 (160)
169 PF02085 Cytochrom_CIII: Class 20.3 19 0.0004 21.7 -1.2 8 94-101 65-72 (102)
170 PRK14891 50S ribosomal protein 20.3 70 0.0015 20.6 1.4 24 3-26 5-31 (131)
171 PF05502 Dynactin_p62: Dynacti 20.3 62 0.0013 25.7 1.4 36 5-41 29-64 (483)
172 KOG2893|consensus 20.2 31 0.00067 24.8 -0.2 36 78-116 12-47 (341)
173 PHA00626 hypothetical protein 20.1 1E+02 0.0023 16.8 1.8 36 4-44 2-38 (59)
174 PF08274 PhnA_Zn_Ribbon: PhnA 20.1 43 0.00094 15.7 0.3 6 78-83 21-26 (30)
No 1
>KOG1701|consensus
Probab=99.93 E-value=1.9e-27 Score=173.62 Aligned_cols=118 Identities=27% Similarity=0.662 Sum_probs=105.4
Q ss_pred CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc--CcCCeeecccCcCCCCCCCCCCCccccCCCCcccc
Q psy4437 2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF--SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISC 79 (131)
Q Consensus 2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f--~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C 79 (131)
+.+|..|+++|.|. ++.|+|+.||+.||+|..|.+.|.+..| ..++++||..||+++|+++|+.|+++|.+.+..
T Consensus 334 lekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~-- 410 (468)
T KOG1701|consen 334 LEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGK-- 410 (468)
T ss_pred HHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCC--
Confidence 35799999999988 7899999999999999999999999988 377999999999999999999999999987653
Q ss_pred ccCCcccccceeeeecCCcccccCccccccccccccc-----eeccCCeeecCCC
Q psy4437 80 AGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-----CFSREGKLFCRND 129 (131)
Q Consensus 80 ~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-----~~~~~g~~~C~~c 129 (131)
.+...|.++++.||.+|++|..|+..|+.+ .|..||.++|+.|
T Consensus 411 -------~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~C 458 (468)
T KOG1701|consen 411 -------DETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTC 458 (468)
T ss_pred -------cceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeechh
Confidence 134456899999999999999999999832 7999999999987
No 2
>KOG4577|consensus
Probab=99.93 E-value=9.4e-29 Score=172.76 Aligned_cols=115 Identities=37% Similarity=0.986 Sum_probs=108.2
Q ss_pred CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCcccccc
Q psy4437 2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAG 81 (131)
Q Consensus 2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~ 81 (131)
.++|++|++.|.++.++.++++.||..|++|+.|..+|.+..|.++|.+||+++|.++|+.+|++|..+|.+..+++
T Consensus 33 ip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVR--- 109 (383)
T KOG4577|consen 33 IPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVR--- 109 (383)
T ss_pred cccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHH---
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999877665
Q ss_pred CCcccccceeeeecCCcccccCccccccccccccc--ee-ccCCeeecCCCC
Q psy4437 82 CEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CF-SREGKLFCRNDF 130 (131)
Q Consensus 82 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~-~~~g~~~C~~cy 130 (131)
.|.+..||.+||.|..|++.|..+ || +.|+++.|+.+|
T Consensus 110 -----------kAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DY 150 (383)
T KOG4577|consen 110 -----------KAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDY 150 (383)
T ss_pred -----------HhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhH
Confidence 899999999999999999999988 65 578999999987
No 3
>KOG1701|consensus
Probab=99.92 E-value=1.3e-27 Score=174.50 Aligned_cols=112 Identities=26% Similarity=0.692 Sum_probs=101.6
Q ss_pred CccccCCccccCce-eEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCCCCccccc
Q psy4437 3 ISCAGCEKPILDKF-LLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCA 80 (131)
Q Consensus 3 ~~C~~C~~~I~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~ 80 (131)
.+|.+|+|.|+++. .+.||++.||..||+|..|++.|.++.| .+|+++||+.||+.. +.+|.
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t----------------lekC~ 338 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT----------------LEKCN 338 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH----------------HHHHh
Confidence 48999999998754 4889999999999999999999999877 899999999999754 47899
Q ss_pred cCCcccccceeeeecCCcccccCccccccccccccc-eec-cCCeeecCCCCC
Q psy4437 81 GCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFS-REGKLFCRNDFF 131 (131)
Q Consensus 81 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~-~~g~~~C~~cy~ 131 (131)
.|+++|+++.+ .|+|+.||+.||+|..|.+.|++. |.. .++++||..||+
T Consensus 339 ~Cg~~I~d~iL-rA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh 390 (468)
T KOG1701|consen 339 KCGEPIMDRIL-RALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFH 390 (468)
T ss_pred hhhhHHHHHHH-HhcccccCCCceEEEEeccccCCccccccCCCceeeehhhh
Confidence 99999999888 999999999999999999999998 654 689999999985
No 4
>KOG2272|consensus
Probab=99.91 E-value=1.6e-26 Score=159.14 Aligned_cols=127 Identities=23% Similarity=0.680 Sum_probs=108.8
Q ss_pred CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCC--------------------
Q psy4437 2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSP-------------------- 60 (131)
Q Consensus 2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~-------------------- 60 (131)
++-|++|++.|.++ +|.+++.+||+.||+|..|++.|++..| ...|..+|..|..+..
T Consensus 73 aPcC~kC~EFiiGr-VikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~ 151 (332)
T KOG2272|consen 73 APCCGKCGEFIIGR-VIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQP 151 (332)
T ss_pred chhhcccccchhhH-HHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccccc
Confidence 46799999999988 7899999999999999999999999877 5678888888876522
Q ss_pred -----------CCCCCCCccccCCC-----------------CccccccCCcccccceeeeecCCcccccCccccccccc
Q psy4437 61 -----------VRFPSGCGVGLSSS-----------------MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHT 112 (131)
Q Consensus 61 -----------~~~C~~c~~~i~~~-----------------~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~ 112 (131)
..+|..|++.+.+. ..++|..|.+||.++.+ .++|++||.++|+|+.|.+|
T Consensus 152 l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi-~amgKhWHveHFvCa~CekP 230 (332)
T KOG2272|consen 152 LTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVI-FAMGKHWHVEHFVCAKCEKP 230 (332)
T ss_pred ccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHHHHH-HHhccccchhheeehhcCCc
Confidence 24677777666542 34899999999998777 99999999999999999999
Q ss_pred cccc-eeccCCeeecCCCC
Q psy4437 113 LSDK-CFSREGKLFCRNDF 130 (131)
Q Consensus 113 l~~~-~~~~~g~~~C~~cy 130 (131)
+-+. .|++.|.+||+.+|
T Consensus 231 FlGHrHYEkkGlaYCe~h~ 249 (332)
T KOG2272|consen 231 FLGHRHYEKKGLAYCETHY 249 (332)
T ss_pred ccchhhhhhcCchhHHHHH
Confidence 9887 89999999999987
No 5
>KOG2272|consensus
Probab=99.86 E-value=2.2e-24 Score=148.55 Aligned_cols=112 Identities=18% Similarity=0.619 Sum_probs=98.2
Q ss_pred CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCC-CccCcCCeeecccCcCCCCCCCCCCCccccCCCCccccc
Q psy4437 2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD-KCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCA 80 (131)
Q Consensus 2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~ 80 (131)
.++|+.|.++|.++ +|.++|+.||.+.|+|+.|.+|+-+ +.|++.|.+||+.+|.++++..|..|...|.+
T Consensus 195 ipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G------- 266 (332)
T KOG2272|consen 195 IPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGG------- 266 (332)
T ss_pred CcccccccCchHHH-HHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCc-------
Confidence 47899999999766 6889999999999999999999887 56799999999999999999766666655543
Q ss_pred cCCcccccceeeeecCCcccccCccccccccccccc--eeccCCeeecCCCC
Q psy4437 81 GCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRNDF 130 (131)
Q Consensus 81 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~~~~g~~~C~~cy 130 (131)
..+ ++.++.|-++||+|+.|++.|... |++.|.+|.|+.||
T Consensus 267 --------~vv-~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy 309 (332)
T KOG2272|consen 267 --------DVV-SALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCY 309 (332)
T ss_pred --------cHH-HHhhhhhccccccccccccccccccceeeeccchHHHHHH
Confidence 333 999999999999999999999877 99999999999887
No 6
>KOG1044|consensus
Probab=99.85 E-value=1.5e-22 Score=152.54 Aligned_cols=112 Identities=22% Similarity=0.581 Sum_probs=96.3
Q ss_pred CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCcccccc
Q psy4437 2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAG 81 (131)
Q Consensus 2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~ 81 (131)
+..|++|++.|..+.++.|+++.||..||+|..|+..|.+++..+||.|||+.||++.|+.+|..|.+.|.+
T Consensus 133 ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fisg-------- 204 (670)
T KOG1044|consen 133 PSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISG-------- 204 (670)
T ss_pred CccccchhhhhhccceeeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhhhh--------
Confidence 457999999998888888999999999999999999999999999999999999999999766666665554
Q ss_pred CCcccccceeeeecCCcccccCccccccccccccc--eeccCCeeecCCC
Q psy4437 82 CEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRND 129 (131)
Q Consensus 82 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~~~~g~~~C~~c 129 (131)
+.+ .|.|++|||.|-+|++|+.+++.+ +|+....++=..|
T Consensus 205 -------kvL-qag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C 246 (670)
T KOG1044|consen 205 -------KVL-QAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDC 246 (670)
T ss_pred -------hhh-hccCcccCcchhhhhhhccccccchheeeccccccCCcc
Confidence 333 899999999999999999999987 7777666654443
No 7
>KOG1703|consensus
Probab=99.82 E-value=2.2e-21 Score=148.27 Aligned_cols=114 Identities=26% Similarity=0.634 Sum_probs=99.3
Q ss_pred CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCCCCccccc
Q psy4437 2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCA 80 (131)
Q Consensus 2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~ 80 (131)
.+.|.+|+++|.++ .|.++++.||++||.|..|.++|.+..| ..++.+||+.||.+++.++|..|..++...+
T Consensus 363 ~p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~----- 436 (479)
T KOG1703|consen 363 RPNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGS----- 436 (479)
T ss_pred CccccccCCchHHh-HhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhh-----
Confidence 57899999999888 5778899999999999999999998766 8999999999999999877666666554322
Q ss_pred cCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437 81 GCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF 130 (131)
Q Consensus 81 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy 130 (131)
..+ .+++..||.+||+|+.|.+.|.++ |+...++|+|.+|+
T Consensus 437 --------~~i-e~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 437 --------RQI-EADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred --------hHh-hccCccccccceehhhhhccccCCceeecCCccccccCC
Confidence 222 899999999999999999999988 99999999999987
No 8
>KOG1703|consensus
Probab=99.81 E-value=4.5e-21 Score=146.57 Aligned_cols=113 Identities=23% Similarity=0.558 Sum_probs=100.2
Q ss_pred CccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCCCCcccccc
Q psy4437 3 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAG 81 (131)
Q Consensus 3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~ 81 (131)
+.|..|++.|.+..++.++++.||+.+|.|..|...+....+ ..+|++||..|+.+.+.++|.+|+++|.+..
T Consensus 304 p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~------ 377 (479)
T KOG1703|consen 304 PLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEG------ 377 (479)
T ss_pred ccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhH------
Confidence 679999999988557889999999999999999999988777 8999999999999999987777666665443
Q ss_pred CCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCCC
Q psy4437 82 CEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDFF 131 (131)
Q Consensus 82 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy~ 131 (131)
+ .+.++.||++||.|+.|+++|..+ |++.+|.+||+.||+
T Consensus 378 ---------v-~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~ 418 (479)
T KOG1703|consen 378 ---------V-CALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYK 418 (479)
T ss_pred ---------h-hhccCeechhceeeecccCCCCCCcccccCCccchhhhHh
Confidence 3 777999999999999999999988 999999999999884
No 9
>KOG1044|consensus
Probab=99.73 E-value=2.1e-18 Score=130.47 Aligned_cols=128 Identities=25% Similarity=0.630 Sum_probs=101.5
Q ss_pred CccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcC-CeeecccCc------------CCCCCCCCCC--
Q psy4437 3 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SRE-GKLFCRNDF------------FRSPVRFPSG-- 66 (131)
Q Consensus 3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~-~~~~C~~c~------------~~~~~~~C~~-- 66 (131)
..|..|.+.-.+. ++.+.++.||..||+|..|+..|....| .++ ..+|+.... -+.+.++|+.
T Consensus 17 i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs 95 (670)
T KOG1044|consen 17 IKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCS 95 (670)
T ss_pred eehhhhCCccccc-eeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceec
Confidence 4688999988666 7899999999999999999999998644 554 456765332 1223344443
Q ss_pred -CccccCCC---------------------------CccccccCCcccccceeeeecCCcccccCcccccccccccccee
Q psy4437 67 -CGVGLSSS---------------------------MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF 118 (131)
Q Consensus 67 -c~~~i~~~---------------------------~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~ 118 (131)
|..+..++ ....|+.|++.|..++.+.|+++.||..||+|..|+..|.++|+
T Consensus 96 ~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~gey~ 175 (670)
T KOG1044|consen 96 TCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGEYM 175 (670)
T ss_pred ccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccceee
Confidence 33444322 34689999999999888899999999999999999999999999
Q ss_pred ccCCeeecCCCCC
Q psy4437 119 SREGKLFCRNDFF 131 (131)
Q Consensus 119 ~~~g~~~C~~cy~ 131 (131)
.+||.|||++||+
T Consensus 176 skdg~pyce~dy~ 188 (670)
T KOG1044|consen 176 SKDGVPYCEKDYQ 188 (670)
T ss_pred ccCCCcchhhhhh
Confidence 9999999999984
No 10
>KOG1700|consensus
Probab=99.63 E-value=5e-17 Score=111.45 Aligned_cols=130 Identities=25% Similarity=0.497 Sum_probs=108.1
Q ss_pred CCCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccc---cCC---
Q psy4437 1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVG---LSS--- 73 (131)
Q Consensus 1 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~---i~~--- 73 (131)
|...|.+|++.++-.+.+...|..||+.||+|..|.+.|....+ .+++.+||+.+|...+++.-..-+.. +.+
T Consensus 6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (200)
T KOG1700|consen 6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGK 85 (200)
T ss_pred ccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCc
Confidence 34589999999987777778899999999999999999998766 89999999998777766554444432 111
Q ss_pred --------------------CCccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437 74 --------------------SMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF 130 (131)
Q Consensus 74 --------------------~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy 130 (131)
+....|..|++.+++.+.+...+..||..||+|+.|+..|+.. +...+|.+||..++
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~ 163 (200)
T KOG1700|consen 86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHF 163 (200)
T ss_pred ccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhh
Confidence 1347899999999998888999999999999999999999998 78889999987765
No 11
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.63 E-value=6.6e-17 Score=90.20 Aligned_cols=56 Identities=30% Similarity=0.869 Sum_probs=49.8
Q ss_pred cccCCccccCceeE-eecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCC
Q psy4437 5 CAGCEKPILDKFLL-NVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSP 60 (131)
Q Consensus 5 C~~C~~~I~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~ 60 (131)
|.+|+++|.+++++ .++|+.||++||+|+.|+++|.+..| ..+|++||++||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 78999999877665 69999999999999999999998766 8999999999987643
No 12
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.59 E-value=3.1e-16 Score=87.45 Aligned_cols=52 Identities=31% Similarity=0.963 Sum_probs=46.6
Q ss_pred cccCCcccccceee-eecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437 79 CAGCEKPILDKFLL-NVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF 130 (131)
Q Consensus 79 C~~C~~~I~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy 130 (131)
|.+|+++|.+...+ .++|+.||++||+|+.|+++|.++ +++.+|+|||+.||
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~ 54 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCY 54 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHH
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHH
Confidence 67788888876664 699999999999999999999988 89999999999887
No 13
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=99.09 E-value=1e-10 Score=59.58 Aligned_cols=37 Identities=41% Similarity=1.078 Sum_probs=33.6
Q ss_pred ccccCCccccCc-eeEeecCCccccCCcccCCCcCcCC
Q psy4437 4 SCAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLS 40 (131)
Q Consensus 4 ~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~ 40 (131)
+|.+|+++|.+. ..+.++++.||++||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999886 6788899999999999999999986
No 14
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=99.01 E-value=2.7e-10 Score=57.99 Aligned_cols=36 Identities=42% Similarity=1.107 Sum_probs=30.9
Q ss_pred cccCCcccccc-eeeeecCCcccccCccccccccccc
Q psy4437 79 CAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLS 114 (131)
Q Consensus 79 C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~ 114 (131)
|..|+++|.+. ..+.+.++.||++||+|..|+++|.
T Consensus 2 C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 67788888775 5558899999999999999999986
No 15
>KOG4577|consensus
Probab=98.94 E-value=2.2e-11 Score=86.09 Aligned_cols=57 Identities=54% Similarity=1.371 Sum_probs=53.8
Q ss_pred CccccccCCcccccceeeeecCCcccccCccccccccccccceeccCCeeecCCCCC
Q psy4437 75 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 131 (131)
Q Consensus 75 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~g~~~C~~cy~ 131 (131)
+.++|+.|.+.|+++.++.+++++||..|++|+.|+.+|....|.++|.+||+++||
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFf 88 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFF 88 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHH
Confidence 457899999999999999999999999999999999999999999999999999986
No 16
>KOG0490|consensus
Probab=98.20 E-value=1.3e-07 Score=66.23 Aligned_cols=107 Identities=31% Similarity=0.712 Sum_probs=80.3
Q ss_pred cCCccccCceeEeecCCccccCCcccCCCcCcCC--CCccCcCCeeecccCcCC--CCCCCCCCCccccCCCCccccccC
Q psy4437 7 GCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFSREGKLFCRNDFFR--SPVRFPSGCGVGLSSSMLISCAGC 82 (131)
Q Consensus 7 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~~~f~~~~~~~C~~c~~~--~~~~~C~~c~~~i~~~~~~~C~~C 82 (131)
.|+..|.+...+.+.+..||..|..|..|...|. ...|.++|..||..++.+ .+..+|.+|...+...+...
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~le---- 76 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELE---- 76 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHH----
Confidence 4778888888788889999999999999999998 677766999999999998 66667777776664433221
Q ss_pred CcccccceeeeecCCcccccCccccccccccccc--eecc-CCeeecCC
Q psy4437 83 EKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSR-EGKLFCRN 128 (131)
Q Consensus 83 ~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~~~-~g~~~C~~ 128 (131)
.+..+. |..||.|..|...+... +.+. ..+..+.+
T Consensus 77 ----------r~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak 114 (235)
T KOG0490|consen 77 ----------RAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAK 114 (235)
T ss_pred ----------HhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHh
Confidence 556666 99999999988877655 4332 33555543
No 17
>KOG1702|consensus
Probab=98.11 E-value=2.4e-07 Score=63.06 Aligned_cols=60 Identities=22% Similarity=0.535 Sum_probs=52.9
Q ss_pred CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCC
Q psy4437 2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPV 61 (131)
Q Consensus 2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~ 61 (131)
...|..|++.++..+.|.-+++.||..||+|..|+.+|..+.+ .-+.++||..+|.+..+
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 4457889999988777888999999999999999999999888 68999999999987654
No 18
>KOG1700|consensus
Probab=98.09 E-value=7.8e-07 Score=61.27 Aligned_cols=59 Identities=29% Similarity=0.584 Sum_probs=51.8
Q ss_pred CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCC
Q psy4437 2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSP 60 (131)
Q Consensus 2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~ 60 (131)
...|..|.+.+++.+.+...+..||..||+|+.|+..|+...+ ..++.+||...+...+
T Consensus 108 ~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 108 KEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred ccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence 4679999999998877888999999999999999999999888 7888998887776654
No 19
>KOG1702|consensus
Probab=97.65 E-value=5.4e-06 Score=56.56 Aligned_cols=54 Identities=24% Similarity=0.579 Sum_probs=46.4
Q ss_pred cccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437 77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF 130 (131)
Q Consensus 77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy 130 (131)
..+..|++.+++.+.+.-+++.||..||+|..|+.+|.-. +-..+.++||..+|
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hY 59 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHY 59 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccc
Confidence 3467788888876666889999999999999999999877 66789999999887
No 20
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=95.51 E-value=0.012 Score=31.83 Aligned_cols=40 Identities=23% Similarity=0.605 Sum_probs=24.7
Q ss_pred CCCCCCCccccC-CCCccccccCCcccccceeeeecCCcccccCc----cccc--ccccc
Q psy4437 61 VRFPSGCGVGLS-SSMLISCAGCEKPILDKFLLNVLERTWHADCV----RCYD--CHHTL 113 (131)
Q Consensus 61 ~~~C~~c~~~i~-~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf----~C~~--C~~~l 113 (131)
+.+|..|++.+. +.+.++|+.|+. .||++|. .|.. |+.++
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cga-------------pyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGA-------------PYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCC-------------cccHHHHhhCCceEeccCCCCc
Confidence 456777777765 445566666654 4898887 3554 55443
No 21
>KOG0490|consensus
Probab=93.81 E-value=0.013 Score=40.85 Aligned_cols=50 Identities=46% Similarity=1.270 Sum_probs=40.7
Q ss_pred CCcccccceeeeecCCcccccCccccccccccc--cceeccCCeeecCCCCC
Q psy4437 82 CEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFSREGKLFCRNDFF 131 (131)
Q Consensus 82 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~g~~~C~~cy~ 131 (131)
|+..|.+...+.+.+..||..|..|..|...+. ...+..+|..||..+|.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~ 53 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQ 53 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccch
Confidence 566777777778889999999999999999998 44444499999998773
No 22
>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=92.03 E-value=0.098 Score=26.08 Aligned_cols=25 Identities=16% Similarity=0.429 Sum_probs=18.7
Q ss_pred cccCCccccCcee-EeecCCccccCC
Q psy4437 5 CAGCEKPILDKFL-LNVLERTWHADC 29 (131)
Q Consensus 5 C~~C~~~I~~~~~-~~~~~~~~H~~C 29 (131)
|.-|+.+|.+..+ +...++.|+.-|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC 26 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCC 26 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEEC
Confidence 6789999987654 666788887544
No 23
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.51 E-value=0.27 Score=22.38 Aligned_cols=14 Identities=29% Similarity=0.536 Sum_probs=9.7
Q ss_pred CCCccccCCccccC
Q psy4437 1 MLISCAGCEKPILD 14 (131)
Q Consensus 1 ~~~~C~~C~~~I~~ 14 (131)
|...|..|+..|.+
T Consensus 1 m~~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 1 MEMFCPNCGAEIDP 14 (26)
T ss_pred CcCCCcccCCcCCc
Confidence 66778888876643
No 24
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=88.80 E-value=0.62 Score=26.17 Aligned_cols=45 Identities=16% Similarity=0.208 Sum_probs=19.6
Q ss_pred cccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCCC
Q psy4437 30 VRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSS 74 (131)
Q Consensus 30 f~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~ 74 (131)
++|+.|...|....- ..=+.+||..|-.+.++..|..|..|....
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~q 53 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQ 53 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-S
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHH
Confidence 578888777765322 344677888888776666566666555443
No 25
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.06 E-value=0.52 Score=20.81 Aligned_cols=9 Identities=22% Similarity=0.671 Sum_probs=3.6
Q ss_pred CCCCccccC
Q psy4437 64 PSGCGVGLS 72 (131)
Q Consensus 64 C~~c~~~i~ 72 (131)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 333444443
No 26
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=86.75 E-value=0.59 Score=28.42 Aligned_cols=29 Identities=21% Similarity=0.576 Sum_probs=19.4
Q ss_pred cccccCCcccccceeeee-cCCcccccCcc
Q psy4437 77 ISCAGCEKPILDKFLLNV-LERTWHADCVR 105 (131)
Q Consensus 77 ~~C~~C~~~I~~~~~~~~-~~~~~H~~Cf~ 105 (131)
..|+.|+++|.....+.+ .|..+|..|++
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 568888888876554344 45667887753
No 27
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=86.23 E-value=0.23 Score=30.42 Aligned_cols=29 Identities=31% Similarity=0.600 Sum_probs=22.8
Q ss_pred ccccCCcccccceeeeec-CCcccccCccc
Q psy4437 78 SCAGCEKPILDKFLLNVL-ERTWHADCVRC 106 (131)
Q Consensus 78 ~C~~C~~~I~~~~~~~~~-~~~~H~~Cf~C 106 (131)
.|..|+++|..++.+++. +..-|.+||+=
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~ 33 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE 33 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence 588899999887777764 46779999874
No 28
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=85.79 E-value=0.55 Score=28.24 Aligned_cols=44 Identities=25% Similarity=0.588 Sum_probs=26.7
Q ss_pred ccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccc
Q psy4437 24 TWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDK 89 (131)
Q Consensus 24 ~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~ 89 (131)
.|-+.=-.|..|...+.. .|.-||..|..+. -+|+.|++.|.+.
T Consensus 39 Py~~~~~~C~~CK~~v~q-----~g~~YCq~CAYkk-----------------GiCamCGKki~dt 82 (90)
T PF10235_consen 39 PYAPYSSKCKICKTKVHQ-----PGAKYCQTCAYKK-----------------GICAMCGKKILDT 82 (90)
T ss_pred cccccCcccccccccccc-----CCCccChhhhccc-----------------CcccccCCeeccc
Confidence 344433456667655532 3667888887664 3577777777653
No 29
>PF12773 DZR: Double zinc ribbon
Probab=85.07 E-value=1.4 Score=23.08 Aligned_cols=9 Identities=22% Similarity=0.671 Sum_probs=4.0
Q ss_pred cccccCCcc
Q psy4437 77 ISCAGCEKP 85 (131)
Q Consensus 77 ~~C~~C~~~ 85 (131)
..|..|+..
T Consensus 30 ~~C~~Cg~~ 38 (50)
T PF12773_consen 30 KICPNCGAE 38 (50)
T ss_pred CCCcCCcCC
Confidence 344444443
No 30
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=84.70 E-value=0.3 Score=24.12 Aligned_cols=33 Identities=33% Similarity=0.753 Sum_probs=19.6
Q ss_pred CCCccccCCccc-cCceeEeecCCccccCCcccCCCcCc
Q psy4437 1 MLISCAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHT 38 (131)
Q Consensus 1 ~~~~C~~C~~~I-~~~~~~~~~~~~~H~~Cf~C~~C~~~ 38 (131)
|...|..|+... .+.+.|...+.. ++|+.|+..
T Consensus 1 M~i~Cp~C~~~y~i~d~~ip~~g~~-----v~C~~C~~~ 34 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDEKIPPKGRK-----VRCSKCGHV 34 (36)
T ss_pred CEEECCCCCCEEeCCHHHCCCCCcE-----EECCCCCCE
Confidence 667788888764 233334444443 677777654
No 31
>KOG2462|consensus
Probab=84.52 E-value=0.68 Score=33.44 Aligned_cols=90 Identities=21% Similarity=0.404 Sum_probs=50.8
Q ss_pred cCCcccCCCcCcCCCCc-cCcCCe-------------eecccCcCCCC-----------CCCCCCCccccC---------
Q psy4437 27 ADCVRCYDCHHTLSDKC-FSREGK-------------LFCRNDFFRSP-----------VRFPSGCGVGLS--------- 72 (131)
Q Consensus 27 ~~Cf~C~~C~~~l~~~~-f~~~~~-------------~~C~~c~~~~~-----------~~~C~~c~~~i~--------- 72 (131)
...++|..|++.++... ..+... .+|..-|..+- .-.|..|++.+.
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHi 207 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHI 207 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhccc
Confidence 34588899998887632 122222 23333332221 136777777653
Q ss_pred ----CCCccccccCCcccccceeeeec-CCcccccCccccccccccccc
Q psy4437 73 ----SSMLISCAGCEKPILDKFLLNVL-ERTWHADCVRCYDCHHTLSDK 116 (131)
Q Consensus 73 ----~~~~~~C~~C~~~I~~~~~~~~~-~~~~H~~Cf~C~~C~~~l~~~ 116 (131)
|+..+.|+.|+|...|+--++|. .-+=+..=|.|..|++.++..
T Consensus 208 RTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~ 256 (279)
T KOG2462|consen 208 RTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALK 256 (279)
T ss_pred ccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHH
Confidence 34457888888888776443432 122233457788888877654
No 32
>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=83.76 E-value=0.34 Score=23.93 Aligned_cols=34 Identities=29% Similarity=0.512 Sum_probs=19.4
Q ss_pred CCCccccCCcccc-CceeEeecCCccccCCcccCCCcCcC
Q psy4437 1 MLISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTL 39 (131)
Q Consensus 1 ~~~~C~~C~~~I~-~~~~~~~~~~~~H~~Cf~C~~C~~~l 39 (131)
|...|..|+..+. +.+.+...+. -++|..|+..+
T Consensus 1 M~~~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~ 35 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW 35 (38)
T ss_pred CEEECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence 6678888888752 2212222221 26778887665
No 33
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=83.19 E-value=0.39 Score=29.46 Aligned_cols=30 Identities=30% Similarity=0.548 Sum_probs=22.7
Q ss_pred ccccCCccccCceeEee-cCCccccCCcccC
Q psy4437 4 SCAGCEKPILDKFLLNV-LERTWHADCVRCY 33 (131)
Q Consensus 4 ~C~~C~~~I~~~~~~~~-~~~~~H~~Cf~C~ 33 (131)
+|..|+++|..++..++ .+..-|-.||+=.
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 68899999988777555 3567888888654
No 34
>KOG1813|consensus
Probab=83.03 E-value=0.89 Score=33.22 Aligned_cols=46 Identities=15% Similarity=0.327 Sum_probs=36.1
Q ss_pred cccCCCcCcCCCCccCcCCeeecccCcCCCC--CCCCCCCccccCCCC
Q psy4437 30 VRCYDCHHTLSDKCFSREGKLFCRNDFFRSP--VRFPSGCGVGLSSSM 75 (131)
Q Consensus 30 f~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~--~~~C~~c~~~i~~~~ 75 (131)
|.|..|++.........-+..+|+.|..+.+ +++|..|++.+.+..
T Consensus 242 f~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~ 289 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSF 289 (313)
T ss_pred ccccccccccccchhhcCCceeehhhhccccccCCcceeccccccccc
Confidence 7888888887765556678899999998776 468888888887643
No 35
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=81.99 E-value=2.2 Score=34.82 Aligned_cols=37 Identities=16% Similarity=0.306 Sum_probs=21.6
Q ss_pred ecccCcCCCCCCCCCCCccccCCCCccccccCCccccc
Q psy4437 51 FCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILD 88 (131)
Q Consensus 51 ~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~ 88 (131)
||..|-.+.-...|..|+..+.++.. -|..|+.+...
T Consensus 17 FC~~CG~~l~~~~Cp~CG~~~~~~~~-fC~~CG~~~~~ 53 (645)
T PRK14559 17 FCQKCGTSLTHKPCPQCGTEVPVDEA-HCPNCGAETGT 53 (645)
T ss_pred cccccCCCCCCCcCCCCCCCCCcccc-cccccCCcccc
Confidence 44444433333467777777665554 57777776543
No 36
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=81.12 E-value=0.55 Score=23.27 Aligned_cols=34 Identities=32% Similarity=0.658 Sum_probs=19.3
Q ss_pred CCCccccCCcccc-CceeEeecCCccccCCcccCCCcCcC
Q psy4437 1 MLISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTL 39 (131)
Q Consensus 1 ~~~~C~~C~~~I~-~~~~~~~~~~~~H~~Cf~C~~C~~~l 39 (131)
|..+|..|+.... +.+.+...+.. .+|+.|+..+
T Consensus 1 M~i~CP~C~~~f~v~~~~l~~~~~~-----vrC~~C~~~f 35 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDDKLPAGGRK-----VRCPKCGHVF 35 (37)
T ss_pred CEEECCCCCceEEcCHHHcccCCcE-----EECCCCCcEe
Confidence 6778888887642 22224333332 6677776543
No 37
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=80.01 E-value=1.4 Score=24.24 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=7.4
Q ss_pred CccccCCccccCc
Q psy4437 3 ISCAGCEKPILDK 15 (131)
Q Consensus 3 ~~C~~C~~~I~~~ 15 (131)
+.|..|+..|.+.
T Consensus 8 ~~CtSCg~~i~~~ 20 (59)
T PRK14890 8 PKCTSCGIEIAPR 20 (59)
T ss_pred ccccCCCCcccCC
Confidence 3566666666443
No 38
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=79.28 E-value=1.8 Score=23.37 Aligned_cols=26 Identities=23% Similarity=0.471 Sum_probs=19.4
Q ss_pred CccccCCccccCceeEeecCCccccC
Q psy4437 3 ISCAGCEKPILDKFLLNVLERTWHAD 28 (131)
Q Consensus 3 ~~C~~C~~~I~~~~~~~~~~~~~H~~ 28 (131)
.+|..|+++|.+...+...+..-|+.
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~g 27 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHPG 27 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCcH
Confidence 57889999998776666666677774
No 39
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=79.07 E-value=1.4 Score=28.42 Aligned_cols=23 Identities=30% Similarity=0.830 Sum_probs=18.6
Q ss_pred ccCCCcCcCCCCccCcCCeeecccCcC
Q psy4437 31 RCYDCHHTLSDKCFSREGKLFCRNDFF 57 (131)
Q Consensus 31 ~C~~C~~~l~~~~f~~~~~~~C~~c~~ 57 (131)
.|..|+.+| |.++|.+||..|-.
T Consensus 30 hCp~Cg~PL----F~KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL----FRKDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc----eeeCCeEECCCCCc
Confidence 477888888 56899999988864
No 40
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=78.34 E-value=1.4 Score=30.48 Aligned_cols=30 Identities=23% Similarity=0.419 Sum_probs=25.4
Q ss_pred cccCCCcCcCCCCcc-CcCCeeecccCcCCC
Q psy4437 30 VRCYDCHHTLSDKCF-SREGKLFCRNDFFRS 59 (131)
Q Consensus 30 f~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~ 59 (131)
-+|+.|+.......- ..+|++.|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 689999998887655 789999999999754
No 41
>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=76.86 E-value=1.9 Score=21.22 Aligned_cols=22 Identities=23% Similarity=0.552 Sum_probs=13.8
Q ss_pred cccccccccccceeccCCeeecCCC
Q psy4437 105 RCYDCHHTLSDKCFSREGKLFCRND 129 (131)
Q Consensus 105 ~C~~C~~~l~~~~~~~~g~~~C~~c 129 (131)
.|..|+.. .+...||..||..|
T Consensus 10 ~C~~C~~~---~~~~~dG~~yC~~c 31 (36)
T PF11781_consen 10 PCPVCGSR---WFYSDDGFYYCDRC 31 (36)
T ss_pred cCCCCCCe---EeEccCCEEEhhhC
Confidence 46666543 35667888888544
No 42
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=74.42 E-value=2 Score=21.86 Aligned_cols=21 Identities=33% Similarity=0.844 Sum_probs=12.4
Q ss_pred ccccccccccceeccCCeeecCCC
Q psy4437 106 CYDCHHTLSDKCFSREGKLFCRND 129 (131)
Q Consensus 106 C~~C~~~l~~~~~~~~g~~~C~~c 129 (131)
|..|+.||- -.++|+.||..|
T Consensus 20 Cp~C~~PL~---~~k~g~~~Cv~C 40 (41)
T PF06677_consen 20 CPDCGTPLM---RDKDGKIYCVSC 40 (41)
T ss_pred cCCCCCeeE---EecCCCEECCCC
Confidence 555654442 246777777665
No 43
>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=73.78 E-value=2.2 Score=22.93 Aligned_cols=22 Identities=27% Similarity=0.910 Sum_probs=11.7
Q ss_pred ccccccccccc-eeccCCeeecC
Q psy4437 106 CYDCHHTLSDK-CFSREGKLFCR 127 (131)
Q Consensus 106 C~~C~~~l~~~-~~~~~g~~~C~ 127 (131)
|..|...++.. -+.+||+.||.
T Consensus 10 C~~C~C~V~~~~Ai~~dGk~YCS 32 (52)
T PF02069_consen 10 CPSCSCVVSEEEAIQKDGKYYCS 32 (52)
T ss_dssp STT----B-TTTSEESSS-EESS
T ss_pred CCCCEeEECchHhHHhCCEeeec
Confidence 56777777755 77888888884
No 44
>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=73.55 E-value=3.9 Score=32.16 Aligned_cols=38 Identities=18% Similarity=0.377 Sum_probs=22.6
Q ss_pred ccccCCcccccceeeeecCCcccccCccccccccccccc
Q psy4437 78 SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK 116 (131)
Q Consensus 78 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 116 (131)
.|+.|-..+-..++ .+.+..--.+||.|..|..+|+..
T Consensus 28 yCp~CL~~~p~~e~-~~~~nrC~r~Cf~CP~C~~~L~~~ 65 (483)
T PF05502_consen 28 YCPNCLFEVPSSEA-RSEKNRCSRNCFDCPICFSPLSVR 65 (483)
T ss_pred ECccccccCChhhh-eeccceeccccccCCCCCCcceeE
Confidence 45555544443332 344444445888888888888755
No 45
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=69.14 E-value=2.5 Score=29.31 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=22.0
Q ss_pred ccccccccccccc-eeccCCeeecCCCC
Q psy4437 104 VRCYDCHHTLSDK-CFSREGKLFCRNDF 130 (131)
Q Consensus 104 f~C~~C~~~l~~~-~~~~~g~~~C~~cy 130 (131)
-+|..|+..+... -...+|+++|..||
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~ 200 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCA 200 (206)
T ss_pred eeccccCcccccchhhhcCCceeccccc
Confidence 5788898887766 56678999999987
No 46
>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=69.04 E-value=4.5 Score=24.42 Aligned_cols=26 Identities=19% Similarity=0.410 Sum_probs=15.7
Q ss_pred ccCCCcCcCCCCcc--CcCCeeecccCc
Q psy4437 31 RCYDCHHTLSDKCF--SREGKLFCRNDF 56 (131)
Q Consensus 31 ~C~~C~~~l~~~~f--~~~~~~~C~~c~ 56 (131)
.|..|+++|....| ..+|.++...|.
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEecccc
Confidence 46777777766555 245566655554
No 47
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=68.27 E-value=2.5 Score=25.84 Aligned_cols=27 Identities=19% Similarity=0.483 Sum_probs=19.2
Q ss_pred Cccccccccccccc--eeccCCeeecCCC
Q psy4437 103 CVRCYDCHHTLSDK--CFSREGKLFCRND 129 (131)
Q Consensus 103 Cf~C~~C~~~l~~~--~~~~~g~~~C~~c 129 (131)
=|+|+.|=..-... -...+|+++|..|
T Consensus 70 EFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEechhhhccccCCCEecccc
Confidence 48888885544333 3467899999987
No 48
>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=67.59 E-value=1.6 Score=25.39 Aligned_cols=9 Identities=33% Similarity=0.697 Sum_probs=6.6
Q ss_pred CcccccCcc
Q psy4437 97 RTWHADCVR 105 (131)
Q Consensus 97 ~~~H~~Cf~ 105 (131)
.-||.+||.
T Consensus 39 ~W~H~~C~~ 47 (82)
T PF00645_consen 39 KWYHWDCFF 47 (82)
T ss_dssp EEEEHHHHH
T ss_pred ceECccccc
Confidence 456888887
No 49
>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=65.31 E-value=5.7 Score=17.75 Aligned_cols=8 Identities=38% Similarity=0.978 Sum_probs=3.2
Q ss_pred cCCccccc
Q psy4437 81 GCEKPILD 88 (131)
Q Consensus 81 ~C~~~I~~ 88 (131)
+|+.+|.+
T Consensus 3 sC~~~i~~ 10 (24)
T PF07754_consen 3 SCGRPIAP 10 (24)
T ss_pred cCCCcccC
Confidence 34444433
No 50
>PRK00420 hypothetical protein; Validated
Probab=65.05 E-value=5 Score=25.18 Aligned_cols=10 Identities=20% Similarity=0.797 Sum_probs=4.5
Q ss_pred cCCeeecCCC
Q psy4437 120 REGKLFCRND 129 (131)
Q Consensus 120 ~~g~~~C~~c 129 (131)
++|+.||..|
T Consensus 37 k~g~~~Cp~C 46 (112)
T PRK00420 37 KDGEVVCPVH 46 (112)
T ss_pred CCCceECCCC
Confidence 4444444443
No 51
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=64.57 E-value=2.2 Score=22.26 Aligned_cols=29 Identities=28% Similarity=0.438 Sum_probs=16.8
Q ss_pred ccCCCcCcCCCCccCcCCee-ecccCcCCC
Q psy4437 31 RCYDCHHTLSDKCFSREGKL-FCRNDFFRS 59 (131)
Q Consensus 31 ~C~~C~~~l~~~~f~~~~~~-~C~~c~~~~ 59 (131)
.|..|.....+..+..=|.. +|..|..+.
T Consensus 4 ~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~ 33 (50)
T PF13920_consen 4 ECPICFENPRDVVLLPCGHLCFCEECAERL 33 (50)
T ss_dssp B-TTTSSSBSSEEEETTCEEEEEHHHHHHH
T ss_pred CCccCCccCCceEEeCCCChHHHHHHhHHh
Confidence 45666665554434444666 888887654
No 52
>KOG0978|consensus
Probab=63.74 E-value=0.88 Score=37.12 Aligned_cols=47 Identities=17% Similarity=0.429 Sum_probs=31.8
Q ss_pred cccCCCcCcCCCCccCcCCeeecccCcCCCCC---CCCCCCccccCCCCc
Q psy4437 30 VRCYDCHHTLSDKCFSREGKLFCRNDFFRSPV---RFPSGCGVGLSSSML 76 (131)
Q Consensus 30 f~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~---~~C~~c~~~i~~~~~ 76 (131)
++|+.|+....+....+=+..||..|-..++. .+|..|+.++.+++.
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence 68888886665544456678889998877664 366666666655543
No 53
>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=63.63 E-value=0.69 Score=22.66 Aligned_cols=25 Identities=20% Similarity=0.549 Sum_probs=11.5
Q ss_pred cCCCcCcCCCCcc-CcCCeeecccCc
Q psy4437 32 CYDCHHTLSDKCF-SREGKLFCRNDF 56 (131)
Q Consensus 32 C~~C~~~l~~~~f-~~~~~~~C~~c~ 56 (131)
|..|+.++..... ...+..+|..|.
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~ 31 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQ 31 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHh
Confidence 5555555554433 345555555443
No 54
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=63.41 E-value=2.7 Score=25.46 Aligned_cols=36 Identities=14% Similarity=0.298 Sum_probs=25.4
Q ss_pred cccccCCcccccceeeeec-CCcccccCccccccccc
Q psy4437 77 ISCAGCEKPILDKFLLNVL-ERTWHADCVRCYDCHHT 112 (131)
Q Consensus 77 ~~C~~C~~~I~~~~~~~~~-~~~~H~~Cf~C~~C~~~ 112 (131)
..|..|+.+|..++.+++- ..+-|-+||.=+.=+++
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKP 43 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCc
Confidence 4688999988877665653 56789999875544443
No 55
>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=62.00 E-value=4.5 Score=20.84 Aligned_cols=8 Identities=13% Similarity=0.409 Sum_probs=4.1
Q ss_pred eecccCcC
Q psy4437 50 LFCRNDFF 57 (131)
Q Consensus 50 ~~C~~c~~ 57 (131)
-+|.+||.
T Consensus 24 dLC~~Cf~ 31 (46)
T cd02249 24 DLCSSCYA 31 (46)
T ss_pred cCHHHHHC
Confidence 34555554
No 56
>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=61.37 E-value=4.1 Score=18.91 Aligned_cols=9 Identities=22% Similarity=0.593 Sum_probs=1.6
Q ss_pred CCCCccccC
Q psy4437 64 PSGCGVGLS 72 (131)
Q Consensus 64 C~~c~~~i~ 72 (131)
|..|++++.
T Consensus 3 C~~C~~~~~ 11 (30)
T PF07649_consen 3 CDACGKPID 11 (30)
T ss_dssp -TTTS----
T ss_pred CCcCCCcCC
Confidence 334444433
No 57
>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=61.22 E-value=3 Score=20.44 Aligned_cols=31 Identities=29% Similarity=0.682 Sum_probs=18.3
Q ss_pred cccCCccccCceeEeecCCccccCCcccCCCcCcCC
Q psy4437 5 CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS 40 (131)
Q Consensus 5 C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 40 (131)
|..|.+.+.+ ..++.||..=..|..|+-.++
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 5556555543 357899999999999987664
No 58
>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=60.38 E-value=5.4 Score=19.38 Aligned_cols=8 Identities=25% Similarity=0.737 Sum_probs=4.6
Q ss_pred cccCCccc
Q psy4437 5 CAGCEKPI 12 (131)
Q Consensus 5 C~~C~~~I 12 (131)
|..|.+.+
T Consensus 2 C~iC~~~~ 9 (45)
T cd00162 2 CPICLEEF 9 (45)
T ss_pred CCcCchhh
Confidence 55566555
No 59
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=59.68 E-value=9 Score=18.32 Aligned_cols=14 Identities=36% Similarity=0.674 Sum_probs=7.3
Q ss_pred CCccccccCCcccc
Q psy4437 74 SMLISCAGCEKPIL 87 (131)
Q Consensus 74 ~~~~~C~~C~~~I~ 87 (131)
.+.++|..|+-.|+
T Consensus 15 ~~~irC~~CG~RIl 28 (32)
T PF03604_consen 15 GDPIRCPECGHRIL 28 (32)
T ss_dssp SSTSSBSSSS-SEE
T ss_pred CCcEECCcCCCeEE
Confidence 34456666666554
No 60
>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=59.10 E-value=4.3 Score=21.96 Aligned_cols=29 Identities=14% Similarity=0.228 Sum_probs=18.9
Q ss_pred cccCCCcCcCCCCccCcCCeeecccCcCC
Q psy4437 30 VRCYDCHHTLSDKCFSREGKLFCRNDFFR 58 (131)
Q Consensus 30 f~C~~C~~~l~~~~f~~~~~~~C~~c~~~ 58 (131)
|.|..|+..+.+......|..||..+..+
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~ 30 (63)
T smart00504 2 FLCPISLEVMKDPVILPSGQTYERRAIEK 30 (63)
T ss_pred cCCcCCCCcCCCCEECCCCCEEeHHHHHH
Confidence 46777777776543355678888777643
No 61
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=57.80 E-value=2.5 Score=22.53 Aligned_cols=28 Identities=21% Similarity=0.594 Sum_probs=18.1
Q ss_pred ccCCCcCcCCC-Ccc-CcCCeeecccCcCCC
Q psy4437 31 RCYDCHHTLSD-KCF-SREGKLFCRNDFFRS 59 (131)
Q Consensus 31 ~C~~C~~~l~~-~~f-~~~~~~~C~~c~~~~ 59 (131)
.|..|++.+.- ..+ ..|| ..|.+|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 36777777765 235 5666 5788887654
No 62
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=57.56 E-value=5.3 Score=21.98 Aligned_cols=22 Identities=36% Similarity=0.822 Sum_probs=15.1
Q ss_pred ccccccccccc---eeccCCeeecC
Q psy4437 106 CYDCHHTLSDK---CFSREGKLFCR 127 (131)
Q Consensus 106 C~~C~~~l~~~---~~~~~g~~~C~ 127 (131)
|..|++.|..+ |.-+..+.+|.
T Consensus 19 C~~C~k~L~~~~DiymYrGd~aFCS 43 (58)
T PF04570_consen 19 CYLCKKKLDPGKDIYMYRGDKAFCS 43 (58)
T ss_pred HHccCCCCCCCCCeeeecccccccc
Confidence 66678888854 55566777774
No 63
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=56.78 E-value=1.9 Score=29.87 Aligned_cols=44 Identities=18% Similarity=0.241 Sum_probs=28.8
Q ss_pred cccCCCcCcCCCCccCcCCeeecccCcCCCC--CCCCCCCccccCC
Q psy4437 30 VRCYDCHHTLSDKCFSREGKLFCRNDFFRSP--VRFPSGCGVGLSS 73 (131)
Q Consensus 30 f~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~--~~~C~~c~~~i~~ 73 (131)
|.|..|.+...+.....=|..+|..|+.+.+ ++.|..|++...+
T Consensus 197 F~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 197 FLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred eeehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 7788887776554334557788888887655 4566666655443
No 64
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=55.68 E-value=7.1 Score=20.12 Aligned_cols=14 Identities=29% Similarity=0.589 Sum_probs=8.9
Q ss_pred CccccccCCccccc
Q psy4437 75 MLISCAGCEKPILD 88 (131)
Q Consensus 75 ~~~~C~~C~~~I~~ 88 (131)
+...|..|+-.|+-
T Consensus 18 ~~irC~~CG~rIly 31 (44)
T smart00659 18 DVVRCRECGYRILY 31 (44)
T ss_pred CceECCCCCceEEE
Confidence 44667777776654
No 65
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=54.99 E-value=1.7 Score=26.45 Aligned_cols=35 Identities=14% Similarity=0.286 Sum_probs=16.2
Q ss_pred cCCccccCceeEeecCCccccCCcccCCCcCcCCC
Q psy4437 7 GCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD 41 (131)
Q Consensus 7 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 41 (131)
.|+..+.+-......-..+++.+..|-.|++.|+-
T Consensus 40 ~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~ 74 (105)
T COG4357 40 HCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTR 74 (105)
T ss_pred HHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhH
Confidence 34444433333333334455555555555555544
No 66
>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=54.45 E-value=4.5 Score=18.71 Aligned_cols=9 Identities=33% Similarity=0.734 Sum_probs=3.1
Q ss_pred ccccCCccc
Q psy4437 4 SCAGCEKPI 12 (131)
Q Consensus 4 ~C~~C~~~I 12 (131)
.|..|+..|
T Consensus 3 ~C~rC~~~~ 11 (30)
T PF06827_consen 3 KCPRCWNYI 11 (30)
T ss_dssp B-TTT--BB
T ss_pred cCccCCCcc
Confidence 455555554
No 67
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=53.92 E-value=2 Score=26.09 Aligned_cols=22 Identities=14% Similarity=0.332 Sum_probs=10.7
Q ss_pred cCCcccccCccccccccccccc
Q psy4437 95 LERTWHADCVRCYDCHHTLSDK 116 (131)
Q Consensus 95 ~~~~~H~~Cf~C~~C~~~l~~~ 116 (131)
.-..+++.+..|..|.+.|+-.
T Consensus 54 ~~~~~~~~~iiCGvC~~~LT~~ 75 (105)
T COG4357 54 GLQEFNPKAIICGVCRKLLTRA 75 (105)
T ss_pred ChhhcCCccEEhhhhhhhhhHH
Confidence 3344455555555555555433
No 68
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=52.71 E-value=5.3 Score=22.85 Aligned_cols=37 Identities=24% Similarity=0.450 Sum_probs=16.8
Q ss_pred ccCCCcCcCCCCccCcCCeeecccCcCCCC-CCCCCCCcccc
Q psy4437 31 RCYDCHHTLSDKCFSREGKLFCRNDFFRSP-VRFPSGCGVGL 71 (131)
Q Consensus 31 ~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~-~~~C~~c~~~i 71 (131)
.|..|+.+|.. .++..+|..|...-. ...|..|++++
T Consensus 3 ~CP~C~~~L~~----~~~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEW----QGGHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEE----ETTEEEETTT--EEEEEEE-TTT-SB-
T ss_pred cCCCCCCccEE----eCCEEECccccccceecccCCCcccHH
Confidence 56778777754 246777877754311 23444444443
No 69
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=52.14 E-value=14 Score=19.02 Aligned_cols=6 Identities=33% Similarity=1.149 Sum_probs=2.9
Q ss_pred cccCCc
Q psy4437 5 CAGCEK 10 (131)
Q Consensus 5 C~~C~~ 10 (131)
|..|++
T Consensus 2 C~vC~~ 7 (51)
T PF00628_consen 2 CPVCGQ 7 (51)
T ss_dssp BTTTTS
T ss_pred CcCCCC
Confidence 444555
No 70
>KOG3476|consensus
Probab=51.90 E-value=0.68 Score=27.51 Aligned_cols=14 Identities=43% Similarity=0.581 Sum_probs=9.9
Q ss_pred cccccCCcccccce
Q psy4437 77 ISCAGCEKPILDKF 90 (131)
Q Consensus 77 ~~C~~C~~~I~~~~ 90 (131)
-+|+-|++.|.+..
T Consensus 80 giCAMCGKki~nTK 93 (100)
T KOG3476|consen 80 GICAMCGKKILNTK 93 (100)
T ss_pred hHHHHhhhHhhccc
Confidence 46888888877643
No 71
>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=51.59 E-value=8.5 Score=19.59 Aligned_cols=9 Identities=22% Similarity=0.596 Sum_probs=4.9
Q ss_pred eecccCcCC
Q psy4437 50 LFCRNDFFR 58 (131)
Q Consensus 50 ~~C~~c~~~ 58 (131)
-+|.+||.+
T Consensus 28 dlC~~Cf~~ 36 (44)
T smart00291 28 DLCQSCFAK 36 (44)
T ss_pred cchHHHHhC
Confidence 356666643
No 72
>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=51.03 E-value=7.1 Score=19.73 Aligned_cols=11 Identities=18% Similarity=0.570 Sum_probs=5.7
Q ss_pred cccccCCcccc
Q psy4437 77 ISCAGCEKPIL 87 (131)
Q Consensus 77 ~~C~~C~~~I~ 87 (131)
..|..|+....
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 34566665443
No 73
>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=50.89 E-value=5.4 Score=24.01 Aligned_cols=12 Identities=42% Similarity=0.711 Sum_probs=7.1
Q ss_pred cccCCCcCcCCC
Q psy4437 30 VRCYDCHHTLSD 41 (131)
Q Consensus 30 f~C~~C~~~l~~ 41 (131)
-.|..|+++|.-
T Consensus 34 S~C~~C~~~L~~ 45 (92)
T PF06750_consen 34 SHCPHCGHPLSW 45 (92)
T ss_pred CcCcCCCCcCcc
Confidence 456666666653
No 74
>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=50.24 E-value=13 Score=18.97 Aligned_cols=10 Identities=50% Similarity=1.381 Sum_probs=5.2
Q ss_pred ccccCCcccc
Q psy4437 4 SCAGCEKPIL 13 (131)
Q Consensus 4 ~C~~C~~~I~ 13 (131)
.|.+|+++|.
T Consensus 2 ~Cd~C~~~i~ 11 (43)
T cd02340 2 ICDGCQGPIV 11 (43)
T ss_pred CCCCCCCcCc
Confidence 4555655443
No 75
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=50.11 E-value=6.5 Score=20.18 Aligned_cols=29 Identities=24% Similarity=0.388 Sum_probs=15.5
Q ss_pred CccccCCccccCceeEeecCCccccCCcccCCCcCcCC
Q psy4437 3 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS 40 (131)
Q Consensus 3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 40 (131)
-+|..|+..+.-.... + =++|..|+.++.
T Consensus 4 y~C~~CG~~~~~~~~~---~------~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYG---T------GVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCC---C------ceECCCCCCeEE
Confidence 4577777765322111 0 267777766553
No 76
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=49.25 E-value=12 Score=20.67 Aligned_cols=10 Identities=20% Similarity=0.537 Sum_probs=4.9
Q ss_pred CCCCCCcccc
Q psy4437 62 RFPSGCGVGL 71 (131)
Q Consensus 62 ~~C~~c~~~i 71 (131)
+.|..|+..|
T Consensus 10 ~~CtSCg~~i 19 (61)
T COG2888 10 PVCTSCGREI 19 (61)
T ss_pred ceeccCCCEe
Confidence 4455555444
No 77
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=48.67 E-value=15 Score=20.75 Aligned_cols=21 Identities=19% Similarity=0.494 Sum_probs=12.2
Q ss_pred cccccccccccc----eeccCCeee
Q psy4437 105 RCYDCHHTLSDK----CFSREGKLF 125 (131)
Q Consensus 105 ~C~~C~~~l~~~----~~~~~g~~~ 125 (131)
+|+-|+..|..+ |+..||.++
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~ 29 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVL 29 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEE
Confidence 366667776554 344566654
No 78
>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=46.41 E-value=13 Score=18.09 Aligned_cols=13 Identities=38% Similarity=1.170 Sum_probs=4.6
Q ss_pred ccccCCccccCce
Q psy4437 4 SCAGCEKPILDKF 16 (131)
Q Consensus 4 ~C~~C~~~I~~~~ 16 (131)
.|..|++++.+.+
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 4555555555443
No 79
>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=45.94 E-value=20 Score=18.05 Aligned_cols=13 Identities=23% Similarity=0.675 Sum_probs=8.2
Q ss_pred ccccccccccccc
Q psy4437 104 VRCYDCHHTLSDK 116 (131)
Q Consensus 104 f~C~~C~~~l~~~ 116 (131)
+.|..|+..|...
T Consensus 20 ~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 20 LVCPNCGLVLEEN 32 (43)
T ss_dssp EEETTT-BBEE-T
T ss_pred EECCCCCCEeecc
Confidence 5788888877654
No 80
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=45.74 E-value=15 Score=19.69 Aligned_cols=24 Identities=21% Similarity=0.519 Sum_probs=17.0
Q ss_pred ccccCCcccccceeeeecCCcccc
Q psy4437 78 SCAGCEKPILDKFLLNVLERTWHA 101 (131)
Q Consensus 78 ~C~~C~~~I~~~~~~~~~~~~~H~ 101 (131)
+|..|+.||...-.+......-|+
T Consensus 3 iCvvCK~Pi~~al~v~T~~Gpvh~ 26 (53)
T PHA02610 3 ICVVCKQPIEKALVVETEKGPVHP 26 (53)
T ss_pred eeeeeCCchhhceEEecCCCCCCC
Confidence 577788888666666666677776
No 81
>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=44.95 E-value=13 Score=19.41 Aligned_cols=9 Identities=22% Similarity=0.490 Sum_probs=3.4
Q ss_pred CCCCCcccc
Q psy4437 63 FPSGCGVGL 71 (131)
Q Consensus 63 ~C~~c~~~i 71 (131)
.|..|++.|
T Consensus 13 ~C~~C~~~i 21 (53)
T PF00130_consen 13 YCDVCGKFI 21 (53)
T ss_dssp B-TTSSSBE
T ss_pred CCcccCccc
Confidence 344444444
No 82
>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=44.64 E-value=11 Score=18.50 Aligned_cols=12 Identities=17% Similarity=0.484 Sum_probs=7.4
Q ss_pred cccccCCccccc
Q psy4437 77 ISCAGCEKPILD 88 (131)
Q Consensus 77 ~~C~~C~~~I~~ 88 (131)
..|..|++.+..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 457777775543
No 83
>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=44.36 E-value=22 Score=23.62 Aligned_cols=11 Identities=36% Similarity=1.029 Sum_probs=5.3
Q ss_pred cccCCccccCc
Q psy4437 5 CAGCEKPILDK 15 (131)
Q Consensus 5 C~~C~~~I~~~ 15 (131)
|..|+-+|.+.
T Consensus 42 Cp~C~~~IrG~ 52 (158)
T PF10083_consen 42 CPNCSTPIRGD 52 (158)
T ss_pred CcCCCCCCCCc
Confidence 44455555443
No 84
>KOG3579|consensus
Probab=44.22 E-value=11 Score=27.67 Aligned_cols=29 Identities=21% Similarity=0.497 Sum_probs=15.9
Q ss_pred cccCCccccCceeEeecCCccccCCcccC
Q psy4437 5 CAGCEKPILDKFLLNVLERTWHADCVRCY 33 (131)
Q Consensus 5 C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~ 33 (131)
|.-|++.+.|.-.|.--.-.-|+-||-|+
T Consensus 271 CTLC~ERLEDTHFVQCPSVp~HKFCFPCS 299 (352)
T KOG3579|consen 271 CTLCHERLEDTHFVQCPSVPSHKFCFPCS 299 (352)
T ss_pred ehhhhhhhccCceeecCCCcccceecccC
Confidence 55566666555444444455566666554
No 85
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=44.08 E-value=10 Score=20.07 Aligned_cols=13 Identities=38% Similarity=0.570 Sum_probs=7.5
Q ss_pred ccccccCCccccc
Q psy4437 76 LISCAGCEKPILD 88 (131)
Q Consensus 76 ~~~C~~C~~~I~~ 88 (131)
...|+.|+-.|+-
T Consensus 24 ~irCp~Cg~rIl~ 36 (49)
T COG1996 24 GIRCPYCGSRILV 36 (49)
T ss_pred ceeCCCCCcEEEE
Confidence 3566666665543
No 86
>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=43.44 E-value=18 Score=17.99 Aligned_cols=29 Identities=21% Similarity=0.461 Sum_probs=11.5
Q ss_pred ccccCCcccccceeeeecCCcccccCcccccccc
Q psy4437 78 SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHH 111 (131)
Q Consensus 78 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~ 111 (131)
+|..|+..|-.-..+...++.| +|..|+.
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred ccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 4555555554433334445554 5665554
No 87
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=42.13 E-value=18 Score=19.52 Aligned_cols=33 Identities=27% Similarity=0.442 Sum_probs=18.9
Q ss_pred CCCccccCCccccCceeEeecCCccccCCcccCCCcCcCC
Q psy4437 1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS 40 (131)
Q Consensus 1 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 40 (131)
|...|..|+..|.-.... .|. -..|..|+..|.
T Consensus 1 ~~~~CP~CG~~iev~~~~--~Ge-----iV~Cp~CGaele 33 (54)
T TIGR01206 1 MQFECPDCGAEIELENPE--LGE-----LVICDECGAELE 33 (54)
T ss_pred CccCCCCCCCEEecCCCc--cCC-----EEeCCCCCCEEE
Confidence 566788888877322211 132 246777777664
No 88
>KOG0320|consensus
Probab=41.89 E-value=4.5 Score=27.50 Aligned_cols=52 Identities=23% Similarity=0.457 Sum_probs=33.4
Q ss_pred ccCCcccCCCcCcCCCCc-c-CcCCeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccce
Q psy4437 26 HADCVRCYDCHHTLSDKC-F-SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKF 90 (131)
Q Consensus 26 H~~Cf~C~~C~~~l~~~~-f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~ 90 (131)
-..++.|-.|-.....+. + .+=|.+||..|...... ....|+.|+|.|..++
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk-------------~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALK-------------NTNKCPTCRKKITHKQ 181 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHH-------------hCCCCCCcccccchhh
Confidence 345788888877776644 5 56688999888754321 1246777777665544
No 89
>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=41.70 E-value=11 Score=19.71 Aligned_cols=30 Identities=20% Similarity=0.598 Sum_probs=19.7
Q ss_pred ccccCCccccCceeEeecCCccccCCcccCCCcCcCCC
Q psy4437 4 SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD 41 (131)
Q Consensus 4 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 41 (131)
.|..|+++..++ +.+.++ |.|..|.+.|..
T Consensus 1 ~CiiC~~~~~~G--I~I~~~------fIC~~CE~~iv~ 30 (46)
T PF10764_consen 1 KCIICGKEKEEG--IHIYGK------FICSDCEKEIVN 30 (46)
T ss_pred CeEeCCCcCCCC--EEEECe------EehHHHHHHhcc
Confidence 366777777665 334444 788888777754
No 90
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=41.62 E-value=40 Score=29.99 Aligned_cols=37 Identities=14% Similarity=0.225 Sum_probs=19.9
Q ss_pred eecccCcCCCCCCCCCCCccccCCCCccccccCCccccc
Q psy4437 50 LFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILD 88 (131)
Q Consensus 50 ~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~ 88 (131)
..|.+|-...+..+|..|+....+ ...|+.|+..+..
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~te~--vy~CPsCGaev~~ 704 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHTEP--VYVCPDCGAEVPP 704 (1337)
T ss_pred EECCCCCCccccccCcccCCcCCC--ceeCccCCCccCC
Confidence 455555544444566666665533 2356666665543
No 91
>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=41.39 E-value=9.4 Score=16.01 Aligned_cols=13 Identities=31% Similarity=0.674 Sum_probs=9.2
Q ss_pred ccccccccccccc
Q psy4437 104 VRCYDCHHTLSDK 116 (131)
Q Consensus 104 f~C~~C~~~l~~~ 116 (131)
|+|..|++.+...
T Consensus 1 y~C~~C~~~f~~~ 13 (23)
T PF00096_consen 1 YKCPICGKSFSSK 13 (23)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCccCCH
Confidence 5678888777654
No 92
>PRK00807 50S ribosomal protein L24e; Validated
Probab=41.20 E-value=21 Score=19.05 Aligned_cols=9 Identities=44% Similarity=0.814 Sum_probs=4.1
Q ss_pred cccCCcccc
Q psy4437 79 CAGCEKPIL 87 (131)
Q Consensus 79 C~~C~~~I~ 87 (131)
|+.|+..|.
T Consensus 4 C~fcG~~I~ 12 (52)
T PRK00807 4 CSFCGKEIE 12 (52)
T ss_pred cCCCCCeEc
Confidence 444444444
No 93
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=40.04 E-value=14 Score=19.33 Aligned_cols=12 Identities=17% Similarity=0.484 Sum_probs=7.7
Q ss_pred cccccCCccccc
Q psy4437 77 ISCAGCEKPILD 88 (131)
Q Consensus 77 ~~C~~C~~~I~~ 88 (131)
..|..|+.....
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 467788775543
No 94
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=39.50 E-value=14 Score=21.36 Aligned_cols=32 Identities=16% Similarity=0.084 Sum_probs=10.5
Q ss_pred CCCCCCCCccccCCCCccccccCCccccccee
Q psy4437 60 PVRFPSGCGVGLSSSMLISCAGCEKPILDKFL 91 (131)
Q Consensus 60 ~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~ 91 (131)
+..+|.+|..........-|+.|+..-+.+..
T Consensus 8 ~vlrC~aCf~~t~~~~k~FCp~CGn~TL~rvs 39 (73)
T PF08772_consen 8 WVLRCHACFKITKDMTKQFCPKCGNATLKRVS 39 (73)
T ss_dssp EEEE-SSS--EES-SS--S-SSS--S--EEEE
T ss_pred eeEEccccccCcCCCCceeCcccCCCcceEEE
Confidence 34455555555444444556666665444433
No 95
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=39.29 E-value=13 Score=20.28 Aligned_cols=22 Identities=23% Similarity=0.276 Sum_probs=12.4
Q ss_pred eecccCcCCCCCCCCCCCcccc
Q psy4437 50 LFCRNDFFRSPVRFPSGCGVGL 71 (131)
Q Consensus 50 ~~C~~c~~~~~~~~C~~c~~~i 71 (131)
.||.+|........|..|+..+
T Consensus 30 TFC~~C~e~~l~~~CPNCgGel 51 (57)
T PF06906_consen 30 TFCADCAETMLNGVCPNCGGEL 51 (57)
T ss_pred cccHHHHHHHhcCcCcCCCCcc
Confidence 3566666655555555555544
No 96
>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=39.18 E-value=15 Score=19.04 Aligned_cols=28 Identities=11% Similarity=0.444 Sum_probs=17.5
Q ss_pred ccCCCcCcCCCCcc--Cc-CCeeecccCcCC
Q psy4437 31 RCYDCHHTLSDKCF--SR-EGKLFCRNDFFR 58 (131)
Q Consensus 31 ~C~~C~~~l~~~~f--~~-~~~~~C~~c~~~ 58 (131)
.|..|+..++...| .+ .+..+|.+||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 46777777776444 22 245678888764
No 97
>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=39.18 E-value=18 Score=20.01 Aligned_cols=12 Identities=33% Similarity=0.567 Sum_probs=6.5
Q ss_pred CCccccCCcccc
Q psy4437 2 LISCAGCEKPIL 13 (131)
Q Consensus 2 ~~~C~~C~~~I~ 13 (131)
+.+|..||++|.
T Consensus 4 PVRCFTCGkvi~ 15 (60)
T PF01194_consen 4 PVRCFTCGKVIG 15 (60)
T ss_dssp SSS-STTTSBTC
T ss_pred ceecCCCCCChh
Confidence 455666666663
No 98
>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=39.00 E-value=10 Score=22.61 Aligned_cols=16 Identities=19% Similarity=0.069 Sum_probs=11.9
Q ss_pred cCCCCCCCCCCCcccc
Q psy4437 56 FFRSPVRFPSGCGVGL 71 (131)
Q Consensus 56 ~~~~~~~~C~~c~~~i 71 (131)
|...|..+|..|++.+
T Consensus 49 Y~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLL 64 (90)
T ss_pred HhhhccchhhHHHhHh
Confidence 5667777888888777
No 99
>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=38.39 E-value=28 Score=18.11 Aligned_cols=19 Identities=26% Similarity=0.683 Sum_probs=8.7
Q ss_pred CCCCccccCCCCccccccC
Q psy4437 64 PSGCGVGLSSSMLISCAGC 82 (131)
Q Consensus 64 C~~c~~~i~~~~~~~C~~C 82 (131)
|.+|.+.+..+....|..|
T Consensus 3 Cd~C~~~~~~g~r~~C~~C 21 (49)
T cd02335 3 CDYCSKDITGTIRIKCAEC 21 (49)
T ss_pred CCCcCCCCCCCcEEECCCC
Confidence 4455544444333444444
No 100
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=38.32 E-value=26 Score=16.83 Aligned_cols=7 Identities=29% Similarity=0.842 Sum_probs=3.3
Q ss_pred ccccCCc
Q psy4437 78 SCAGCEK 84 (131)
Q Consensus 78 ~C~~C~~ 84 (131)
.|+.|+.
T Consensus 20 ~CP~Cg~ 26 (34)
T cd00729 20 KCPICGA 26 (34)
T ss_pred cCcCCCC
Confidence 4444443
No 101
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=38.07 E-value=13 Score=18.75 Aligned_cols=29 Identities=21% Similarity=0.495 Sum_probs=14.5
Q ss_pred cCCCcCcCCC--Ccc-CcCCeeecccCcCCCC
Q psy4437 32 CYDCHHTLSD--KCF-SREGKLFCRNDFFRSP 60 (131)
Q Consensus 32 C~~C~~~l~~--~~f-~~~~~~~C~~c~~~~~ 60 (131)
|..|...+++ ..+ ..=|..+|..|..+..
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc
Confidence 4455555522 122 2336667777765544
No 102
>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=37.61 E-value=8.1 Score=21.15 Aligned_cols=15 Identities=27% Similarity=0.735 Sum_probs=12.3
Q ss_pred cccCCCcCcCCCCcc
Q psy4437 30 VRCYDCHHTLSDKCF 44 (131)
Q Consensus 30 f~C~~C~~~l~~~~f 44 (131)
+.|++|+..|+++.|
T Consensus 5 lvCSTCGrDlSeeRy 19 (63)
T PF05864_consen 5 LVCSTCGRDLSEERY 19 (63)
T ss_pred eeecccCCcchHHHH
Confidence 578999999988655
No 103
>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=37.27 E-value=8.3 Score=19.67 Aligned_cols=26 Identities=19% Similarity=0.460 Sum_probs=9.2
Q ss_pred cccCCccccCceeEee--cCCccccCCc
Q psy4437 5 CAGCEKPILDKFLLNV--LERTWHADCV 30 (131)
Q Consensus 5 C~~C~~~I~~~~~~~~--~~~~~H~~Cf 30 (131)
|..|++.++-+..-.- =+..||..|+
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~ 28 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCF 28 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHH
Confidence 5667776655533211 1234565554
No 104
>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=36.60 E-value=6.7 Score=19.69 Aligned_cols=27 Identities=22% Similarity=0.476 Sum_probs=12.9
Q ss_pred ccccCCccccCceeEeec--CCccccCCc
Q psy4437 4 SCAGCEKPILDKFLLNVL--ERTWHADCV 30 (131)
Q Consensus 4 ~C~~C~~~I~~~~~~~~~--~~~~H~~Cf 30 (131)
.|..|.+.+.+++.+..+ +-.||.+|+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci 30 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCI 30 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHH
Confidence 466677777432222222 444555443
No 105
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=35.99 E-value=8.6 Score=21.04 Aligned_cols=15 Identities=27% Similarity=0.735 Sum_probs=12.3
Q ss_pred cccCCCcCcCCCCcc
Q psy4437 30 VRCYDCHHTLSDKCF 44 (131)
Q Consensus 30 f~C~~C~~~l~~~~f 44 (131)
++|++|+..|+++.|
T Consensus 5 lVCsTCGrDlSeeRy 19 (63)
T PHA03082 5 LVCSTCGRDLSEERY 19 (63)
T ss_pred eeecccCcchhHHHH
Confidence 579999999988655
No 106
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=35.88 E-value=21 Score=19.11 Aligned_cols=28 Identities=25% Similarity=0.526 Sum_probs=14.1
Q ss_pred cccCCcccccceeeeecCCcccccCccc
Q psy4437 79 CAGCEKPILDKFLLNVLERTWHADCVRC 106 (131)
Q Consensus 79 C~~C~~~I~~~~~~~~~~~~~H~~Cf~C 106 (131)
|+-|+.+|.-..-.+..++.|=.+|-.|
T Consensus 3 CPyCge~~~~~iD~s~~~Q~yiEDC~vC 30 (52)
T PF14255_consen 3 CPYCGEPIEILIDPSAGDQEYIEDCQVC 30 (52)
T ss_pred CCCCCCeeEEEEecCCCCeeEEeehhhc
Confidence 4555555543222244566666666554
No 107
>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=35.66 E-value=27 Score=18.40 Aligned_cols=8 Identities=38% Similarity=1.103 Sum_probs=4.4
Q ss_pred ecccCcCC
Q psy4437 51 FCRNDFFR 58 (131)
Q Consensus 51 ~C~~c~~~ 58 (131)
+|..||..
T Consensus 26 LC~~Cf~~ 33 (49)
T cd02334 26 LCQSCFFS 33 (49)
T ss_pred chHHHHhC
Confidence 56666643
No 108
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=34.85 E-value=18 Score=19.31 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=14.6
Q ss_pred cccccccccccc-eec---cCCeeecCCC
Q psy4437 105 RCYDCHHTLSDK-CFS---REGKLFCRND 129 (131)
Q Consensus 105 ~C~~C~~~l~~~-~~~---~~g~~~C~~c 129 (131)
+|..|...|+.. +.. .++.++|+.|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~C 52 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNC 52 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCC
Confidence 577777777666 221 2355667665
No 109
>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=34.69 E-value=33 Score=17.07 Aligned_cols=8 Identities=13% Similarity=0.239 Sum_probs=3.3
Q ss_pred CCCCcccc
Q psy4437 64 PSGCGVGL 71 (131)
Q Consensus 64 C~~c~~~i 71 (131)
|..|.+.|
T Consensus 14 C~~C~~~i 21 (49)
T smart00109 14 CCVCRKSI 21 (49)
T ss_pred cccccccc
Confidence 44444433
No 110
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=34.20 E-value=11 Score=24.58 Aligned_cols=34 Identities=18% Similarity=0.371 Sum_probs=15.8
Q ss_pred ccccCCccccCceeEeecCCccccCCcccCCCcCcCC
Q psy4437 4 SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS 40 (131)
Q Consensus 4 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 40 (131)
.|..|+...+..+++...+. ..=|.|..|+..|.
T Consensus 101 ~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 101 KCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred ECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 35666655543332222121 22266666666664
No 111
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=33.79 E-value=21 Score=29.60 Aligned_cols=82 Identities=24% Similarity=0.484 Sum_probs=46.9
Q ss_pred CccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCccccccC
Q psy4437 3 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGC 82 (131)
Q Consensus 3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C 82 (131)
.+|..|-+.|.+. .++.||--=-.|+.|+-.++- ....|| .+... .-.+.++|..|
T Consensus 102 a~C~~Cl~Ei~dp-----~~rrY~YPF~~CT~CGPRfTI----i~alPY-----DR~nT----------sM~~F~lC~~C 157 (750)
T COG0068 102 ATCEDCLEEIFDP-----NSRRYLYPFINCTNCGPRFTI----IEALPY-----DRENT----------SMADFPLCPFC 157 (750)
T ss_pred hhhHHHHHHhcCC-----CCcceeccccccCCCCcceee----eccCCC-----CcccC----------ccccCcCCHHH
Confidence 4577777777554 466777776778888755542 222221 11100 00223456666
Q ss_pred CcccccceeeeecCCcccccCcccccccccc
Q psy4437 83 EKPILDKFLLNVLERTWHADCVRCYDCHHTL 113 (131)
Q Consensus 83 ~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l 113 (131)
.+. +....++.||..=..|..|+-.+
T Consensus 158 ~~E-----Y~dP~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 158 DKE-----YKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred HHH-----hcCccccccccccccCcccCCCe
Confidence 542 11567888999888899987644
No 112
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=33.68 E-value=24 Score=18.47 Aligned_cols=8 Identities=13% Similarity=0.704 Sum_probs=4.1
Q ss_pred ecccCcCC
Q psy4437 51 FCRNDFFR 58 (131)
Q Consensus 51 ~C~~c~~~ 58 (131)
+|.+||.+
T Consensus 28 lC~~C~~~ 35 (48)
T cd02341 28 LCQDCVVK 35 (48)
T ss_pred cCHHHHhC
Confidence 45555543
No 113
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=33.57 E-value=23 Score=24.43 Aligned_cols=29 Identities=24% Similarity=0.460 Sum_probs=19.8
Q ss_pred CcccCCCcCcCCCCccCcCCeeecccCcC
Q psy4437 29 CVRCYDCHHTLSDKCFSREGKLFCRNDFF 57 (131)
Q Consensus 29 Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~ 57 (131)
-|.|..|...+.+.....=|..||..|..
T Consensus 18 ~~~CpICld~~~dPVvT~CGH~FC~~CI~ 46 (193)
T PLN03208 18 DFDCNICLDQVRDPVVTLCGHLFCWPCIH 46 (193)
T ss_pred ccCCccCCCcCCCcEEcCCCchhHHHHHH
Confidence 47788887776554334567788888864
No 114
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=33.49 E-value=17 Score=20.25 Aligned_cols=11 Identities=36% Similarity=0.785 Sum_probs=6.1
Q ss_pred CccccCCcccc
Q psy4437 3 ISCAGCEKPIL 13 (131)
Q Consensus 3 ~~C~~C~~~I~ 13 (131)
.+|..||++|.
T Consensus 5 vRCFTCGkvi~ 15 (62)
T PRK04016 5 VRCFTCGKVIA 15 (62)
T ss_pred eEecCCCCChH
Confidence 45555665553
No 115
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=33.32 E-value=18 Score=20.77 Aligned_cols=12 Identities=33% Similarity=0.567 Sum_probs=7.6
Q ss_pred CCccccCCcccc
Q psy4437 2 LISCAGCEKPIL 13 (131)
Q Consensus 2 ~~~C~~C~~~I~ 13 (131)
+.+|..||++|.
T Consensus 4 PVRCFTCGkvig 15 (71)
T PLN00032 4 PVRCFTCGKVIG 15 (71)
T ss_pred ceeecCCCCCcH
Confidence 456677777663
No 116
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=33.08 E-value=54 Score=27.05 Aligned_cols=40 Identities=23% Similarity=0.496 Sum_probs=25.8
Q ss_pred CCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCccccccccccccc
Q psy4437 61 VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK 116 (131)
Q Consensus 61 ~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 116 (131)
+..|..|+.++.. ..|..|+..+..... .|..|+..++..
T Consensus 15 akFC~~CG~~l~~---~~Cp~CG~~~~~~~~-------------fC~~CG~~~~~~ 54 (645)
T PRK14559 15 NRFCQKCGTSLTH---KPCPQCGTEVPVDEA-------------HCPNCGAETGTI 54 (645)
T ss_pred CccccccCCCCCC---CcCCCCCCCCCcccc-------------cccccCCcccch
Confidence 5578888777643 368888887544332 367777777654
No 117
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=32.84 E-value=18 Score=21.19 Aligned_cols=28 Identities=25% Similarity=0.571 Sum_probs=19.4
Q ss_pred ccCCCcCcCCCCc-c--CcCC---eeecccCcCC
Q psy4437 31 RCYDCHHTLSDKC-F--SREG---KLFCRNDFFR 58 (131)
Q Consensus 31 ~C~~C~~~l~~~~-f--~~~~---~~~C~~c~~~ 58 (131)
.|..|+.||.... + ..|| .-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 4788999998754 3 2343 4699999865
No 118
>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=32.26 E-value=42 Score=15.09 Aligned_cols=6 Identities=33% Similarity=1.016 Sum_probs=2.5
Q ss_pred ccccCC
Q psy4437 78 SCAGCE 83 (131)
Q Consensus 78 ~C~~C~ 83 (131)
.|+.|+
T Consensus 16 ~Cp~CG 21 (26)
T PF10571_consen 16 FCPHCG 21 (26)
T ss_pred cCCCCC
Confidence 344443
No 119
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=32.14 E-value=24 Score=17.07 Aligned_cols=8 Identities=38% Similarity=1.281 Sum_probs=2.2
Q ss_pred cccCCccc
Q psy4437 79 CAGCEKPI 86 (131)
Q Consensus 79 C~~C~~~I 86 (131)
|+.|+.++
T Consensus 3 C~~CG~~l 10 (34)
T PF14803_consen 3 CPQCGGPL 10 (34)
T ss_dssp -TTT--B-
T ss_pred cccccChh
Confidence 55555554
No 120
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=31.54 E-value=26 Score=26.97 Aligned_cols=26 Identities=19% Similarity=0.395 Sum_probs=14.3
Q ss_pred CCCCCccccCCCCccccccCCccccc
Q psy4437 63 FPSGCGVGLSSSMLISCAGCEKPILD 88 (131)
Q Consensus 63 ~C~~c~~~i~~~~~~~C~~C~~~I~~ 88 (131)
.|..|+..+.+++...|++|+..+..
T Consensus 217 ~C~~Cd~~~~~~~~a~CpRC~~~L~~ 242 (403)
T TIGR00155 217 SCSACHTTILPAQEPVCPRCSTPLYV 242 (403)
T ss_pred cCCCCCCccCCCCCcCCcCCCCcccC
Confidence 35555554444444566666666543
No 121
>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=30.86 E-value=19 Score=14.70 Aligned_cols=13 Identities=23% Similarity=0.613 Sum_probs=6.8
Q ss_pred ccccccccccccc
Q psy4437 104 VRCYDCHHTLSDK 116 (131)
Q Consensus 104 f~C~~C~~~l~~~ 116 (131)
|.|..|+..+...
T Consensus 1 ~~C~~C~~~~~~~ 13 (24)
T PF13894_consen 1 FQCPICGKSFRSK 13 (24)
T ss_dssp EE-SSTS-EESSH
T ss_pred CCCcCCCCcCCcH
Confidence 4677777766543
No 122
>PRK12496 hypothetical protein; Provisional
Probab=30.46 E-value=30 Score=23.13 Aligned_cols=26 Identities=19% Similarity=0.390 Sum_probs=14.7
Q ss_pred CCCCCCccccCCC-CccccccCCcccc
Q psy4437 62 RFPSGCGVGLSSS-MLISCAGCEKPIL 87 (131)
Q Consensus 62 ~~C~~c~~~i~~~-~~~~C~~C~~~I~ 87 (131)
.+|.+|++..... ....|+.||.++.
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChhh
Confidence 4566666655432 2245777776654
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=30.24 E-value=1.1e+02 Score=27.49 Aligned_cols=53 Identities=17% Similarity=0.356 Sum_probs=32.8
Q ss_pred CcccCCCcCcCCCCccCcCCeeecccCcCCCC-CCCCCCCccccCCCC--ccccccCCcccccc
Q psy4437 29 CVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP-VRFPSGCGVGLSSSM--LISCAGCEKPILDK 89 (131)
Q Consensus 29 Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~-~~~C~~c~~~i~~~~--~~~C~~C~~~I~~~ 89 (131)
=++|..|+..... .+|..|-.... ...|..|+..+.+.+ ...|+.|+.++...
T Consensus 667 ~rkCPkCG~~t~~--------~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~~ 722 (1337)
T PRK14714 667 RRRCPSCGTETYE--------NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTPY 722 (1337)
T ss_pred EEECCCCCCcccc--------ccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCccccc
Confidence 3778888775432 16777654432 236888887765432 34788888777653
No 124
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=29.93 E-value=70 Score=23.14 Aligned_cols=36 Identities=19% Similarity=0.561 Sum_probs=21.6
Q ss_pred CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCC
Q psy4437 2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD 41 (131)
Q Consensus 2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 41 (131)
.++|.+|.+.-.. | ..++.|=..=|.|..|+..+.+
T Consensus 132 VSRCr~C~~rYDP---V-P~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 132 VSRCRKCRKRYDP---V-PCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccccccccccCC---C-ccccccceeeeecccccccchh
Confidence 3566677664311 1 1456666666788888777765
No 125
>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 KOG3497|consensus
Probab=29.35 E-value=20 Score=19.90 Aligned_cols=13 Identities=46% Similarity=0.667 Sum_probs=7.5
Q ss_pred CCccccCCccccC
Q psy4437 2 LISCAGCEKPILD 14 (131)
Q Consensus 2 ~~~C~~C~~~I~~ 14 (131)
+.+|..|++.|.+
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 3456666666643
No 127
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=29.31 E-value=21 Score=18.62 Aligned_cols=10 Identities=40% Similarity=0.979 Sum_probs=5.0
Q ss_pred cccccccccc
Q psy4437 104 VRCYDCHHTL 113 (131)
Q Consensus 104 f~C~~C~~~l 113 (131)
++|..|...|
T Consensus 32 lrCGaCs~vl 41 (46)
T PF11331_consen 32 LRCGACSEVL 41 (46)
T ss_pred EeCCCCceeE
Confidence 4455555444
No 128
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=28.93 E-value=31 Score=24.23 Aligned_cols=28 Identities=21% Similarity=0.387 Sum_probs=15.5
Q ss_pred cCccccccccccccc-eeccCCeeecCCC
Q psy4437 102 DCVRCYDCHHTLSDK-CFSREGKLFCRND 129 (131)
Q Consensus 102 ~Cf~C~~C~~~l~~~-~~~~~g~~~C~~c 129 (131)
+=..|..|++++... |...+|.++|..|
T Consensus 148 ~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c 176 (247)
T PRK00085 148 DLDHCAVCGAPGDHRYFSPKEGGAVCSEC 176 (247)
T ss_pred chhhHhcCCCCCCceEEecccCCcccccc
Confidence 334566666665533 3345666666555
No 129
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=28.85 E-value=37 Score=22.10 Aligned_cols=12 Identities=33% Similarity=0.753 Sum_probs=6.6
Q ss_pred cccCCCcCcCCC
Q psy4437 30 VRCYDCHHTLSD 41 (131)
Q Consensus 30 f~C~~C~~~l~~ 41 (131)
-+|..|+.+|..
T Consensus 92 sRC~~CN~~L~~ 103 (147)
T PF01927_consen 92 SRCPKCNGPLRP 103 (147)
T ss_pred CccCCCCcEeee
Confidence 456666665543
No 130
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=28.82 E-value=20 Score=15.64 Aligned_cols=13 Identities=31% Similarity=0.710 Sum_probs=9.9
Q ss_pred ccccccccccccc
Q psy4437 104 VRCYDCHHTLSDK 116 (131)
Q Consensus 104 f~C~~C~~~l~~~ 116 (131)
|.|..|++.+...
T Consensus 2 ~~C~~C~~~F~~~ 14 (27)
T PF13912_consen 2 FECDECGKTFSSL 14 (27)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCccCCccCCh
Confidence 5788888888765
No 131
>PRK12495 hypothetical protein; Provisional
Probab=28.36 E-value=40 Score=23.82 Aligned_cols=27 Identities=26% Similarity=0.716 Sum_probs=17.2
Q ss_pred cccccCCcccccceeeeecCCcccccCccccccccccc
Q psy4437 77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS 114 (131)
Q Consensus 77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 114 (131)
..|..|+.||. . ++.+-.|..|+....
T Consensus 43 ~hC~~CG~PIp----------a-~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 43 AHCDECGDPIF----------R-HDGQEFCPTCQQPVT 69 (226)
T ss_pred hhcccccCccc----------C-CCCeeECCCCCCccc
Confidence 56888888876 1 144556777776554
No 132
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=28.34 E-value=34 Score=17.23 Aligned_cols=6 Identities=17% Similarity=0.163 Sum_probs=2.2
Q ss_pred CCCCcc
Q psy4437 64 PSGCGV 69 (131)
Q Consensus 64 C~~c~~ 69 (131)
|..|.+
T Consensus 14 C~~C~~ 19 (50)
T cd00029 14 CDVCRK 19 (50)
T ss_pred hhhcch
Confidence 333333
No 133
>PF05810 NinF: NinF protein; InterPro: IPR008712 This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
Probab=28.19 E-value=13 Score=20.24 Aligned_cols=19 Identities=26% Similarity=0.602 Sum_probs=10.6
Q ss_pred CCCCccccCCCCccccccC
Q psy4437 64 PSGCGVGLSSSMLISCAGC 82 (131)
Q Consensus 64 C~~c~~~i~~~~~~~C~~C 82 (131)
|.+|++.+.+.+...|..|
T Consensus 20 Ca~C~~~L~~~E~h~Ce~C 38 (58)
T PF05810_consen 20 CANCGQKLHPDETHVCEEC 38 (58)
T ss_pred HhccCcccccchhhHHHHH
Confidence 5666666655555444444
No 134
>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=28.02 E-value=28 Score=18.14 Aligned_cols=8 Identities=13% Similarity=0.513 Sum_probs=4.5
Q ss_pred ecccCcCC
Q psy4437 51 FCRNDFFR 58 (131)
Q Consensus 51 ~C~~c~~~ 58 (131)
+|.+||..
T Consensus 26 lC~~Cf~~ 33 (49)
T cd02338 26 LCADCYDS 33 (49)
T ss_pred cchhHHhC
Confidence 56666643
No 135
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=27.95 E-value=23 Score=18.87 Aligned_cols=6 Identities=50% Similarity=1.425 Sum_probs=1.5
Q ss_pred cccccc
Q psy4437 105 RCYDCH 110 (131)
Q Consensus 105 ~C~~C~ 110 (131)
+|.+|+
T Consensus 23 ~C~~C~ 28 (51)
T PF07975_consen 23 RCPKCK 28 (51)
T ss_dssp --TTTT
T ss_pred ECCCCC
Confidence 333333
No 136
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.49 E-value=72 Score=26.42 Aligned_cols=55 Identities=20% Similarity=0.188 Sum_probs=29.7
Q ss_pred eeEeecCCccccCCcccCCCcCcCCC----C--cc-CcCCeeecccCcCCCCCCCCCCCccc
Q psy4437 16 FLLNVLERTWHADCVRCYDCHHTLSD----K--CF-SREGKLFCRNDFFRSPVRFPSGCGVG 70 (131)
Q Consensus 16 ~~~~~~~~~~H~~Cf~C~~C~~~l~~----~--~f-~~~~~~~C~~c~~~~~~~~C~~c~~~ 70 (131)
.++..+++.-...=+.|..|+..+.= . .| ..++.+.|.-|-.......|..|+..
T Consensus 370 qvll~lnRrGyap~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 370 PVLVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred cEEEEecCCCCCCeeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 34444444323333555555554431 1 12 34567888888665556678888764
No 137
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=27.26 E-value=44 Score=24.44 Aligned_cols=26 Identities=23% Similarity=0.395 Sum_probs=13.1
Q ss_pred cccccCCcccccceeeeecCCcccccC
Q psy4437 77 ISCAGCEKPILDKFLLNVLERTWHADC 103 (131)
Q Consensus 77 ~~C~~C~~~I~~~~~~~~~~~~~H~~C 103 (131)
..|.+|+.+|.-..+ .-.+..|.|.|
T Consensus 246 epC~~CGt~I~k~~~-~gR~t~~CP~C 271 (273)
T COG0266 246 EPCRRCGTPIEKIKL-GGRSTFYCPVC 271 (273)
T ss_pred CCCCccCCEeEEEEE-cCCcCEeCCCC
Confidence 445556555544433 44455554444
No 138
>KOG3579|consensus
Probab=27.24 E-value=41 Score=24.83 Aligned_cols=35 Identities=20% Similarity=0.429 Sum_probs=28.7
Q ss_pred CCccccccCCcccccceeeeecCCcccccCccccc
Q psy4437 74 SMLISCAGCEKPILDKFLLNVLERTWHADCVRCYD 108 (131)
Q Consensus 74 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~ 108 (131)
+....|.-|++.+.|...|.--.-.-|+=||-|++
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR 300 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR 300 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCH
Confidence 34468999999999988777778888999999975
No 139
>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=27.20 E-value=35 Score=15.01 Aligned_cols=13 Identities=23% Similarity=0.595 Sum_probs=9.9
Q ss_pred ccccccccccccc
Q psy4437 104 VRCYDCHHTLSDK 116 (131)
Q Consensus 104 f~C~~C~~~l~~~ 116 (131)
|.|..|++.+.+.
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 5688888888765
No 140
>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=27.10 E-value=21 Score=18.33 Aligned_cols=8 Identities=25% Similarity=0.546 Sum_probs=4.4
Q ss_pred eecccCcC
Q psy4437 50 LFCRNDFF 57 (131)
Q Consensus 50 ~~C~~c~~ 57 (131)
-+|.+||.
T Consensus 29 dLC~~C~~ 36 (46)
T PF00569_consen 29 DLCEDCFS 36 (46)
T ss_dssp EEEHHHHH
T ss_pred chhhHHHh
Confidence 35666654
No 141
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=27.08 E-value=31 Score=24.66 Aligned_cols=29 Identities=14% Similarity=0.434 Sum_probs=17.7
Q ss_pred ccCccccccccccccc-eeccCCeeecCCC
Q psy4437 101 ADCVRCYDCHHTLSDK-CFSREGKLFCRND 129 (131)
Q Consensus 101 ~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~c 129 (131)
++=-.|+.|+.+.... +..+.|...|..|
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~ 181 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKC 181 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhc
Confidence 3334567777777654 5566666666654
No 142
>PHA02929 N1R/p28-like protein; Provisional
Probab=27.08 E-value=32 Score=24.61 Aligned_cols=39 Identities=23% Similarity=0.572 Sum_probs=25.7
Q ss_pred cccccCCcccccce-------eeeecCCcccccCc--------ccccccccccc
Q psy4437 77 ISCAGCEKPILDKF-------LLNVLERTWHADCV--------RCYDCHHTLSD 115 (131)
Q Consensus 77 ~~C~~C~~~I~~~~-------~~~~~~~~~H~~Cf--------~C~~C~~~l~~ 115 (131)
..|+.|...+.+.. ++..=+..||.+|+ +|..|..++..
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 46777777665432 22334677888887 68888877764
No 143
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=26.79 E-value=27 Score=19.41 Aligned_cols=12 Identities=33% Similarity=0.609 Sum_probs=6.9
Q ss_pred CCccccCCcccc
Q psy4437 2 LISCAGCEKPIL 13 (131)
Q Consensus 2 ~~~C~~C~~~I~ 13 (131)
+.+|..||++|.
T Consensus 4 PiRCFsCGkvi~ 15 (63)
T COG1644 4 PVRCFSCGKVIG 15 (63)
T ss_pred ceEeecCCCCHH
Confidence 345666666663
No 144
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=26.73 E-value=23 Score=15.08 Aligned_cols=13 Identities=23% Similarity=0.613 Sum_probs=9.6
Q ss_pred ccccccccccccc
Q psy4437 104 VRCYDCHHTLSDK 116 (131)
Q Consensus 104 f~C~~C~~~l~~~ 116 (131)
|.|..|++.+.+.
T Consensus 1 ~~C~~C~~~f~s~ 13 (25)
T PF12874_consen 1 FYCDICNKSFSSE 13 (25)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCCcCCH
Confidence 5688888877765
No 145
>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=26.65 E-value=28 Score=28.97 Aligned_cols=81 Identities=25% Similarity=0.545 Sum_probs=40.6
Q ss_pred ccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCccccccCC
Q psy4437 4 SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCE 83 (131)
Q Consensus 4 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~ 83 (131)
+|..|-+.|.+. .++.|+-.=..|+.|+-..+- ....|| .+. ...+ .+..+|..|.
T Consensus 70 ~C~~Cl~E~~dp-----~~Rry~YpF~nCt~CGPr~~i----~~~lpy-----dr~--------~t~m--~~f~~C~~C~ 125 (711)
T TIGR00143 70 TCSDCLEEMLDK-----NDRRYLYPFISCTHCGPRFTI----IEALPY-----DRE--------NTSM--ADFPLCPDCA 125 (711)
T ss_pred hHHHHHHHhcCC-----CcccccCCcccccCCCCCeEE----eecCCC-----CCC--------CcCC--CCCcCCHHHH
Confidence 456666655443 356666666677777654332 111111 000 0011 2234566665
Q ss_pred cccccceeeeecCCcccccCcccccccccc
Q psy4437 84 KPILDKFLLNVLERTWHADCVRCYDCHHTL 113 (131)
Q Consensus 84 ~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l 113 (131)
+... ...++.||-.=-.|..|+-.|
T Consensus 126 ~ey~-----~p~~rr~h~~~~~C~~Cgp~l 150 (711)
T TIGR00143 126 KEYK-----DPLDRRFHAQPIACPRCGPQL 150 (711)
T ss_pred HHhc-----CCccccCCCCCccCCCCCcEE
Confidence 5432 224567777767777776655
No 146
>PRK04023 DNA polymerase II large subunit; Validated
Probab=26.63 E-value=98 Score=27.12 Aligned_cols=21 Identities=19% Similarity=0.028 Sum_probs=10.1
Q ss_pred eecccCcCCCCCCCCCCCccc
Q psy4437 50 LFCRNDFFRSPVRFPSGCGVG 70 (131)
Q Consensus 50 ~~C~~c~~~~~~~~C~~c~~~ 70 (131)
.+|..|-...+..+|..|+..
T Consensus 627 RfCpsCG~~t~~frCP~CG~~ 647 (1121)
T PRK04023 627 RKCPSCGKETFYRRCPFCGTH 647 (1121)
T ss_pred ccCCCCCCcCCcccCCCCCCC
Confidence 345555444444455555543
No 147
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=25.54 E-value=45 Score=17.58 Aligned_cols=12 Identities=17% Similarity=0.711 Sum_probs=4.4
Q ss_pred CcCCeeecccCc
Q psy4437 45 SREGKLFCRNDF 56 (131)
Q Consensus 45 ~~~~~~~C~~c~ 56 (131)
+..|.+-|.++|
T Consensus 11 ~~k~Li~C~dHY 22 (50)
T PF03854_consen 11 ANKGLIKCSDHY 22 (50)
T ss_dssp --SSEEE-SS-E
T ss_pred cCCCeeeecchh
Confidence 445555555555
No 148
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=24.69 E-value=58 Score=21.95 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=14.5
Q ss_pred CCCCCccccCCCCccccccCCcc
Q psy4437 63 FPSGCGVGLSSSMLISCAGCEKP 85 (131)
Q Consensus 63 ~C~~c~~~i~~~~~~~C~~C~~~ 85 (131)
+|..|+-...+.....|+.|+.|
T Consensus 136 vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 136 VCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EcCCCCCcccCCCCCcCCCCCCh
Confidence 56666666655555677777654
No 149
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.45 E-value=98 Score=24.61 Aligned_cols=54 Identities=22% Similarity=0.349 Sum_probs=29.2
Q ss_pred eEeecCCccccCCcccCCCcCcCCC------Ccc-CcCCeeecccCcCC-CCCCCCCCCccc
Q psy4437 17 LLNVLERTWHADCVRCYDCHHTLSD------KCF-SREGKLFCRNDFFR-SPVRFPSGCGVG 70 (131)
Q Consensus 17 ~~~~~~~~~H~~Cf~C~~C~~~l~~------~~f-~~~~~~~C~~c~~~-~~~~~C~~c~~~ 70 (131)
++.+.++.-...-..|..|+..+.= -.| ..++.+.|..|-.. .....|..|+..
T Consensus 201 vLvflnrrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 201 SILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred EEEEEeCCcCCCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 4434443322233555555555431 122 45678889888554 345678888764
No 150
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=24.31 E-value=72 Score=17.44 Aligned_cols=28 Identities=21% Similarity=0.338 Sum_probs=13.4
Q ss_pred CCCCCCCccccCCCCc--cccccCCccccc
Q psy4437 61 VRFPSGCGVGLSSSML--ISCAGCEKPILD 88 (131)
Q Consensus 61 ~~~C~~c~~~i~~~~~--~~C~~C~~~I~~ 88 (131)
.+.|..|++-|=..+. ..|..|+.++..
T Consensus 18 ~~NCl~CGkIiC~~Eg~~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 18 APNCLNCGKIICEQEGPLGPCPFCGTPLLS 47 (57)
T ss_pred cccccccChhhcccccCcCcCCCCCCcccC
Confidence 4455555554432222 356666655543
No 151
>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=24.06 E-value=41 Score=17.28 Aligned_cols=7 Identities=29% Similarity=0.548 Sum_probs=3.4
Q ss_pred ecccCcC
Q psy4437 51 FCRNDFF 57 (131)
Q Consensus 51 ~C~~c~~ 57 (131)
+|+.||.
T Consensus 26 LC~~C~~ 32 (43)
T cd02342 26 LCTICFS 32 (43)
T ss_pred cHHHHhh
Confidence 4555543
No 152
>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=23.93 E-value=26 Score=17.95 Aligned_cols=19 Identities=26% Similarity=0.927 Sum_probs=9.1
Q ss_pred ccccccccccceeccCCeeecC
Q psy4437 106 CYDCHHTLSDKCFSREGKLFCR 127 (131)
Q Consensus 106 C~~C~~~l~~~~~~~~g~~~C~ 127 (131)
|..|.+.+.. ..++.+||.
T Consensus 9 C~~Cdk~~~~---~~~~~lYCS 27 (43)
T PF12855_consen 9 CIVCDKQIDP---PDDGSLYCS 27 (43)
T ss_pred HHHhhccccC---CCCCccccC
Confidence 3445555532 334556663
No 153
>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=23.92 E-value=53 Score=15.05 Aligned_cols=12 Identities=17% Similarity=0.570 Sum_probs=6.5
Q ss_pred cccCCCcCcCCC
Q psy4437 30 VRCYDCHHTLSD 41 (131)
Q Consensus 30 f~C~~C~~~l~~ 41 (131)
|.|..|++.+.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF03107_consen 1 FWCDVCRRKIDG 12 (30)
T ss_pred CCCCCCCCCcCC
Confidence 345566555544
No 154
>smart00214 VWC von Willebrand factor (vWF) type C domain.
Probab=23.61 E-value=50 Score=17.69 Aligned_cols=14 Identities=36% Similarity=0.795 Sum_probs=10.8
Q ss_pred eecCCccccc-Cccc
Q psy4437 93 NVLERTWHAD-CVRC 106 (131)
Q Consensus 93 ~~~~~~~H~~-Cf~C 106 (131)
...|..|+++ |..|
T Consensus 8 y~~G~~W~~~~C~~C 22 (59)
T smart00214 8 YNDGETWKPDPCQIC 22 (59)
T ss_pred eCCCCEECCCCCeEC
Confidence 5678899998 6665
No 155
>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=23.31 E-value=60 Score=18.02 Aligned_cols=13 Identities=31% Similarity=0.437 Sum_probs=9.2
Q ss_pred eeccCCeeecCCC
Q psy4437 117 CFSREGKLFCRND 129 (131)
Q Consensus 117 ~~~~~g~~~C~~c 129 (131)
+...+|.++|.+|
T Consensus 47 ~~i~eg~L~Cp~c 59 (68)
T PF03966_consen 47 VEIVEGELICPEC 59 (68)
T ss_dssp EETTTTEEEETTT
T ss_pred ccccCCEEEcCCC
Confidence 3456788888776
No 156
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=22.95 E-value=25 Score=23.87 Aligned_cols=11 Identities=36% Similarity=0.854 Sum_probs=6.9
Q ss_pred cccCCCcCcCC
Q psy4437 30 VRCYDCHHTLS 40 (131)
Q Consensus 30 f~C~~C~~~l~ 40 (131)
|.|..|+.+|.
T Consensus 137 F~Cp~Cg~~L~ 147 (178)
T PRK06266 137 FRCPQCGEMLE 147 (178)
T ss_pred CcCCCCCCCCe
Confidence 66666666664
No 157
>PF11077 DUF2616: Protein of unknown function (DUF2616); InterPro: IPR020201 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Probab=22.89 E-value=52 Score=22.36 Aligned_cols=31 Identities=29% Similarity=0.562 Sum_probs=19.3
Q ss_pred ccCccccccccccccc-eeccCCeeecCCCCC
Q psy4437 101 ADCVRCYDCHHTLSDK-CFSREGKLFCRNDFF 131 (131)
Q Consensus 101 ~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy~ 131 (131)
..|+.|..=....+.. ++-.|-+++|..|+|
T Consensus 137 ~kC~QC~~~~~~~~~~~~~~F~~~lFC~~ClF 168 (173)
T PF11077_consen 137 DKCVQCSQKCENVGAKIFTYFNFNLFCKNCLF 168 (173)
T ss_pred cccCcCCCCcccccceeEEecChhhcccccCc
Confidence 3455554432333333 566899999999986
No 158
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.41 E-value=88 Score=14.90 Aligned_cols=11 Identities=9% Similarity=0.042 Sum_probs=5.5
Q ss_pred ccCCeeecCCC
Q psy4437 119 SREGKLFCRND 129 (131)
Q Consensus 119 ~~~g~~~C~~c 129 (131)
..++..+|..|
T Consensus 17 ~~~~~~~C~~C 27 (33)
T PF08792_consen 17 KEDDYEVCIFC 27 (33)
T ss_pred ecCCeEEcccC
Confidence 44555555544
No 159
>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=22.32 E-value=31 Score=18.45 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=5.2
Q ss_pred cccCCCcCcCC
Q psy4437 30 VRCYDCHHTLS 40 (131)
Q Consensus 30 f~C~~C~~~l~ 40 (131)
++|..|++.|.
T Consensus 5 iRC~~CnklLa 15 (51)
T PF10122_consen 5 IRCGHCNKLLA 15 (51)
T ss_pred eeccchhHHHh
Confidence 34455554443
No 160
>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=22.32 E-value=60 Score=17.49 Aligned_cols=10 Identities=30% Similarity=0.650 Sum_probs=4.7
Q ss_pred ccccCCcccc
Q psy4437 78 SCAGCEKPIL 87 (131)
Q Consensus 78 ~C~~C~~~I~ 87 (131)
.|.-|+..|.
T Consensus 5 ~C~f~g~~I~ 14 (54)
T cd00472 5 KCSFCGYKIY 14 (54)
T ss_pred EecCcCCeec
Confidence 3444444444
No 161
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.16 E-value=39 Score=21.24 Aligned_cols=11 Identities=27% Similarity=0.724 Sum_probs=5.0
Q ss_pred ccccCCccccc
Q psy4437 78 SCAGCEKPILD 88 (131)
Q Consensus 78 ~C~~C~~~I~~ 88 (131)
.|+.|+..|.+
T Consensus 14 ~C~~C~t~i~G 24 (113)
T PF09862_consen 14 KCPSCGTEIEG 24 (113)
T ss_pred EcCCCCCEEEe
Confidence 34444444443
No 162
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=22.12 E-value=40 Score=18.42 Aligned_cols=13 Identities=38% Similarity=0.905 Sum_probs=6.5
Q ss_pred CCCccccCCcccc
Q psy4437 1 MLISCAGCEKPIL 13 (131)
Q Consensus 1 ~~~~C~~C~~~I~ 13 (131)
|...|..|++++.
T Consensus 1 m~v~CP~C~k~~~ 13 (57)
T PF03884_consen 1 MTVKCPICGKPVE 13 (57)
T ss_dssp -EEE-TTT--EEE
T ss_pred CcccCCCCCCeec
Confidence 6677888887763
No 163
>KOG2932|consensus
Probab=21.99 E-value=45 Score=24.96 Aligned_cols=41 Identities=12% Similarity=0.185 Sum_probs=24.2
Q ss_pred ccCCCcCcCCCC-ccCcCCeeecccCcCCCCCCCCCCCcccc
Q psy4437 31 RCYDCHHTLSDK-CFSREGKLFCRNDFFRSPVRFPSGCGVGL 71 (131)
Q Consensus 31 ~C~~C~~~l~~~-~f~~~~~~~C~~c~~~~~~~~C~~c~~~i 71 (131)
-|..|+.++.-- ...-=+.+||.+|........|..|...+
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRV 133 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHH
Confidence 467777776531 11223456788887665555666666544
No 164
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=21.80 E-value=58 Score=19.62 Aligned_cols=12 Identities=17% Similarity=0.661 Sum_probs=7.6
Q ss_pred cccCCCcCcCCC
Q psy4437 30 VRCYDCHHTLSD 41 (131)
Q Consensus 30 f~C~~C~~~l~~ 41 (131)
|+|+.|+...++
T Consensus 6 F~C~~C~~~W~S 17 (98)
T PF13695_consen 6 FQCSKCSRGWTS 17 (98)
T ss_pred EECCCCCCCCcc
Confidence 666667666655
No 165
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.52 E-value=1.1e+02 Score=15.54 Aligned_cols=7 Identities=29% Similarity=0.942 Sum_probs=3.0
Q ss_pred cccCCcc
Q psy4437 5 CAGCEKP 11 (131)
Q Consensus 5 C~~C~~~ 11 (131)
|..|+..
T Consensus 3 Cp~Cg~~ 9 (52)
T smart00661 3 CPKCGNM 9 (52)
T ss_pred CCCCCCc
Confidence 4444443
No 166
>KOG2114|consensus
Probab=21.15 E-value=42 Score=28.54 Aligned_cols=36 Identities=25% Similarity=0.698 Sum_probs=19.1
Q ss_pred CccccCCccccCceeEeec-CCccccCCcc-----cCCCcCcC
Q psy4437 3 ISCAGCEKPILDKFLLNVL-ERTWHADCVR-----CYDCHHTL 39 (131)
Q Consensus 3 ~~C~~C~~~I~~~~~~~~~-~~~~H~~Cf~-----C~~C~~~l 39 (131)
.+|..|..++.-. .|..+ +-.||..||. |..|...+
T Consensus 841 skCs~C~~~LdlP-~VhF~CgHsyHqhC~e~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 841 SKCSACEGTLDLP-FVHFLCGHSYHQHCLEDKEDKCPKCLPEL 882 (933)
T ss_pred eeecccCCccccc-eeeeecccHHHHHhhccCcccCCccchhh
Confidence 4566666665333 23333 5666666665 55554433
No 167
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=21.11 E-value=75 Score=19.56 Aligned_cols=13 Identities=23% Similarity=0.639 Sum_probs=8.9
Q ss_pred eeccCCeeecCCC
Q psy4437 117 CFSREGKLFCRND 129 (131)
Q Consensus 117 ~~~~~g~~~C~~c 129 (131)
|+..++++.|..|
T Consensus 46 Y~q~g~~lvC~~C 58 (102)
T PF10080_consen 46 YYQEGDQLVCKNC 58 (102)
T ss_pred eEEECCEEEEecC
Confidence 6666777777665
No 168
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.95 E-value=1.1e+02 Score=19.67 Aligned_cols=11 Identities=27% Similarity=0.649 Sum_probs=5.0
Q ss_pred cccCCccccCc
Q psy4437 5 CAGCEKPILDK 15 (131)
Q Consensus 5 C~~C~~~I~~~ 15 (131)
|..|+-+|.+.
T Consensus 42 cp~csasirgd 52 (160)
T COG4306 42 CPICSASIRGD 52 (160)
T ss_pred CCccCCccccc
Confidence 44444444443
No 169
>PF02085 Cytochrom_CIII: Class III cytochrome C family; InterPro: IPR020942 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes []. Ambler [] recognised four classes of cytC. Class III comprises the low redox potential multiple haem cytochromes: cyt C7 (trihaem), C3 (tetrahaem), and high-molecular-weight cytC, HMC (hexadecahaem), with only 30-40 residues per haem group. The haem c groups, all bis-histidinyl coordinated, are structurally and functionally nonequivalent and present different redox potentials in the range 0 to -400 mV []. The 3D structures of a number of cyt C3 proteins have been determined. The proteins consist of 4-5 alpha-helices and 2 beta-strands wrapped around a compact core of four non-parallel haems, which present a relatively high degree of exposure to the solvent. The overall protein architecture, haem plane orientations and iron-iron distances are highly conserved [].; GO: 0009055 electron carrier activity, 0020037 heme binding; PDB: 1AQE_A 1CZJ_A 1H29_B 1GWS_A 2CVC_A 2KMY_A 1DUW_A 1UPD_A 1I77_A 1GMB_A ....
Probab=20.33 E-value=19 Score=21.73 Aligned_cols=8 Identities=13% Similarity=0.621 Sum_probs=4.5
Q ss_pred ecCCcccc
Q psy4437 94 VLERTWHA 101 (131)
Q Consensus 94 ~~~~~~H~ 101 (131)
.....||.
T Consensus 65 ~~~~a~H~ 72 (102)
T PF02085_consen 65 SFKKAFHQ 72 (102)
T ss_dssp BHHHHHHH
T ss_pred hHHHHhcC
Confidence 33556666
No 170
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=20.31 E-value=70 Score=20.62 Aligned_cols=24 Identities=13% Similarity=0.133 Sum_probs=15.6
Q ss_pred CccccCCccccCc---eeEeecCCccc
Q psy4437 3 ISCAGCEKPILDK---FLLNVLERTWH 26 (131)
Q Consensus 3 ~~C~~C~~~I~~~---~~~~~~~~~~H 26 (131)
.+|..|+..|..+ ..|...|+.|+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEE
Confidence 3588999999643 33555666664
No 171
>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=20.26 E-value=62 Score=25.66 Aligned_cols=36 Identities=19% Similarity=0.391 Sum_probs=21.2
Q ss_pred cccCCccccCceeEeecCCccccCCcccCCCcCcCCC
Q psy4437 5 CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD 41 (131)
Q Consensus 5 C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 41 (131)
|..|-..+...+ +...+..=..+||.|-.|...|..
T Consensus 29 Cp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 29 CPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred CccccccCChhh-heeccceeccccccCCCCCCccee
Confidence 455555554443 223334445588888888888865
No 172
>KOG2893|consensus
Probab=20.24 E-value=31 Score=24.80 Aligned_cols=36 Identities=25% Similarity=0.450 Sum_probs=19.8
Q ss_pred ccccCCcccccceeeeecCCcccccCccccccccccccc
Q psy4437 78 SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK 116 (131)
Q Consensus 78 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 116 (131)
-|.-|++...+..++....+ ..+|+|..|.+.|-++
T Consensus 12 wcwycnrefddekiliqhqk---akhfkchichkkl~sg 47 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK---AKHFKCHICHKKLFSG 47 (341)
T ss_pred eeeecccccchhhhhhhhhh---hccceeeeehhhhccC
Confidence 34555555555444333222 3468888888777544
No 173
>PHA00626 hypothetical protein
Probab=20.09 E-value=1e+02 Score=16.82 Aligned_cols=36 Identities=28% Similarity=0.476 Sum_probs=21.6
Q ss_pred ccccCCcc-ccCceeEeecCCccccCCcccCCCcCcCCCCcc
Q psy4437 4 SCAGCEKP-ILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF 44 (131)
Q Consensus 4 ~C~~C~~~-I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f 44 (131)
.|..|+.. |.-...+.- +..=++|..|+-..+...|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~-----~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRG-----WSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCceeeeeceecc-----cCcceEcCCCCCeechhhh
Confidence 57888873 532222222 2334789999888876666
No 174
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=20.05 E-value=43 Score=15.70 Aligned_cols=6 Identities=33% Similarity=1.149 Sum_probs=2.4
Q ss_pred ccccCC
Q psy4437 78 SCAGCE 83 (131)
Q Consensus 78 ~C~~C~ 83 (131)
+|+.|+
T Consensus 21 vCp~C~ 26 (30)
T PF08274_consen 21 VCPECG 26 (30)
T ss_dssp EETTTT
T ss_pred eCCccc
Confidence 344443
Done!