Query 028299
Match_columns 211
No_of_seqs 115 out of 207
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 09:21:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028299.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028299hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3277 Uncharacterized conser 100.0 2.4E-39 5.2E-44 269.6 8.6 114 87-211 48-165 (165)
2 PF05180 zf-DNL: DNL zinc fing 100.0 1.2E-37 2.5E-42 227.2 2.1 66 124-189 1-66 (66)
3 PF05207 zf-CSL: CSL zinc fing 94.0 0.03 6.6E-07 39.3 1.5 34 125-161 16-49 (55)
4 PF01096 TFIIS_C: Transcriptio 89.8 0.22 4.7E-06 32.7 1.7 34 128-161 1-37 (39)
5 smart00440 ZnF_C2C2 C2C2 Zinc 89.3 0.33 7.1E-06 32.1 2.2 34 128-161 1-37 (40)
6 TIGR01206 lysW lysine biosynth 87.8 0.42 9.2E-06 34.0 2.1 35 126-165 1-35 (54)
7 KOG2923 Uncharacterized conser 85.2 0.58 1.2E-05 35.3 1.8 31 127-160 22-52 (67)
8 PRK00398 rpoP DNA-directed RNA 85.0 0.82 1.8E-05 30.3 2.3 38 126-170 2-39 (46)
9 TIGR00416 sms DNA repair prote 83.5 0.82 1.8E-05 43.2 2.4 30 126-166 6-35 (454)
10 TIGR02098 MJ0042_CXXC MJ0042 f 81.7 1.3 2.7E-05 28.0 2.1 34 126-161 1-34 (38)
11 PRK11823 DNA repair protein Ra 81.4 1.1 2.4E-05 42.1 2.4 31 125-166 5-35 (446)
12 TIGR01385 TFSII transcription 79.9 1.4 3E-05 40.2 2.5 35 127-161 258-295 (299)
13 PF13717 zinc_ribbon_4: zinc-r 78.5 1.9 4.2E-05 27.9 2.2 33 126-160 1-33 (36)
14 COG2956 Predicted N-acetylgluc 78.1 1.4 3.1E-05 42.1 2.1 35 124-169 351-385 (389)
15 smart00834 CxxC_CXXC_SSSS Puta 77.2 1.4 3E-05 27.7 1.2 31 126-160 4-34 (41)
16 PF13719 zinc_ribbon_5: zinc-r 76.3 2.3 5E-05 27.5 2.1 32 127-160 2-33 (37)
17 TIGR02605 CxxC_CxxC_SSSS putat 75.6 1.7 3.6E-05 28.9 1.3 32 126-161 4-35 (52)
18 COG1066 Sms Predicted ATP-depe 74.9 2.1 4.5E-05 41.8 2.3 30 126-166 6-35 (456)
19 cd01121 Sms Sms (bacterial rad 74.4 1.9 4.1E-05 39.9 1.8 28 128-166 1-28 (372)
20 PF07295 DUF1451: Protein of u 72.8 2 4.3E-05 35.7 1.4 29 127-162 112-140 (146)
21 PF13719 zinc_ribbon_5: zinc-r 72.5 2 4.2E-05 27.8 1.0 17 151-167 1-17 (37)
22 PF09723 Zn-ribbon_8: Zinc rib 72.3 2.2 4.9E-05 28.1 1.3 32 126-161 4-35 (42)
23 PRK11788 tetratricopeptide rep 72.0 3.1 6.7E-05 35.5 2.4 32 128-170 355-386 (389)
24 PRK11032 hypothetical protein; 70.4 2.3 5.1E-05 36.0 1.3 28 127-161 124-151 (160)
25 PRK14892 putative transcriptio 70.3 4.4 9.6E-05 31.9 2.8 37 123-164 17-54 (99)
26 COG5216 Uncharacterized conser 69.4 4.2 9.1E-05 30.6 2.3 44 116-166 12-55 (67)
27 PF04161 Arv1: Arv1-like famil 66.9 3.7 8E-05 34.9 1.8 32 128-160 1-32 (208)
28 PF05129 Elf1: Transcription e 66.2 2.3 4.9E-05 32.0 0.4 40 121-163 16-57 (81)
29 PRK00564 hypA hydrogenase nick 64.2 3.9 8.4E-05 32.3 1.4 32 123-162 67-98 (117)
30 smart00659 RPOLCX RNA polymera 63.4 7.2 0.00016 26.5 2.4 31 126-164 1-31 (44)
31 TIGR00100 hypA hydrogenase nic 61.7 4.7 0.0001 31.7 1.4 31 123-162 66-96 (115)
32 COG1645 Uncharacterized Zn-fin 61.4 3.6 7.8E-05 34.2 0.7 33 122-163 23-55 (131)
33 PRK12495 hypothetical protein; 61.0 4.7 0.0001 36.3 1.5 30 122-160 37-66 (226)
34 PF03367 zf-ZPR1: ZPR1 zinc-fi 58.4 7.6 0.00017 32.3 2.2 31 122-152 25-56 (161)
35 PF14354 Lar_restr_allev: Rest 56.8 11 0.00024 25.6 2.4 31 130-160 6-37 (61)
36 KOG2703 C4-type Zn-finger prot 56.1 11 0.00023 37.0 3.0 36 121-156 62-97 (460)
37 PF08996 zf-DNA_Pol: DNA Polym 55.9 7.3 0.00016 32.6 1.7 39 123-161 14-54 (188)
38 smart00249 PHD PHD zinc finger 55.7 9.3 0.0002 23.1 1.8 23 129-161 1-23 (47)
39 PF01927 Mut7-C: Mut7-C RNAse 55.5 9.2 0.0002 30.7 2.1 32 129-161 93-133 (147)
40 KOG3134 Predicted membrane pro 53.5 5.6 0.00012 35.8 0.7 31 128-160 1-32 (225)
41 PRK03824 hypA hydrogenase nick 52.5 12 0.00025 30.3 2.3 36 124-162 67-117 (135)
42 smart00653 eIF2B_5 domain pres 52.4 11 0.00025 29.8 2.2 30 128-161 81-110 (110)
43 smart00350 MCM minichromosome 51.0 12 0.00025 35.7 2.4 36 124-162 34-71 (509)
44 PRK03681 hypA hydrogenase nick 49.6 11 0.00024 29.6 1.7 32 123-162 66-97 (114)
45 KOG2186 Cell growth-regulating 49.3 7 0.00015 36.2 0.6 36 125-160 1-37 (276)
46 PRK03988 translation initiatio 49.1 14 0.00031 30.4 2.3 33 128-164 103-135 (138)
47 PRK00464 nrdR transcriptional 49.0 12 0.00026 31.4 1.9 34 129-162 2-38 (154)
48 PF02146 SIR2: Sir2 family; I 48.3 8.5 0.00018 31.1 0.9 45 127-174 105-149 (178)
49 PRK12336 translation initiatio 47.7 15 0.00033 31.5 2.4 36 128-167 99-134 (201)
50 COG2023 RPR2 RNase P subunit R 47.7 11 0.00024 30.5 1.4 39 128-166 57-96 (105)
51 PF03604 DNA_RNApol_7kD: DNA d 47.5 11 0.00023 24.4 1.1 29 128-164 1-29 (32)
52 PF13453 zf-TFIIB: Transcripti 47.0 18 0.00038 23.5 2.1 27 130-161 2-28 (41)
53 PF01873 eIF-5_eIF-2B: Domain 46.6 12 0.00026 30.3 1.5 30 129-162 95-124 (125)
54 PF01155 HypA: Hydrogenase exp 46.4 13 0.00027 29.0 1.6 32 123-163 66-97 (113)
55 PRK12380 hydrogenase nickel in 46.3 11 0.00025 29.5 1.3 30 123-161 66-95 (113)
56 KOG4216 Steroid hormone nuclea 45.7 9.9 0.00021 37.3 1.1 26 127-160 46-71 (479)
57 PF05876 Terminase_GpA: Phage 45.5 18 0.00038 35.3 2.7 46 114-161 189-238 (557)
58 PF05907 DUF866: Eukaryotic pr 44.9 10 0.00022 31.6 0.9 45 121-165 58-112 (161)
59 PF00628 PHD: PHD-finger; Int 44.5 23 0.00049 23.0 2.3 24 129-162 1-24 (51)
60 COG1503 eRF1 Peptide chain rel 43.7 13 0.00028 36.0 1.5 47 120-170 320-366 (411)
61 TIGR00340 zpr1_rel ZPR1-relate 43.7 20 0.00043 30.3 2.4 26 122-147 23-48 (163)
62 KOG1105 Transcription elongati 43.7 19 0.0004 33.5 2.5 43 121-163 249-294 (296)
63 PF10058 DUF2296: Predicted in 43.2 32 0.0007 24.2 3.1 36 121-161 18-53 (54)
64 PRK00241 nudC NADH pyrophospha 43.1 19 0.00041 31.7 2.3 15 128-142 118-132 (256)
65 COG1326 Uncharacterized archae 42.9 21 0.00046 31.8 2.6 36 124-162 3-40 (201)
66 TIGR00340 zpr1_rel ZPR1-relate 41.7 18 0.0004 30.5 1.9 12 152-163 28-39 (163)
67 smart00709 Zpr1 Duplicated dom 41.6 19 0.00042 30.1 2.0 31 122-152 24-55 (160)
68 PRK00762 hypA hydrogenase nick 40.4 20 0.00044 28.5 1.9 36 123-162 66-102 (124)
69 TIGR00311 aIF-2beta translatio 39.9 24 0.00052 29.0 2.3 33 128-164 98-130 (133)
70 COG4888 Uncharacterized Zn rib 39.8 25 0.00054 28.5 2.3 46 124-170 19-64 (104)
71 COG2816 NPY1 NTP pyrophosphohy 39.8 22 0.00048 32.8 2.3 55 130-191 114-201 (279)
72 PHA02998 RNA polymerase subuni 39.7 22 0.00047 31.6 2.1 36 126-161 142-180 (195)
73 PF04032 Rpr2: RNAse P Rpr2/Rp 39.3 22 0.00047 25.3 1.8 31 129-159 48-84 (85)
74 PRK00420 hypothetical protein; 39.2 18 0.00039 29.2 1.4 34 125-166 21-54 (112)
75 COG1996 RPC10 DNA-directed RNA 38.6 36 0.00078 24.2 2.7 35 123-164 2-36 (49)
76 TIGR01384 TFS_arch transcripti 38.4 24 0.00051 26.4 1.9 34 127-160 62-98 (104)
77 PF00935 Ribosomal_L44: Riboso 37.6 23 0.00051 27.0 1.8 20 122-141 48-67 (77)
78 TIGR00310 ZPR1_znf ZPR1 zinc f 37.5 24 0.00052 30.5 2.1 20 122-141 25-44 (192)
79 PF08271 TF_Zn_Ribbon: TFIIB z 37.4 27 0.00059 22.8 1.8 32 128-167 1-32 (43)
80 KOG1507 Nucleosome assembly pr 37.3 54 0.0012 31.5 4.5 59 119-185 199-269 (358)
81 PF11023 DUF2614: Protein of u 37.2 17 0.00037 29.9 1.0 33 151-183 68-102 (114)
82 KOG4846 Nuclear receptor [Sign 36.9 78 0.0017 31.7 5.6 50 88-160 108-157 (538)
83 PHA02942 putative transposase; 36.9 26 0.00057 32.6 2.4 27 128-162 326-352 (383)
84 COG1631 RPL42A Ribosomal prote 36.4 25 0.00054 28.1 1.8 19 121-139 62-80 (94)
85 PF04690 YABBY: YABBY protein; 36.4 18 0.00039 31.2 1.1 32 129-161 14-45 (170)
86 COG2051 RPS27A Ribosomal prote 36.4 29 0.00063 26.3 2.1 17 150-166 17-33 (67)
87 PF00096 zf-C2H2: Zinc finger, 36.4 18 0.00038 20.0 0.7 10 128-137 1-10 (23)
88 PF07028 DUF1319: Protein of u 36.3 21 0.00046 29.7 1.5 22 60-81 83-104 (126)
89 COG0675 Transposase and inacti 36.1 26 0.00056 29.1 2.0 22 129-162 311-332 (364)
90 COG0846 SIR2 NAD-dependent pro 35.5 22 0.00048 31.8 1.6 49 126-176 121-169 (250)
91 PF13894 zf-C2H2_4: C2H2-type 35.1 21 0.00046 19.0 0.9 11 128-138 1-11 (24)
92 PF01667 Ribosomal_S27e: Ribos 34.5 30 0.00066 24.9 1.9 17 151-167 6-22 (55)
93 PF07282 OrfB_Zn_ribbon: Putat 32.7 34 0.00074 23.7 1.8 26 129-161 30-55 (69)
94 PRK00415 rps27e 30S ribosomal 32.5 39 0.00084 24.9 2.1 17 151-167 10-26 (59)
95 PF09332 Mcm10: Mcm10 replicat 32.2 30 0.00066 32.6 2.0 43 125-167 250-300 (344)
96 PF12874 zf-met: Zinc-finger o 31.9 23 0.00049 19.9 0.7 9 128-136 1-9 (25)
97 TIGR01384 TFS_arch transcripti 31.9 39 0.00085 25.2 2.2 20 118-137 81-100 (104)
98 cd07160 NR_DBD_LXR DNA-binding 31.5 18 0.00039 28.2 0.3 28 128-163 19-46 (101)
99 COG5254 ARV1 Predicted membran 30.8 17 0.00036 33.0 0.0 31 129-160 2-32 (239)
100 cd01408 SIRT1 SIRT1: Eukaryoti 29.9 16 0.00034 31.6 -0.3 44 128-174 117-160 (235)
101 KOG2907 RNA polymerase I trans 29.4 42 0.00091 27.7 2.1 38 124-161 71-111 (116)
102 cd01407 SIR2-fam SIR2 family o 29.0 24 0.00052 29.7 0.6 44 128-174 110-153 (218)
103 COG1571 Predicted DNA-binding 28.8 20 0.00043 34.8 0.2 35 127-164 367-404 (421)
104 PF13912 zf-C2H2_6: C2H2-type 28.8 28 0.0006 19.9 0.7 9 128-136 2-10 (27)
105 PRK14138 NAD-dependent deacety 28.4 24 0.00051 30.7 0.5 44 128-174 120-163 (244)
106 smart00531 TFIIE Transcription 28.4 36 0.00079 27.4 1.6 40 125-167 97-138 (147)
107 PF14311 DUF4379: Domain of un 28.4 38 0.00082 23.0 1.4 35 120-158 21-55 (55)
108 COG3357 Predicted transcriptio 28.0 34 0.00075 27.5 1.4 38 127-180 58-96 (97)
109 PF03330 DPBB_1: Rare lipoprot 27.7 46 0.00099 23.6 1.8 14 150-163 43-56 (78)
110 PRK00481 NAD-dependent deacety 27.2 33 0.00071 29.4 1.2 40 128-174 123-162 (242)
111 PRK14714 DNA polymerase II lar 27.1 43 0.00093 36.9 2.3 33 127-160 667-700 (1337)
112 PF05605 zf-Di19: Drought indu 26.9 16 0.00035 24.7 -0.6 31 127-160 2-39 (54)
113 cd01410 SIRT7 SIRT7: Eukaryoti 26.8 22 0.00049 30.1 0.1 45 128-174 96-140 (206)
114 COG0484 DnaJ DnaJ-class molecu 26.6 36 0.00078 32.5 1.4 15 122-136 178-192 (371)
115 PF12760 Zn_Tnp_IS1595: Transp 26.5 43 0.00093 22.2 1.4 10 128-137 19-28 (46)
116 cd07170 NR_DBD_ERR DNA-binding 26.3 23 0.0005 27.4 0.1 26 130-163 7-32 (97)
117 PF09986 DUF2225: Uncharacteri 26.3 46 0.001 28.6 1.9 40 127-166 5-62 (214)
118 PRK03976 rpl37ae 50S ribosomal 26.3 51 0.0011 25.9 2.0 31 123-160 32-62 (90)
119 TIGR00244 transcriptional regu 25.6 51 0.0011 28.0 2.0 34 129-162 2-38 (147)
120 TIGR03655 anti_R_Lar restricti 25.5 75 0.0016 21.6 2.5 32 130-161 4-35 (53)
121 COG1198 PriA Primosomal protei 25.4 41 0.00088 34.6 1.7 21 149-169 472-492 (730)
122 PF01396 zf-C4_Topoisom: Topoi 25.4 52 0.0011 21.5 1.6 32 129-165 3-37 (39)
123 PF12322 T4_baseplate: T4 bact 25.2 40 0.00087 29.2 1.4 22 123-144 74-95 (205)
124 COG0551 TopA Zn-finger domain 25.1 53 0.0012 25.9 2.0 43 124-166 14-75 (140)
125 smart00661 RPOL9 RNA polymeras 24.8 81 0.0017 20.5 2.5 30 130-164 3-32 (52)
126 PF13465 zf-H2C2_2: Zinc-finge 24.8 36 0.00079 20.1 0.8 9 128-136 15-23 (26)
127 cd07168 NR_DBD_DHR4_like DNA-b 24.6 28 0.00062 26.4 0.3 26 130-163 9-34 (90)
128 TIGR00280 L37a ribosomal prote 24.6 58 0.0013 25.7 2.0 32 123-161 31-62 (91)
129 PRK02935 hypothetical protein; 24.3 43 0.00093 27.5 1.3 34 150-183 68-103 (110)
130 cd01411 SIR2H SIR2H: Uncharact 24.2 49 0.0011 28.3 1.7 38 128-174 119-156 (225)
131 cd01412 SIRT5_Af1_CobB SIRT5_A 24.2 37 0.0008 28.5 1.0 42 128-175 110-151 (224)
132 cd06965 NR_DBD_Ppar DNA-bindin 24.1 24 0.00051 26.4 -0.2 33 130-170 2-34 (84)
133 PTZ00083 40S ribosomal protein 24.0 64 0.0014 25.3 2.2 12 123-134 31-42 (85)
134 PLN00209 ribosomal protein S27 23.9 64 0.0014 25.4 2.2 12 123-134 32-43 (86)
135 PRK04351 hypothetical protein; 23.9 75 0.0016 26.3 2.7 34 123-163 108-143 (149)
136 KOG0179 20S proteasome, regula 23.8 47 0.001 30.3 1.6 38 50-87 158-212 (235)
137 KOG3507 DNA-directed RNA polym 23.7 1.1E+02 0.0024 23.0 3.2 34 122-163 15-48 (62)
138 smart00067 GHA Glycoprotein ho 22.8 52 0.0011 26.0 1.5 26 130-159 2-27 (87)
139 KOG4323 Polycomb-like PHD Zn-f 22.7 55 0.0012 32.3 1.9 31 121-161 164-194 (464)
140 cd07161 NR_DBD_EcR DNA-binding 22.7 30 0.00064 26.4 0.1 25 130-162 4-28 (91)
141 PF01780 Ribosomal_L37ae: Ribo 22.4 45 0.00098 26.2 1.1 29 125-160 33-61 (90)
142 PTZ00255 60S ribosomal protein 22.2 68 0.0015 25.3 2.0 32 123-161 32-63 (90)
143 PF04810 zf-Sec23_Sec24: Sec23 22.2 48 0.001 21.6 1.0 12 127-138 24-35 (40)
144 cd02335 ZZ_ADA2 Zinc finger, Z 22.1 69 0.0015 21.6 1.8 26 128-163 1-26 (49)
145 cd01409 SIRT4 SIRT4: Eukaryoti 21.7 71 0.0015 28.1 2.3 21 152-174 169-189 (260)
146 COG0602 NrdG Organic radical a 21.5 62 0.0013 27.8 1.8 28 155-183 36-63 (212)
147 PF09332 Mcm10: Mcm10 replicat 21.4 54 0.0012 31.0 1.5 53 126-187 284-337 (344)
148 cd07157 2DBD_NR_DBD1 The first 21.4 37 0.00079 25.6 0.4 33 129-169 2-34 (86)
149 TIGR02159 PA_CoA_Oxy4 phenylac 21.3 25 0.00054 29.0 -0.6 34 128-161 106-139 (146)
150 cd07158 NR_DBD_Ppar_like The D 21.1 26 0.00055 25.3 -0.5 29 130-166 1-29 (73)
151 PF04216 FdhE: Protein involve 20.7 48 0.001 29.3 1.0 41 129-170 213-255 (290)
152 cd07163 NR_DBD_TLX DNA-binding 20.7 44 0.00095 25.4 0.7 36 127-170 6-41 (92)
153 PF13597 NRDD: Anaerobic ribon 20.6 64 0.0014 31.6 1.9 22 129-162 493-514 (546)
154 COG1997 RPL43A Ribosomal prote 20.6 63 0.0014 25.7 1.5 32 123-161 31-62 (89)
155 PF06839 zf-GRF: GRF zinc fing 20.5 82 0.0018 20.8 1.9 30 130-160 3-33 (45)
156 PTZ00157 60S ribosomal protein 20.3 75 0.0016 24.9 1.9 19 122-140 64-82 (84)
157 COG5109 Uncharacterized conser 20.2 67 0.0014 31.1 1.9 60 109-169 319-393 (396)
158 PF05876 Terminase_GpA: Phage 20.2 45 0.00098 32.6 0.8 21 150-170 198-219 (557)
No 1
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.4e-39 Score=269.64 Aligned_cols=114 Identities=36% Similarity=0.667 Sum_probs=93.4
Q ss_pred CCCCCCCCCCCCCCCCCCCcccccccccccccCCCcceEEEEEcccCCCccccccCcccccCccEEEEcCCCCccceeee
Q 028299 87 GSGMEGPSVPAGAEEGSSTEKVSTFPWSLFTKSPRRRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVD 166 (211)
Q Consensus 87 ~S~~eGP~~~a~~~~~s~~~~~s~~P~s~~~k~prr~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIAD 166 (211)
.++|++|+.+++.++ ..+. -|.+.|+++|+|.|||++|++|++|+|||+||++|||||||+||+|+|||||
T Consensus 48 ~~~s~s~se~~~~~s----~t~l-----~~~~~~kp~m~l~yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~HliaD 118 (165)
T KOG3277|consen 48 GTGSRSPSEAAKTDS----ATVL-----TFFKVPKPRMQLAYTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHHLIAD 118 (165)
T ss_pred ccCcccccccCCCCc----cccc-----ccccCCCcceEEEEEeeccCCccccccChhhhhCceEEEECCCCccceeehh
Confidence 456677777765332 1111 1357889999999999999999999999999999999999999999999999
Q ss_pred cccccccCCCC--cchhhhcCCCCccccccccCCCC--CCCCCCCcccC
Q 028299 167 NLNLFHEMKCY--VNPSFNYRDAKWDVGFKLFDMDD--DDDDGNNVFRI 211 (211)
Q Consensus 167 NLgwF~e~~~t--IEdi~k~KGe~v~kg~~~~D~~d--d~d~~~~~fp~ 211 (211)
|||||+|.+++ |||||++|||+|.+. +.|+.+ .-++.+++||+
T Consensus 119 nL~~F~d~~~~~nied~l~~kge~v~~~--~g~~~~e~i~~~~~d~f~~ 165 (165)
T KOG3277|consen 119 NLGWFHDLKGKRNIEDILAAKGEQVKRN--LGDGEDEDIPEDSKDVFPL 165 (165)
T ss_pred hhcccccccccccHHHHHHhccceeeee--ccccccccccccccccCCC
Confidence 99999999988 999999999999886 333332 33457899986
No 2
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=100.00 E-value=1.2e-37 Score=227.15 Aligned_cols=66 Identities=36% Similarity=0.688 Sum_probs=52.5
Q ss_pred eEEEEEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccCCCCcchhhhcCCCCc
Q 028299 124 MRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEMKCYVNPSFNYRDAKW 189 (211)
Q Consensus 124 ~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~~~tIEdi~k~KGe~v 189 (211)
|+|+|||++|++|++|+|||+||++||||||||||+|+||||||||||.|.+.+|||||++|||+|
T Consensus 1 ~~l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlIaDnLg~f~e~~~~iE~~l~~kge~v 66 (66)
T PF05180_consen 1 YQLTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLIADNLGWFGENKRNIEDILKEKGEKV 66 (66)
T ss_dssp EEEEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES--SS-SGGGS---HHHHHHHH----
T ss_pred CeEEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeeehhhhcccccCCCCHHHHHHHcCCcC
Confidence 789999999999999999999999999999999999999999999999999999999999999986
No 3
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=93.96 E-value=0.03 Score=39.28 Aligned_cols=34 Identities=29% Similarity=0.761 Sum_probs=29.1
Q ss_pred EEEEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 125 RVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 125 ~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
...|.| .||.. -.|++.-.+.|.++|+|++|.-+
T Consensus 16 ~~~y~C-RCG~~--f~i~e~~l~~~~~iv~C~sCSL~ 49 (55)
T PF05207_consen 16 VYSYPC-RCGGE--FEISEEDLEEGEVIVQCDSCSLW 49 (55)
T ss_dssp EEEEEE-TTSSE--EEEEHHHHHCT--EEEETTTTEE
T ss_pred EEEEcC-CCCCE--EEEcchhccCcCEEEECCCCccE
Confidence 589999 99998 88999999999999999999865
No 4
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=89.81 E-value=0.22 Score=32.71 Aligned_cols=34 Identities=26% Similarity=0.592 Sum_probs=24.4
Q ss_pred EEcccCCCcccccc---CcccccCccEEEEcCCCCcc
Q 028299 128 FTCNVCGQRTTRAI---NPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 128 FTC~~C~tRS~k~i---SK~AY~~GvViVqC~GC~n~ 161 (211)
++|..|+++.+..+ .|.|-+.-++|..|..|..+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 46889999888777 55677788999999988753
No 5
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.32 E-value=0.33 Score=32.11 Aligned_cols=34 Identities=29% Similarity=0.499 Sum_probs=26.4
Q ss_pred EEcccCCCcccccc---CcccccCccEEEEcCCCCcc
Q 028299 128 FTCNVCGQRTTRAI---NPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 128 FTC~~C~tRS~k~i---SK~AY~~GvViVqC~GC~n~ 161 (211)
|.|.+|+++.+..+ .|.|-+.=++|..|..|..+
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 47899998888766 45677777899999999753
No 6
>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=87.77 E-value=0.42 Score=34.03 Aligned_cols=35 Identities=26% Similarity=0.619 Sum_probs=24.8
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCccceee
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLV 165 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIA 165 (211)
|+|+|..|+..- .+. ..+. |- ||.|+.|...+-|+
T Consensus 1 ~~~~CP~CG~~i--ev~-~~~~-Ge-iV~Cp~CGaeleVv 35 (54)
T TIGR01206 1 MQFECPDCGAEI--ELE-NPEL-GE-LVICDECGAELEVV 35 (54)
T ss_pred CccCCCCCCCEE--ecC-CCcc-CC-EEeCCCCCCEEEEE
Confidence 479999999944 232 2233 65 67999999987665
No 7
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.20 E-value=0.58 Score=35.27 Aligned_cols=31 Identities=26% Similarity=0.706 Sum_probs=26.7
Q ss_pred EEEcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 127 AFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 127 ~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
.|-| .||-| -.|++.-.+.|-.+++||+|.-
T Consensus 22 ~yPC-pCGDr--f~It~edL~~ge~Va~CpsCSL 52 (67)
T KOG2923|consen 22 YYPC-PCGDR--FQITLEDLENGEDVARCPSCSL 52 (67)
T ss_pred EcCC-CCCCe--eeecHHHHhCCCeeecCCCceE
Confidence 3444 79999 7899999999999999999974
No 8
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=84.99 E-value=0.82 Score=30.30 Aligned_cols=38 Identities=16% Similarity=0.344 Sum_probs=27.6
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccc
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNL 170 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgw 170 (211)
+.|.|..||....- ...+..++||.|.+.-++.|+=..
T Consensus 2 ~~y~C~~CG~~~~~-------~~~~~~~~Cp~CG~~~~~~~~~~~ 39 (46)
T PRK00398 2 AEYKCARCGREVEL-------DEYGTGVRCPYCGYRILFKERPPV 39 (46)
T ss_pred CEEECCCCCCEEEE-------CCCCCceECCCCCCeEEEccCCCc
Confidence 68999999986542 233337899999988877776443
No 9
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=83.49 E-value=0.82 Score=43.17 Aligned_cols=30 Identities=20% Similarity=0.687 Sum_probs=25.0
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCccceeee
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVD 166 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIAD 166 (211)
..|.|..||..+.+- .-|||+|..|--+.-
T Consensus 6 ~~y~C~~Cg~~~~~~-----------~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 6 SKFVCQHCGADSPKW-----------QGKCPACHAWNTITE 35 (454)
T ss_pred CeEECCcCCCCCccc-----------cEECcCCCCccccch
Confidence 469999999887764 579999999987765
No 10
>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=81.66 E-value=1.3 Score=28.00 Aligned_cols=34 Identities=18% Similarity=0.350 Sum_probs=22.1
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
|.++|..|++...-.-.+. ...|. -|+|+.|...
T Consensus 1 M~~~CP~C~~~~~v~~~~~-~~~~~-~v~C~~C~~~ 34 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQL-GANGG-KVRCGKCGHV 34 (38)
T ss_pred CEEECCCCCCEEEeCHHHc-CCCCC-EEECCCCCCE
Confidence 4589999998754332222 23443 7999999864
No 11
>PRK11823 DNA repair protein RadA; Provisional
Probab=81.40 E-value=1.1 Score=42.11 Aligned_cols=31 Identities=26% Similarity=0.799 Sum_probs=25.5
Q ss_pred EEEEEcccCCCccccccCcccccCccEEEEcCCCCccceeee
Q 028299 125 RVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVD 166 (211)
Q Consensus 125 ~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIAD 166 (211)
...|.|..||..+.+- +-|||.|..|--+.-
T Consensus 5 ~~~y~C~~Cg~~~~~~-----------~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 5 KTAYVCQECGAESPKW-----------LGRCPECGAWNTLVE 35 (446)
T ss_pred CCeEECCcCCCCCccc-----------CeeCcCCCCccceee
Confidence 3569999999887764 479999999987765
No 12
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=79.87 E-value=1.4 Score=40.20 Aligned_cols=35 Identities=31% Similarity=0.502 Sum_probs=28.4
Q ss_pred EEEcccCCCcccccc---CcccccCccEEEEcCCCCcc
Q 028299 127 AFTCNVCGQRTTRAI---NPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 127 ~FTC~~C~tRS~k~i---SK~AY~~GvViVqC~GC~n~ 161 (211)
.|+|..|+++....+ .|.|=+-=++|++|..|.++
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~ 295 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNR 295 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCe
Confidence 599999999888544 55666666999999999865
No 13
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=78.49 E-value=1.9 Score=27.90 Aligned_cols=33 Identities=21% Similarity=0.463 Sum_probs=19.2
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
|..+|..|+++-. |.-..--.+-+-|||+.|..
T Consensus 1 M~i~Cp~C~~~y~--i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 1 MIITCPNCQAKYE--IDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred CEEECCCCCCEEe--CCHHHCCCCCcEEECCCCCC
Confidence 3567777777543 33332334445778888864
No 14
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=78.14 E-value=1.4 Score=42.12 Aligned_cols=35 Identities=17% Similarity=0.550 Sum_probs=27.1
Q ss_pred eEEEEEcccCCCccccccCcccccCccEEEEcCCCCccceeeeccc
Q 028299 124 MRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLN 169 (211)
Q Consensus 124 ~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLg 169 (211)
-...|+|..||.++. +..-+||+|+.|--|.-+.+
T Consensus 351 ~~~~YRC~~CGF~a~-----------~l~W~CPsC~~W~TikPir~ 385 (389)
T COG2956 351 RKPRYRCQNCGFTAH-----------TLYWHCPSCRAWETIKPIRG 385 (389)
T ss_pred hcCCceecccCCcce-----------eeeeeCCCcccccccCCccc
Confidence 345699999997754 45789999999987776554
No 15
>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=77.21 E-value=1.4 Score=27.67 Aligned_cols=31 Identities=16% Similarity=0.423 Sum_probs=21.5
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
..|.|..||++-....+-.. --.+.||.|..
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISD----DPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCEEEEEEecCC----CCCCCCCCCCC
Confidence 47999999996554332211 35678999987
No 16
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=76.30 E-value=2.3 Score=27.49 Aligned_cols=32 Identities=25% Similarity=0.496 Sum_probs=19.5
Q ss_pred EEEcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 127 AFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 127 ~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
..+|..|+++-. |.....-.+-..|+|+.|+.
T Consensus 2 ~i~CP~C~~~f~--v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 2 IITCPNCQTRFR--VPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EEECCCCCceEE--cCHHHcccCCcEEECCCCCc
Confidence 457888877543 33333334455788888874
No 17
>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=75.57 E-value=1.7 Score=28.95 Aligned_cols=32 Identities=19% Similarity=0.449 Sum_probs=21.2
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
-.|.|+.|+++-....+-.. --.+.||.|...
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~~ 35 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSD----DPLATCPECGGE 35 (52)
T ss_pred EEEEeCCCCCEeEEEEecCC----CCCCCCCCCCCC
Confidence 47999999986654422111 234679999974
No 18
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=74.90 E-value=2.1 Score=41.82 Aligned_cols=30 Identities=30% Similarity=0.796 Sum_probs=25.1
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCccceeee
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVD 166 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIAD 166 (211)
-.|.|+.||.-+.|-+ -|||+|..|--+..
T Consensus 6 t~f~C~~CG~~s~KW~-----------GkCp~Cg~Wns~vE 35 (456)
T COG1066 6 TAFVCQECGYVSPKWL-----------GKCPACGAWNTLVE 35 (456)
T ss_pred cEEEcccCCCCCcccc-----------ccCCCCCCccceEE
Confidence 6799999999888754 68999999976654
No 19
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=74.40 E-value=1.9 Score=39.90 Aligned_cols=28 Identities=25% Similarity=0.756 Sum_probs=23.7
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeee
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVD 166 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIAD 166 (211)
|.|..||..+.|- .-|||+|..|.-+.-
T Consensus 1 ~~c~~cg~~~~~~-----------~g~cp~c~~w~~~~e 28 (372)
T cd01121 1 YVCSECGYVSPKW-----------LGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCCc-----------cEECcCCCCceeeee
Confidence 7899999887764 579999999988875
No 20
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=72.80 E-value=2 Score=35.68 Aligned_cols=29 Identities=21% Similarity=0.542 Sum_probs=22.9
Q ss_pred EEEcccCCCccccccCcccccCccEEEEcCCCCccc
Q 028299 127 AFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 127 ~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H 162 (211)
.|+|..||+.. .|.+-.+|..||.|....
T Consensus 112 ~l~C~~Cg~~~-------~~~~~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 112 TLVCENCGHEV-------ELTHPERLPPCPKCGHTE 140 (146)
T ss_pred eEecccCCCEE-------EecCCCcCCCCCCCCCCe
Confidence 58999999864 455567899999998753
No 21
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=72.45 E-value=2 Score=27.84 Aligned_cols=17 Identities=18% Similarity=0.647 Sum_probs=14.9
Q ss_pred EEEEcCCCCccceeeec
Q 028299 151 VFVQCCGCNVFHKLVDN 167 (211)
Q Consensus 151 ViVqC~GC~n~HLIADN 167 (211)
.+|+||.|+....|.|.
T Consensus 1 M~i~CP~C~~~f~v~~~ 17 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDD 17 (37)
T ss_pred CEEECCCCCceEEcCHH
Confidence 37999999999999884
No 22
>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=72.31 E-value=2.2 Score=28.13 Aligned_cols=32 Identities=19% Similarity=0.392 Sum_probs=23.2
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
-.|.|..||+.-....+-.. --.+.||.|...
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISE----DDPVPCPECGST 35 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCC----CCCCcCCCCCCC
Confidence 47999999987776554333 446789999873
No 23
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=71.96 E-value=3.1 Score=35.48 Aligned_cols=32 Identities=19% Similarity=0.600 Sum_probs=25.9
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccc
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNL 170 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgw 170 (211)
|.|..||+.+.+. .-.||+|..+|-|-=.+|+
T Consensus 355 ~~c~~cg~~~~~~-----------~~~c~~c~~~~~~~~~~~~ 386 (389)
T PRK11788 355 YRCRNCGFTARTL-----------YWHCPSCKAWETIKPIRGL 386 (389)
T ss_pred EECCCCCCCCccc-----------eeECcCCCCccCcCCcccC
Confidence 7799999988764 3589999999988766665
No 24
>PRK11032 hypothetical protein; Provisional
Probab=70.39 E-value=2.3 Score=35.99 Aligned_cols=28 Identities=21% Similarity=0.496 Sum_probs=23.6
Q ss_pred EEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 127 AFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 127 ~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
.+.|..||+.. .|.+-.+|..||.|...
T Consensus 124 ~LvC~~Cg~~~-------~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 124 NLVCEKCHHHL-------AFYTPEVLPLCPKCGHD 151 (160)
T ss_pred eEEecCCCCEE-------EecCCCcCCCCCCCCCC
Confidence 57899999865 57788899999999864
No 25
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=70.31 E-value=4.4 Score=31.92 Aligned_cols=37 Identities=19% Similarity=0.679 Sum_probs=26.3
Q ss_pred ceEEEEEcccCCCcccc-ccCcccccCccEEEEcCCCCcccee
Q 028299 123 RMRVAFTCNVCGQRTTR-AINPHAYTDGTVFVQCCGCNVFHKL 164 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k-~iSK~AY~~GvViVqC~GC~n~HLI 164 (211)
++--.|+|..|+..+.. .|.| |+..+.|+.|...+--
T Consensus 17 klpt~f~CP~Cge~~v~v~~~k-----~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 17 KLPKIFECPRCGKVSISVKIKK-----NIAIITCGNCGLYTEF 54 (99)
T ss_pred CCCcEeECCCCCCeEeeeecCC-----CcceEECCCCCCccCE
Confidence 34457999999963332 3444 8999999999886543
No 26
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=69.43 E-value=4.2 Score=30.59 Aligned_cols=44 Identities=30% Similarity=0.623 Sum_probs=32.3
Q ss_pred cccCCCcceEEEEEcccCCCccccccCcccccCccEEEEcCCCCccceeee
Q 028299 116 FTKSPRRRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVD 166 (211)
Q Consensus 116 ~~k~prr~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIAD 166 (211)
|+-++ ..-...|-| .||-|- .||-.-...|-|..+||+|. ||++
T Consensus 12 ftf~~-e~~~ftyPC-PCGDRF--eIsLeDl~~GE~VArCPSCS---Liv~ 55 (67)
T COG5216 12 FTFSR-EEKTFTYPC-PCGDRF--EISLEDLRNGEVVARCPSCS---LIVC 55 (67)
T ss_pred eEEcC-CCceEEecC-CCCCEe--EEEHHHhhCCceEEEcCCce---EEEE
Confidence 44443 345667888 599885 57778889999999999996 4544
No 27
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=66.85 E-value=3.7 Score=34.93 Aligned_cols=32 Identities=16% Similarity=0.456 Sum_probs=23.4
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
|-|-.||++....+.+-. .+.+-+.+|+.|+.
T Consensus 1 miCIeCg~~v~~Ly~~Ys-~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYS-PGNIRLTKCPNCGK 32 (208)
T ss_pred CEeccCCCcchhhhhccC-CCcEEEeeccccCC
Confidence 469999999765555432 33488999999974
No 28
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=66.23 E-value=2.3 Score=32.05 Aligned_cols=40 Identities=18% Similarity=0.537 Sum_probs=20.4
Q ss_pred CcceEEEEEcccCCCcccc--ccCcccccCccEEEEcCCCCccce
Q 028299 121 RRRMRVAFTCNVCGQRTTR--AINPHAYTDGTVFVQCCGCNVFHK 163 (211)
Q Consensus 121 rr~~~l~FTC~~C~tRS~k--~iSK~AY~~GvViVqC~GC~n~HL 163 (211)
.+++.-.|+|-.|++..+- .|.|. .|+-.+.|.-|...+-
T Consensus 16 ~~~l~~~F~CPfC~~~~sV~v~idkk---~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 16 KPKLPKVFDCPFCNHEKSVSVKIDKK---EGIGILSCRVCGESFQ 57 (81)
T ss_dssp ----SS----TTT--SS-EEEEEETT---TTEEEEEESSS--EEE
T ss_pred CCCCCceEcCCcCCCCCeEEEEEEcc---CCEEEEEecCCCCeEE
Confidence 4566678999999965542 45444 8999999999976553
No 29
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=64.21 E-value=3.9 Score=32.28 Aligned_cols=32 Identities=22% Similarity=0.559 Sum_probs=20.9
Q ss_pred ceEEEEEcccCCCccccccCcccccCccEEEEcCCCCccc
Q 028299 123 RMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H 162 (211)
..-+.+.|+.|++. +....| .+.+||.|....
T Consensus 67 ~vp~~~~C~~Cg~~----~~~~~~----~~~~CP~Cgs~~ 98 (117)
T PRK00564 67 DEKVELECKDCSHV----FKPNAL----DYGVCEKCHSKN 98 (117)
T ss_pred ecCCEEEhhhCCCc----cccCCc----cCCcCcCCCCCc
Confidence 45568999999943 332222 235799999764
No 30
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=63.42 E-value=7.2 Score=26.50 Aligned_cols=31 Identities=19% Similarity=0.509 Sum_probs=22.4
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCcccee
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKL 164 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLI 164 (211)
+.|.|..||+...-. ..=-|+|+.|..+=|.
T Consensus 1 ~~Y~C~~Cg~~~~~~--------~~~~irC~~CG~rIly 31 (44)
T smart00659 1 MIYICGECGRENEIK--------SKDVVRCRECGYRILY 31 (44)
T ss_pred CEEECCCCCCEeecC--------CCCceECCCCCceEEE
Confidence 479999999976533 1134899999977654
No 31
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=61.72 E-value=4.7 Score=31.66 Aligned_cols=31 Identities=19% Similarity=0.511 Sum_probs=20.9
Q ss_pred ceEEEEEcccCCCccccccCcccccCccEEEEcCCCCccc
Q 028299 123 RMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H 162 (211)
..-+.+.|+.|++... ...| ...||.|....
T Consensus 66 ~~p~~~~C~~Cg~~~~----~~~~-----~~~CP~Cgs~~ 96 (115)
T TIGR00100 66 DEPVECECEDCSEEVS----PEID-----LYRCPKCHGIM 96 (115)
T ss_pred eeCcEEEcccCCCEEe----cCCc-----CccCcCCcCCC
Confidence 4556799999994433 2222 46799999864
No 32
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=61.40 E-value=3.6 Score=34.21 Aligned_cols=33 Identities=33% Similarity=0.569 Sum_probs=26.0
Q ss_pred cceEEEEEcccCCCccccccCcccccCccEEEEcCCCCccce
Q 028299 122 RRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHK 163 (211)
Q Consensus 122 r~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HL 163 (211)
+--+|..+|.+||+.=.+ +.|.|+ ||-|..+-.
T Consensus 23 GAkML~~hCp~Cg~PLF~-------KdG~v~--CPvC~~~~~ 55 (131)
T COG1645 23 GAKMLAKHCPKCGTPLFR-------KDGEVF--CPVCGYREV 55 (131)
T ss_pred hhHHHHhhCcccCCccee-------eCCeEE--CCCCCceEE
Confidence 456789999999998765 578775 999996443
No 33
>PRK12495 hypothetical protein; Provisional
Probab=61.00 E-value=4.7 Score=36.30 Aligned_cols=30 Identities=23% Similarity=0.471 Sum_probs=24.0
Q ss_pred cceEEEEEcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 122 RRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 122 r~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
+--++.|.|.+||..-. +| .|+| .|+.|+.
T Consensus 37 gatmsa~hC~~CG~PIp------a~-pG~~--~Cp~CQ~ 66 (226)
T PRK12495 37 GATMTNAHCDECGDPIF------RH-DGQE--FCPTCQQ 66 (226)
T ss_pred hcccchhhcccccCccc------CC-CCee--ECCCCCC
Confidence 45678899999999877 56 7875 5999983
No 34
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=58.43 E-value=7.6 Score=32.32 Aligned_cols=31 Identities=16% Similarity=0.433 Sum_probs=20.9
Q ss_pred cceEEEEEcccCCCccccccCcccc-cCccEE
Q 028299 122 RRMRVAFTCNVCGQRTTRAINPHAY-TDGTVF 152 (211)
Q Consensus 122 r~~~l~FTC~~C~tRS~k~iSK~AY-~~GvVi 152 (211)
.-+.+.|.|..||.|+....+-.++ .+|+.+
T Consensus 25 evii~sf~C~~CGyk~~ev~~~~~~~~~G~r~ 56 (161)
T PF03367_consen 25 EVIIMSFECEHCGYKNNEVKSGGQIQPKGVRI 56 (161)
T ss_dssp EEEEEEEE-TTT--EEEEEEEECSS-SSEEEE
T ss_pred eEEEEEeECCCCCCEeeeEEECccCCCCceEE
Confidence 4689999999999999987776666 444444
No 35
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=56.76 E-value=11 Score=25.64 Aligned_cols=31 Identities=23% Similarity=0.693 Sum_probs=22.0
Q ss_pred cccCCCccccccCcccccCcc-EEEEcCCCCc
Q 028299 130 CNVCGQRTTRAINPHAYTDGT-VFVQCCGCNV 160 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~Gv-ViVqC~GC~n 160 (211)
|.-||..............|. +.|.|..|..
T Consensus 6 CPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 6 CPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 888977666655544444443 8899999988
No 36
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=56.13 E-value=11 Score=37.05 Aligned_cols=36 Identities=19% Similarity=0.479 Sum_probs=31.8
Q ss_pred CcceEEEEEcccCCCccccccCcccccCccEEEEcC
Q 028299 121 RRRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCC 156 (211)
Q Consensus 121 rr~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~ 156 (211)
|.-+.+.|-|..||++|....++..-..|-|-+.|.
T Consensus 62 REvVimSF~CpHCG~kN~eiQ~a~~iQ~~Gvri~l~ 97 (460)
T KOG2703|consen 62 REVVIMSFECPHCGHKNNEIQSAEEIQEGGVRIELR 97 (460)
T ss_pred heeeeEEeecCccCCccccccchhccccCceEEEEE
Confidence 456899999999999999999999999888877664
No 37
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=55.95 E-value=7.3 Score=32.65 Aligned_cols=39 Identities=18% Similarity=0.319 Sum_probs=20.9
Q ss_pred ceEEEEEcccCCCccc-cccCc-ccccCccEEEEcCCCCcc
Q 028299 123 RMRVAFTCNVCGQRTT-RAINP-HAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~-k~iSK-~AY~~GvViVqC~GC~n~ 161 (211)
---+.|+|..|++... ..+.+ .....-....+|+.|+..
T Consensus 14 c~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~ 54 (188)
T PF08996_consen 14 CEPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTP 54 (188)
T ss_dssp ---EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B
T ss_pred CCceEeECCCCCCCccccccccCCccccccCcCcCCCCCCc
Confidence 3468999999999885 33333 444444568999999983
No 38
>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 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=55.55 E-value=9.2 Score=30.72 Aligned_cols=32 Identities=22% Similarity=0.577 Sum_probs=22.6
Q ss_pred EcccCCCccccccCcc---------cccCccEEEEcCCCCcc
Q 028299 129 TCNVCGQRTTRAINPH---------AYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~---------AY~~GvViVqC~GC~n~ 161 (211)
-|-+||.+-. .++|. .|...-.|-+|++|...
T Consensus 93 RC~~CN~~L~-~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 93 RCPKCNGPLR-PVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred ccCCCCcEee-echhhccccccCccccccCCeEEECCCCCCE
Confidence 5999999543 34443 55566679999999864
No 40
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=53.50 E-value=5.6 Score=35.82 Aligned_cols=31 Identities=23% Similarity=0.694 Sum_probs=26.4
Q ss_pred EEcccCCCccccccCcccccCc-cEEEEcCCCCc
Q 028299 128 FTCNVCGQRTTRAINPHAYTDG-TVFVQCCGCNV 160 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~G-vViVqC~GC~n 160 (211)
|+|-.||.+....+.+ |-+| +=+.+|++|+.
T Consensus 1 ~~CVeCg~~vksLy~~--Ys~g~irlt~C~nC~e 32 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQ--YSPGNIRLTKCPNCQE 32 (225)
T ss_pred CcccccCchHHHHHHh--cCCCcEEEeeCCchhh
Confidence 6899999999888865 7788 67889999985
No 41
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.54 E-value=12 Score=30.26 Aligned_cols=36 Identities=19% Similarity=0.516 Sum_probs=21.4
Q ss_pred eEEEEEcccCCCccccc---------------cCcccccCccEEEEcCCCCccc
Q 028299 124 MRVAFTCNVCGQRTTRA---------------INPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 124 ~~l~FTC~~C~tRS~k~---------------iSK~AY~~GvViVqC~GC~n~H 162 (211)
.-..+.|..||..-... +.+..+. -+.+||.|..++
T Consensus 67 ~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~CP~Cgs~~ 117 (135)
T PRK03824 67 EEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVH---AFLKCPKCGSRD 117 (135)
T ss_pred cceEEECCCCCCEEecccccccccccccccccccccccc---cCcCCcCCCCCC
Confidence 34679999999543321 1121112 235799999865
No 42
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=52.38 E-value=11 Score=29.83 Aligned_cols=30 Identities=27% Similarity=0.656 Sum_probs=25.0
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
=.|..|+...++.+-. .++.+.+|..|.++
T Consensus 81 VlC~~C~spdT~l~k~----~r~~~l~C~aCGa~ 110 (110)
T smart00653 81 VLCPECGSPDTELIKE----NRLFFLKCEACGAR 110 (110)
T ss_pred EECCCCCCCCcEEEEe----CCeEEEEccccCCC
Confidence 3699999998887754 78999999999763
No 43
>smart00350 MCM minichromosome maintenance proteins.
Probab=51.01 E-value=12 Score=35.71 Aligned_cols=36 Identities=28% Similarity=0.452 Sum_probs=25.5
Q ss_pred eEEEEEcccCCCccccccCcccccCccEEEEcCC--CCccc
Q 028299 124 MRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCG--CNVFH 162 (211)
Q Consensus 124 ~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~G--C~n~H 162 (211)
....|.|..|++.....+....|. .-..|++ |++.+
T Consensus 34 ~~~~f~C~~C~~~~~~~~~~~~~~---~p~~C~~~~C~~~~ 71 (509)
T smart00350 34 KRASFTCEKCGATLGPEIQSGRET---EPTVCPPRECQSPT 71 (509)
T ss_pred EEEEEEecCCCCEEeEEecCCccc---CCCcCCCCcCCCCC
Confidence 357899999999876665433332 3467998 99865
No 44
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=49.56 E-value=11 Score=29.63 Aligned_cols=32 Identities=16% Similarity=0.275 Sum_probs=20.6
Q ss_pred ceEEEEEcccCCCccccccCcccccCccEEEEcCCCCccc
Q 028299 123 RMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H 162 (211)
..-+.+.|+.|++. +....+ -+.+||.|....
T Consensus 66 ~~p~~~~C~~Cg~~----~~~~~~----~~~~CP~Cgs~~ 97 (114)
T PRK03681 66 EQEAECWCETCQQY----VTLLTQ----RVRRCPQCHGDM 97 (114)
T ss_pred eeCcEEEcccCCCe----eecCCc----cCCcCcCcCCCC
Confidence 45578999999952 222111 125799999765
No 45
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=49.30 E-value=7 Score=36.15 Aligned_cols=36 Identities=31% Similarity=0.731 Sum_probs=21.7
Q ss_pred EEEEEcccCCCcccc-ccCcccccCccEEEEcCCCCc
Q 028299 125 RVAFTCNVCGQRTTR-AINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 125 ~l~FTC~~C~tRS~k-~iSK~AY~~GvViVqC~GC~n 160 (211)
++.|||++||.---| .+-||.|.=-=--..|--|.+
T Consensus 1 MV~FtCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k 37 (276)
T KOG2186|consen 1 MVFFTCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGK 37 (276)
T ss_pred CeEEehhhhhhhccccchHHHHHhccCCeeEEeeccc
Confidence 478999999986654 556665531113344555544
No 46
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=49.11 E-value=14 Score=30.42 Aligned_cols=33 Identities=21% Similarity=0.522 Sum_probs=27.5
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCcccee
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKL 164 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLI 164 (211)
=.|..|+...++.+- +..+.+.+|..|.+..-+
T Consensus 103 VlC~~C~spdT~l~k----~~r~~~l~C~ACGa~~~V 135 (138)
T PRK03988 103 VICPECGSPDTKLIK----EGRIWVLKCEACGAETPV 135 (138)
T ss_pred EECCCCCCCCcEEEE----cCCeEEEEcccCCCCCcC
Confidence 379999999998874 377899999999987654
No 47
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=48.97 E-value=12 Score=31.35 Aligned_cols=34 Identities=29% Similarity=0.700 Sum_probs=27.6
Q ss_pred EcccCCCccccccCcccccCccEE---EEcCCCCccc
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVF---VQCCGCNVFH 162 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvVi---VqC~GC~n~H 162 (211)
.|.-|++.-++.++-..+..|-++ -||+.|.-..
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 599999988888888888888444 6999998654
No 48
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=48.30 E-value=8.5 Score=31.15 Aligned_cols=45 Identities=22% Similarity=0.412 Sum_probs=28.2
Q ss_pred EEEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccC
Q 028299 127 AFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEM 174 (211)
Q Consensus 127 ~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~ 174 (211)
.+.|..|+......--...+..+.+ .+|+.|.. +|-.|.=||+|.
T Consensus 105 ~~~C~~C~~~~~~~~~~~~~~~~~~-~~C~~C~~--~lrp~vv~fgE~ 149 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVDSIDEEEP-PRCPKCGG--LLRPDVVLFGES 149 (178)
T ss_dssp EEEETTTSBEEEGHHHHHHHHTTSS-CBCTTTSC--BEEEEE--BTSB
T ss_pred eeeecCCCccccchhhccccccccc-ccccccCc--cCCCCeeecCCC
Confidence 4689999997654322222222221 19999998 688999999875
No 49
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=47.74 E-value=15 Score=31.49 Aligned_cols=36 Identities=22% Similarity=0.621 Sum_probs=30.1
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeeec
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDN 167 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADN 167 (211)
=.|..|+...++.+-. ..+.+.+|..|.+.+-+.-+
T Consensus 99 V~C~~C~~pdT~l~k~----~~~~~l~C~aCGa~~~v~~~ 134 (201)
T PRK12336 99 VICSECGLPDTRLVKE----DRVLMLRCDACGAHRPVKKR 134 (201)
T ss_pred EECCCCCCCCcEEEEc----CCeEEEEcccCCCCcccccc
Confidence 3699999999988743 58999999999999888754
No 50
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=47.65 E-value=11 Score=30.47 Aligned_cols=39 Identities=21% Similarity=0.388 Sum_probs=23.4
Q ss_pred EEcccCCCccccccC-cccccCccEEEEcCCCCccceeee
Q 028299 128 FTCNVCGQRTTRAIN-PHAYTDGTVFVQCCGCNVFHKLVD 166 (211)
Q Consensus 128 FTC~~C~tRS~k~iS-K~AY~~GvViVqC~GC~n~HLIAD 166 (211)
.+|+.|.+-=..-.| +.-..+|.|+|+|..|....=+..
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p~ 96 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYPY 96 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEecc
Confidence 579999983111111 122334559999999987654443
No 51
>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=47.55 E-value=11 Score=24.39 Aligned_cols=29 Identities=24% Similarity=0.695 Sum_probs=18.4
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCcccee
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKL 164 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLI 164 (211)
|.|..|+.... +.. ... |+|+.|..+.|.
T Consensus 1 Y~C~~Cg~~~~--~~~---~~~---irC~~CG~RIly 29 (32)
T PF03604_consen 1 YICGECGAEVE--LKP---GDP---IRCPECGHRILY 29 (32)
T ss_dssp EBESSSSSSE---BST---SST---SSBSSSS-SEEB
T ss_pred CCCCcCCCeeE--cCC---CCc---EECCcCCCeEEE
Confidence 67999998877 222 111 599999887764
No 52
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=46.98 E-value=18 Score=23.48 Aligned_cols=27 Identities=22% Similarity=0.600 Sum_probs=18.8
Q ss_pred cccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 130 CNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
|..|++ . +.+..+ .++.+-+|++|.-.
T Consensus 2 CP~C~~-~---l~~~~~-~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 2 CPRCGT-E---LEPVRL-GDVEIDVCPSCGGI 28 (41)
T ss_pred cCCCCc-c---cceEEE-CCEEEEECCCCCeE
Confidence 788877 2 223333 77889999999754
No 53
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=46.56 E-value=12 Score=30.27 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=25.7
Q ss_pred EcccCCCccccccCcccccCccEEEEcCCCCccc
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H 162 (211)
.|..|+...+..+-+ .++.+.+|..|...+
T Consensus 95 lC~~C~spdT~l~k~----~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 95 LCPECGSPDTELIKE----GRLIFLKCKACGASR 124 (125)
T ss_dssp SCTSTSSSSEEEEEE----TTCCEEEETTTSCEE
T ss_pred EcCCCCCCccEEEEc----CCEEEEEecccCCcC
Confidence 699999998877655 899999999998764
No 54
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=46.37 E-value=13 Score=29.03 Aligned_cols=32 Identities=16% Similarity=0.316 Sum_probs=18.2
Q ss_pred ceEEEEEcccCCCccccccCcccccCccEEEEcCCCCccce
Q 028299 123 RMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHK 163 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HL 163 (211)
..-+.+.|+.|++...-.-.. ..||.|....+
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~---------~~CP~Cgs~~~ 97 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDEFD---------FSCPRCGSPDV 97 (113)
T ss_dssp EE--EEEETTTS-EEECHHCC---------HH-SSSSSS-E
T ss_pred ecCCcEECCCCCCEEecCCCC---------CCCcCCcCCCc
Confidence 466789999999865422211 23999999863
No 55
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.28 E-value=11 Score=29.48 Aligned_cols=30 Identities=23% Similarity=0.218 Sum_probs=19.5
Q ss_pred ceEEEEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 123 RMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
..-+.+.|+.|++... ... ...+||.|...
T Consensus 66 ~vp~~~~C~~Cg~~~~----~~~-----~~~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVVE----IHQ-----HDAQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEEe----cCC-----cCccCcCCCCC
Confidence 4567899999994322 211 23359999965
No 56
>KOG4216 consensus Steroid hormone nuclear receptor [Transcription]
Probab=45.68 E-value=9.9 Score=37.32 Aligned_cols=26 Identities=27% Similarity=0.908 Sum_probs=20.0
Q ss_pred EEEcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 127 AFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 127 ~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
.--||+||-.|. .-|-|| |+|.||+-
T Consensus 46 vIPCKiCGDKSS------GiHYGV--ITCEGCKG 71 (479)
T KOG4216|consen 46 IIPCKICGDKSS------GIHYGV--ITCEGCKG 71 (479)
T ss_pred EEeeeeccCCCC------cceeee--EeeccchH
Confidence 357999999875 456675 68999973
No 57
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=45.54 E-value=18 Score=35.31 Aligned_cols=46 Identities=24% Similarity=0.477 Sum_probs=36.0
Q ss_pred cccccCCCcceEEEEEcccCCCccccccCcccccCc----cEEEEcCCCCcc
Q 028299 114 SLFTKSPRRRMRVAFTCNVCGQRTTRAINPHAYTDG----TVFVQCCGCNVF 161 (211)
Q Consensus 114 s~~~k~prr~~~l~FTC~~C~tRS~k~iSK~AY~~G----vViVqC~GC~n~ 161 (211)
.++..+.++++ .-.|..|++...-.+...-|.+| .|..+|+.|...
T Consensus 189 ~~~~~sdqr~~--~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~ 238 (557)
T PF05876_consen 189 RLYEESDQRRY--YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCE 238 (557)
T ss_pred HHHHhCCceEE--EccCCCCCCCccccccceeecCCCCccceEEECCCCcCC
Confidence 34556666644 55799999999988888888866 899999999853
No 58
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=44.94 E-value=10 Score=31.60 Aligned_cols=45 Identities=20% Similarity=0.388 Sum_probs=22.6
Q ss_pred CcceEEEEEcccCCCccccccCc---cccc-------CccEEEEcCCCCccceee
Q 028299 121 RRRMRVAFTCNVCGQRTTRAINP---HAYT-------DGTVFVQCCGCNVFHKLV 165 (211)
Q Consensus 121 rr~~~l~FTC~~C~tRS~k~iSK---~AY~-------~GvViVqC~GC~n~HLIA 165 (211)
|+...+.++|+.|+..+.-.|.+ .+|. .-+|..-|.||.-.-.+-
T Consensus 58 rG~aNfv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~i~~fdCRG~e~~~f~p 112 (161)
T PF05907_consen 58 RGTANFVMKCKFCKRESSIDIIPGKGKPYTAEDSGKFVPILAFDCRGLEPVEFSP 112 (161)
T ss_dssp S-EESEEE--SSSS--EEEEEE--TTTEEEGGGTTS-EEEEEEEEESEEEEEE--
T ss_pred ccceEeEecCcCcCCccEEEEEecCccccccccccCCceEEEEECCCcEeEEEec
Confidence 56677777888887766654433 4565 235666777775444333
No 59
>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=44.50 E-value=23 Score=22.99 Aligned_cols=24 Identities=42% Similarity=0.869 Sum_probs=17.5
Q ss_pred EcccCCCccccccCcccccCccEEEEcCCCCccc
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H 162 (211)
+|.+|+. ...+--+|+|.+|..+.
T Consensus 1 ~C~vC~~----------~~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 1 YCPVCGQ----------SDDDGDMIQCDSCNRWY 24 (51)
T ss_dssp EBTTTTS----------SCTTSSEEEBSTTSCEE
T ss_pred eCcCCCC----------cCCCCCeEEcCCCChhh
Confidence 4778887 34455688999998753
No 60
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=43.74 E-value=13 Score=35.97 Aligned_cols=47 Identities=21% Similarity=0.460 Sum_probs=36.5
Q ss_pred CCcceEEEEEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccc
Q 028299 120 PRRRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNL 170 (211)
Q Consensus 120 prr~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgw 170 (211)
-.+...+.|.|..|+..+.++....... =+ +|+.|..-|...+--..
T Consensus 320 dl~~~r~~~~c~~~~~e~~~t~~~~~~~---~~-~~~~~~~e~~~v~~~d~ 366 (411)
T COG1503 320 DLEKERVTYKCPTCGYENLKSKREFEQK---RF-RCPECGSEMEEVEVSDL 366 (411)
T ss_pred cccccceeecCCCcchhhhhcccccccc---cc-cCccccccccchhhhhH
Confidence 3456778999999999998876666555 34 99999999988765433
No 61
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=43.71 E-value=20 Score=30.27 Aligned_cols=26 Identities=23% Similarity=0.488 Sum_probs=19.7
Q ss_pred cceEEEEEcccCCCccccccCccccc
Q 028299 122 RRMRVAFTCNVCGQRTTRAINPHAYT 147 (211)
Q Consensus 122 r~~~l~FTC~~C~tRS~k~iSK~AY~ 147 (211)
.-+.+.|.|..||.|+....+=.+..
T Consensus 23 evii~sf~C~~CGyr~~ev~~~~~~~ 48 (163)
T TIGR00340 23 KIMLSTYICEKCGYRSTDVYQLEEKE 48 (163)
T ss_pred eEEEEEEECCCCCCchhheeEcCCcC
Confidence 46888999999999988665544443
No 62
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=43.71 E-value=19 Score=33.51 Aligned_cols=43 Identities=23% Similarity=0.394 Sum_probs=32.7
Q ss_pred CcceEEEEEcccCCCccc---cccCcccccCccEEEEcCCCCccce
Q 028299 121 RRRMRVAFTCNVCGQRTT---RAINPHAYTDGTVFVQCCGCNVFHK 163 (211)
Q Consensus 121 rr~~~l~FTC~~C~tRS~---k~iSK~AY~~GvViVqC~GC~n~HL 163 (211)
.+.---.|+|.+|+.++- ..=+|.+=+-=+-||+|..|.|+-.
T Consensus 249 ~gt~td~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ecgnrWk 294 (296)
T KOG1105|consen 249 QGTQTDLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNECGNRWK 294 (296)
T ss_pred ccccccceeeccccccceeEEeeccCCCCCCcceeeeecccCCccc
Confidence 334444799999999775 3556777777889999999999743
No 63
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=43.19 E-value=32 Score=24.25 Aligned_cols=36 Identities=17% Similarity=0.432 Sum_probs=24.5
Q ss_pred CcceEEEEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 121 RRRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 121 rr~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
..+|.|. |..|..-+.-.. ++.|.. |.-+|+.|..+
T Consensus 18 ~~r~aLI--C~~C~~hNGla~-~~~~~~--i~y~C~~Cg~~ 53 (54)
T PF10058_consen 18 SNRYALI--CSKCFSHNGLAP-KEEFEE--IQYRCPYCGAL 53 (54)
T ss_pred cCceeEE--Ccccchhhcccc-cccCCc--eEEEcCCCCCc
Confidence 3455554 999988776544 555554 47899999764
No 64
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=43.07 E-value=19 Score=31.75 Aligned_cols=15 Identities=27% Similarity=0.538 Sum_probs=7.5
Q ss_pred EEcccCCCccccccC
Q 028299 128 FTCNVCGQRTTRAIN 142 (211)
Q Consensus 128 FTC~~C~tRS~k~iS 142 (211)
..|..|+.+....++
T Consensus 118 ~~C~~c~~~~yp~~~ 132 (256)
T PRK00241 118 MLCPHCRERYYPRIA 132 (256)
T ss_pred EECCCCCCEECCCCC
Confidence 456666655444333
No 65
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=42.95 E-value=21 Score=31.79 Aligned_cols=36 Identities=19% Similarity=0.542 Sum_probs=26.3
Q ss_pred eEEEEEcccCCCccc-cccCcc-cccCccEEEEcCCCCccc
Q 028299 124 MRVAFTCNVCGQRTT-RAINPH-AYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 124 ~~l~FTC~~C~tRS~-k~iSK~-AY~~GvViVqC~GC~n~H 162 (211)
+.+.+-|.-|+.-.+ |.+=|. .++ ++++|..|..-|
T Consensus 3 ~~iy~~Cp~Cg~eev~hEVik~~g~~---~lvrC~eCG~V~ 40 (201)
T COG1326 3 EEIYIECPSCGSEEVSHEVIKERGRE---PLVRCEECGTVH 40 (201)
T ss_pred ceEEEECCCCCcchhhHHHHHhcCCc---eEEEccCCCcEe
Confidence 467789999994333 444444 555 999999999888
No 66
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=41.69 E-value=18 Score=30.48 Aligned_cols=12 Identities=17% Similarity=0.271 Sum_probs=8.6
Q ss_pred EEEcCCCCccce
Q 028299 152 FVQCCGCNVFHK 163 (211)
Q Consensus 152 iVqC~GC~n~HL 163 (211)
-..|+.|.-+|-
T Consensus 28 sf~C~~CGyr~~ 39 (163)
T TIGR00340 28 TYICEKCGYRST 39 (163)
T ss_pred EEECCCCCCchh
Confidence 357888887764
No 67
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=41.61 E-value=19 Score=30.12 Aligned_cols=31 Identities=23% Similarity=0.454 Sum_probs=21.0
Q ss_pred cceEEEEEcccCCCccccccCcc-cccCccEE
Q 028299 122 RRMRVAFTCNVCGQRTTRAINPH-AYTDGTVF 152 (211)
Q Consensus 122 r~~~l~FTC~~C~tRS~k~iSK~-AY~~GvVi 152 (211)
.-+.+.|+|..||.|+....+=. -=.+|+.+
T Consensus 24 evii~sf~C~~CGyk~~ev~~~~~~~p~G~r~ 55 (160)
T smart00709 24 EVIIMSFECEHCGYRNNEVKSGGAIEPKGTRI 55 (160)
T ss_pred eEEEEEEECCCCCCccceEEECcccCCCceEE
Confidence 46888999999999998653322 23345443
No 68
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.39 E-value=20 Score=28.53 Aligned_cols=36 Identities=19% Similarity=0.434 Sum_probs=20.3
Q ss_pred ceEEEEEcccCCCccccc-cCcccccCccEEEEcCCCCccc
Q 028299 123 RMRVAFTCNVCGQRTTRA-INPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~-iSK~AY~~GvViVqC~GC~n~H 162 (211)
..-+.+.| .|+....-. +....| ....+||.|...+
T Consensus 66 ~vp~~~~C-~Cg~~~~~~~~~~~~~---~~~~~CP~Cgs~~ 102 (124)
T PRK00762 66 MIPVEIEC-ECGYEGVVDEDEIDHY---AAVIECPVCGNKR 102 (124)
T ss_pred ecCeeEEe-eCcCcccccccchhcc---ccCCcCcCCCCCC
Confidence 45678999 999542211 111111 0146799999654
No 69
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=39.88 E-value=24 Score=28.95 Aligned_cols=33 Identities=24% Similarity=0.559 Sum_probs=26.3
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCcccee
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKL 164 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLI 164 (211)
=.|..|+..-++.+ | ...+.+.+|..|....-+
T Consensus 98 VlC~~C~sPdT~l~-k---~~r~~~l~C~ACGa~~~v 130 (133)
T TIGR00311 98 VICRECNRPDTRII-K---EGRVSLLKCEACGAKAPL 130 (133)
T ss_pred EECCCCCCCCcEEE-E---eCCeEEEecccCCCCCcc
Confidence 37999999999877 3 256668899999987755
No 70
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=39.84 E-value=25 Score=28.55 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=31.6
Q ss_pred eEEEEEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccc
Q 028299 124 MRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNL 170 (211)
Q Consensus 124 ~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgw 170 (211)
|-=.|||-.||+-+.-.-+ .--..++-.+.|..|...|-.-=|-+|
T Consensus 19 L~k~FtCp~Cghe~vs~ct-vkk~~~~g~~~Cg~CGls~e~ev~~l~ 64 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCT-VKKTVNIGTAVCGNCGLSFECEVPELS 64 (104)
T ss_pred CCceEecCccCCeeeeEEE-EEecCceeEEEcccCcceEEEeccccc
Confidence 6678999999997653111 112345667889999999976555555
No 71
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=39.80 E-value=22 Score=32.77 Aligned_cols=55 Identities=24% Similarity=0.314 Sum_probs=35.4
Q ss_pred cccCCCccccccCcccccCccEEEEcCCCCccc------------------eeeecccccc----------cCCCCcc--
Q 028299 130 CNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH------------------KLVDNLNLFH----------EMKCYVN-- 179 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H------------------LIADNLgwF~----------e~~~tIE-- 179 (211)
|..||+++. .+ .|=.-.+|++|.+.| |++-+-.+|. |.+-|||
T Consensus 114 Cg~CG~~~~------~~-~~g~~~~C~~cg~~~fPR~dP~vIv~v~~~~~ilLa~~~~h~~g~yS~LAGFVE~GETlE~A 186 (279)
T COG2816 114 CGRCGTKTY------PR-EGGWARVCPKCGHEHFPRIDPCVIVAVIRGDEILLARHPRHFPGMYSLLAGFVEPGETLEQA 186 (279)
T ss_pred CCCCCCcCc------cc-cCceeeeCCCCCCccCCCCCCeEEEEEecCCceeecCCCCCCCcceeeeeecccCCccHHHH
Confidence 888888764 23 344456899999987 5666666653 4445555
Q ss_pred ---hhhhcCCCCccc
Q 028299 180 ---PSFNYRDAKWDV 191 (211)
Q Consensus 180 ---di~k~KGe~v~k 191 (211)
+++.+-|-+|++
T Consensus 187 V~REv~EE~Gi~V~~ 201 (279)
T COG2816 187 VAREVFEEVGIKVKN 201 (279)
T ss_pred HHHHHHHhhCeEEee
Confidence 456666666543
No 72
>PHA02998 RNA polymerase subunit; Provisional
Probab=39.69 E-value=22 Score=31.59 Aligned_cols=36 Identities=19% Similarity=0.313 Sum_probs=28.3
Q ss_pred EEEEcccCCCccccccC---cccccCccEEEEcCCCCcc
Q 028299 126 VAFTCNVCGQRTTRAIN---PHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iS---K~AY~~GvViVqC~GC~n~ 161 (211)
..-+|..|+++.+..+. |.|=+--++|.+|..|.++
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~ 180 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKH 180 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCc
Confidence 34679999999987554 4466777999999999875
No 73
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=39.30 E-value=22 Score=25.31 Aligned_cols=31 Identities=19% Similarity=0.511 Sum_probs=15.4
Q ss_pred EcccCCCccccc------cCcccccCccEEEEcCCCC
Q 028299 129 TCNVCGQRTTRA------INPHAYTDGTVFVQCCGCN 159 (211)
Q Consensus 129 TC~~C~tRS~k~------iSK~AY~~GvViVqC~GC~ 159 (211)
-|+.|++--.-- |-|..-..+.|+++|-.|.
T Consensus 48 ~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~ 84 (85)
T PF04032_consen 48 ICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCG 84 (85)
T ss_dssp B-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTT
T ss_pred cccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccC
Confidence 588888732222 2233556789999999996
No 74
>PRK00420 hypothetical protein; Validated
Probab=39.16 E-value=18 Score=29.22 Aligned_cols=34 Identities=24% Similarity=0.307 Sum_probs=25.3
Q ss_pred EEEEEcccCCCccccccCcccccCccEEEEcCCCCccceeee
Q 028299 125 RVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVD 166 (211)
Q Consensus 125 ~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIAD 166 (211)
++.-+|.+||+.-.+. .+| -++||.|.....+.+
T Consensus 21 ml~~~CP~Cg~pLf~l------k~g--~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 21 MLSKHCPVCGLPLFEL------KDG--EVVCPVHGKVYIVKS 54 (112)
T ss_pred HccCCCCCCCCcceec------CCC--ceECCCCCCeeeecc
Confidence 4789999999876653 234 367999999766655
No 75
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=38.59 E-value=36 Score=24.16 Aligned_cols=35 Identities=17% Similarity=0.415 Sum_probs=24.9
Q ss_pred ceEEEEEcccCCCccccccCcccccCccEEEEcCCCCcccee
Q 028299 123 RMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKL 164 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLI 164 (211)
..++.|.|-.|+..-. -....--|+||-|..+=|+
T Consensus 2 ~~~~~Y~C~~Cg~~~~-------~~~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 2 EAMMEYKCARCGREVE-------LDQETRGIRCPYCGSRILV 36 (49)
T ss_pred cceEEEEhhhcCCeee-------hhhccCceeCCCCCcEEEE
Confidence 3578999999998761 1223445899999977655
No 76
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=38.42 E-value=24 Score=26.43 Aligned_cols=34 Identities=24% Similarity=0.509 Sum_probs=23.3
Q ss_pred EEEcccCCCcccccc---CcccccCccEEEEcCCCCc
Q 028299 127 AFTCNVCGQRTTRAI---NPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 127 ~FTC~~C~tRS~k~i---SK~AY~~GvViVqC~GC~n 160 (211)
...|.+||++-+.-+ .|.|=+-=++|-.|..|..
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~ 98 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGY 98 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCC
Confidence 357888887776544 4555566678888888864
No 77
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=37.63 E-value=23 Score=27.01 Aligned_cols=20 Identities=20% Similarity=0.629 Sum_probs=15.6
Q ss_pred cceEEEEEcccCCCcccccc
Q 028299 122 RRMRVAFTCNVCGQRTTRAI 141 (211)
Q Consensus 122 r~~~l~FTC~~C~tRS~k~i 141 (211)
.+..|.|+|.+|+....+.+
T Consensus 48 KKi~Lrl~C~~C~~~~~~~~ 67 (77)
T PF00935_consen 48 KKIVLRLECTECGKAHMRPG 67 (77)
T ss_dssp EBBEEEEEETTTS-EEEEE-
T ss_pred ccEEEEEEeCCCCccccccc
Confidence 47999999999998877665
No 78
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=37.47 E-value=24 Score=30.45 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=16.8
Q ss_pred cceEEEEEcccCCCcccccc
Q 028299 122 RRMRVAFTCNVCGQRTTRAI 141 (211)
Q Consensus 122 r~~~l~FTC~~C~tRS~k~i 141 (211)
.-+.+.|.|..||.|+.-..
T Consensus 25 evii~sf~C~~CGyr~~ev~ 44 (192)
T TIGR00310 25 EVLETSTICEHCGYRSNDVK 44 (192)
T ss_pred eEEEEEEECCCCCCccceeE
Confidence 46889999999999987543
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=37.41 E-value=27 Score=22.76 Aligned_cols=32 Identities=25% Similarity=0.616 Sum_probs=18.3
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeeec
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDN 167 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADN 167 (211)
|+|..|+.+.. +. -+..|-+ -|+.|. .+|.|+
T Consensus 1 m~Cp~Cg~~~~--~~--D~~~g~~--vC~~CG--~Vl~e~ 32 (43)
T PF08271_consen 1 MKCPNCGSKEI--VF--DPERGEL--VCPNCG--LVLEEN 32 (43)
T ss_dssp ESBTTTSSSEE--EE--ETTTTEE--EETTT---BBEE-T
T ss_pred CCCcCCcCCce--EE--cCCCCeE--ECCCCC--CEeecc
Confidence 67888988662 11 1555655 688884 344444
No 80
>KOG1507 consensus Nucleosome assembly protein NAP-1 [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=37.34 E-value=54 Score=31.48 Aligned_cols=59 Identities=14% Similarity=0.180 Sum_probs=39.0
Q ss_pred CCCcceEEEEEcccCC-------CccccccCccccc-----CccEEEEcCCCCccceeeecccccccCCCCcchhhhcC
Q 028299 119 SPRRRMRVAFTCNVCG-------QRTTRAINPHAYT-----DGTVFVQCCGCNVFHKLVDNLNLFHEMKCYVNPSFNYR 185 (211)
Q Consensus 119 ~prr~~~l~FTC~~C~-------tRS~k~iSK~AY~-----~GvViVqC~GC~n~HLIADNLgwF~e~~~tIEdi~k~K 185 (211)
.|+..|.|.|-=..=. |.+-++.++-.|. .|-.|.+|-||. ..|....+.|+--+.+.|
T Consensus 199 ~~~~~fklEFhFd~N~YFtN~vLTKTY~l~~~~D~~~P~~~~G~~i~~~~Gc~--------IdW~~gknlT~kti~kKq 269 (358)
T KOG1507|consen 199 DGQVGFKLEFHFDPNPYFTNEVLTKTYFLKSEPDEDDPFAFDGPEIEKCEGCE--------IDWKPGKNLTVKTIKKKQ 269 (358)
T ss_pred CCccceEEEEEcCCCccccccceeeeeeeeccCCCcCCcccCCceEEeeecCe--------eeccCCCccchhhhhhhc
Confidence 4556788887665422 2233333222221 378999999994 679999999998888874
No 81
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=37.16 E-value=17 Score=29.86 Aligned_cols=33 Identities=21% Similarity=0.410 Sum_probs=20.4
Q ss_pred EEEEcCCCCccceeeec--ccccccCCCCcchhhh
Q 028299 151 VFVQCCGCNVFHKLVDN--LNLFHEMKCYVNPSFN 183 (211)
Q Consensus 151 ViVqC~GC~n~HLIADN--LgwF~e~~~tIEdi~k 183 (211)
|.|+||+|...+++--. .-.|=....++++-++
T Consensus 68 v~V~CP~C~K~TKmLGr~D~CM~C~~pLTLd~~le 102 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRVDACMHCKEPLTLDPSLE 102 (114)
T ss_pred eeeECCCCCChHhhhchhhccCcCCCcCccCchhh
Confidence 88999999998865322 2223345555555443
No 82
>KOG4846 consensus Nuclear receptor [Signal transduction mechanisms]
Probab=36.92 E-value=78 Score=31.69 Aligned_cols=50 Identities=26% Similarity=0.519 Sum_probs=31.6
Q ss_pred CCCCCCCCCCCCCCCCCCcccccccccccccCCCcceEEEEEcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 88 SGMEGPSVPAGAEEGSSTEKVSTFPWSLFTKSPRRRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 88 S~~eGP~~~a~~~~~s~~~~~s~~P~s~~~k~prr~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
+.|||-+--+.+++-|++-++ .. +.--|++||-.. ..||.||- -|.||+-
T Consensus 108 ~A~e~Ssslsp~~s~Sn~t~~-------------~~--~~~lCkVCgDkA------SGfHYGV~--aCEGCKG 157 (538)
T KOG4846|consen 108 SATEVSSSLSPPDSLSNTTQI-------------GK--AISLCKVCGDKA------SGFHYGVT--ACEGCKG 157 (538)
T ss_pred hhhccccccCCcccccchhcc-------------cc--eeEeehhhcccc------ccceecee--ecccchH
Confidence 456666655555554543332 12 233599999865 47999974 6999984
No 83
>PHA02942 putative transposase; Provisional
Probab=36.89 E-value=26 Score=32.64 Aligned_cols=27 Identities=22% Similarity=0.689 Sum_probs=18.4
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccc
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H 162 (211)
=||..||+... ..+. =...|+.|...|
T Consensus 326 q~Cs~CG~~~~-~l~~-------r~f~C~~CG~~~ 352 (383)
T PHA02942 326 VSCPKCGHKMV-EIAH-------RYFHCPSCGYEN 352 (383)
T ss_pred ccCCCCCCccC-cCCC-------CEEECCCCCCEe
Confidence 47999998763 2221 157899998765
No 84
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=36.40 E-value=25 Score=28.13 Aligned_cols=19 Identities=21% Similarity=0.754 Sum_probs=16.1
Q ss_pred CcceEEEEEcccCCCcccc
Q 028299 121 RRRMRVAFTCNVCGQRTTR 139 (211)
Q Consensus 121 rr~~~l~FTC~~C~tRS~k 139 (211)
-.++.|.|+|.+|+...++
T Consensus 62 tKKv~Lr~~Ct~Cgkah~~ 80 (94)
T COG1631 62 TKKVDLRLRCTECGKAHQR 80 (94)
T ss_pred cceEEEEEEehhhcccccc
Confidence 4589999999999987665
No 85
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=36.39 E-value=18 Score=31.17 Aligned_cols=32 Identities=25% Similarity=0.471 Sum_probs=23.3
Q ss_pred EcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
-||-|+|-=+-.+--.. ---+|-|||..|.|.
T Consensus 14 hCnFC~TiLaVsVP~ss-L~~~VTVRCGHCtNL 45 (170)
T PF04690_consen 14 HCNFCNTILAVSVPCSS-LLKTVTVRCGHCTNL 45 (170)
T ss_pred EcCCcCeEEEEecchhh-hhhhhceeccCccce
Confidence 69999997664443222 336899999999985
No 86
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=36.38 E-value=29 Score=26.25 Aligned_cols=17 Identities=18% Similarity=0.344 Sum_probs=9.1
Q ss_pred cEEEEcCCCCccceeee
Q 028299 150 TVFVQCCGCNVFHKLVD 166 (211)
Q Consensus 150 vViVqC~GC~n~HLIAD 166 (211)
-+-|+|++|.|.-.+=+
T Consensus 17 Fl~VkCpdC~N~q~vFs 33 (67)
T COG2051 17 FLRVKCPDCGNEQVVFS 33 (67)
T ss_pred EEEEECCCCCCEEEEec
Confidence 34556666665555433
No 87
>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=36.37 E-value=18 Score=20.01 Aligned_cols=10 Identities=30% Similarity=1.202 Sum_probs=7.5
Q ss_pred EEcccCCCcc
Q 028299 128 FTCNVCGQRT 137 (211)
Q Consensus 128 FTC~~C~tRS 137 (211)
|+|..|+..-
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 7888888653
No 88
>PF07028 DUF1319: Protein of unknown function (DUF1319); InterPro: IPR010746 This entry is represented by Commelina yellow mottle virus, Orf1. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains a number of viral proteins of unknown function approximately 200 residues long. Family members seem to be restricted to badnaviruses.
Probab=36.35 E-value=21 Score=29.68 Aligned_cols=22 Identities=23% Similarity=0.376 Sum_probs=19.4
Q ss_pred cccCCCCChHHHhhhhhhhhcc
Q 028299 60 LFGNQTLSKDEAMGLVLSAASV 81 (211)
Q Consensus 60 ~~~~~~ls~~~~~~lvlsaa~~ 81 (211)
|+.++|||+++...||+.++.-
T Consensus 83 ~l~rRPLtk~dVeeLV~~IseQ 104 (126)
T PF07028_consen 83 YLERRPLTKEDVEELVLRISEQ 104 (126)
T ss_pred HHHcCCCCHHHHHHHHHHHHhC
Confidence 6889999999999999988743
No 89
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.06 E-value=26 Score=29.05 Aligned_cols=22 Identities=32% Similarity=0.940 Sum_probs=15.2
Q ss_pred EcccCCCccccccCcccccCccEEEEcCCCCccc
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H 162 (211)
||..||. ++ .=...|+.|...|
T Consensus 311 ~C~~cg~-----~~-------~r~~~C~~cg~~~ 332 (364)
T COG0675 311 TCPCCGH-----LS-------GRLFKCPRCGFVH 332 (364)
T ss_pred cccccCC-----cc-------ceeEECCCCCCee
Confidence 6999999 22 1135799998754
No 90
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=35.54 E-value=22 Score=31.79 Aligned_cols=49 Identities=16% Similarity=0.270 Sum_probs=32.3
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccCCC
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEMKC 176 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~~~ 176 (211)
..+.|..|+......- ...+....-+-+|+.|... +|-=+.=||+|.--
T Consensus 121 ~~~~C~~C~~~~~~~~-~~~~~~~~~~p~C~~Cg~~-~lrP~VV~fGE~lp 169 (250)
T COG0846 121 KRVRCSKCGNQYYDED-VIKFIEDGLIPRCPKCGGP-VLRPDVVWFGEPLP 169 (250)
T ss_pred eeeEeCCCcCccchhh-hhhhcccCCCCcCccCCCc-cccCCEEEeCCCCC
Confidence 4577999986654211 1222333378899999997 66667779988643
No 91
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=35.13 E-value=21 Score=18.95 Aligned_cols=11 Identities=36% Similarity=1.141 Sum_probs=6.5
Q ss_pred EEcccCCCccc
Q 028299 128 FTCNVCGQRTT 138 (211)
Q Consensus 128 FTC~~C~tRS~ 138 (211)
|.|..|+.+..
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 78999987543
No 92
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=34.48 E-value=30 Score=24.93 Aligned_cols=17 Identities=24% Similarity=0.604 Sum_probs=10.6
Q ss_pred EEEEcCCCCccceeeec
Q 028299 151 VFVQCCGCNVFHKLVDN 167 (211)
Q Consensus 151 ViVqC~GC~n~HLIADN 167 (211)
+-|+|++|.|.-.|=+|
T Consensus 6 m~VkCp~C~~~q~vFSh 22 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSH 22 (55)
T ss_dssp EEEE-TTT-SEEEEETT
T ss_pred EEEECCCCCCeeEEEec
Confidence 56788888887776554
No 93
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=32.66 E-value=34 Score=23.66 Aligned_cols=26 Identities=27% Similarity=0.672 Sum_probs=15.5
Q ss_pred EcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
||..||.+..+..+.. ...|+.|...
T Consensus 30 ~C~~CG~~~~~~~~~r-------~~~C~~Cg~~ 55 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGR-------VFTCPNCGFE 55 (69)
T ss_pred CccCcccccccccccc-------eEEcCCCCCE
Confidence 6778888777622222 3467777653
No 94
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=32.48 E-value=39 Score=24.86 Aligned_cols=17 Identities=18% Similarity=0.409 Sum_probs=9.2
Q ss_pred EEEEcCCCCccceeeec
Q 028299 151 VFVQCCGCNVFHKLVDN 167 (211)
Q Consensus 151 ViVqC~GC~n~HLIADN 167 (211)
+-|+|++|.|.-.|=+|
T Consensus 10 ~~VkCp~C~n~q~vFsh 26 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSH 26 (59)
T ss_pred EEEECCCCCCeEEEEec
Confidence 34566666665555444
No 95
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=32.21 E-value=30 Score=32.59 Aligned_cols=43 Identities=21% Similarity=0.413 Sum_probs=20.2
Q ss_pred EEEEEcccCCCcccccc-----Cccccc--Ccc-EEEEcCCCCccceeeec
Q 028299 125 RVAFTCNVCGQRTTRAI-----NPHAYT--DGT-VFVQCCGCNVFHKLVDN 167 (211)
Q Consensus 125 ~l~FTC~~C~tRS~k~i-----SK~AY~--~Gv-ViVqC~GC~n~HLIADN 167 (211)
.=+|+|..|.....+.- .+|.|+ +++ =|.+|.+|+++-.--|.
T Consensus 250 ~kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~sl~r 300 (344)
T PF09332_consen 250 CKAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTISLER 300 (344)
T ss_dssp EEEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEESSS
T ss_pred EEEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeeeccc
Confidence 45799999975443322 233333 222 26799999998554443
No 96
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=31.89 E-value=23 Score=19.93 Aligned_cols=9 Identities=33% Similarity=1.298 Sum_probs=7.2
Q ss_pred EEcccCCCc
Q 028299 128 FTCNVCGQR 136 (211)
Q Consensus 128 FTC~~C~tR 136 (211)
|+|.+|+..
T Consensus 1 ~~C~~C~~~ 9 (25)
T PF12874_consen 1 FYCDICNKS 9 (25)
T ss_dssp EEETTTTEE
T ss_pred CCCCCCCCC
Confidence 789999754
No 97
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=31.88 E-value=39 Score=25.23 Aligned_cols=20 Identities=15% Similarity=0.366 Sum_probs=15.9
Q ss_pred cCCCcceEEEEEcccCCCcc
Q 028299 118 KSPRRRMRVAFTCNVCGQRT 137 (211)
Q Consensus 118 k~prr~~~l~FTC~~C~tRS 137 (211)
.+....|.+-|+|..|+++-
T Consensus 81 RsadE~~T~fy~C~~C~~~w 100 (104)
T TIGR01384 81 RRADEPETRFYKCTKCGYVW 100 (104)
T ss_pred CCCCCCcEEEEEeCCCCCee
Confidence 44456799999999999863
No 98
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=31.47 E-value=18 Score=28.24 Aligned_cols=28 Identities=29% Similarity=0.860 Sum_probs=21.7
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccce
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHK 163 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HL 163 (211)
--|.+|+.. -..||.|+. .|.+|...+-
T Consensus 19 ~~C~VCg~~------a~g~hyGv~--sC~aCk~FFR 46 (101)
T cd07160 19 EVCSVCGDK------ASGFHYNVL--SCEGCKGFFR 46 (101)
T ss_pred CCCeecCCc------CcceEECcc--eehhhhhhhh
Confidence 359999963 357999985 7999998764
No 99
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=30.80 E-value=17 Score=33.04 Aligned_cols=31 Identities=26% Similarity=0.562 Sum_probs=27.7
Q ss_pred EcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
.|-.||.|-.+.+.+.+ +..+=+.|||.|+.
T Consensus 2 vCIeCg~~vdsLyt~ys-ts~iqls~Cp~C~~ 32 (239)
T COG5254 2 VCIECGSRVDSLYTRYS-TSAIQLSRCPSCNR 32 (239)
T ss_pred eeeEcCCccceeeeecc-CcceehhcCchHHH
Confidence 58899999999998888 78889999999986
No 100
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=29.95 E-value=16 Score=31.57 Aligned_cols=44 Identities=14% Similarity=0.265 Sum_probs=27.4
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccC
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEM 174 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~ 174 (211)
..|..|+.+-....-+.....+ .+-+|+.|. .++-+|.=||+|.
T Consensus 117 ~~C~~C~~~~~~~~~~~~~~~~-~~p~C~~Cg--g~lrP~Vv~FGE~ 160 (235)
T cd01408 117 AHCIKCKHKYPGDWMREDIFNQ-EVPKCPRCG--GLVKPDIVFFGES 160 (235)
T ss_pred cccccCCCcCCHHHHHHHHhCC-CCccCCCCC--CCccCcEEECCCC
Confidence 4698999854321100111112 146899997 6699999999984
No 101
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=29.42 E-value=42 Score=27.74 Aligned_cols=38 Identities=24% Similarity=0.412 Sum_probs=28.4
Q ss_pred eEEEEEcccCCCccc--c-ccCcccccCccEEEEcCCCCcc
Q 028299 124 MRVAFTCNVCGQRTT--R-AINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 124 ~~l~FTC~~C~tRS~--k-~iSK~AY~~GvViVqC~GC~n~ 161 (211)
-.|.-.|.+||+--. + +=.|.|=+--+||-.|+.|+-+
T Consensus 71 a~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k 111 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYK 111 (116)
T ss_pred cchhccCcccCCchhhhhhhhcccccCCceEEEEcCcccee
Confidence 345567999998644 2 3356777888999999999864
No 102
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=28.95 E-value=24 Score=29.71 Aligned_cols=44 Identities=20% Similarity=0.397 Sum_probs=27.9
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccC
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEM 174 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~ 174 (211)
..|..|+.+....--...+.... +-+|+.|. ..+-.|.=||+|.
T Consensus 110 ~~C~~C~~~~~~~~~~~~~~~~~-~p~C~~Cg--~~lrP~Vv~fgE~ 153 (218)
T cd01407 110 VRCTKCGKEYPRDELQADIDREE-VPRCPKCG--GLLRPDVVFFGES 153 (218)
T ss_pred ceeCCCcCCCcHHHHhHhhccCC-CCcCCCCC--CccCCCeEECCCC
Confidence 45989987644321001122332 56899997 5688888899885
No 103
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=28.82 E-value=20 Score=34.84 Aligned_cols=35 Identities=23% Similarity=0.469 Sum_probs=19.5
Q ss_pred EEEcccCCCccccccC---cccccCccEEEEcCCCCcccee
Q 028299 127 AFTCNVCGQRTTRAIN---PHAYTDGTVFVQCCGCNVFHKL 164 (211)
Q Consensus 127 ~FTC~~C~tRS~k~iS---K~AY~~GvViVqC~GC~n~HLI 164 (211)
-|.|++|++|..+..= +.+...|+ .-|-|.-+||-
T Consensus 367 g~rC~kCg~~~~~~~~~~v~r~l~~g~---evp~~arRHLs 404 (421)
T COG1571 367 GFRCKKCGTRARETLIKEVPRDLEPGV---EVPPVARRHLS 404 (421)
T ss_pred CcccccccccCCcccccccccccCCCC---cCCchhhhhcc
Confidence 5777777776553222 23344454 45666667763
No 104
>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=28.80 E-value=28 Score=19.94 Aligned_cols=9 Identities=44% Similarity=1.409 Sum_probs=7.3
Q ss_pred EEcccCCCc
Q 028299 128 FTCNVCGQR 136 (211)
Q Consensus 128 FTC~~C~tR 136 (211)
|+|..|+..
T Consensus 2 ~~C~~C~~~ 10 (27)
T PF13912_consen 2 FECDECGKT 10 (27)
T ss_dssp EEETTTTEE
T ss_pred CCCCccCCc
Confidence 789999864
No 105
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=28.43 E-value=24 Score=30.74 Aligned_cols=44 Identities=23% Similarity=0.424 Sum_probs=28.1
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccC
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEM 174 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~ 174 (211)
..|..|+.+-...--......+. +-+|+.|.. .+-.|.=||+|.
T Consensus 120 ~~C~~C~~~~~~~~~~~~~~~~~-~p~Cp~Cgg--~lrP~Vv~FgE~ 163 (244)
T PRK14138 120 YYCVRCGKRYTVEDVIEKLEKSD-VPRCDDCSG--LIRPNIVFFGEA 163 (244)
T ss_pred eEECCCCCcccHHHHHHHHhcCC-CCCCCCCCC--eECCCEEECCCc
Confidence 55989997644211111222232 478999974 788999999984
No 106
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=28.41 E-value=36 Score=27.38 Aligned_cols=40 Identities=23% Similarity=0.272 Sum_probs=24.6
Q ss_pred EEEEEcccCCCccccccCccccc--CccEEEEcCCCCccceeeec
Q 028299 125 RVAFTCNVCGQRTTRAINPHAYT--DGTVFVQCCGCNVFHKLVDN 167 (211)
Q Consensus 125 ~l~FTC~~C~tRS~k~iSK~AY~--~GvViVqC~GC~n~HLIADN 167 (211)
...|.|..|+.+-.- . .|.. +-..-.+||.|...=...||
T Consensus 97 ~~~Y~Cp~C~~~y~~--~-ea~~~~d~~~~f~Cp~Cg~~l~~~dn 138 (147)
T smart00531 97 NAYYKCPNCQSKYTF--L-EANQLLDMDGTFTCPRCGEELEEDDN 138 (147)
T ss_pred CcEEECcCCCCEeeH--H-HHHHhcCCCCcEECCCCCCEEEEcCc
Confidence 458999999866541 1 1211 11333889999887666665
No 107
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=28.36 E-value=38 Score=22.99 Aligned_cols=35 Identities=23% Similarity=0.481 Sum_probs=23.3
Q ss_pred CCcceEEEEEcccCCCccccccCcccccCccEEEEcCCC
Q 028299 120 PRRRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGC 158 (211)
Q Consensus 120 prr~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC 158 (211)
+.....+.+.|..|++.=...|+... .--..||-|
T Consensus 21 ~~s~~~v~W~C~~Cgh~w~~~v~~R~----~~~~~CP~C 55 (55)
T PF14311_consen 21 PGSNKKVWWKCPKCGHEWKASVNDRT----RRGKGCPYC 55 (55)
T ss_pred cCCCCEEEEECCCCCCeeEccHhhhc----cCCCCCCCC
Confidence 34578899999999987666666543 122346665
No 108
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=28.02 E-value=34 Score=27.50 Aligned_cols=38 Identities=18% Similarity=0.452 Sum_probs=25.9
Q ss_pred EEEcccCCCcccc-ccCcccccCccEEEEcCCCCccceeeecccccccCCCCcch
Q 028299 127 AFTCNVCGQRTTR-AINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEMKCYVNP 180 (211)
Q Consensus 127 ~FTC~~C~tRS~k-~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~~~tIEd 180 (211)
-=.|+.||.--.. .|++- -+||.|+. .|..+.++.|+.
T Consensus 58 Pa~CkkCGfef~~~~ik~p--------SRCP~CKS--------E~Ie~prF~ie~ 96 (97)
T COG3357 58 PARCKKCGFEFRDDKIKKP--------SRCPKCKS--------EWIEEPRFVIES 96 (97)
T ss_pred ChhhcccCccccccccCCc--------ccCCcchh--------hcccCCceeecc
Confidence 3479999974433 44433 48999986 577777777764
No 109
>PF03330 DPBB_1: Rare lipoprotein A (RlpA)-like double-psi beta-barrel; InterPro: IPR009009 Beta barrels are commonly observed in protein structures. They are classified in terms of two integral parameters: the number of strands in the sheet, n, and the shear number, S, a measure of the stagger of the strands in the beta-sheet. These two parameters have been shown to determine the major geometrical features of beta-barrels. Six-stranded beta-barrels with a pseudo-twofold axis are found in several proteins. One involving parallel strands forming two psi structures is known as the double-psi barrel. The first psi structure consists of the loop connecting strands beta1 and beta2 (a 'psi loop') and the strand beta5, whereas the second psi structure consists of the loop connecting strands beta4 and beta5 and the strand beta2. All the psi structures in double-psi barrels have a unique handedness, in that beta1 (beta4), beta2 (beta5) and the loop following beta5 (beta2) form a right-handed helix. The unique handedness may be related to the fact that the twisting angle between the parallel pair of strands is always larger than that between the antiparallel pair [].; PDB: 1N10_B 3D30_A 2BH0_A 2HCZ_X.
Probab=27.72 E-value=46 Score=23.63 Aligned_cols=14 Identities=43% Similarity=0.695 Sum_probs=10.4
Q ss_pred cEEEEcCCCCccce
Q 028299 150 TVFVQCCGCNVFHK 163 (211)
Q Consensus 150 vViVqC~GC~n~HL 163 (211)
+|.=+||+|...||
T Consensus 43 ~V~D~Cp~~~~~~l 56 (78)
T PF03330_consen 43 TVVDRCPGCPPNHL 56 (78)
T ss_dssp EEEEE-TTSSSSEE
T ss_pred EEEccCCCCcCCEE
Confidence 45558999999997
No 110
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=27.21 E-value=33 Score=29.41 Aligned_cols=40 Identities=30% Similarity=0.504 Sum_probs=25.4
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccC
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEM 174 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~ 174 (211)
..|..|+.+-.. ..+... -+.+|+.|. +.+-.|.=||+|.
T Consensus 123 ~~C~~C~~~~~~----~~~~~~-~~p~C~~Cg--g~lrP~Vv~fge~ 162 (242)
T PRK00481 123 ARCTKCGQTYDL----DEYLKP-EPPRCPKCG--GILRPDVVLFGEM 162 (242)
T ss_pred eeeCCCCCCcCh----hhhccC-CCCCCCCCC--CccCCCeEECCCC
Confidence 569999765321 111111 145699996 7788888899875
No 111
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.11 E-value=43 Score=36.94 Aligned_cols=33 Identities=24% Similarity=0.481 Sum_probs=19.0
Q ss_pred EEEcccCCCccccccCcc-cccCccEEEEcCCCCc
Q 028299 127 AFTCNVCGQRTTRAINPH-AYTDGTVFVQCCGCNV 160 (211)
Q Consensus 127 ~FTC~~C~tRS~k~iSK~-AY~~GvViVqC~GC~n 160 (211)
.|.|..||+.+...+-+. ..+.-.+ ..|+.|..
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~te~v-y~CPsCGa 700 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHTEPV-YVCPDCGA 700 (1337)
T ss_pred EEECCCCCCccccccCcccCCcCCCc-eeCccCCC
Confidence 488999998766555552 2222222 25666655
No 112
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=26.87 E-value=16 Score=24.69 Aligned_cols=31 Identities=29% Similarity=0.575 Sum_probs=21.0
Q ss_pred EEEcccCCCccc-------cccCcccccCccEEEEcCCCCc
Q 028299 127 AFTCNVCGQRTT-------RAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 127 ~FTC~~C~tRS~-------k~iSK~AY~~GvViVqC~GC~n 160 (211)
.|+|..|+. .. |-..+|.+... -|.||=|..
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~--~v~CPiC~~ 39 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESK--NVVCPICSS 39 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCC--CccCCCchh
Confidence 489999998 42 22345555544 478999986
No 113
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=26.77 E-value=22 Score=30.11 Aligned_cols=45 Identities=24% Similarity=0.349 Sum_probs=27.0
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccC
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEM 174 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~ 174 (211)
..|..|+++-...--.......-.+.+|+.|. .++-.+.=||+|.
T Consensus 96 ~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cg--g~lrP~VV~FgE~ 140 (206)
T cd01410 96 EVCKSCGPEYVRDDVVETRGDKETGRRCHACG--GILKDTIVDFGER 140 (206)
T ss_pred ccCCCCCCccchHHHHHHhhcCCCCCcCCCCc--CccCCcEEECCCC
Confidence 45999997643211000111111246799997 5689999999984
No 114
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=26.56 E-value=36 Score=32.51 Aligned_cols=15 Identities=20% Similarity=0.408 Sum_probs=9.1
Q ss_pred cceEEEEEcccCCCc
Q 028299 122 RRMRVAFTCNVCGQR 136 (211)
Q Consensus 122 r~~~l~FTC~~C~tR 136 (211)
..++++=||..|+.+
T Consensus 178 g~~~~~~~C~~C~G~ 192 (371)
T COG0484 178 GFFSFQQTCPTCNGT 192 (371)
T ss_pred eEEEEEEECCCCccc
Confidence 345666666666654
No 115
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=26.51 E-value=43 Score=22.17 Aligned_cols=10 Identities=40% Similarity=1.125 Sum_probs=5.6
Q ss_pred EEcccCCCcc
Q 028299 128 FTCNVCGQRT 137 (211)
Q Consensus 128 FTC~~C~tRS 137 (211)
|+|..|+...
T Consensus 19 ~~CP~Cg~~~ 28 (46)
T PF12760_consen 19 FVCPHCGSTK 28 (46)
T ss_pred CCCCCCCCee
Confidence 4566666553
No 116
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=26.33 E-value=23 Score=27.45 Aligned_cols=26 Identities=38% Similarity=0.929 Sum_probs=19.9
Q ss_pred cccCCCccccccCcccccCccEEEEcCCCCccce
Q 028299 130 CNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHK 163 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HL 163 (211)
|.+|+..+ ..||.||+ .|.+|+..+-
T Consensus 7 C~VCg~~a------~g~hyGv~--sC~aCk~FFR 32 (97)
T cd07170 7 CLVCGDIA------SGYHYGVA--SCEACKAFFK 32 (97)
T ss_pred CeecCCcC------cceEECce--eehhhhHHHH
Confidence 99998644 47888874 7999988663
No 117
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=26.33 E-value=46 Score=28.58 Aligned_cols=40 Identities=23% Similarity=0.348 Sum_probs=23.5
Q ss_pred EEEcccCCCcccc--ccCcc-----------cccCcc-----EEEEcCCCCccceeee
Q 028299 127 AFTCNVCGQRTTR--AINPH-----------AYTDGT-----VFVQCCGCNVFHKLVD 166 (211)
Q Consensus 127 ~FTC~~C~tRS~k--~iSK~-----------AY~~Gv-----ViVqC~GC~n~HLIAD 166 (211)
.+||.+|++.-.. ..|.. .+.+|| +++.||.|.---.-.|
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~ 62 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEED 62 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccc
Confidence 4799999984332 12211 122332 6788999986655444
No 118
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=26.32 E-value=51 Score=25.92 Aligned_cols=31 Identities=32% Similarity=0.746 Sum_probs=24.4
Q ss_pred ceEEEEEcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 123 RMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
++.-.|+|..|+....+. .++=|-+|..|..
T Consensus 32 ~q~a~y~CpfCgk~~vkR-------~a~GIW~C~~C~~ 62 (90)
T PRK03976 32 KMRAKHVCPVCGRPKVKR-------VGTGIWECRKCGA 62 (90)
T ss_pred HHhcCccCCCCCCCceEE-------EEEEEEEcCCCCC
Confidence 455679999998777664 3688999999975
No 119
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=25.61 E-value=51 Score=28.00 Aligned_cols=34 Identities=24% Similarity=0.606 Sum_probs=29.5
Q ss_pred EcccCCCccccccCcccccCccEEE---EcCCCCccc
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVFV---QCCGCNVFH 162 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvViV---qC~GC~n~H 162 (211)
.|..|++-.++-|.-..-+.|..|- .|..|..+.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 4999999999999888889999994 599998875
No 120
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=25.48 E-value=75 Score=21.59 Aligned_cols=32 Identities=19% Similarity=0.439 Sum_probs=15.0
Q ss_pred cccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 130 CNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
|..||...........-..+.-++.|..|...
T Consensus 4 CPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 4 CPFCGGADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence 66666644433222222223333467777654
No 121
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=25.41 E-value=41 Score=34.65 Aligned_cols=21 Identities=14% Similarity=0.150 Sum_probs=14.3
Q ss_pred ccEEEEcCCCCccceeeeccc
Q 028299 149 GTVFVQCCGCNVFHKLVDNLN 169 (211)
Q Consensus 149 GvViVqC~GC~n~HLIADNLg 169 (211)
.-+--+||.|...||.+==.|
T Consensus 472 ~~~p~~Cp~Cgs~~L~~~G~G 492 (730)
T COG1198 472 EPIPQSCPECGSEHLRAVGPG 492 (730)
T ss_pred CCCCCCCCCCCCCeeEEeccc
Confidence 345567888888888765444
No 122
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=25.37 E-value=52 Score=21.51 Aligned_cols=32 Identities=22% Similarity=0.508 Sum_probs=19.5
Q ss_pred EcccCCCccccccCcccccCccEEEEcCC---CCccceee
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVFVQCCG---CNVFHKLV 165 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvViVqC~G---C~n~HLIA 165 (211)
.|.+|+..-...-+|.. .|+-|.+ |+...-|-
T Consensus 3 ~CP~Cg~~lv~r~~k~g-----~F~~Cs~yP~C~~~~~~~ 37 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGKKG-----KFLGCSNYPECKYTEPLP 37 (39)
T ss_pred CCCCCCceeEEEECCCC-----CEEECCCCCCcCCeEeCC
Confidence 58888854444444433 7788876 77655443
No 123
>PF12322 T4_baseplate: T4 bacteriophage base plate protein; InterPro: IPR024364 Proteins in this family are found in T4-like viruses. They have a single completely conserved residue S that may be functionally important. The family includes the two base plate proteins from bacteriophage T4: Gp51 and Gp26, encoded by late genes []. Gp26 is a structural component of central hub of the baseplate. It associates with Gp25 (tail lysozyme) in the assembly process. Gp51 is essential for the formation of the central hub of the phage baseplate, playing a catalytic role for the central hub formation. It may be also a structural component of the hub.
Probab=25.16 E-value=40 Score=29.22 Aligned_cols=22 Identities=32% Similarity=0.702 Sum_probs=17.0
Q ss_pred ceEEEEEcccCCCccccccCcc
Q 028299 123 RMRVAFTCNVCGQRTTRAINPH 144 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~ 144 (211)
.+.+.|||..||++..-.|+-.
T Consensus 74 ~v~~~~~C~~cg~~~~~~i~l~ 95 (205)
T PF12322_consen 74 KVPVNYTCPDCGEEVKVPINLD 95 (205)
T ss_pred cceEEEECCCCCcEEEEEecch
Confidence 4899999999999666665543
No 124
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=25.05 E-value=53 Score=25.87 Aligned_cols=43 Identities=19% Similarity=0.458 Sum_probs=26.6
Q ss_pred eEEEEEcccCCCccccccCccc-------------cc--CccE---EEEcCCCCc-cceeee
Q 028299 124 MRVAFTCNVCGQRTTRAINPHA-------------YT--DGTV---FVQCCGCNV-FHKLVD 166 (211)
Q Consensus 124 ~~l~FTC~~C~tRS~k~iSK~A-------------Y~--~GvV---iVqC~GC~n-~HLIAD 166 (211)
....-.|.+|++.-...+++.. |. ++.+ -++||.|.. .+++..
T Consensus 14 ~~~~~~Cp~Cg~~m~~~~~~~g~f~gCs~yP~C~~~~~~~~~~~~~~~~Cp~C~~~~~~~k~ 75 (140)
T COG0551 14 LKTGQICPKCGKNMVKKFGKYGIFLGCSNYPKCDYYEPEKAIAEKTGVKCPKCGKGLLVLKK 75 (140)
T ss_pred cccCccCCcCCCeeEEEEccCCeEEEeCCCCCCCCCcccccccccCceeCCCCCCCceEEEe
Confidence 3445678888887777666622 22 4455 389999995 444444
No 125
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.79 E-value=81 Score=20.51 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=16.2
Q ss_pred cccCCCccccccCcccccCccEEEEcCCCCcccee
Q 028299 130 CNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKL 164 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLI 164 (211)
|..||..-...- ... .-...|+.|...|-|
T Consensus 3 Cp~Cg~~l~~~~----~~~-~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 3 CPKCGNMLIPKE----GKE-KRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCcccccc----CCC-CCEEECCcCCCeEEC
Confidence 777877332221 111 125569999866544
No 126
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=24.77 E-value=36 Score=20.11 Aligned_cols=9 Identities=33% Similarity=1.261 Sum_probs=7.8
Q ss_pred EEcccCCCc
Q 028299 128 FTCNVCGQR 136 (211)
Q Consensus 128 FTC~~C~tR 136 (211)
|.|..|+.+
T Consensus 15 ~~C~~C~k~ 23 (26)
T PF13465_consen 15 YKCPYCGKS 23 (26)
T ss_dssp EEESSSSEE
T ss_pred CCCCCCcCe
Confidence 899999865
No 127
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=24.64 E-value=28 Score=26.36 Aligned_cols=26 Identities=31% Similarity=0.907 Sum_probs=20.3
Q ss_pred cccCCCccccccCcccccCccEEEEcCCCCccce
Q 028299 130 CNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHK 163 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HL 163 (211)
|.+|+..+ ..||.|+ +.|.+|+..+-
T Consensus 9 C~VCg~~~------~g~hyGv--~sC~aCk~FFR 34 (90)
T cd07168 9 CSICEDKA------TGLHYGI--ITCEGCKGFFK 34 (90)
T ss_pred CcccCCcC------cceEECc--eehhhhhHhhh
Confidence 99998643 4789997 47999998763
No 128
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=24.62 E-value=58 Score=25.71 Aligned_cols=32 Identities=22% Similarity=0.632 Sum_probs=24.4
Q ss_pred ceEEEEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 123 RMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
++.-.|+|..|+....+. .++=|-+|..|...
T Consensus 31 ~q~a~y~CpfCgk~~vkR-------~a~GIW~C~~C~~~ 62 (91)
T TIGR00280 31 QQKAKYVCPFCGKKTVKR-------GSTGIWTCRKCGAK 62 (91)
T ss_pred HHhcCccCCCCCCCceEE-------EeeEEEEcCCCCCE
Confidence 455679999999766554 36789999999753
No 129
>PRK02935 hypothetical protein; Provisional
Probab=24.29 E-value=43 Score=27.49 Aligned_cols=34 Identities=18% Similarity=0.286 Sum_probs=19.4
Q ss_pred cEEEEcCCCCccceeeec--ccccccCCCCcchhhh
Q 028299 150 TVFVQCCGCNVFHKLVDN--LNLFHEMKCYVNPSFN 183 (211)
Q Consensus 150 vViVqC~GC~n~HLIADN--LgwF~e~~~tIEdi~k 183 (211)
.|.|+||+|+..-..--. .-.|=+...++++-++
T Consensus 68 avqV~CP~C~K~TKmLGrvD~CM~C~~PLTLd~~le 103 (110)
T PRK02935 68 AVQVICPSCEKPTKMLGRVDACMHCNQPLTLDRSLE 103 (110)
T ss_pred ceeeECCCCCchhhhccceeecCcCCCcCCcCcccc
Confidence 478999999875543221 2224455556655444
No 130
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=24.21 E-value=49 Score=28.29 Aligned_cols=38 Identities=24% Similarity=0.532 Sum_probs=26.2
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccC
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEM 174 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~ 174 (211)
..|..|+.+-.. ..|.+ +-+|+.|. .++-.|.=||+|.
T Consensus 119 ~~C~~C~~~~~~----~~~~~---~p~C~~Cg--g~lrP~vv~fge~ 156 (225)
T cd01411 119 IYCTVCGKTVDW----EEYLK---SPYHAKCG--GVIRPDIVLYEEM 156 (225)
T ss_pred eEeCCCCCccch----hhcCC---CCCCCCCC--CEeCCCEEEcCCC
Confidence 569999754321 22322 36899997 6888888899875
No 131
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=24.20 E-value=37 Score=28.54 Aligned_cols=42 Identities=19% Similarity=0.382 Sum_probs=27.4
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccCC
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEMK 175 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~~ 175 (211)
..|..|+.+-... ..+... -+-+|+.|. +.+-.|.=||+|.-
T Consensus 110 ~~C~~C~~~~~~~---~~~~~~-~~p~C~~Cg--g~lrp~Vv~fge~~ 151 (224)
T cd01412 110 VRCSSCGYVGENN---EEIPEE-ELPRCPKCG--GLLRPGVVWFGESL 151 (224)
T ss_pred cccCCCCCCCCcc---hhhhcc-CCCCCCCCC--CccCCceEECCCCC
Confidence 4589998875442 111111 257899996 66778888998753
No 132
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=24.13 E-value=24 Score=26.40 Aligned_cols=33 Identities=33% Similarity=0.796 Sum_probs=22.4
Q ss_pred cccCCCccccccCcccccCccEEEEcCCCCccceeeecccc
Q 028299 130 CNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNL 170 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgw 170 (211)
|.+|+. ..+.||.|+. .|.+|+..+--+=+.++
T Consensus 2 C~VCg~------~~~g~hyGv~--sC~aCk~FFRR~v~~~~ 34 (84)
T cd06965 2 CRVCGD------KASGFHYGVH--ACEGCKGFFRRTIRLKL 34 (84)
T ss_pred CcccCc------cCcceEEChh--hhhhhhhheeeeeecCC
Confidence 778886 3357888874 79999987755443333
No 133
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=24.00 E-value=64 Score=25.35 Aligned_cols=12 Identities=17% Similarity=0.476 Sum_probs=6.4
Q ss_pred ceEEEEEcccCC
Q 028299 123 RMRVAFTCNVCG 134 (211)
Q Consensus 123 ~~~l~FTC~~C~ 134 (211)
++.|.-.|..|+
T Consensus 31 S~Fm~VkCp~C~ 42 (85)
T PTZ00083 31 SYFMDVKCPGCS 42 (85)
T ss_pred CeEEEEECCCCC
Confidence 455555555554
No 134
>PLN00209 ribosomal protein S27; Provisional
Probab=23.94 E-value=64 Score=25.41 Aligned_cols=12 Identities=17% Similarity=0.415 Sum_probs=6.3
Q ss_pred ceEEEEEcccCC
Q 028299 123 RMRVAFTCNVCG 134 (211)
Q Consensus 123 ~~~l~FTC~~C~ 134 (211)
++.|.-.|..|+
T Consensus 32 S~Fm~VkCp~C~ 43 (86)
T PLN00209 32 SFFMDVKCQGCF 43 (86)
T ss_pred CEEEEEECCCCC
Confidence 455555555554
No 135
>PRK04351 hypothetical protein; Provisional
Probab=23.87 E-value=75 Score=26.34 Aligned_cols=34 Identities=29% Similarity=0.554 Sum_probs=23.0
Q ss_pred ceEEEEEcccCCC--ccccccCcccccCccEEEEcCCCCccce
Q 028299 123 RMRVAFTCNVCGQ--RTTRAINPHAYTDGTVFVQCCGCNVFHK 163 (211)
Q Consensus 123 ~~~l~FTC~~C~t--RS~k~iSK~AY~~GvViVqC~GC~n~HL 163 (211)
.....|.|..|++ ...+.+++ ---+|..|.-.=.
T Consensus 108 ~~~y~Y~C~~Cg~~~~r~Rr~n~-------~~yrCg~C~g~L~ 143 (149)
T PRK04351 108 KKNYLYECQSCGQQYLRKRRINT-------KRYRCGKCRGKLK 143 (149)
T ss_pred CceEEEECCCCCCEeeeeeecCC-------CcEEeCCCCcEee
Confidence 3557999999998 33355554 3447888876443
No 136
>KOG0179 consensus 20S proteasome, regulatory subunit beta type PSMB1/PRE7 [Posttranslational modification, protein turnover, chaperones]
Probab=23.79 E-value=47 Score=30.29 Aligned_cols=38 Identities=39% Similarity=0.480 Sum_probs=27.7
Q ss_pred cCCCCCcccccccCC--------------CCChHHHhhhhhhh---hccCCcccC
Q 028299 50 SNSKETSIVPLFGNQ--------------TLSKDEAMGLVLSA---ASVRGWTTG 87 (211)
Q Consensus 50 ~~~~~~~~~p~~~~~--------------~ls~~~~~~lvlsa---a~~r~w~t~ 87 (211)
+-+-.+-|.|+|.|+ +||.|+||.||-.+ |..|.-.||
T Consensus 158 gGsa~~mI~PfLDnQi~~kn~~~e~~~~~~Ls~e~ai~lv~d~F~SAaERdI~tG 212 (235)
T KOG0179|consen 158 GGSAASMIQPFLDNQIGHKNQNLENAERTPLSLERAIRLVKDAFTSAAERDIYTG 212 (235)
T ss_pred CCcchhhhhhhhhhhccCcCcccccCcccccCHHHHHHHHHHHhhhhhhcccccC
Confidence 344567788888776 89999999998765 345555554
No 137
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=23.66 E-value=1.1e+02 Score=22.96 Aligned_cols=34 Identities=26% Similarity=0.611 Sum_probs=24.7
Q ss_pred cceEEEEEcccCCCccccccCcccccCccEEEEcCCCCccce
Q 028299 122 RRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHK 163 (211)
Q Consensus 122 r~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HL 163 (211)
+.-.|.|-|-.|+.++.-. .|= .|||..|.-+-|
T Consensus 15 r~~~miYiCgdC~~en~lk-------~~D-~irCReCG~RIl 48 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTLK-------RGD-VIRCRECGYRIL 48 (62)
T ss_pred CcccEEEEecccccccccc-------CCC-cEehhhcchHHH
Confidence 5678999999999988621 222 479999986543
No 138
>smart00067 GHA Glycoprotein hormone alpha chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology.
Probab=22.84 E-value=52 Score=26.01 Aligned_cols=26 Identities=27% Similarity=0.744 Sum_probs=21.3
Q ss_pred cccCCCccccccCcccccCccEEEEcCCCC
Q 028299 130 CNVCGQRTTRAINPHAYTDGTVFVQCCGCN 159 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~GvViVqC~GC~ 159 (211)
|..|.-|-.+.||| .|.-|-||-||=
T Consensus 2 C~EC~L~~N~~FS~----~~~PiyQC~GCC 27 (87)
T smart00067 2 CPECTLKENKIFSK----PGAPIYQCMGCC 27 (87)
T ss_pred CccceeccccccCC----CCCceeEeccee
Confidence 77888888888888 377888999984
No 139
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=22.74 E-value=55 Score=32.31 Aligned_cols=31 Identities=26% Similarity=0.545 Sum_probs=19.8
Q ss_pred CcceEEEEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 121 RRRMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 121 rr~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
.+++.++ |-+|..--.-..+ =+|||.+|.++
T Consensus 164 ~~~~n~q--c~vC~~g~~~~~N--------rmlqC~~C~~~ 194 (464)
T KOG4323|consen 164 GHKVNLQ--CSVCYCGGPGAGN--------RMLQCDKCRQW 194 (464)
T ss_pred cccccce--eeeeecCCcCccc--------eeeeecccccH
Confidence 4455555 9998643322222 37999999985
No 140
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=22.67 E-value=30 Score=26.44 Aligned_cols=25 Identities=40% Similarity=0.999 Sum_probs=18.9
Q ss_pred cccCCCccccccCcccccCccEEEEcCCCCccc
Q 028299 130 CNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H 162 (211)
|.+|+..+ +.||.|++ .|.+|...+
T Consensus 4 C~VCg~~a------~g~hyGv~--sC~aCk~FF 28 (91)
T cd07161 4 CLVCGDRA------SGYHYNAL--TCEGCKGFF 28 (91)
T ss_pred CeeCCCcC------cceEECce--eehhhHHHH
Confidence 88888643 47888874 799998865
No 141
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=22.37 E-value=45 Score=26.23 Aligned_cols=29 Identities=24% Similarity=0.714 Sum_probs=21.9
Q ss_pred EEEEEcccCCCccccccCcccccCccEEEEcCCCCc
Q 028299 125 RVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 125 ~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n 160 (211)
.-.|+|..|+....+.. ++=|-+|..|..
T Consensus 33 ~~ky~Cp~Cgk~~vkR~-------a~GIW~C~~C~~ 61 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRV-------ATGIWKCKKCGK 61 (90)
T ss_dssp HS-BEESSSSSSEEEEE-------ETTEEEETTTTE
T ss_pred hCCCcCCCCCCceeEEe-------eeEEeecCCCCC
Confidence 34699999999886653 456789999984
No 142
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=22.18 E-value=68 Score=25.26 Aligned_cols=32 Identities=19% Similarity=0.568 Sum_probs=24.0
Q ss_pred ceEEEEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 123 RMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
++.-.|+|..|+.-..+.. ++=|-+|..|...
T Consensus 32 ~q~a~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~ 63 (90)
T PTZ00255 32 SQHAKYFCPFCGKHAVKRQ-------AVGIWRCKGCKKT 63 (90)
T ss_pred HHhCCccCCCCCCCceeee-------eeEEEEcCCCCCE
Confidence 3456799999997666543 5678999999753
No 143
>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=22.16 E-value=48 Score=21.63 Aligned_cols=12 Identities=33% Similarity=1.121 Sum_probs=8.2
Q ss_pred EEEcccCCCccc
Q 028299 127 AFTCNVCGQRTT 138 (211)
Q Consensus 127 ~FTC~~C~tRS~ 138 (211)
.++|+.|++++.
T Consensus 24 ~w~C~~C~~~N~ 35 (40)
T PF04810_consen 24 TWICNFCGTKNP 35 (40)
T ss_dssp EEEETTT--EEE
T ss_pred EEECcCCCCcCC
Confidence 489999999764
No 144
>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=22.08 E-value=69 Score=21.56 Aligned_cols=26 Identities=27% Similarity=0.867 Sum_probs=16.6
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCccce
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHK 163 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HL 163 (211)
|+|+.|.... .+-+-++|..|.+..|
T Consensus 1 ~~Cd~C~~~~----------~~g~r~~C~~C~d~dL 26 (49)
T cd02335 1 YHCDYCSKDI----------TGTIRIKCAECPDFDL 26 (49)
T ss_pred CCCCCcCCCC----------CCCcEEECCCCCCcch
Confidence 5788887521 2236788888876554
No 145
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=21.72 E-value=71 Score=28.14 Aligned_cols=21 Identities=24% Similarity=0.456 Sum_probs=17.9
Q ss_pred EEEcCCCCccceeeecccccccC
Q 028299 152 FVQCCGCNVFHKLVDNLNLFHEM 174 (211)
Q Consensus 152 iVqC~GC~n~HLIADNLgwF~e~ 174 (211)
+-+|+.|. .+|-.+.=||+|.
T Consensus 169 ~p~C~~Cg--g~lrP~VV~FGE~ 189 (260)
T cd01409 169 VPECERCG--GVLKPDVVFFGEN 189 (260)
T ss_pred CCCCCCCC--CEECCCEEECCCC
Confidence 46799997 6899999999984
No 146
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=21.50 E-value=62 Score=27.79 Aligned_cols=28 Identities=14% Similarity=0.144 Sum_probs=15.4
Q ss_pred cCCCCccceeeecccccccCCCCcchhhh
Q 028299 155 CCGCNVFHKLVDNLNLFHEMKCYVNPSFN 183 (211)
Q Consensus 155 C~GC~n~HLIADNLgwF~e~~~tIEdi~k 183 (211)
|++|.+.|-...+-+ +......+++|++
T Consensus 36 C~~Cdt~~t~~~~~~-~~~~~~~~~~I~~ 63 (212)
T COG0602 36 CPGCDTKYTWDFNYG-KPGTPMSADEILA 63 (212)
T ss_pred CCCCCChhhhccccc-CCCCccCHHHHHH
Confidence 889988876544331 1123345555554
No 147
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=21.39 E-value=54 Score=30.99 Aligned_cols=53 Identities=21% Similarity=0.432 Sum_probs=16.8
Q ss_pred EEEEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccccccCCCCcc-hhhhcCCC
Q 028299 126 VAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNLFHEMKCYVN-PSFNYRDA 187 (211)
Q Consensus 126 l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgwF~e~~~tIE-di~k~KGe 187 (211)
=-|.|.-|+.|++ .+-+ |- ...|++|...- -..-|++.|.+..+. +.|--+|+
T Consensus 284 RFFkC~~C~~Rt~-sl~r--~P----~~~C~~Cg~~~--wer~~M~~ek~~~~~~e~L~~RG~ 337 (344)
T PF09332_consen 284 RFFKCKDCGNRTI-SLER--LP----KKHCSNCGSSK--WERTGMLKEKKGKLGGETLLPRGE 337 (344)
T ss_dssp EEEE-T-TS-EEE-ESSS--S------S--TTT-S-----EEE---SSS--------------
T ss_pred eeEECCCCCCeee-eccc--CC----CCCCCcCCcCc--eeehhhhhhhcccCCccccccccc
Confidence 3599999999976 3333 32 24899998642 234455666555442 34444443
No 148
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=21.38 E-value=37 Score=25.56 Aligned_cols=33 Identities=30% Similarity=0.700 Sum_probs=23.3
Q ss_pred EcccCCCccccccCcccccCccEEEEcCCCCccceeeeccc
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLN 169 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLg 169 (211)
.|.+|+..+ ..||.|++ .|.+|+..+--+=+.+
T Consensus 2 ~C~VCg~~a------~g~hyGv~--sC~aCk~FFRR~~~~~ 34 (86)
T cd07157 2 TCQVCGEPA------AGFHHGAY--VCEACKKFFMRSSNAI 34 (86)
T ss_pred CCcccCCcC------cccEECcc--eeeEeeeEEecceecC
Confidence 488998643 46788975 7999999775544433
No 149
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=21.25 E-value=25 Score=29.02 Aligned_cols=34 Identities=21% Similarity=0.414 Sum_probs=28.1
Q ss_pred EEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 128 FTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 128 FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
-.|..||.+.++.+|+-.=+----+-+|..|..-
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~ep 139 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEP 139 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCc
Confidence 5799999999999998877766667788888753
No 150
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=21.15 E-value=26 Score=25.27 Aligned_cols=29 Identities=31% Similarity=0.856 Sum_probs=20.0
Q ss_pred cccCCCccccccCcccccCccEEEEcCCCCccceeee
Q 028299 130 CNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVD 166 (211)
Q Consensus 130 C~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIAD 166 (211)
|.+|+.... .||.|+. .|.+|+..+--+-
T Consensus 1 C~VCg~~~~------g~hyGv~--~C~aC~~FFRR~v 29 (73)
T cd07158 1 CKVCGDKAS------GFHYGVH--SCEGCKGFFRRTI 29 (73)
T ss_pred CcccCccCc------ceEECcc--hhhHHHHHHhhhh
Confidence 677876443 5888874 6999988764433
No 151
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=20.67 E-value=48 Score=29.26 Aligned_cols=41 Identities=20% Similarity=0.379 Sum_probs=21.5
Q ss_pred EcccCCCccccccCcc--cccCccEEEEcCCCCccceeeecccc
Q 028299 129 TCNVCGQRTTRAINPH--AYTDGTVFVQCCGCNVFHKLVDNLNL 170 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~--AY~~GvViVqC~GC~n~HLIADNLgw 170 (211)
+|..||......+.-. --+.++-+-.|..|+.+-++.| ...
T Consensus 213 ~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd-~~~ 255 (290)
T PF04216_consen 213 KCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD-REK 255 (290)
T ss_dssp S-TTT---SS-EEE--------SEEEEEETTTTEEEEEEE-TTT
T ss_pred CCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHh-hhh
Confidence 4555665544322221 2234788889999999999999 543
No 152
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=20.67 E-value=44 Score=25.44 Aligned_cols=36 Identities=31% Similarity=0.582 Sum_probs=25.9
Q ss_pred EEEcccCCCccccccCcccccCccEEEEcCCCCccceeeecccc
Q 028299 127 AFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLNL 170 (211)
Q Consensus 127 ~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLgw 170 (211)
.-.|.+|+. ..+.||-|+. .|.+|+..+--+-..++
T Consensus 6 ~~~C~VCg~------~a~g~hyGv~--sC~aCk~FFRR~v~~~~ 41 (92)
T cd07163 6 DIPCKVCGD------RSSGKHYGIY--ACDGCSGFFKRSIRRNR 41 (92)
T ss_pred CCCCcccCC------cCcccEECce--eeeeeeeEEeeeecCCC
Confidence 345999986 3467899984 89999998755544444
No 153
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=20.65 E-value=64 Score=31.55 Aligned_cols=22 Identities=27% Similarity=0.537 Sum_probs=9.5
Q ss_pred EcccCCCccccccCcccccCccEEEEcCCCCccc
Q 028299 129 TCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVFH 162 (211)
Q Consensus 129 TC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~H 162 (211)
.|..||... |- --+||.|.+.+
T Consensus 493 ~C~~CG~~~-----------~~-~~~CP~CGs~~ 514 (546)
T PF13597_consen 493 ICPDCGYIG-----------GE-GDKCPKCGSEN 514 (546)
T ss_dssp EETTT---S--------------EEE-CCC----
T ss_pred cccCCCcCC-----------CC-CCCCCCCCCcc
Confidence 499998643 33 56799999997
No 154
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=20.57 E-value=63 Score=25.66 Aligned_cols=32 Identities=28% Similarity=0.625 Sum_probs=24.4
Q ss_pred ceEEEEEcccCCCccccccCcccccCccEEEEcCCCCcc
Q 028299 123 RMRVAFTCNVCGQRTTRAINPHAYTDGTVFVQCCGCNVF 161 (211)
Q Consensus 123 ~~~l~FTC~~C~tRS~k~iSK~AY~~GvViVqC~GC~n~ 161 (211)
++.-.|.|..|+....+.+ ++=|-+|..|...
T Consensus 31 ~~~~~~~Cp~C~~~~VkR~-------a~GIW~C~kCg~~ 62 (89)
T COG1997 31 QQRAKHVCPFCGRTTVKRI-------ATGIWKCRKCGAK 62 (89)
T ss_pred HHhcCCcCCCCCCcceeee-------ccCeEEcCCCCCe
Confidence 4555789999999866665 3568899999754
No 155
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=20.51 E-value=82 Score=20.77 Aligned_cols=30 Identities=23% Similarity=0.543 Sum_probs=25.8
Q ss_pred cccCCCccccccCc-ccccCccEEEEcCCCCc
Q 028299 130 CNVCGQRTTRAINP-HAYTDGTVFVQCCGCNV 160 (211)
Q Consensus 130 C~~C~tRS~k~iSK-~AY~~GvViVqC~GC~n 160 (211)
|. ||.+....+++ ..-..|=.+-.|+....
T Consensus 3 C~-Cg~~~~~~~s~k~~~N~GR~Fy~C~~~~~ 33 (45)
T PF06839_consen 3 CP-CGEPAVRRTSKKTGPNPGRRFYKCPNYKD 33 (45)
T ss_pred CC-CCCEeEEEEEeCCCCCCCCcceECCCCCC
Confidence 77 99988887777 99999999999997665
No 156
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=20.29 E-value=75 Score=24.87 Aligned_cols=19 Identities=11% Similarity=0.621 Sum_probs=15.5
Q ss_pred cceEEEEEcccCCCccccc
Q 028299 122 RRMRVAFTCNVCGQRTTRA 140 (211)
Q Consensus 122 r~~~l~FTC~~C~tRS~k~ 140 (211)
.+..|.|+|.+|+......
T Consensus 64 KKi~Lrl~C~~C~~~~~~~ 82 (84)
T PTZ00157 64 KKIVLKLECTKCKSKRQKV 82 (84)
T ss_pred ceeEEEEEecccCceeEec
Confidence 4789999999999876543
No 157
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=20.25 E-value=67 Score=31.10 Aligned_cols=60 Identities=22% Similarity=0.412 Sum_probs=39.8
Q ss_pred ccccccccccCCCcceEEEEEccc---------------CCCccccccCcccccCccEEEEcCCCCccceeeeccc
Q 028299 109 STFPWSLFTKSPRRRMRVAFTCNV---------------CGQRTTRAINPHAYTDGTVFVQCCGCNVFHKLVDNLN 169 (211)
Q Consensus 109 s~~P~s~~~k~prr~~~l~FTC~~---------------C~tRS~k~iSK~AY~~GvViVqC~GC~n~HLIADNLg 169 (211)
+.+|..++....+ .+-=.|+|.+ ||+.-.+.--++--.+|+.--+||-|-+.-.-+|-+.
T Consensus 319 ~eLP~eIklp~~~-hfHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~~~~~~~~r 393 (396)
T COG5109 319 SELPMEIKLPKGR-HFHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEMSKYENILR 393 (396)
T ss_pred CCCceEEecCCcc-cccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcchhhhhhhc
Confidence 4566666655544 7888999983 5544333222233468999999999988776666543
No 158
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=20.23 E-value=45 Score=32.55 Aligned_cols=21 Identities=29% Similarity=0.513 Sum_probs=18.5
Q ss_pred cEEEEcCCCCccceee-ecccc
Q 028299 150 TVFVQCCGCNVFHKLV-DNLNL 170 (211)
Q Consensus 150 vViVqC~GC~n~HLIA-DNLgw 170 (211)
.-.|.||.|..+|.+. +||.|
T Consensus 198 ~~~vpCPhCg~~~~l~~~~l~w 219 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLEWENLKW 219 (557)
T ss_pred EEEccCCCCCCCccccccceee
Confidence 4589999999999998 78888
Done!