Query 026819
Match_columns 232
No_of_seqs 145 out of 189
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 13:10:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026819.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026819hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04161 Arv1: Arv1-like famil 100.0 8.5E-58 1.8E-62 395.9 17.7 194 3-196 1-208 (208)
2 KOG3134 Predicted membrane pro 100.0 1.6E-41 3.5E-46 293.3 14.9 200 3-205 1-212 (225)
3 COG5254 ARV1 Predicted membran 100.0 3.3E-38 7.1E-43 269.9 11.8 194 3-201 1-220 (239)
4 KOG3134 Predicted membrane pro 96.6 0.0084 1.8E-07 53.0 7.6 114 112-225 100-218 (225)
5 smart00834 CxxC_CXXC_SSSS Puta 93.0 0.037 8.1E-07 35.4 0.6 34 2-38 5-38 (41)
6 PF08271 TF_Zn_Ribbon: TFIIB z 92.6 0.086 1.9E-06 34.7 1.9 33 3-40 1-33 (43)
7 PRK00398 rpoP DNA-directed RNA 92.0 0.074 1.6E-06 35.4 1.0 31 1-37 2-32 (46)
8 smart00659 RPOLCX RNA polymera 91.5 0.11 2.4E-06 34.8 1.5 28 1-35 1-28 (44)
9 PF09723 Zn-ribbon_8: Zinc rib 90.2 0.11 2.4E-06 34.2 0.5 34 2-38 5-39 (42)
10 TIGR02605 CxxC_CxxC_SSSS putat 89.2 0.16 3.4E-06 34.3 0.7 30 2-34 5-34 (52)
11 PF13248 zf-ribbon_3: zinc-rib 88.8 0.19 4.1E-06 29.7 0.8 24 1-34 1-24 (26)
12 PF03604 DNA_RNApol_7kD: DNA d 88.7 0.27 5.8E-06 30.9 1.4 25 3-34 1-25 (32)
13 PF14319 Zn_Tnp_IS91: Transpos 87.3 0.46 9.9E-06 37.6 2.3 52 2-67 42-95 (111)
14 COG1996 RPC10 DNA-directed RNA 87.3 0.2 4.4E-06 34.5 0.3 28 1-34 5-32 (49)
15 PF05180 zf-DNL: DNL zinc fing 86.5 0.33 7.1E-06 35.4 1.0 36 2-38 4-44 (66)
16 cd00729 rubredoxin_SM Rubredox 85.0 0.35 7.6E-06 30.5 0.5 32 2-41 2-33 (34)
17 PF07282 OrfB_Zn_ribbon: Putat 82.5 0.77 1.7E-05 32.6 1.5 30 3-38 29-58 (69)
18 PF01286 XPA_N: XPA protein N- 81.2 0.57 1.2E-05 29.9 0.4 28 1-33 2-31 (34)
19 PF04216 FdhE: Protein involve 80.5 1.4 3.1E-05 39.9 2.8 35 3-37 212-252 (290)
20 PF12773 DZR: Double zinc ribb 80.5 0.85 1.8E-05 30.4 1.0 31 2-39 12-42 (50)
21 PF12647 RNHCP: RNHCP domain; 80.3 0.89 1.9E-05 35.2 1.2 29 1-33 3-31 (92)
22 PRK00464 nrdR transcriptional 78.5 1.2 2.6E-05 37.5 1.5 44 3-46 1-48 (154)
23 PF01927 Mut7-C: Mut7-C RNAse 77.4 1.2 2.7E-05 36.5 1.3 33 3-35 92-133 (147)
24 PF13240 zinc_ribbon_2: zinc-r 76.1 1.1 2.3E-05 26.0 0.4 21 4-34 1-21 (23)
25 PRK12495 hypothetical protein; 74.2 1.6 3.5E-05 38.8 1.3 29 2-38 42-70 (226)
26 PF04981 NMD3: NMD3 family ; 73.7 1.7 3.8E-05 38.3 1.4 38 5-42 1-53 (236)
27 COG3364 Zn-ribbon containing p 73.6 1.1 2.4E-05 35.5 0.1 37 1-43 1-37 (112)
28 PF13453 zf-TFIIB: Transcripti 73.6 3 6.4E-05 27.0 2.1 27 5-35 2-28 (41)
29 smart00401 ZnF_GATA zinc finge 73.1 2 4.4E-05 29.4 1.3 32 2-35 3-34 (52)
30 PF10571 UPF0547: Uncharacteri 70.9 2 4.3E-05 25.7 0.7 22 4-35 2-23 (26)
31 PF14803 Nudix_N_2: Nudix N-te 70.1 2.4 5.2E-05 26.9 1.0 30 4-35 2-31 (34)
32 PF02591 DUF164: Putative zinc 70.1 1.3 2.8E-05 30.5 -0.3 33 2-35 22-55 (56)
33 PRK00420 hypothetical protein; 69.0 2.7 6E-05 33.6 1.4 28 3-37 24-51 (112)
34 TIGR02098 MJ0042_CXXC MJ0042 f 68.8 2.3 5.1E-05 26.7 0.8 35 1-36 1-35 (38)
35 PF12760 Zn_Tnp_IS1595: Transp 67.6 3.9 8.4E-05 27.1 1.7 29 1-34 17-45 (46)
36 PRK03564 formate dehydrogenase 67.6 5.8 0.00013 36.9 3.4 63 3-66 227-301 (309)
37 COG1656 Uncharacterized conser 66.2 2.5 5.5E-05 36.0 0.7 33 3-35 98-139 (165)
38 COG2331 Uncharacterized protei 65.9 1.3 2.7E-05 33.4 -1.0 34 2-38 12-45 (82)
39 cd00350 rubredoxin_like Rubred 65.0 2.9 6.3E-05 25.9 0.7 31 3-41 2-32 (33)
40 PF14446 Prok-RING_1: Prokaryo 64.4 4.3 9.2E-05 28.5 1.4 27 1-35 4-30 (54)
41 PF09845 DUF2072: Zn-ribbon co 63.9 2.6 5.6E-05 34.7 0.4 28 2-35 1-28 (131)
42 COG2260 Predicted Zn-ribbon RN 63.8 3.3 7.2E-05 29.5 0.8 18 27-44 18-46 (59)
43 PF09082 DUF1922: Domain of un 63.2 2.6 5.7E-05 30.9 0.2 26 3-36 4-29 (68)
44 cd01121 Sms Sms (bacterial rad 61.6 4.1 8.9E-05 38.6 1.3 23 3-35 1-23 (372)
45 PF14353 CpXC: CpXC protein 61.5 5.9 0.00013 31.4 2.0 56 3-68 2-70 (128)
46 PF09538 FYDLN_acid: Protein o 61.0 3.8 8.3E-05 32.5 0.8 28 3-37 10-37 (108)
47 PF14149 YhfH: YhfH-like prote 59.9 1.6 3.5E-05 28.4 -1.2 24 3-32 14-37 (37)
48 PF07754 DUF1610: Domain of un 59.0 6.8 0.00015 23.1 1.4 24 5-34 1-24 (24)
49 COG4888 Uncharacterized Zn rib 58.9 5.3 0.00011 31.6 1.2 53 3-55 23-80 (104)
50 PRK00423 tfb transcription ini 58.7 6.6 0.00014 36.1 2.1 34 2-40 11-45 (310)
51 PF14255 Cys_rich_CPXG: Cystei 57.8 7.2 0.00016 27.0 1.7 40 4-43 2-41 (52)
52 COG0846 SIR2 NAD-dependent pro 57.6 4.3 9.3E-05 36.6 0.6 33 3-35 123-155 (250)
53 PF13719 zinc_ribbon_5: zinc-r 57.5 5.1 0.00011 25.5 0.8 34 1-35 1-34 (37)
54 TIGR01562 FdhE formate dehydro 57.5 11 0.00023 35.1 3.2 62 3-66 225-301 (305)
55 smart00531 TFIIE Transcription 55.7 4 8.6E-05 33.5 0.1 36 2-38 99-135 (147)
56 TIGR00416 sms DNA repair prote 55.5 5.7 0.00012 38.6 1.1 24 2-35 7-30 (454)
57 PHA02942 putative transposase; 54.0 7.5 0.00016 37.0 1.6 29 3-38 326-354 (383)
58 PF13717 zinc_ribbon_4: zinc-r 53.2 7.3 0.00016 24.7 1.0 32 1-35 1-34 (36)
59 PRK11823 DNA repair protein Ra 53.1 6.6 0.00014 38.0 1.1 29 2-41 7-35 (446)
60 COG1997 RPL43A Ribosomal prote 50.6 9.3 0.0002 29.4 1.4 28 1-35 34-62 (89)
61 COG2888 Predicted Zn-ribbon RN 50.3 9.2 0.0002 27.5 1.2 39 2-40 9-52 (61)
62 PF11023 DUF2614: Protein of u 48.7 6.5 0.00014 31.6 0.3 25 3-35 70-94 (114)
63 COG5254 ARV1 Predicted membran 47.4 12 0.00026 33.2 1.7 46 152-197 143-189 (239)
64 PRK00564 hypA hydrogenase nick 47.2 8.9 0.00019 30.5 0.9 26 3-35 72-97 (117)
65 PF12156 ATPase-cat_bd: Putati 47.0 6.6 0.00014 29.7 0.1 34 4-37 2-37 (88)
66 COG4031 Predicted metal-bindin 46.5 9.1 0.0002 33.6 0.8 30 3-44 1-34 (227)
67 PRK03681 hypA hydrogenase nick 45.6 11 0.00023 29.9 1.1 26 3-35 71-96 (114)
68 smart00661 RPOL9 RNA polymeras 45.4 13 0.00028 24.5 1.4 28 4-35 2-29 (52)
69 PRK07591 threonine synthase; V 44.8 11 0.00024 36.1 1.3 30 3-43 19-48 (421)
70 PRK14890 putative Zn-ribbon RN 44.6 15 0.00032 26.3 1.6 38 2-39 7-49 (59)
71 TIGR02300 FYDLN_acid conserved 44.3 10 0.00022 31.1 0.8 27 3-36 10-36 (129)
72 PRK14892 putative transcriptio 44.2 11 0.00024 29.5 0.9 50 3-55 22-76 (99)
73 KOG1597 Transcription initiati 44.2 14 0.00031 34.4 1.8 29 4-35 2-30 (308)
74 COG1066 Sms Predicted ATP-depe 44.1 11 0.00023 36.9 1.1 23 2-34 7-29 (456)
75 cd00202 ZnF_GATA Zinc finger D 44.0 7.1 0.00015 27.0 -0.1 34 4-39 1-34 (54)
76 COG1405 SUA7 Transcription ini 43.4 14 0.00031 33.9 1.7 37 2-43 1-38 (285)
77 COG3357 Predicted transcriptio 42.9 12 0.00025 29.2 0.9 26 2-34 58-84 (97)
78 PRK12336 translation initiatio 42.2 20 0.00043 31.2 2.3 36 4-42 100-137 (201)
79 PRK05978 hypothetical protein; 41.9 12 0.00027 31.3 0.9 27 3-34 34-60 (148)
80 PRK12380 hydrogenase nickel in 40.4 13 0.00029 29.3 0.9 25 3-35 71-95 (113)
81 PRK04136 rpl40e 50S ribosomal 39.8 16 0.00035 25.1 1.1 23 2-34 14-36 (48)
82 PF09297 zf-NADH-PPase: NADH p 38.6 11 0.00023 23.1 0.0 27 3-35 4-30 (32)
83 PHA02768 hypothetical protein; 38.4 7.3 0.00016 27.4 -0.8 40 2-42 5-50 (55)
84 PRK03824 hypA hydrogenase nick 38.4 15 0.00032 30.0 0.9 33 3-35 71-116 (135)
85 KOG3277 Uncharacterized conser 37.4 20 0.00044 30.4 1.6 36 2-38 79-119 (165)
86 COG1645 Uncharacterized Zn-fin 36.5 19 0.00041 29.7 1.2 24 3-34 29-52 (131)
87 COG3880 Modulator of heat shoc 36.5 24 0.00052 30.4 1.9 41 3-43 1-43 (176)
88 PF02146 SIR2: Sir2 family; I 36.1 6.4 0.00014 32.9 -1.7 30 3-34 106-137 (178)
89 PF09151 DUF1936: Domain of un 36.0 36 0.00078 21.5 2.1 27 3-31 2-29 (36)
90 PF09567 RE_MamI: MamI restric 35.6 16 0.00034 33.6 0.6 21 4-34 84-104 (314)
91 PF07191 zinc-ribbons_6: zinc- 35.5 21 0.00045 26.4 1.2 34 3-36 2-40 (70)
92 PF10122 Mu-like_Com: Mu-like 34.6 24 0.00052 24.5 1.3 30 2-35 4-33 (51)
93 COG1499 NMD3 NMD protein affec 34.2 25 0.00053 33.5 1.8 32 2-33 6-50 (355)
94 TIGR01206 lysW lysine biosynth 33.9 29 0.00064 24.2 1.7 30 2-35 2-31 (54)
95 PF06542 PHA-1: Regulator prot 33.9 10 0.00022 36.4 -0.9 39 28-66 123-161 (390)
96 COG1545 Predicted nucleic-acid 33.3 22 0.00048 29.1 1.2 31 3-43 30-61 (140)
97 PRK04023 DNA polymerase II lar 33.3 25 0.00054 37.9 1.8 16 27-42 664-679 (1121)
98 TIGR00100 hypA hydrogenase nic 33.0 19 0.00041 28.5 0.7 26 3-36 71-96 (115)
99 PF00320 GATA: GATA zinc finge 32.6 9.6 0.00021 24.1 -0.9 32 5-38 1-32 (36)
100 PF05191 ADK_lid: Adenylate ki 32.5 24 0.00053 22.4 1.0 28 3-34 2-29 (36)
101 PRK02935 hypothetical protein; 32.5 23 0.0005 28.2 1.1 24 4-35 72-95 (110)
102 PRK03976 rpl37ae 50S ribosomal 32.4 33 0.00071 26.5 1.9 28 2-36 36-64 (90)
103 TIGR03829 YokU_near_AblA uncha 32.2 52 0.0011 25.3 3.0 50 5-54 2-60 (89)
104 PRK06266 transcription initiat 31.9 17 0.00037 31.0 0.3 32 2-38 117-148 (178)
105 PF10083 DUF2321: Uncharacteri 31.5 20 0.00044 30.4 0.6 31 5-35 42-77 (158)
106 PF01155 HypA: Hydrogenase exp 30.4 17 0.00038 28.5 0.1 25 3-35 71-95 (113)
107 COG1571 Predicted DNA-binding 30.2 27 0.00058 34.0 1.3 29 2-37 350-378 (421)
108 COG1552 RPL40A Ribosomal prote 30.0 14 0.0003 25.5 -0.4 22 3-34 15-36 (50)
109 PF03691 UPF0167: Uncharacteri 29.6 20 0.00042 30.9 0.3 37 2-39 24-65 (176)
110 PF09332 Mcm10: Mcm10 replicat 29.4 21 0.00047 33.8 0.5 27 3-35 286-312 (344)
111 COG0375 HybF Zn finger protein 29.4 26 0.00056 28.2 0.9 29 3-39 71-99 (115)
112 PRK00762 hypA hydrogenase nick 29.2 26 0.00057 28.1 0.9 30 3-35 71-101 (124)
113 PF09889 DUF2116: Uncharacteri 29.1 23 0.0005 25.2 0.5 12 3-14 4-15 (59)
114 cd01407 SIR2-fam SIR2 family o 28.3 21 0.00045 30.9 0.2 31 3-35 110-142 (218)
115 cd01408 SIRT1 SIRT1: Eukaryoti 28.1 18 0.00039 31.9 -0.2 12 23-34 113-124 (235)
116 PF10058 DUF2296: Predicted in 28.1 43 0.00092 23.2 1.7 30 3-34 23-52 (54)
117 PRK14714 DNA polymerase II lar 28.0 33 0.00072 37.8 1.7 14 28-41 711-724 (1337)
118 PF04810 zf-Sec23_Sec24: Sec23 27.8 26 0.00056 22.5 0.5 18 27-44 3-20 (40)
119 PRK06386 replication factor A; 27.8 28 0.00061 33.1 1.0 24 3-39 237-260 (358)
120 TIGR00280 L37a ribosomal prote 27.8 43 0.00094 25.9 1.8 28 2-36 35-63 (91)
121 PRK07218 replication factor A; 27.6 29 0.00063 33.7 1.1 20 47-66 324-343 (423)
122 CHL00174 accD acetyl-CoA carbo 27.5 14 0.00029 34.4 -1.2 25 4-34 40-65 (296)
123 PF10977 DUF2797: Protein of u 27.3 24 0.00052 31.6 0.4 29 4-32 13-43 (235)
124 PRK14559 putative protein seri 27.1 29 0.00062 35.5 1.0 7 28-34 29-35 (645)
125 PRK04023 DNA polymerase II lar 26.9 36 0.00079 36.7 1.7 35 2-39 626-664 (1121)
126 PRK00019 rpmE 50S ribosomal pr 26.9 47 0.001 24.5 1.9 29 4-34 15-43 (72)
127 PF13913 zf-C2HC_2: zinc-finge 26.8 27 0.00059 20.3 0.5 9 26-34 2-10 (25)
128 smart00709 Zpr1 Duplicated dom 26.4 46 0.001 28.0 1.9 30 4-33 2-36 (160)
129 COG2816 NPY1 NTP pyrophosphohy 26.4 40 0.00087 31.1 1.7 27 3-35 112-138 (279)
130 PF03367 zf-ZPR1: ZPR1 zinc-fi 26.4 37 0.00081 28.5 1.4 31 3-33 2-37 (161)
131 PTZ00255 60S ribosomal protein 26.1 50 0.0011 25.5 1.9 28 2-36 36-64 (90)
132 COG1644 RPB10 DNA-directed RNA 26.0 15 0.00033 26.5 -0.8 19 3-21 5-23 (63)
133 PTZ00410 NAD-dependent SIR2; P 26.0 24 0.00052 33.5 0.2 30 3-34 148-179 (349)
134 KOG2682 NAD-dependent histone 25.9 15 0.00033 33.6 -1.1 37 3-39 153-190 (314)
135 PRK06393 rpoE DNA-directed RNA 25.7 12 0.00026 27.2 -1.4 34 3-49 6-39 (64)
136 PF01194 RNA_pol_N: RNA polyme 25.3 20 0.00044 25.6 -0.3 16 4-19 6-21 (60)
137 PRK06260 threonine synthase; V 25.1 33 0.00072 32.4 0.9 28 2-37 3-30 (397)
138 PF05129 Elf1: Transcription e 24.8 50 0.0011 24.7 1.7 33 3-35 23-55 (81)
139 PRK04016 DNA-directed RNA poly 24.7 18 0.00039 26.1 -0.7 17 4-20 6-22 (62)
140 cd01411 SIR2H SIR2H: Uncharact 24.4 33 0.00071 30.0 0.7 26 3-34 119-144 (225)
141 PRK06424 transcription factor; 24.4 32 0.00069 28.5 0.6 37 5-42 3-39 (144)
142 PRK14559 putative protein seri 24.2 40 0.00087 34.5 1.4 14 26-39 41-54 (645)
143 COG3478 Predicted nucleic-acid 24.2 42 0.0009 24.6 1.1 9 4-12 6-14 (68)
144 PRK13130 H/ACA RNA-protein com 24.0 39 0.00084 23.8 0.9 18 28-45 19-47 (56)
145 TIGR00310 ZPR1_znf ZPR1 zinc f 23.8 55 0.0012 28.4 2.0 31 4-34 2-38 (192)
146 PRK00504 rpmG 50S ribosomal pr 23.7 60 0.0013 22.3 1.8 33 3-35 8-43 (50)
147 PF08792 A2L_zn_ribbon: A2L zi 23.5 48 0.001 20.7 1.2 27 3-35 4-30 (33)
148 PF14311 DUF4379: Domain of un 23.1 39 0.00085 22.9 0.8 8 4-11 30-37 (55)
149 PRK14704 anaerobic ribonucleos 23.1 37 0.00079 34.6 0.9 22 3-35 560-581 (618)
150 COG0254 RpmE Ribosomal protein 22.9 61 0.0013 24.2 1.8 29 4-33 16-44 (75)
151 PRK12286 rpmF 50S ribosomal pr 22.8 55 0.0012 23.0 1.5 23 4-37 29-51 (57)
152 cd04476 RPA1_DBD_C RPA1_DBD_C: 22.7 42 0.0009 27.6 1.0 28 3-37 35-62 (166)
153 PF06827 zf-FPG_IleRS: Zinc fi 22.6 63 0.0014 19.1 1.6 29 3-35 2-30 (30)
154 PRK01397 50S ribosomal protein 22.4 71 0.0015 23.9 2.1 15 20-34 28-42 (78)
155 KOG0477 DNA replication licens 22.1 44 0.00096 34.6 1.2 33 2-35 292-324 (854)
156 PRK07218 replication factor A; 22.0 47 0.001 32.3 1.3 20 20-39 291-310 (423)
157 COG2995 PqiA Uncharacterized p 21.4 49 0.0011 32.1 1.3 26 4-35 20-47 (418)
158 PF04135 Nop10p: Nucleolar RNA 21.3 57 0.0012 22.7 1.3 18 27-44 18-46 (53)
159 PRK08402 replication factor A; 21.2 43 0.00093 31.8 0.9 9 4-12 214-222 (355)
160 PLN00032 DNA-directed RNA poly 21.0 24 0.00052 26.1 -0.7 18 4-21 6-23 (71)
161 cd01412 SIRT5_Af1_CobB SIRT5_A 20.9 45 0.00099 28.8 0.9 29 3-34 110-138 (224)
162 COG3809 Uncharacterized protei 20.7 57 0.0012 24.9 1.2 37 3-43 2-44 (88)
163 smart00507 HNHc HNH nucleases. 20.5 43 0.00094 20.9 0.5 11 3-13 11-21 (52)
164 PF10217 DUF2039: Uncharacteri 20.3 15 0.00033 28.5 -1.9 33 3-35 56-90 (92)
165 PF03833 PolC_DP2: DNA polymer 20.1 34 0.00075 36.1 0.0 41 3-43 668-709 (900)
No 1
>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=100.00 E-value=8.5e-58 Score=395.89 Aligned_cols=194 Identities=41% Similarity=0.643 Sum_probs=166.9
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccccccccchhHHHHHHHHhcCcchhheeeccccccccc--------hh
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETV--------NL 74 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayrHllfN~~~~~~~--------~~ 74 (232)
++|||||+||++||++|||||||+|+|++||++||||||+|+++++||++|+|||||||++||+.+++.+ +.
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDkYiE~d~vil~IDLlLlK~~AYRHllfN~~~~~~~~~~~~~~~~~ 80 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADKYIEYDNVILFIDLLLLKPQAYRHLLFNRLEPELSKFQVKNWFSK 80 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCcccceeccccHHHHHHHHHcchhhHHHhhccCCccccccchhhhhhhh
Confidence 5899999999999999999999999999999999999999999999999999999999999999887765 44
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhccCCCCCC---chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-CCChh
Q 026819 75 KGILWKSTVGFLLLDAYRSLLLSRSNEGQSS---SMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTS-AGASS 150 (232)
Q Consensus 75 ~~~l~kl~vl~lL~eay~~~~~~~~~~~~~~---s~~~~~~~~~~~~~l~~~~l~~~~f~~~~~l~~~~~l~~~-~~~~~ 150 (232)
.+.+||++++++++|||+.|..++++.+... .....+...++..++...++++++|+..+.+..+...+++ ....+
T Consensus 81 ~~~~~rl~il~ll~eayl~w~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (208)
T PF04161_consen 81 FKSLWRLVILLLLFEAYLRWASEEKSSQSSQLMSSILSQSIYMQYLFFLIYCLLENLLFHLFIALLIRFWLKWGQQYKYR 160 (208)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhccccccchhhhhhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccchh
Confidence 5689999999999999999987666543221 0111233455556778888899999988888888888887 55678
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCCchh--HHHHHHHHHHHHHHH
Q 026819 151 FKDFLLAVLISSYFKIFLVAMMVWNFPSSVI--YIIDLFVLSSNTVAL 196 (232)
Q Consensus 151 ~~~ll~alllSS~~KLf~ilmlIW~~~~s~~--~li~~~vl~snv~Al 196 (232)
++.+++|+++||++|+|+++|+||+||.+.. .++++++++||+|||
T Consensus 161 ~~~l~~alllSs~~Klf~ilmlIW~~~~~~~~~~ii~~~v~~~~~~aL 208 (208)
T PF04161_consen 161 FRVLLTALLLSSYGKLFPILMLIWPYDSSPISLSIIDWFVLLSNIEAL 208 (208)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999999999996544 599999999999996
No 2
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=1.6e-41 Score=293.28 Aligned_cols=200 Identities=37% Similarity=0.601 Sum_probs=148.5
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccccccccchhHHHHHHHHhcCcchhheeeccccccccchhhhHHHHHH
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKST 82 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayrHllfN~~~~~~~~~~~~l~kl~ 82 (232)
++|||||+++++||++||+||+|+|+||||+++||||||+|+||++||++|+|||||||+|||..++++.+....+||+.
T Consensus 1 ~~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~vDkYiE~d~vii~IDliL~k~qaYRHlLfN~~~~~~~~~~~~l~~~~ 80 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVVDKYIELDVVIIFIDLILLKAQAYRHLLFNSLIQRTKNVFCLLWKLV 80 (225)
T ss_pred CcccccCchHHHHHHhcCCCcEEEeeCCchhhHHHhHeehhhHHHHHHHHHHhHHHHHHHHHHhhhHHhHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999988888899988
Q ss_pred HHHHHHHHHHHHHhhcc-CCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc--------CCChhHHH
Q 026819 83 VGFLLLDAYRSLLLSRS-NEGQSSSMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTS--------AGASSFKD 153 (232)
Q Consensus 83 vl~lL~eay~~~~~~~~-~~~~~~s~~~~~~~~~~~~~l~~~~l~~~~f~~~~~l~~~~~l~~~--------~~~~~~~~ 153 (232)
...++++-+.....+.+ ++|+.+++++. ....+++......+++|.+.+...-..+.+.. ..+..+..
T Consensus 81 ~~~~lL~~~~~~l~~~~~~~e~~~~~~~~---~~~~~~~~~~i~~~~l~~f~~~~~~~~~~~l~~~~lLl~~~~~~syi~ 157 (225)
T KOG3134|consen 81 FAWLLLQDFESLLLWLSEDDEWVFYRSFA---LPALEVLSSLIERQYLFVFLWCNRETTFVQLSSALLLLKTLLLKSYIS 157 (225)
T ss_pred HHHHHHHHhHhhcccccCCCcchhhhhHH---HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHH
Confidence 88888887766555555 45555555431 11112222211113333322211111111110 01123333
Q ss_pred -HHHHHHHHHHHHHHHHHHhhccCCCc--hhHHHHHHHHHHHHHHHHHHhhcchh
Q 026819 154 -FLLAVLISSYFKIFLVAMMVWNFPSS--VIYIIDLFVLSSNTVALKVITESAMN 205 (232)
Q Consensus 154 -ll~alllSS~~KLf~ilmlIW~~~~s--~~~li~~~vl~snv~Al~vv~~~~~~ 205 (232)
+......||+.|.++|.|++|++|.+ +...+.|..++++++|++++++.++.
T Consensus 158 ~i~~~~~~s~~~~v~~Ifml~~~~~~~~v~~~~v~~~~~~a~l~~l~i~s~~~~~ 212 (225)
T KOG3134|consen 158 VISLLVILSSCVKVNPIFMLISCYQTSRVALGIVYWVSFLAVLLALKILSTSRYF 212 (225)
T ss_pred HHHHHHHHHHhhhhhheeeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67778888888899999999999975 45789999999999999999877764
No 3
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=100.00 E-value=3.3e-38 Score=269.86 Aligned_cols=194 Identities=21% Similarity=0.321 Sum_probs=134.3
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccccccccchhHHHHHHHHhcCcchhheeeccccccccchhhhHHHH--
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWK-- 80 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayrHllfN~~~~~~~~~~~~l~k-- 80 (232)
++|||||.||++||++||.++||+++||+|++.+|||+|.|+|+++||++|+|||+|||++||+++.++...+....|
T Consensus 1 mvCIeCg~~vdsLyt~ysts~iqls~Cp~C~~~~DkY~Eld~vl~~iDllLlK~~iyRHllFNsl~artf~nd~~c~~~v 80 (239)
T COG5254 1 MVCIECGSRVDSLYTRYSTSAIQLSRCPSCNRKMDKYFELDGVLKLIDLLLLKRRIYRHLLFNSLRARTFTNDVLCMLAV 80 (239)
T ss_pred CeeeEcCCccceeeeeccCcceehhcCchHHHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHhhHhHHHHHhHHHHHHHH
Confidence 589999999999999999999999999999999999999999999999999999999999999988554221111111
Q ss_pred ------HHHHHHHHHHHHHHHhhccCCCCCCchhh-----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026819 81 ------STVGFLLLDAYRSLLLSRSNEGQSSSMSF-----------------SLLAWIFQKMLKDVVLGNVMFLGVFLHA 137 (232)
Q Consensus 81 ------l~vl~lL~eay~~~~~~~~~~~~~~s~~~-----------------~~~~~~~~~~l~~~~l~~~~f~~~~~l~ 137 (232)
+..+...++.|.+|-..++. +...+.+ .....++......++.+..+|.....+-
T Consensus 81 ~~Fc~~~~~l~~~f~~~L~w~~~E~~--~~~~~a~~~~~~pes~~~~s~ilr~~~s~qyl~~~~vcl~~~~l~~~f~~lf 158 (239)
T COG5254 81 RMFCEPILQLHEAFGLLLSWGPGEGV--SIAEMATICRDVPESLMETSLILRLVFSMQYLHAGFVCLSSALLLSSFYYLF 158 (239)
T ss_pred HHHHHHHHHHHHHhhhheeecccccc--chHHHHHhhhhhHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22344455555555322221 0000100 0011122333344445555555443333
Q ss_pred HHHHhhccCCChhHHHHHHHHHHHHHHHHHHHHHhhccCCCc-hhHHHHHHHHHHHHHHHHHHhh
Q 026819 138 SRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSS-VIYIIDLFVLSSNTVALKVITE 201 (232)
Q Consensus 138 ~~~~l~~~~~~~~~~~ll~alllSS~~KLf~ilmlIW~~~~s-~~~li~~~vl~snv~Al~vv~~ 201 (232)
....++|.. ....-..++.+|+.+|.+|++|+||+||.+ ++..|+|.++.+|+++++++|.
T Consensus 159 ~~~~~~Wk~---~~~~s~~~I~ls~~a~~~pV~m~Iw~yd~~Ia~~~I~wv~~~~~~~~l~Ilt~ 220 (239)
T COG5254 159 MFIMTMWKY---QCEESLLVIELSCVACNSPVIMEIWLYDNEIALGCIYWVKFAAGLVCLRILTT 220 (239)
T ss_pred HHHHHHHHH---HhhhcchheeeecchhcchhheeehhcchHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 333333321 112233589999999999999999999974 4679999999999999999996
No 4
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=96.62 E-value=0.0084 Score=52.96 Aligned_cols=114 Identities=17% Similarity=0.101 Sum_probs=77.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHhhcc---CCChhHHHHHHHHHHHHHHH-HHHHHHhhccCCCchhHHHHH
Q 026819 112 LAWIFQKMLKDVVLGNVMFLGVFLHASR-ILLNTS---AGASSFKDFLLAVLISSYFK-IFLVAMMVWNFPSSVIYIIDL 186 (232)
Q Consensus 112 ~~~~~~~~l~~~~l~~~~f~~~~~l~~~-~~l~~~---~~~~~~~~ll~alllSS~~K-Lf~ilmlIW~~~~s~~~li~~ 186 (232)
.+|.++..+.....+...+.+.-.+... .+.... .+.++...+++++.++||+| .+...+..|..+...+++++|
T Consensus 100 ~e~~~~~~~~~~~~~~~~~~i~~~~l~~f~~~~~~~~~~~l~~~~lLl~~~~~~syi~~i~~~~~~s~~~~v~~Ifml~~ 179 (225)
T KOG3134|consen 100 DEWVFYRSFALPALEVLSSLIERQYLFVFLWCNRETTFVQLSSALLLLKTLLLKSYISVISLLVILSSCVKVNPIFMLIS 179 (225)
T ss_pred CcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhheeeeeh
Confidence 3677888777777777776654333332 222222 23567788999999999999 788888888777666677777
Q ss_pred HHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHHhhh
Q 026819 187 FVLSSNTVALKVITESAMNRILGVCLVAHAVKFFVVQGL 225 (232)
Q Consensus 187 ~vl~snv~Al~vv~~~~~~~~~~~~~~a~~~r~~~~~~~ 225 (232)
-..++++.+-.+-.-.--....+.+++++..|+++..+.
T Consensus 180 ~~~~~~v~~~~v~~~~~~a~l~~l~i~s~~~~~l~~s~~ 218 (225)
T KOG3134|consen 180 CYQTSRVALGIVYWVSFLAVLLALKILSTSRYFLFDSIC 218 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 766666655554443333356677788999999887653
No 5
>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=93.00 E-value=0.037 Score=35.36 Aligned_cols=34 Identities=32% Similarity=0.640 Sum_probs=23.7
Q ss_pred CccccccCcccccceeeccCCceEeecCCCccccccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (232)
+|+|.+||+..+.+... + + -....||+||.-+.|
T Consensus 5 ~y~C~~Cg~~fe~~~~~-~-~-~~~~~CP~Cg~~~~r 38 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI-S-D-DPLATCPECGGDVRR 38 (41)
T ss_pred EEEcCCCCCEEEEEEec-C-C-CCCCCCCCCCCccee
Confidence 47999999987765322 1 1 367789999985443
No 6
>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=92.60 E-value=0.086 Score=34.65 Aligned_cols=33 Identities=30% Similarity=0.729 Sum_probs=23.4
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYI 40 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYi 40 (232)
++|.+||... +..++..+.+ .|++||.+.|..+
T Consensus 1 m~Cp~Cg~~~--~~~D~~~g~~---vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 1 MKCPNCGSKE--IVFDPERGEL---VCPNCGLVLEENI 33 (43)
T ss_dssp ESBTTTSSSE--EEEETTTTEE---EETTT-BBEE-TT
T ss_pred CCCcCCcCCc--eEEcCCCCeE---ECCCCCCEeeccc
Confidence 5799999965 6666766653 8999998877554
No 7
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=91.96 E-value=0.074 Score=35.41 Aligned_cols=31 Identities=23% Similarity=0.573 Sum_probs=22.7
Q ss_pred CCccccccCcccccceeeccCCceEeecCCCcccccc
Q 026819 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (232)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (232)
++|+|.+||..++- .++. ....||+||...+
T Consensus 2 ~~y~C~~CG~~~~~-----~~~~-~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVEL-----DEYG-TGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEE-----CCCC-CceECCCCCCeEE
Confidence 46899999998643 2222 2679999998766
No 8
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=91.48 E-value=0.11 Score=34.75 Aligned_cols=28 Identities=29% Similarity=0.647 Sum_probs=20.4
Q ss_pred CCccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
+.|+|-+||+.++.- +.+ .-+|++||.-
T Consensus 1 ~~Y~C~~Cg~~~~~~----~~~---~irC~~CG~r 28 (44)
T smart00659 1 MIYICGECGRENEIK----SKD---VVRCRECGYR 28 (44)
T ss_pred CEEECCCCCCEeecC----CCC---ceECCCCCce
Confidence 579999999987642 232 3479999963
No 9
>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=90.22 E-value=0.11 Score=34.16 Aligned_cols=34 Identities=29% Similarity=0.641 Sum_probs=24.7
Q ss_pred CccccccCcccccceeeccCCceEeecCCCccc-cccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA-VADE 38 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~-~~Dk 38 (232)
+|+|-+||+.-+.+.. .+. -....||+||. -+.|
T Consensus 5 ey~C~~Cg~~fe~~~~-~~~--~~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQS-ISE--DDPVPCPECGSTEVRR 39 (42)
T ss_pred EEEeCCCCCEEEEEEE-cCC--CCCCcCCCCCCCceEE
Confidence 5899999998877643 222 46779999998 4443
No 10
>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=89.22 E-value=0.16 Score=34.32 Aligned_cols=30 Identities=40% Similarity=0.877 Sum_probs=22.3
Q ss_pred CccccccCcccccceeeccCCceEeecCCCccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
+|+|-+||+..+.+ ...+. -....||+||.
T Consensus 5 ey~C~~Cg~~fe~~-~~~~~--~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVL-QKMSD--DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEE-EecCC--CCCCCCCCCCC
Confidence 58999999987765 33332 25678999997
No 11
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=88.77 E-value=0.19 Score=29.75 Aligned_cols=24 Identities=42% Similarity=0.796 Sum_probs=17.7
Q ss_pred CCccccccCcccccceeeccCCceEeecCCCccc
Q 026819 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
|+..|.+||++++. .-.-|++||+
T Consensus 1 m~~~Cp~Cg~~~~~----------~~~fC~~CG~ 24 (26)
T PF13248_consen 1 MEMFCPNCGAEIDP----------DAKFCPNCGA 24 (26)
T ss_pred CcCCCcccCCcCCc----------ccccChhhCC
Confidence 56789999997643 2347999986
No 12
>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=88.65 E-value=0.27 Score=30.87 Aligned_cols=25 Identities=28% Similarity=0.826 Sum_probs=17.0
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
|+|-+||+.++ + -..+. .+|++||.
T Consensus 1 Y~C~~Cg~~~~-~---~~~~~---irC~~CG~ 25 (32)
T PF03604_consen 1 YICGECGAEVE-L---KPGDP---IRCPECGH 25 (32)
T ss_dssp EBESSSSSSE--B---STSST---SSBSSSS-
T ss_pred CCCCcCCCeeE-c---CCCCc---EECCcCCC
Confidence 68999999998 2 22333 38999985
No 13
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=87.28 E-value=0.46 Score=37.61 Aligned_cols=52 Identities=29% Similarity=0.623 Sum_probs=34.1
Q ss_pred CccccccCcccccceeeccCCceEeecCCCccccccccccchhHHHHHHHHhcC--cchhheeecccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHK--PQAYRHLLYNVL 67 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k--~~ayrHllfN~~ 67 (232)
.+.|.+||+.-.. |.+..-| .||+|+..+ .-.++|-...+ |-.|||++|=..
T Consensus 42 ~~~C~~Cg~~~~~----~~SCk~R--~CP~C~~~~--------~~~W~~~~~~~ll~~~y~HvVFTlP 95 (111)
T PF14319_consen 42 RYRCEDCGHEKIV----YNSCKNR--HCPSCQAKA--------TEQWIEKQREDLLPVPYFHVVFTLP 95 (111)
T ss_pred eeecCCCCceEEe----cCcccCc--CCCCCCChH--------HHHHHHHHHhhCCCCCeEEEEEcCc
Confidence 5789999987522 4444334 899999753 33444443333 588999999763
No 14
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=87.28 E-value=0.2 Score=34.46 Aligned_cols=28 Identities=32% Similarity=0.860 Sum_probs=19.9
Q ss_pred CCccccccCcccccceeeccCCceEeecCCCccc
Q 026819 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
++|+|..||..++.+ . .-+--.||.||.
T Consensus 5 ~~Y~C~~Cg~~~~~~---~---~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVELD---Q---ETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeehh---h---ccCceeCCCCCc
Confidence 469999999999543 1 123348999985
No 15
>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=86.49 E-value=0.33 Score=35.40 Aligned_cols=36 Identities=33% Similarity=0.905 Sum_probs=24.7
Q ss_pred CccccccCcccccceee--ccCCceEeecCCCccc---cccc
Q 026819 2 EYRCVKCGFRIKTLFVQ--YSPGNIRLMKCENCRA---VADE 38 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~--y~~~~i~l~~C~~C~~---~~Dk 38 (232)
.+-|-.|+++....+.+ |.+|. .+.+||+|++ +||.
T Consensus 4 ~FTC~~C~~Rs~~~~sk~aY~~Gv-Viv~C~gC~~~HlIaDn 44 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSKQAYHKGV-VIVQCPGCKNRHLIADN 44 (66)
T ss_dssp EEEETTTTEEEEEEEEHHHHHTSE-EEEE-TTS--EEES--S
T ss_pred EEEcCCCCCccceeeCHHHHhCCe-EEEECCCCcceeeehhh
Confidence 46799999998887766 66654 8999999986 5664
No 16
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=84.99 E-value=0.35 Score=30.51 Aligned_cols=32 Identities=25% Similarity=0.544 Sum_probs=23.5
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccccccccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE 41 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE 41 (232)
.++|..||+-.+. .-....||.|+...+++.+
T Consensus 2 ~~~C~~CG~i~~g--------~~~p~~CP~Cg~~~~~F~~ 33 (34)
T cd00729 2 VWVCPVCGYIHEG--------EEAPEKCPICGAPKEKFEE 33 (34)
T ss_pred eEECCCCCCEeEC--------CcCCCcCcCCCCchHHcEE
Confidence 4789999976432 1134589999999888765
No 17
>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=82.54 E-value=0.77 Score=32.57 Aligned_cols=30 Identities=33% Similarity=0.688 Sum_probs=24.0
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (232)
-.|-.||++.+. +.+-+.-.|++||...|.
T Consensus 29 q~C~~CG~~~~~------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 29 QTCPRCGHRNKK------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred cCccCccccccc------ccccceEEcCCCCCEECc
Confidence 469999999877 335588899999988775
No 18
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=81.22 E-value=0.57 Score=29.88 Aligned_cols=28 Identities=32% Similarity=0.669 Sum_probs=13.2
Q ss_pred CCccccccCccc--ccceeeccCCceEeecCCCcc
Q 026819 1 MEYRCVKCGFRI--KTLFVQYSPGNIRLMKCENCR 33 (232)
Q Consensus 1 ~~~~Ci~C~~~v--~~l~~~y~~~~i~l~~C~~C~ 33 (232)
+.+.|.|||.+- +-|++ +..+..|.+|.
T Consensus 2 ~~~~C~eC~~~f~dSyL~~-----~F~~~VCD~CR 31 (34)
T PF01286_consen 2 DYPKCDECGKPFMDSYLLN-----NFDLPVCDKCR 31 (34)
T ss_dssp S-EE-TTT--EES-SSCCC-----CTS-S--TTT-
T ss_pred CCchHhHhCCHHHHHHHHH-----hCCcccccccc
Confidence 358999999984 34433 44566888885
No 19
>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=80.50 E-value=1.4 Score=39.94 Aligned_cols=35 Identities=23% Similarity=0.525 Sum_probs=20.2
Q ss_pred ccccccCcccccceeec---cCCceEeecCCCccc---ccc
Q 026819 3 YRCVKCGFRIKTLFVQY---SPGNIRLMKCENCRA---VAD 37 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y---~~~~i~l~~C~~C~~---~~D 37 (232)
-.|..||+.-..-+.-+ ..+..|++.|++||. ..|
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEE
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHh
Confidence 46999999876666555 456899999999994 555
No 20
>PF12773 DZR: Double zinc ribbon
Probab=80.47 E-value=0.85 Score=30.36 Aligned_cols=31 Identities=26% Similarity=0.491 Sum_probs=21.4
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccccccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY 39 (232)
.-.|.+||++++ ........|++|++..++-
T Consensus 12 ~~fC~~CG~~l~-------~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 12 AKFCPHCGTPLP-------PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred ccCChhhcCChh-------hccCCCCCCcCCcCCCcCC
Confidence 346889999887 2222455799999876654
No 21
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=80.34 E-value=0.89 Score=35.24 Aligned_cols=29 Identities=24% Similarity=0.780 Sum_probs=23.0
Q ss_pred CCccccccCcccccceeeccCCceEeecCCCcc
Q 026819 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCR 33 (232)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~ 33 (232)
+.+.|.+||..|.- .++|+-.-..||+|-
T Consensus 3 ~~F~C~~CG~~V~p----~~~g~~~RNHCP~CL 31 (92)
T PF12647_consen 3 ESFTCVHCGLTVSP----LAAGSAHRNHCPSCL 31 (92)
T ss_pred cccCccccCCCccc----CCCCCCccCcCcccc
Confidence 46899999999976 356666667999995
No 22
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=78.52 E-value=1.2 Score=37.45 Aligned_cols=44 Identities=25% Similarity=0.462 Sum_probs=30.9
Q ss_pred ccccccCccc-ccceeec-cCCc-e-EeecCCCccccccccccchhHH
Q 026819 3 YRCVKCGFRI-KTLFVQY-SPGN-I-RLMKCENCRAVADEYIECEIMI 46 (232)
Q Consensus 3 ~~Ci~C~~~v-~~l~~~y-~~~~-i-~l~~C~~C~~~~DkYiE~d~~i 46 (232)
+.|.+||+|- .-.=.+| ++|| + |.-+|++||.-.--|=+.+.++
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 4799999986 3333444 5543 3 4689999999888777776653
No 23
>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=77.42 E-value=1.2 Score=36.48 Aligned_cols=33 Identities=18% Similarity=0.479 Sum_probs=21.8
Q ss_pred ccccccCcccccceee-----cc----CCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQ-----YS----PGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~-----y~----~~~i~l~~C~~C~~~ 35 (232)
-+|..||.+...+=++ -. ..+-+...|++||++
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCE
Confidence 4899999986554222 00 113358899999985
No 24
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=76.11 E-value=1.1 Score=26.00 Aligned_cols=21 Identities=33% Similarity=0.784 Sum_probs=14.8
Q ss_pred cccccCcccccceeeccCCceEeecCCCccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
.|.+||++++. . -..|++||.
T Consensus 1 ~Cp~CG~~~~~------~----~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIED------D----AKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCC------c----CcchhhhCC
Confidence 38899998854 1 225999986
No 25
>PRK12495 hypothetical protein; Provisional
Probab=74.22 E-value=1.6 Score=38.83 Aligned_cols=29 Identities=28% Similarity=0.521 Sum_probs=22.4
Q ss_pred CccccccCcccccceeeccCCceEeecCCCccccccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (232)
...|-.||.|++. | +| .+.|+.|+++++.
T Consensus 42 a~hC~~CG~PIpa----~-pG---~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 42 NAHCDECGDPIFR----H-DG---QEFCPTCQQPVTE 70 (226)
T ss_pred hhhcccccCcccC----C-CC---eeECCCCCCcccc
Confidence 3579999999993 4 43 3579999998773
No 26
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=73.74 E-value=1.7 Score=38.34 Aligned_cols=38 Identities=24% Similarity=0.624 Sum_probs=24.7
Q ss_pred ccccCcccccceeec-------------cCCceEeecCCCccccc--cccccc
Q 026819 5 CVKCGFRIKTLFVQY-------------SPGNIRLMKCENCRAVA--DEYIEC 42 (232)
Q Consensus 5 Ci~C~~~v~~l~~~y-------------~~~~i~l~~C~~C~~~~--DkYiE~ 42 (232)
|..||.|.+.++... =|+.+.++.|+.||+.= .+.++.
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~W~~~ 53 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGRWVDP 53 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCCEeeec
Confidence 777887776653211 24578999999999753 344444
No 27
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=73.65 E-value=1.1 Score=35.45 Aligned_cols=37 Identities=24% Similarity=0.460 Sum_probs=26.1
Q ss_pred CCccccccCcccccceeeccCCceEeecCCCccccccccccch
Q 026819 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (232)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d 43 (232)
|..+|+.||+.-+. .+..-+.-||+||.--=+|+--|
T Consensus 1 MpH~CtrCG~vf~~------g~~~il~GCp~CG~nkF~yv~~e 37 (112)
T COG3364 1 MPHQCTRCGEVFDD------GSEEILSGCPKCGCNKFLYVPEE 37 (112)
T ss_pred CCceeccccccccc------ccHHHHccCccccchheEecccc
Confidence 67899999986433 13445778999997665666555
No 28
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=73.57 E-value=3 Score=26.98 Aligned_cols=27 Identities=22% Similarity=0.859 Sum_probs=20.5
Q ss_pred ccccCcccccceeeccCCceEeecCCCcccc
Q 026819 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 5 Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
|..|++....... +.+.+..|++|+.+
T Consensus 2 CP~C~~~l~~~~~----~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 2 CPRCGTELEPVRL----GDVEIDVCPSCGGI 28 (41)
T ss_pred cCCCCcccceEEE----CCEEEEECCCCCeE
Confidence 8889987554322 56999999999974
No 29
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=73.15 E-value=2 Score=29.45 Aligned_cols=32 Identities=25% Similarity=0.537 Sum_probs=26.4
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
+.+|.+|+..-...|++...+. ...|..|+-.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~--~~LCnaCgl~ 34 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGN--KTLCNACGLY 34 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCC--CcEeecccHH
Confidence 5789999999999998887765 5779999854
No 30
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=70.87 E-value=2 Score=25.67 Aligned_cols=22 Identities=23% Similarity=0.618 Sum_probs=16.6
Q ss_pred cccccCcccccceeeccCCceEeecCCCcccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.|-+|++.|+. .-..||+||..
T Consensus 2 ~CP~C~~~V~~----------~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPE----------SAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchh----------hcCcCCCCCCC
Confidence 58999999854 34479999853
No 31
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=70.07 E-value=2.4 Score=26.91 Aligned_cols=30 Identities=17% Similarity=0.405 Sum_probs=14.9
Q ss_pred cccccCcccccceeeccCCceEeecCCCcccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
-|.+||+|++.- .-.+++-.-..|++|+.+
T Consensus 2 fC~~CG~~l~~~--ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERR--IPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE----TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhh--cCCCCCccceECCCCCCE
Confidence 389999997542 223344455579999865
No 32
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=70.05 E-value=1.3 Score=30.55 Aligned_cols=33 Identities=18% Similarity=0.486 Sum_probs=23.6
Q ss_pred CccccccCccc-ccceeeccCCceEeecCCCcccc
Q 026819 2 EYRCVKCGFRI-KTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 2 ~~~Ci~C~~~v-~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.-+|-.|+..+ ++.+.+-..+ -++..||+||++
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~-~~i~~Cp~CgRi 55 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKG-DEIVFCPNCGRI 55 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcC-CCeEECcCCCcc
Confidence 34788899885 4555555444 478899999985
No 33
>PRK00420 hypothetical protein; Validated
Probab=69.05 E-value=2.7 Score=33.60 Aligned_cols=28 Identities=21% Similarity=0.317 Sum_probs=20.2
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (232)
..|..||.|.-.+ +++ -..||+||++.+
T Consensus 24 ~~CP~Cg~pLf~l---k~g----~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFEL---KDG----EVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceec---CCC----ceECCCCCCeee
Confidence 4799999997655 333 348999998543
No 34
>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=68.82 E-value=2.3 Score=26.73 Aligned_cols=35 Identities=20% Similarity=0.481 Sum_probs=19.2
Q ss_pred CCccccccCcccccceeeccCCceEeecCCCccccc
Q 026819 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (232)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (232)
|...|.+||+...-==.+...+. ..-.|++|+...
T Consensus 1 M~~~CP~C~~~~~v~~~~~~~~~-~~v~C~~C~~~~ 35 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLGANG-GKVRCGKCGHVW 35 (38)
T ss_pred CEEECCCCCCEEEeCHHHcCCCC-CEEECCCCCCEE
Confidence 45679999985211101111111 245699999864
No 35
>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=67.65 E-value=3.9 Score=27.09 Aligned_cols=29 Identities=24% Similarity=0.606 Sum_probs=18.9
Q ss_pred CCccccccCcccccceeeccCCceEeecCCCccc
Q 026819 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
++++|..||+. .. |.-.+-+.-+|.+|++
T Consensus 17 ~g~~CP~Cg~~--~~---~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGST--KH---YRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCe--ee---EEeCCCCeEECCCCCC
Confidence 46789999987 22 2222246678988875
No 36
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=67.56 E-value=5.8 Score=36.94 Aligned_cols=63 Identities=16% Similarity=0.382 Sum_probs=40.6
Q ss_pred ccccccCcccccceeeccC--CceEeecCCCcccc---c----ccccc---chhHHHHHHHHhcCcchhheeeccc
Q 026819 3 YRCVKCGFRIKTLFVQYSP--GNIRLMKCENCRAV---A----DEYIE---CEIMILLIDLILHKPQAYRHLLYNV 66 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~--~~i~l~~C~~C~~~---~----DkYiE---~d~~i~~iDl~L~k~~ayrHllfN~ 66 (232)
-.|.+||..-+--|-...+ ..+|.+.|++|+.- . |+.+| -|.--+.+|++..+ +-|++.=+|-
T Consensus 227 ~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~p~adDlatL~LDl~a~e-~Gy~r~~~Np 301 (309)
T PRK03564 227 VKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQEKDPKVEAVADDLASLVLDARMEQ-EGFARSSINP 301 (309)
T ss_pred ccCCCCCCCCceeeeeecCCCcceEeeecccccccceecccccCCCCCcchhHHhhhHhHHHHHh-cCCCCCCCCc
Confidence 4699999863333332322 47899999999953 2 22221 13456788888855 5788887774
No 37
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=66.24 E-value=2.5 Score=36.01 Aligned_cols=33 Identities=15% Similarity=0.460 Sum_probs=21.7
Q ss_pred ccccccCcccccceeeccC---------CceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSP---------GNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~---------~~i~l~~C~~C~~~ 35 (232)
-+|.+||.+...+.+.=-. ..-....|++||++
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 5899999997665332211 12246779999985
No 38
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.86 E-value=1.3 Score=33.41 Aligned_cols=34 Identities=29% Similarity=0.717 Sum_probs=23.0
Q ss_pred CccccccCcccccceeeccCCceEeecCCCccccccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (232)
.|.|.|||+.-+-+ ...+.+ -+|.|+.|+....|
T Consensus 12 ~Y~c~~cg~~~dvv-q~~~dd--plt~ce~c~a~~kk 45 (82)
T COG2331 12 SYECTECGNRFDVV-QAMTDD--PLTTCEECGARLKK 45 (82)
T ss_pred EEeecccchHHHHH-HhcccC--ccccChhhChHHHH
Confidence 47899999984433 112333 68899999976544
No 39
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=65.03 E-value=2.9 Score=25.92 Aligned_cols=31 Identities=26% Similarity=0.590 Sum_probs=21.6
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccccccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE 41 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE 41 (232)
++|-.||+-.+.- . .-..||.|+.-.+.+.+
T Consensus 2 ~~C~~CGy~y~~~-------~-~~~~CP~Cg~~~~~F~~ 32 (33)
T cd00350 2 YVCPVCGYIYDGE-------E-APWVCPVCGAPKDKFEK 32 (33)
T ss_pred EECCCCCCEECCC-------c-CCCcCcCCCCcHHHcEE
Confidence 7899999763321 1 45589999987776543
No 40
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=64.36 E-value=4.3 Score=28.53 Aligned_cols=27 Identities=26% Similarity=0.655 Sum_probs=19.7
Q ss_pred CCccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
++.+|..||.+++. ++ -+..|+.|+.+
T Consensus 4 ~~~~C~~Cg~~~~~------~d--DiVvCp~Cgap 30 (54)
T PF14446_consen 4 EGCKCPVCGKKFKD------GD--DIVVCPECGAP 30 (54)
T ss_pred cCccChhhCCcccC------CC--CEEECCCCCCc
Confidence 35789999999843 22 45689999865
No 41
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=63.92 E-value=2.6 Score=34.66 Aligned_cols=28 Identities=25% Similarity=0.540 Sum_probs=19.4
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
..+|++||+--+. .+..-|.-||+||.-
T Consensus 1 PH~Ct~Cg~~f~d------gs~eil~GCP~CGg~ 28 (131)
T PF09845_consen 1 PHQCTKCGRVFED------GSKEILSGCPECGGN 28 (131)
T ss_pred CcccCcCCCCcCC------CcHHHHccCcccCCc
Confidence 3689999986432 222467789999953
No 42
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=63.82 E-value=3.3 Score=29.54 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=14.2
Q ss_pred ecCCCccc-----------cccccccchh
Q 026819 27 MKCENCRA-----------VADEYIECEI 44 (232)
Q Consensus 27 ~~C~~C~~-----------~~DkYiE~d~ 44 (232)
++||.||. ..|||-.|-.
T Consensus 18 e~Cp~CG~~t~~~~PprFSPeD~y~kYR~ 46 (59)
T COG2260 18 EKCPVCGGDTKVPHPPRFSPEDKYGKYRR 46 (59)
T ss_pred ccCCCCCCccccCCCCCCCccchHHHHHH
Confidence 68999994 5799988764
No 43
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=63.18 E-value=2.6 Score=30.94 Aligned_cols=26 Identities=31% Similarity=0.848 Sum_probs=18.9
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (232)
++| .||... |++++-+-.+| .||+..
T Consensus 4 frC-~Cgr~l------ya~e~~kTkkC-~CG~~l 29 (68)
T PF09082_consen 4 FRC-DCGRYL------YAKEGAKTKKC-VCGKTL 29 (68)
T ss_dssp EEE-TTS--E------EEETT-SEEEE-TTTEEE
T ss_pred EEe-cCCCEE------EecCCcceeEe-cCCCee
Confidence 578 799876 88888899999 999753
No 44
>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=61.56 E-value=4.1 Score=38.61 Aligned_cols=23 Identities=35% Similarity=0.858 Sum_probs=18.2
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
|+|-+||+..+.- +-+||+|++.
T Consensus 1 ~~c~~cg~~~~~~----------~g~cp~c~~w 23 (372)
T cd01121 1 YVCSECGYVSPKW----------LGKCPECGEW 23 (372)
T ss_pred CCCCCCCCCCCCc----------cEECcCCCCc
Confidence 7899999987663 3479999864
No 45
>PF14353 CpXC: CpXC protein
Probab=61.47 E-value=5.9 Score=31.39 Aligned_cols=56 Identities=20% Similarity=0.551 Sum_probs=36.6
Q ss_pred ccccccCcc-cccceeeccC------------CceEeecCCCccccccccccchhHHHHHHHHhcCcchhheeeccccc
Q 026819 3 YRCVKCGFR-IKTLFVQYSP------------GNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLN 68 (232)
Q Consensus 3 ~~Ci~C~~~-v~~l~~~y~~------------~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayrHllfN~~~ 68 (232)
-.|.+||++ -..+|+.... |.+-.-.||+||+.. +++++ ++-+.++. +-++++..+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~--~~~~p-------~lY~D~~~-~~~i~~~P~ 70 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKF--RLEYP-------LLYHDPEK-KFMIYYFPD 70 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCce--ecCCC-------EEEEcCCC-CEEEEEcCC
Confidence 469999998 4566666543 466688999999876 46665 23344443 455556544
No 46
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=60.96 E-value=3.8 Score=32.46 Aligned_cols=28 Identities=25% Similarity=0.561 Sum_probs=20.3
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (232)
-+|.+||++---| |-.-..||+||..-+
T Consensus 10 R~Cp~CG~kFYDL-------nk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-------NKDPIVCPKCGTEFP 37 (108)
T ss_pred ccCCCCcchhccC-------CCCCccCCCCCCccC
Confidence 4799999998555 224457999998643
No 47
>PF14149 YhfH: YhfH-like protein
Probab=59.93 E-value=1.6 Score=28.39 Aligned_cols=24 Identities=29% Similarity=0.832 Sum_probs=16.6
Q ss_pred ccccccCcccccceeeccCCceEeecCCCc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENC 32 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C 32 (232)
..|.+||..+++-..-|++ .|++|
T Consensus 14 K~C~~CG~~i~EQ~E~Y~n------~C~~C 37 (37)
T PF14149_consen 14 KKCTECGKEIEEQAECYGN------ECDRC 37 (37)
T ss_pred cccHHHHHHHHHHHHHHhC------cCCCC
Confidence 4688888887776666665 46665
No 48
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=58.97 E-value=6.8 Score=23.09 Aligned_cols=24 Identities=29% Similarity=0.638 Sum_probs=14.2
Q ss_pred ccccCcccccceeeccCCceEeecCCCccc
Q 026819 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 5 Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
|+.||.++..- +.-..-.||+||.
T Consensus 1 C~sC~~~i~~r------~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPR------EQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCc------ccCceEeCCCCCC
Confidence 77888876431 1112337999984
No 49
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=58.89 E-value=5.3 Score=31.55 Aligned_cols=53 Identities=19% Similarity=0.337 Sum_probs=34.0
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccc-----cccccchhHHHHHHHHhcC
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA-----DEYIECEIMILLIDLILHK 55 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~-----DkYiE~d~~i~~iDl~L~k 55 (232)
+-|..|||...+.-+.=..+++-...|++||.-. .=.-+.|..-.|+|+-+--
T Consensus 23 FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wvDay~eg 80 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVYSAWVDAYLEG 80 (104)
T ss_pred EecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHHHHHHHHHHhc
Confidence 5699999985543333456688889999999521 1122345556777776643
No 50
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=58.73 E-value=6.6 Score=36.13 Aligned_cols=34 Identities=29% Similarity=0.771 Sum_probs=23.7
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccccc-ccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD-EYI 40 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D-kYi 40 (232)
+.+|.+||. +.+-.+|+.|. ..|.+||-+.+ .-|
T Consensus 11 ~~~Cp~Cg~--~~iv~d~~~Ge---~vC~~CG~Vl~e~~i 45 (310)
T PRK00423 11 KLVCPECGS--DKLIYDYERGE---IVCADCGLVIEENII 45 (310)
T ss_pred CCcCcCCCC--CCeeEECCCCe---EeecccCCccccccc
Confidence 457999996 35656676653 58999998654 344
No 51
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=57.83 E-value=7.2 Score=27.04 Aligned_cols=40 Identities=18% Similarity=0.385 Sum_probs=31.9
Q ss_pred cccccCcccccceeeccCCceEeecCCCccccccccccch
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d 43 (232)
.|..||+++.-+-..-.++.--.+.|+.|.++-.=.++.|
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d 41 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVTVD 41 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEEEC
Confidence 5999999998876666666778999999999866655554
No 52
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=57.56 E-value=4.3 Score=36.64 Aligned_cols=33 Identities=24% Similarity=0.370 Sum_probs=21.1
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.+|+.||...+.-...-...+..+.+|++|+..
T Consensus 123 ~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 155 (250)
T COG0846 123 VRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP 155 (250)
T ss_pred eEeCCCcCccchhhhhhhcccCCCCcCccCCCc
Confidence 579999987653332222223356789999987
No 53
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=57.49 E-value=5.1 Score=25.50 Aligned_cols=34 Identities=24% Similarity=0.472 Sum_probs=19.4
Q ss_pred CCccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
|.-.|.+|++.-+-=-.+-.. .-+.-+|++|+++
T Consensus 1 M~i~CP~C~~~f~v~~~~l~~-~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDDKLPA-GGRKVRCPKCGHV 34 (37)
T ss_pred CEEECCCCCceEEcCHHHccc-CCcEEECCCCCcE
Confidence 345788998862211111222 2356789999975
No 54
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=57.47 E-value=11 Score=35.15 Aligned_cols=62 Identities=16% Similarity=0.401 Sum_probs=39.7
Q ss_pred ccccccCcccccc-eeecc----CCceEeecCCCcccc---ccc----ccc---chhHHHHHHHHhcCcchhheeeccc
Q 026819 3 YRCVKCGFRIKTL-FVQYS----PGNIRLMKCENCRAV---ADE----YIE---CEIMILLIDLILHKPQAYRHLLYNV 66 (232)
Q Consensus 3 ~~Ci~C~~~v~~l-~~~y~----~~~i~l~~C~~C~~~---~Dk----YiE---~d~~i~~iDl~L~k~~ayrHllfN~ 66 (232)
-.|.+||+. +.+ |-... .+.+|.+.|++|+.- .|. -+| -|.--+.+|++..+ +-|+..=+|-
T Consensus 225 ~~C~~Cg~~-~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~~~adDlaSL~LD~~a~e-~Gy~r~~~np 301 (305)
T TIGR01562 225 VKCSHCEES-KHLAYLSLEHDAEKAVLKAETCDSCQGYLKILYQEKDPHADAVADDLASLALDMRMAE-DGYLRRSPNP 301 (305)
T ss_pred ccCCCCCCC-CceeeEeecCCCCCcceEEeeccccccchhhhccccCCccCchHHHHhhhHhhHHHHh-cCCCCCCCCc
Confidence 469999997 334 43332 246899999999953 221 111 24456788888865 5788766663
No 55
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=55.70 E-value=4 Score=33.52 Aligned_cols=36 Identities=22% Similarity=0.420 Sum_probs=21.1
Q ss_pred CccccccCccccccee-eccCCceEeecCCCccccccc
Q 026819 2 EYRCVKCGFRIKTLFV-QYSPGNIRLMKCENCRAVADE 38 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~-~y~~~~i~l~~C~~C~~~~Dk 38 (232)
.|+|.+||...+.+=- .+. +.-..-.||+||.....
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~-d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLL-DMDGTFTCPRCGEELEE 135 (147)
T ss_pred EEECcCCCCEeeHHHHHHhc-CCCCcEECCCCCCEEEE
Confidence 5899999977553211 010 11122679999986543
No 56
>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=55.51 E-value=5.7 Score=38.57 Aligned_cols=24 Identities=29% Similarity=0.668 Sum_probs=19.2
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.|+|-+||+..+.. .-+||.|++.
T Consensus 7 ~y~C~~Cg~~~~~~----------~g~Cp~C~~w 30 (454)
T TIGR00416 7 KFVCQHCGADSPKW----------QGKCPACHAW 30 (454)
T ss_pred eEECCcCCCCCccc----------cEECcCCCCc
Confidence 48999999987764 3479999864
No 57
>PHA02942 putative transposase; Provisional
Probab=54.02 E-value=7.5 Score=37.00 Aligned_cols=29 Identities=28% Similarity=0.728 Sum_probs=21.3
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (232)
-.|-.||+..+.+ ..|.-.|++||...|.
T Consensus 326 q~Cs~CG~~~~~l-------~~r~f~C~~CG~~~dr 354 (383)
T PHA02942 326 VSCPKCGHKMVEI-------AHRYFHCPSCGYENDR 354 (383)
T ss_pred ccCCCCCCccCcC-------CCCEEECCCCCCEeCc
Confidence 4699999877543 2367789999987765
No 58
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=53.19 E-value=7.3 Score=24.73 Aligned_cols=32 Identities=28% Similarity=0.628 Sum_probs=19.7
Q ss_pred CCccccccCcc--cccceeeccCCceEeecCCCcccc
Q 026819 1 MEYRCVKCGFR--IKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 1 ~~~~Ci~C~~~--v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
|.-.|.+|+.. ++. .+- ++.-+--+|++|++.
T Consensus 1 M~i~Cp~C~~~y~i~d--~~i-p~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDD--EKI-PPKGRKVRCSKCGHV 34 (36)
T ss_pred CEEECCCCCCEEeCCH--HHC-CCCCcEEECCCCCCE
Confidence 34578899876 221 111 234467789999974
No 59
>PRK11823 DNA repair protein RadA; Provisional
Probab=53.13 E-value=6.6 Score=38.01 Aligned_cols=29 Identities=31% Similarity=0.740 Sum_probs=21.0
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccccccccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE 41 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE 41 (232)
.|+|-+||+..+.. .-+||.|++. +.+.|
T Consensus 7 ~y~C~~Cg~~~~~~----------~g~Cp~C~~w-~t~~e 35 (446)
T PRK11823 7 AYVCQECGAESPKW----------LGRCPECGAW-NTLVE 35 (446)
T ss_pred eEECCcCCCCCccc----------CeeCcCCCCc-cceee
Confidence 58999999987664 2379999864 34444
No 60
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=50.62 E-value=9.3 Score=29.44 Aligned_cols=28 Identities=29% Similarity=0.660 Sum_probs=20.1
Q ss_pred CCccccccCcc-cccceeeccCCceEeecCCCcccc
Q 026819 1 MEYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 1 ~~~~Ci~C~~~-v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
+.|.|..||.+ |+.+ +. -+=+|++|+..
T Consensus 34 ~~~~Cp~C~~~~VkR~----a~---GIW~C~kCg~~ 62 (89)
T COG1997 34 AKHVCPFCGRTTVKRI----AT---GIWKCRKCGAK 62 (89)
T ss_pred cCCcCCCCCCcceeee----cc---CeEEcCCCCCe
Confidence 36899999998 4433 33 46789999963
No 61
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=50.30 E-value=9.2 Score=27.47 Aligned_cols=39 Identities=26% Similarity=0.702 Sum_probs=23.5
Q ss_pred CccccccCccc--ccceeec---cCCceEeecCCCccccccccc
Q 026819 2 EYRCVKCGFRI--KTLFVQY---SPGNIRLMKCENCRAVADEYI 40 (232)
Q Consensus 2 ~~~Ci~C~~~v--~~l~~~y---~~~~i~l~~C~~C~~~~DkYi 40 (232)
.++|+.||..+ .+-|..+ .=|+..+..|.+|.+....|.
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~ 52 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKLGNPYR 52 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHHcCCceE
Confidence 37899999986 4444444 113455566666666655553
No 62
>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=48.67 E-value=6.5 Score=31.59 Aligned_cols=25 Identities=32% Similarity=0.708 Sum_probs=19.0
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
-+|.||+++.+-|= |...|..|+++
T Consensus 70 V~CP~C~K~TKmLG--------r~D~CM~C~~p 94 (114)
T PF11023_consen 70 VECPNCGKQTKMLG--------RVDACMHCKEP 94 (114)
T ss_pred eECCCCCChHhhhc--------hhhccCcCCCc
Confidence 36999999987761 33589999986
No 63
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=47.37 E-value=12 Score=33.18 Aligned_cols=46 Identities=22% Similarity=0.541 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhccCCCc-hhHHHHHHHHHHHHHHHH
Q 026819 152 KDFLLAVLISSYFKIFLVAMMVWNFPSS-VIYIIDLFVLSSNTVALK 197 (232)
Q Consensus 152 ~~ll~alllSS~~KLf~ilmlIW~~~~s-~~~li~~~vl~snv~Al~ 197 (232)
.-++-|.+++|+..+|.+.|+.|+|..+ ....|++-..+.|.-.+.
T Consensus 143 vcl~~~~l~~~f~~lf~~~~~~Wk~~~~~s~~~I~ls~~a~~~pV~m 189 (239)
T COG5254 143 VCLSSALLLSSFYYLFMFIMTMWKYQCEESLLVIELSCVACNSPVIM 189 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchheeeecchhcchhhe
Confidence 3578889999999999999999999863 333444444444443333
No 64
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.19 E-value=8.9 Score=30.51 Aligned_cols=26 Identities=23% Similarity=0.636 Sum_probs=16.4
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.+|-+||+..+. +......||+||..
T Consensus 72 ~~C~~Cg~~~~~-------~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 72 LECKDCSHVFKP-------NALDYGVCEKCHSK 97 (117)
T ss_pred EEhhhCCCcccc-------CCccCCcCcCCCCC
Confidence 479999954322 12233469999975
No 65
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=47.02 E-value=6.6 Score=29.72 Aligned_cols=34 Identities=26% Similarity=0.619 Sum_probs=25.6
Q ss_pred cccccCcccc--cceeeccCCceEeecCCCcccccc
Q 026819 4 RCVKCGFRIK--TLFVQYSPGNIRLMKCENCRAVAD 37 (232)
Q Consensus 4 ~Ci~C~~~v~--~l~~~y~~~~i~l~~C~~C~~~~D 37 (232)
.|-|||.|++ .-++.--.|.-|.-=|+-|..++.
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~ 37 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQ 37 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHH
Confidence 5999999996 445555555667788999998875
No 66
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=46.48 E-value=9.1 Score=33.64 Aligned_cols=30 Identities=27% Similarity=0.664 Sum_probs=22.7
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccc----cccccccchh
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA----VADEYIECEI 44 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~----~~DkYiE~d~ 44 (232)
++| +||.+++. | ..|++|+. .||-|.|--.
T Consensus 1 ~~C-rCG~~l~~------p-----~~Cl~Cg~~~av~~~vy~~~~r 34 (227)
T COG4031 1 LIC-RCGAELSS------P-----AFCLNCGRRHAVGCGVYVSESR 34 (227)
T ss_pred Ccc-ccCCcccc------c-----chhcccCCcceeEeeeeccccE
Confidence 589 99999864 3 47999997 4777877553
No 67
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=45.57 E-value=11 Score=29.93 Aligned_cols=26 Identities=23% Similarity=0.604 Sum_probs=16.9
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
..|-+||+..+.. ......||+||..
T Consensus 71 ~~C~~Cg~~~~~~-------~~~~~~CP~Cgs~ 96 (114)
T PRK03681 71 CWCETCQQYVTLL-------TQRVRRCPQCHGD 96 (114)
T ss_pred EEcccCCCeeecC-------CccCCcCcCcCCC
Confidence 4799999754331 1123569999975
No 68
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=45.42 E-value=13 Score=24.53 Aligned_cols=28 Identities=25% Similarity=0.538 Sum_probs=16.7
Q ss_pred cccccCcccccceeeccCCceEeecCCCcccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
-|.+||..+ +.+-..++ ..-.|++|+..
T Consensus 2 FCp~Cg~~l---~~~~~~~~-~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNML---IPKEGKEK-RRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCcc---ccccCCCC-CEEECCcCCCe
Confidence 489999965 22222222 25579999953
No 69
>PRK07591 threonine synthase; Validated
Probab=44.82 E-value=11 Score=36.05 Aligned_cols=30 Identities=23% Similarity=0.635 Sum_probs=21.0
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccccccccch
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d 43 (232)
.+|+.||+.- .++. . -.||.|+..-| ++||
T Consensus 19 l~C~~Cg~~~-------~~~~-~-~~C~~cg~~l~--~~y~ 48 (421)
T PRK07591 19 LKCRECGAEY-------PLGP-I-HVCEECFGPLE--VAYD 48 (421)
T ss_pred EEeCCCCCcC-------CCCC-C-ccCCCCCCeEE--EEec
Confidence 6899999763 3332 2 57999998877 4444
No 70
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=44.62 E-value=15 Score=26.27 Aligned_cols=38 Identities=32% Similarity=0.870 Sum_probs=20.8
Q ss_pred CccccccCcccccc--eeecc-C--CceEeecCCCcccccccc
Q 026819 2 EYRCVKCGFRIKTL--FVQYS-P--GNIRLMKCENCRAVADEY 39 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l--~~~y~-~--~~i~l~~C~~C~~~~DkY 39 (232)
.+.|+-||.++... +.++. | |..-+..|++|.+..-.|
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~~~Y 49 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPY 49 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcCCce
Confidence 46799999886421 33331 1 233355566665555555
No 71
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=44.27 E-value=10 Score=31.14 Aligned_cols=27 Identities=19% Similarity=0.119 Sum_probs=20.1
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (232)
.+|.+||++---| |-.-..||+||...
T Consensus 10 r~Cp~cg~kFYDL-------nk~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDL-------NRRPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCcccccc-------CCCCccCCCcCCcc
Confidence 5799999987555 22556899999863
No 72
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=44.21 E-value=11 Score=29.50 Aligned_cols=50 Identities=26% Similarity=0.597 Sum_probs=28.4
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccccc----ccc-chhHHHHHHHHhcC
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE----YIE-CEIMILLIDLILHK 55 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk----YiE-~d~~i~~iDl~L~k 55 (232)
..|.+||+. .+--.-+. ++-...|++||.--.. --| .|..--|||...-+
T Consensus 22 f~CP~Cge~--~v~v~~~k-~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wiD~~~eg 76 (99)
T PRK14892 22 FECPRCGKV--SISVKIKK-NIAIITCGNCGLYTEFEVPSVYDEVDVYNKFIDLYLEG 76 (99)
T ss_pred eECCCCCCe--EeeeecCC-CcceEECCCCCCccCEECCccccchhhHHHHHHHHHhc
Confidence 469999954 22212222 4567789999954222 112 25556677776544
No 73
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=44.17 E-value=14 Score=34.37 Aligned_cols=29 Identities=28% Similarity=0.528 Sum_probs=25.0
Q ss_pred cccccCcccccceeeccCCceEeecCCCcccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.|.+|..+-+.+..+|+.| -|.|+.||.+
T Consensus 2 ~c~~C~~~~~~~V~d~~~g---dtvC~~CGlV 30 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAG---DTVCSECGLV 30 (308)
T ss_pred CCCCCCCCCCCeeeeccCC---ceecccCCee
Confidence 5999999888999999885 4799999964
No 74
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=44.12 E-value=11 Score=36.89 Aligned_cols=23 Identities=35% Similarity=0.853 Sum_probs=17.5
Q ss_pred CccccccCcccccceeeccCCceEeecCCCccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
.|+|-|||..-+. =+-+||+|+.
T Consensus 7 ~f~C~~CG~~s~K----------W~GkCp~Cg~ 29 (456)
T COG1066 7 AFVCQECGYVSPK----------WLGKCPACGA 29 (456)
T ss_pred EEEcccCCCCCcc----------ccccCCCCCC
Confidence 3899999987544 2448999995
No 75
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=44.02 E-value=7.1 Score=27.04 Aligned_cols=34 Identities=21% Similarity=0.461 Sum_probs=26.3
Q ss_pred cccccCcccccceeeccCCceEeecCCCcccccccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY 39 (232)
+|.+||..-..++++..++ .-+.|..|+-.--||
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~--~~~LCNaCgl~~~k~ 34 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSG--GSTLCNACGLYWKKH 34 (54)
T ss_pred CCCCCCCCCCcccccCCCC--cchHHHHHHHHHHhc
Confidence 5999999999999987644 456899998655444
No 76
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=43.45 E-value=14 Score=33.89 Aligned_cols=37 Identities=27% Similarity=0.696 Sum_probs=26.7
Q ss_pred CccccccCcccccceeeccCCceEeecCCCccccc-cccccch
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA-DEYIECE 43 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~-DkYiE~d 43 (232)
++.|-|||.. .+-++|..|. ..|..||-++ |++|..+
T Consensus 1 ~~~CpeCg~~--~~~~d~~~ge---~VC~~CG~Vi~~~~id~g 38 (285)
T COG1405 1 VMSCPECGST--NIITDYERGE---IVCADCGLVLEDSLIDPG 38 (285)
T ss_pred CCCCCCCCCc--cceeeccCCe---EEeccCCEEeccccccCC
Confidence 3689999998 6666776653 4799999854 4466655
No 77
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=42.88 E-value=12 Score=29.19 Aligned_cols=26 Identities=35% Similarity=0.998 Sum_probs=18.8
Q ss_pred CccccccCcccccceeeccCCceE-eecCCCccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIR-LMKCENCRA 34 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~-l~~C~~C~~ 34 (232)
+++|-.||..-.. +.|+ -+.||+|+.
T Consensus 58 Pa~CkkCGfef~~-------~~ik~pSRCP~CKS 84 (97)
T COG3357 58 PARCKKCGFEFRD-------DKIKKPSRCPKCKS 84 (97)
T ss_pred ChhhcccCccccc-------cccCCcccCCcchh
Confidence 5789999976433 3444 679999985
No 78
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=42.24 E-value=20 Score=31.18 Aligned_cols=36 Identities=19% Similarity=0.568 Sum_probs=26.9
Q ss_pred cccccCcccccceeeccCCceEeecCCCccc--cccccccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA--VADEYIEC 42 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~--~~DkYiE~ 42 (232)
.|-+|+.|=..|-++ +.+-..+|..||. .+|+.-+.
T Consensus 100 ~C~~C~~pdT~l~k~---~~~~~l~C~aCGa~~~v~~~~~~ 137 (201)
T PRK12336 100 ICSECGLPDTRLVKE---DRVLMLRCDACGAHRPVKKRKAS 137 (201)
T ss_pred ECCCCCCCCcEEEEc---CCeEEEEcccCCCCccccccccc
Confidence 599999998888654 4566789999996 45655443
No 79
>PRK05978 hypothetical protein; Provisional
Probab=41.91 E-value=12 Score=31.28 Aligned_cols=27 Identities=30% Similarity=0.675 Sum_probs=19.7
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
-+|-+||+. .+|+.|-+ --..|+.||.
T Consensus 34 grCP~CG~G--~LF~g~Lk---v~~~C~~CG~ 60 (148)
T PRK05978 34 GRCPACGEG--KLFRAFLK---PVDHCAACGE 60 (148)
T ss_pred CcCCCCCCC--cccccccc---cCCCccccCC
Confidence 479999985 57777744 3357999996
No 80
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=40.38 E-value=13 Score=29.32 Aligned_cols=25 Identities=16% Similarity=0.484 Sum_probs=15.6
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.+|-+||+..+. +. ....||+||..
T Consensus 71 ~~C~~Cg~~~~~-------~~-~~~~CP~Cgs~ 95 (113)
T PRK12380 71 AWCWDCSQVVEI-------HQ-HDAQCPHCHGE 95 (113)
T ss_pred EEcccCCCEEec-------CC-cCccCcCCCCC
Confidence 479999964322 11 12249999975
No 81
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=39.75 E-value=16 Score=25.07 Aligned_cols=23 Identities=30% Similarity=0.681 Sum_probs=17.8
Q ss_pred CccccccCcccccceeeccCCceEeecCCCccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
..||-.|+.+.+- +-+.|.+||.
T Consensus 14 k~ICrkC~ARnp~----------~A~~CRKCg~ 36 (48)
T PRK04136 14 KKICMRCNARNPW----------RATKCRKCGY 36 (48)
T ss_pred ccchhcccCCCCc----------cccccccCCC
Confidence 4689999887643 6778999985
No 82
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=38.61 E-value=11 Score=23.07 Aligned_cols=27 Identities=26% Similarity=0.540 Sum_probs=13.9
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.-|-.||.|.... + .-.-.+|++|+..
T Consensus 4 rfC~~CG~~t~~~-----~-~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTKPA-----P-GGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEEE------S-SSS-EEESSSS-E
T ss_pred cccCcCCccccCC-----C-CcCEeECCCCcCE
Confidence 3588899997553 2 2245589999863
No 83
>PHA02768 hypothetical protein; Provisional
Probab=38.45 E-value=7.3 Score=27.41 Aligned_cols=40 Identities=33% Similarity=0.650 Sum_probs=23.1
Q ss_pred CccccccCccc---ccceeeccCCceEeecCCCcccc---ccccccc
Q 026819 2 EYRCVKCGFRI---KTLFVQYSPGNIRLMKCENCRAV---ADEYIEC 42 (232)
Q Consensus 2 ~~~Ci~C~~~v---~~l~~~y~~~~i~l~~C~~C~~~---~DkYiE~ 42 (232)
+|.|-+||..- ++|.+--...+ +--+|.+|++. --+|||.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l~~~ 50 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEYIEI 50 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceecccceeEEE
Confidence 57899999873 33322111112 34578888774 3566664
No 84
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.43 E-value=15 Score=30.00 Aligned_cols=33 Identities=21% Similarity=0.588 Sum_probs=18.2
Q ss_pred ccccccCcccccce------------eeccCCc-eEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLF------------VQYSPGN-IRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~------------~~y~~~~-i~l~~C~~C~~~ 35 (232)
.+|-+||+..+.-- ..|.|+. -....||+||..
T Consensus 71 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 71 LKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred EECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 58999996532210 0122221 133569999975
No 85
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.39 E-value=20 Score=30.41 Aligned_cols=36 Identities=28% Similarity=0.748 Sum_probs=25.9
Q ss_pred CccccccCcccccceee--ccCCceEeecCCCccc---cccc
Q 026819 2 EYRCVKCGFRIKTLFVQ--YSPGNIRLMKCENCRA---VADE 38 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~--y~~~~i~l~~C~~C~~---~~Dk 38 (232)
.|.|--||++...-+.+ |.+|. .+-+|+.|+. +||.
T Consensus 79 ~yTCkvCntRs~ktisk~AY~~Gv-VivqC~gC~~~HliaDn 119 (165)
T KOG3277|consen 79 AYTCKVCNTRSTKTISKQAYEKGV-VIVQCPGCKNHHLIADN 119 (165)
T ss_pred EEEeeccCCccccccChhhhhCce-EEEECCCCccceeehhh
Confidence 37899999997655544 66655 6778999985 5664
No 86
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=36.54 E-value=19 Score=29.68 Aligned_cols=24 Identities=29% Similarity=0.634 Sum_probs=17.3
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
..|-.||.|. |+ +.+. ..||.|+.
T Consensus 29 ~hCp~Cg~PL---F~-KdG~----v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPL---FR-KDGE----VFCPVCGY 52 (131)
T ss_pred hhCcccCCcc---ee-eCCe----EECCCCCc
Confidence 5799999995 44 3332 37999994
No 87
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=36.50 E-value=24 Score=30.38 Aligned_cols=41 Identities=24% Similarity=0.452 Sum_probs=31.5
Q ss_pred ccccccCc-ccccceeec-cCCceEeecCCCccccccccccch
Q 026819 3 YRCVKCGF-RIKTLFVQY-SPGNIRLMKCENCRAVADEYIECE 43 (232)
Q Consensus 3 ~~Ci~C~~-~v~~l~~~y-~~~~i~l~~C~~C~~~~DkYiE~d 43 (232)
.+|-+|+. |+.-=|++- +++.+++..|.+|-+.-..|.+-|
T Consensus 1 miCq~CqqnpAti~~tkI~~~~k~e~~vCe~Ca~~~s~a~~~e 43 (176)
T COG3880 1 MICQNCQQNPATIHFTKIINGEKIELYVCETCAKPHSEAYDIE 43 (176)
T ss_pred CcchhhcCCcceEEEEEeecCCeeEeehhhcCCCchhhhccch
Confidence 47999999 777777665 567889999999998755555544
No 88
>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=36.09 E-value=6.4 Score=32.85 Aligned_cols=30 Identities=23% Similarity=0.477 Sum_probs=15.2
Q ss_pred ccccccCcccccce--eeccCCceEeecCCCccc
Q 026819 3 YRCVKCGFRIKTLF--VQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~--~~y~~~~i~l~~C~~C~~ 34 (232)
.+|.+|++..+.-. .....+ ...+|+.|+.
T Consensus 106 ~~C~~C~~~~~~~~~~~~~~~~--~~~~C~~C~~ 137 (178)
T PF02146_consen 106 LRCSKCGKEYDREDIVDSIDEE--EPPRCPKCGG 137 (178)
T ss_dssp EEETTTSBEEEGHHHHHHHHTT--SSCBCTTTSC
T ss_pred eeecCCCccccchhhccccccc--ccccccccCc
Confidence 46777777543321 111122 2237777777
No 89
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=35.98 E-value=36 Score=21.49 Aligned_cols=27 Identities=37% Similarity=0.849 Sum_probs=16.3
Q ss_pred ccccccCcccccceeec-cCCceEeecCCC
Q 026819 3 YRCVKCGFRIKTLFVQY-SPGNIRLMKCEN 31 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y-~~~~i~l~~C~~ 31 (232)
..|..||..| |--.| .+|.|+.-+|+|
T Consensus 2 hlcpkcgvgv--l~pvy~~kgeikvfrcsn 29 (36)
T PF09151_consen 2 HLCPKCGVGV--LEPVYNQKGEIKVFRCSN 29 (36)
T ss_dssp -B-TTTSSSB--EEEEE-TTS-EEEEEES-
T ss_pred ccCCccCceE--EEEeecCCCcEEEEEcCC
Confidence 4699999875 22335 467899998765
No 90
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=35.60 E-value=16 Score=33.58 Aligned_cols=21 Identities=33% Similarity=0.961 Sum_probs=16.8
Q ss_pred cccccCcccccceeeccCCceEeecCCCccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
.|-+||..|..+ . +.||+|+.
T Consensus 84 ~C~~CGa~V~~~----e------~~Cp~C~S 104 (314)
T PF09567_consen 84 KCNNCGANVSRL----E------ESCPNCGS 104 (314)
T ss_pred hhccccceeeeh----h------hcCCCCCc
Confidence 699999999874 2 36999994
No 91
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=35.48 E-value=21 Score=26.39 Aligned_cols=34 Identities=18% Similarity=0.311 Sum_probs=16.4
Q ss_pred ccccccCcccccceeec-----cCCceEeecCCCccccc
Q 026819 3 YRCVKCGFRIKTLFVQY-----SPGNIRLMKCENCRAVA 36 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y-----~~~~i~l~~C~~C~~~~ 36 (232)
-.|..|.++.+.-..+| ..+..+...||.|++.-
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHH
Confidence 35777777755443333 23466777888888753
No 92
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=34.64 E-value=24 Score=24.51 Aligned_cols=30 Identities=23% Similarity=0.545 Sum_probs=17.1
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
+.+|-+|++-.-.- ..|.. ---+||+|+.+
T Consensus 4 eiRC~~CnklLa~~-g~~~~---leIKCpRC~ti 33 (51)
T PF10122_consen 4 EIRCGHCNKLLAKA-GEVIE---LEIKCPRCKTI 33 (51)
T ss_pred ceeccchhHHHhhh-cCccE---EEEECCCCCcc
Confidence 56888888764321 01221 22379999864
No 93
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=34.20 E-value=25 Score=33.47 Aligned_cols=32 Identities=25% Similarity=0.689 Sum_probs=24.1
Q ss_pred CccccccCcccccce---------eec----cCCceEeecCCCcc
Q 026819 2 EYRCVKCGFRIKTLF---------VQY----SPGNIRLMKCENCR 33 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~---------~~y----~~~~i~l~~C~~C~ 33 (232)
.-.|..||.+++.+. ..+ -|+++.+..|.+||
T Consensus 6 ~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cg 50 (355)
T COG1499 6 TILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCG 50 (355)
T ss_pred ccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCC
Confidence 357999999996443 223 24688999999999
No 94
>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=33.88 E-value=29 Score=24.19 Aligned_cols=30 Identities=30% Similarity=0.700 Sum_probs=18.8
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
...|.+||..+.- =.... | .+-.|+.||.-
T Consensus 2 ~~~CP~CG~~iev-~~~~~-G--eiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIEL-ENPEL-G--ELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEec-CCCcc-C--CEEeCCCCCCE
Confidence 4689999998632 11122 2 24489999963
No 95
>PF06542 PHA-1: Regulator protein PHA-1; InterPro: IPR009497 This family represents the protein product of the gene pha-1 which coordinates with lin-35 Rb during animal development. The protein is expressed during embryonic development and functions in the cytoplasm. PHA-1 acts in a parallel pathway with UBC-18 to regulate the activity of a common cellular target [].
Probab=33.85 E-value=10 Score=36.42 Aligned_cols=39 Identities=21% Similarity=0.439 Sum_probs=35.8
Q ss_pred cCCCccccccccccchhHHHHHHHHhcCcchhheeeccc
Q 026819 28 KCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNV 66 (232)
Q Consensus 28 ~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayrHllfN~ 66 (232)
-|++|.++|++-.||.++..=.+.-+-+|.-|++|..+-
T Consensus 123 GC~~C~~ia~~C~eYGPi~~~~~~~~~~~~hfk~L~itD 161 (390)
T PF06542_consen 123 GCEKCSNIAKKCEEYGPIQFSVLQRFKKPKHFKKLIITD 161 (390)
T ss_pred hHHHHHHHHhhhhhcCCccHhHHhccCCCCCCCEEEEcH
Confidence 488999999999999999999988899999999998875
No 96
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=33.30 E-value=22 Score=29.09 Aligned_cols=31 Identities=29% Similarity=0.787 Sum_probs=19.1
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccccc-ccccch
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD-EYIECE 43 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D-kYiE~d 43 (232)
-+|-+||+-- |.|. ..|++|+.-.| +.+|..
T Consensus 30 ~kC~~CG~v~------~PPr----~~Cp~C~~~~~~E~vels 61 (140)
T COG1545 30 TKCKKCGRVY------FPPR----AYCPKCGSETELEWVELS 61 (140)
T ss_pred EEcCCCCeEE------cCCc----ccCCCCCCCCceEEEEeC
Confidence 3577777642 3332 36788887766 777754
No 97
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.27 E-value=25 Score=37.85 Aligned_cols=16 Identities=25% Similarity=0.561 Sum_probs=9.5
Q ss_pred ecCCCccccccccccc
Q 026819 27 MKCENCRAVADEYIEC 42 (232)
Q Consensus 27 ~~C~~C~~~~DkYiE~ 42 (232)
..||+|+.....+-..
T Consensus 664 y~CPKCG~El~~~s~~ 679 (1121)
T PRK04023 664 DECEKCGREPTPYSKR 679 (1121)
T ss_pred CcCCCCCCCCCccceE
Confidence 3577787765554433
No 98
>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=33.01 E-value=19 Score=28.52 Aligned_cols=26 Identities=19% Similarity=0.630 Sum_probs=16.7
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (232)
-+|-+||+..+.- . ....||+||..-
T Consensus 71 ~~C~~Cg~~~~~~-------~-~~~~CP~Cgs~~ 96 (115)
T TIGR00100 71 CECEDCSEEVSPE-------I-DLYRCPKCHGIM 96 (115)
T ss_pred EEcccCCCEEecC-------C-cCccCcCCcCCC
Confidence 4799999654321 1 134699999753
No 99
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=32.61 E-value=9.6 Score=24.06 Aligned_cols=32 Identities=22% Similarity=0.488 Sum_probs=20.2
Q ss_pred ccccCcccccceeeccCCceEeecCCCccccccc
Q 026819 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (232)
Q Consensus 5 Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (232)
|.+|+..-..++++-.+++ .+.|..|+-.-.|
T Consensus 1 C~~C~tt~t~~WR~~~~g~--~~LCn~Cg~~~kk 32 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGN--RTLCNACGLYYKK 32 (36)
T ss_dssp -TTT--ST-SSEEEETTSE--E-EEHHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCC--CHHHHHHHHHHHH
Confidence 8899999999998887664 4479888754333
No 100
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=32.49 E-value=24 Score=22.44 Aligned_cols=28 Identities=29% Similarity=0.457 Sum_probs=16.7
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
.+|.+||+.-.-.|.--. .-.+|++||.
T Consensus 2 r~C~~Cg~~Yh~~~~pP~----~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPK----VEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--S----STTBCTTTTE
T ss_pred cCcCCCCCccccccCCCC----CCCccCCCCC
Confidence 368889876443322222 3348999986
No 101
>PRK02935 hypothetical protein; Provisional
Probab=32.48 E-value=23 Score=28.24 Aligned_cols=24 Identities=29% Similarity=0.533 Sum_probs=17.5
Q ss_pred cccccCcccccceeeccCCceEeecCCCcccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.|.+|+++.+-|= |...|..|+++
T Consensus 72 ~CP~C~K~TKmLG--------rvD~CM~C~~P 95 (110)
T PRK02935 72 ICPSCEKPTKMLG--------RVDACMHCNQP 95 (110)
T ss_pred ECCCCCchhhhcc--------ceeecCcCCCc
Confidence 5888888877761 45578888875
No 102
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=32.38 E-value=33 Score=26.51 Aligned_cols=28 Identities=25% Similarity=0.599 Sum_probs=21.1
Q ss_pred CccccccCcc-cccceeeccCCceEeecCCCccccc
Q 026819 2 EYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAVA 36 (232)
Q Consensus 2 ~~~Ci~C~~~-v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (232)
.|.|..||.+ ++.. ..-+=.|.+|++..
T Consensus 36 ~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~~ 64 (90)
T PRK03976 36 KHVCPVCGRPKVKRV-------GTGIWECRKCGAKF 64 (90)
T ss_pred CccCCCCCCCceEEE-------EEEEEEcCCCCCEE
Confidence 5889999876 5543 55678999999753
No 103
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=32.24 E-value=52 Score=25.33 Aligned_cols=50 Identities=20% Similarity=0.289 Sum_probs=31.3
Q ss_pred ccccCc--cccccee---eccCC----ceEeecCCCccccccccccchhHHHHHHHHhc
Q 026819 5 CVKCGF--RIKTLFV---QYSPG----NIRLMKCENCRAVADEYIECEIMILLIDLILH 54 (232)
Q Consensus 5 Ci~C~~--~v~~l~~---~y~~~----~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~ 54 (232)
|.-|+. ..++.-+ +|++| .||-..|-.|.+--..|++-|.+--+=|.+++
T Consensus 2 C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~dev~~eIE~~l~l 60 (89)
T TIGR03829 2 CRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDDTTVKEIEDQLLL 60 (89)
T ss_pred CcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeecHHHHHHHHhhhEE
Confidence 888944 2444443 34443 45556666677777889998877666665543
No 104
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=31.95 E-value=17 Score=30.99 Aligned_cols=32 Identities=19% Similarity=0.429 Sum_probs=20.1
Q ss_pred CccccccCcccccceeeccCCceEeecCCCccccccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (232)
.|+|.+||.+.+.+=- .+. -=.||.||..--.
T Consensus 117 ~Y~Cp~C~~rytf~eA-~~~----~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA-MEY----GFRCPQCGEMLEE 148 (178)
T ss_pred EEECCCCCcEEeHHHH-hhc----CCcCCCCCCCCee
Confidence 5899999977543310 111 2379999986544
No 105
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=31.46 E-value=20 Score=30.38 Aligned_cols=31 Identities=19% Similarity=0.360 Sum_probs=15.6
Q ss_pred ccccCcccccceee-----ccCCceEeecCCCcccc
Q 026819 5 CVKCGFRIKTLFVQ-----YSPGNIRLMKCENCRAV 35 (232)
Q Consensus 5 Ci~C~~~v~~l~~~-----y~~~~i~l~~C~~C~~~ 35 (232)
|-+|++|+..=|.. +++++-.-.-|.+||+.
T Consensus 42 Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkp 77 (158)
T PF10083_consen 42 CPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKP 77 (158)
T ss_pred CcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCC
Confidence 66666666544321 12333344556666653
No 106
>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=30.35 E-value=17 Score=28.54 Aligned_cols=25 Identities=24% Similarity=0.769 Sum_probs=14.6
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
-+|-+||+.-+- +... ..||+||..
T Consensus 71 ~~C~~Cg~~~~~-------~~~~-~~CP~Cgs~ 95 (113)
T PF01155_consen 71 ARCRDCGHEFEP-------DEFD-FSCPRCGSP 95 (113)
T ss_dssp EEETTTS-EEEC-------HHCC-HH-SSSSSS
T ss_pred EECCCCCCEEec-------CCCC-CCCcCCcCC
Confidence 479999986432 1212 459999986
No 107
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.16 E-value=27 Score=34.00 Aligned_cols=29 Identities=31% Similarity=0.610 Sum_probs=22.0
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (232)
.|+|-.||...++.=+ + =-+|++|+.-+.
T Consensus 350 ~p~Cp~Cg~~m~S~G~-----~--g~rC~kCg~~~~ 378 (421)
T COG1571 350 NPVCPRCGGRMKSAGR-----N--GFRCKKCGTRAR 378 (421)
T ss_pred CCCCCccCCchhhcCC-----C--CcccccccccCC
Confidence 5899999999887522 1 348999997654
No 108
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=30.02 E-value=14 Score=25.51 Aligned_cols=22 Identities=32% Similarity=0.587 Sum_probs=16.9
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
.||-.||...+ .+-|+|.+|+-
T Consensus 15 kIC~rC~Arnp----------~~A~kCRkC~~ 36 (50)
T COG1552 15 KICRRCYARNP----------PRATKCRKCGY 36 (50)
T ss_pred HHHHHhcCCCC----------cchhHHhhccC
Confidence 58899988764 36788999973
No 109
>PF03691 UPF0167: Uncharacterised protein family (UPF0167); InterPro: IPR005363 The proteins in this family are about 200 amino acids long and each contain 3 CXXC motifs.
Probab=29.60 E-value=20 Score=30.89 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=29.1
Q ss_pred CccccccCcccccceee--ccCCceEeecCCCc---ccccccc
Q 026819 2 EYRCVKCGFRIKTLFVQ--YSPGNIRLMKCENC---RAVADEY 39 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~--y~~~~i~l~~C~~C---~~~~DkY 39 (232)
+-+|.-||++..-.|+- |+.+++. ..||-| |+-|+||
T Consensus 24 ~~~C~cCgk~~~~~Y~~~~Y~~~dv~-~lCPwCIAdG~AA~kf 65 (176)
T PF03691_consen 24 EVVCDCCGKARGYYYTGPFYSEEDVE-YLCPWCIADGSAAKKF 65 (176)
T ss_pred CCCcCCCCCCceeEecCCceecCCcc-ccCHhHhcCcHhHHhc
Confidence 34799999998887765 7888888 899999 4566665
No 110
>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=29.43 E-value=21 Score=33.75 Aligned_cols=27 Identities=30% Similarity=0.806 Sum_probs=13.3
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
+.|-+||.+.-++ .+|.+ ..|++||..
T Consensus 286 FkC~~C~~Rt~sl-~r~P~-----~~C~~Cg~~ 312 (344)
T PF09332_consen 286 FKCKDCGNRTISL-ERLPK-----KHCSNCGSS 312 (344)
T ss_dssp EE-T-TS-EEEES-SSS-------S--TTT-S-
T ss_pred EECCCCCCeeeec-ccCCC-----CCCCcCCcC
Confidence 4699999997777 34633 279999964
No 111
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=29.36 E-value=26 Score=28.24 Aligned_cols=29 Identities=21% Similarity=0.678 Sum_probs=18.7
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY 39 (232)
-.|-+|+++++..-..| .||+||..-.+-
T Consensus 71 ~~C~~C~~~~~~e~~~~--------~CP~C~s~~~~i 99 (115)
T COG0375 71 CWCLDCGQEVELEELDY--------RCPKCGSINLRI 99 (115)
T ss_pred EEeccCCCeecchhhee--------ECCCCCCCceEE
Confidence 36889988875532222 299999765543
No 112
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.23 E-value=26 Score=28.09 Aligned_cols=30 Identities=17% Similarity=0.440 Sum_probs=15.0
Q ss_pred ccccccCcccccceeeccCCceE-eecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIR-LMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~-l~~C~~C~~~ 35 (232)
-+| +||+..+.-- ...+... ...||+||..
T Consensus 71 ~~C-~Cg~~~~~~~--~~~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 71 IEC-ECGYEGVVDE--DEIDHYAAVIECPVCGNK 101 (124)
T ss_pred EEe-eCcCcccccc--cchhccccCCcCcCCCCC
Confidence 479 9996532210 0000001 1369999954
No 113
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=29.11 E-value=23 Score=25.20 Aligned_cols=12 Identities=33% Similarity=0.664 Sum_probs=9.8
Q ss_pred ccccccCccccc
Q 026819 3 YRCVKCGFRIKT 14 (232)
Q Consensus 3 ~~Ci~C~~~v~~ 14 (232)
..|+.||.|++.
T Consensus 4 kHC~~CG~~Ip~ 15 (59)
T PF09889_consen 4 KHCPVCGKPIPP 15 (59)
T ss_pred CcCCcCCCcCCc
Confidence 469999999874
No 114
>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=28.33 E-value=21 Score=30.86 Aligned_cols=31 Identities=23% Similarity=0.534 Sum_probs=17.1
Q ss_pred ccccccCcccccce--eeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLF--VQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~--~~y~~~~i~l~~C~~C~~~ 35 (232)
.+|..|++..+.-. .... .-.+..|++|+..
T Consensus 110 ~~C~~C~~~~~~~~~~~~~~--~~~~p~C~~Cg~~ 142 (218)
T cd01407 110 VRCTKCGKEYPRDELQADID--REEVPRCPKCGGL 142 (218)
T ss_pred ceeCCCcCCCcHHHHhHhhc--cCCCCcCCCCCCc
Confidence 56888887643211 0111 1235678888865
No 115
>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=28.13 E-value=18 Score=31.92 Aligned_cols=12 Identities=17% Similarity=0.636 Sum_probs=5.6
Q ss_pred ceEeecCCCccc
Q 026819 23 NIRLMKCENCRA 34 (232)
Q Consensus 23 ~i~l~~C~~C~~ 34 (232)
++...+|.+|++
T Consensus 113 ~l~~~~C~~C~~ 124 (235)
T cd01408 113 SFATAHCIKCKH 124 (235)
T ss_pred CCCccccccCCC
Confidence 444444555544
No 116
>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=28.12 E-value=43 Score=23.25 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=18.0
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
-||-+|....... .+-..+.+ --+|++|+.
T Consensus 23 LIC~~C~~hNGla-~~~~~~~i-~y~C~~Cg~ 52 (54)
T PF10058_consen 23 LICSKCFSHNGLA-PKEEFEEI-QYRCPYCGA 52 (54)
T ss_pred EECcccchhhccc-ccccCCce-EEEcCCCCC
Confidence 4788887765432 23333344 557888885
No 117
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.01 E-value=33 Score=37.77 Aligned_cols=14 Identities=21% Similarity=0.631 Sum_probs=8.3
Q ss_pred cCCCcccccccccc
Q 026819 28 KCENCRAVADEYIE 41 (232)
Q Consensus 28 ~C~~C~~~~DkYiE 41 (232)
.||+|+...-.|-.
T Consensus 711 ~CP~CGtplv~~~~ 724 (1337)
T PRK14714 711 ECPRCDVELTPYQR 724 (1337)
T ss_pred cCCCCCCcccccce
Confidence 67777765544443
No 118
>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=27.80 E-value=26 Score=22.55 Aligned_cols=18 Identities=22% Similarity=0.709 Sum_probs=11.2
Q ss_pred ecCCCccccccccccchh
Q 026819 27 MKCENCRAVADEYIECEI 44 (232)
Q Consensus 27 ~~C~~C~~~~DkYiE~d~ 44 (232)
-+|++|+...-+|.++|.
T Consensus 3 ~rC~~C~aylNp~~~~~~ 20 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDD 20 (40)
T ss_dssp -B-TTT--BS-TTSEEET
T ss_pred cccCCCCCEECCcceEcC
Confidence 379999999999999884
No 119
>PRK06386 replication factor A; Reviewed
Probab=27.78 E-value=28 Score=33.11 Aligned_cols=24 Identities=25% Similarity=0.498 Sum_probs=0.0
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY 39 (232)
.+|.+|+..++. ..|+.|++ ++.|
T Consensus 237 ~rCP~C~R~l~~------------g~C~~HG~-v~~~ 260 (358)
T PRK06386 237 TKCSVCNKIIED------------GVCKDHPD-APVY 260 (358)
T ss_pred ecCcCCCeEccC------------CcCCCCCC-CCCe
No 120
>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=27.76 E-value=43 Score=25.90 Aligned_cols=28 Identities=29% Similarity=0.660 Sum_probs=20.7
Q ss_pred CccccccCcc-cccceeeccCCceEeecCCCccccc
Q 026819 2 EYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAVA 36 (232)
Q Consensus 2 ~~~Ci~C~~~-v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (232)
.|.|..||.+ ++.. ..-+=+|.+|++..
T Consensus 35 ~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 35 KYVCPFCGKKTVKRG-------STGIWTCRKCGAKF 63 (91)
T ss_pred CccCCCCCCCceEEE-------eeEEEEcCCCCCEE
Confidence 5789999976 4443 45678999999753
No 121
>PRK07218 replication factor A; Provisional
Probab=27.62 E-value=29 Score=33.72 Aligned_cols=20 Identities=20% Similarity=0.227 Sum_probs=12.3
Q ss_pred HHHHHHhcCcchhheeeccc
Q 026819 47 LLIDLILHKPQAYRHLLYNV 66 (232)
Q Consensus 47 ~~iDl~L~k~~ayrHllfN~ 66 (232)
+.|+.+|-.=--+.-.+||+
T Consensus 324 lrik~vLDDGtg~~~~~~~~ 343 (423)
T PRK07218 324 LRIKAILDDGTGSVTVILDR 343 (423)
T ss_pred eEEEEEEECCCCeEEEEECh
Confidence 45556666655666666666
No 122
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=27.46 E-value=14 Score=34.37 Aligned_cols=25 Identities=24% Similarity=0.425 Sum_probs=14.9
Q ss_pred cccccCcccccceeeccCCc-eEeecCCCccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGN-IRLMKCENCRA 34 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~-i~l~~C~~C~~ 34 (232)
.|-+|++.+ |.++- -.+..||+|+.
T Consensus 40 kc~~C~~~~------~~~~l~~~~~vcp~c~~ 65 (296)
T CHL00174 40 QCENCYGLN------YKKFLKSKMNICEQCGY 65 (296)
T ss_pred ECCCccchh------hHHHHHHcCCCCCCCCC
Confidence 577888765 22221 12458999984
No 123
>PF10977 DUF2797: Protein of unknown function (DUF2797); InterPro: IPR021246 This family of proteins has no known function.
Probab=27.29 E-value=24 Score=31.59 Aligned_cols=29 Identities=38% Similarity=0.910 Sum_probs=20.2
Q ss_pred cccccCcccccceee-c-cCCceEeecCCCc
Q 026819 4 RCVKCGFRIKTLFVQ-Y-SPGNIRLMKCENC 32 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~-y-~~~~i~l~~C~~C 32 (232)
.|++||...+.-|.+ | -+.--++.+|+.|
T Consensus 13 ~c~~cG~~~~~s~~qg~C~~C~~~~aqC~~C 43 (235)
T PF10977_consen 13 QCLNCGRKTKKSFRQGYCYPCFQTLAQCDEC 43 (235)
T ss_pred EEecCCccccccCCCCceeCCCCcCccChhH
Confidence 699999998777766 2 1223366678877
No 124
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.14 E-value=29 Score=35.53 Aligned_cols=7 Identities=29% Similarity=1.056 Sum_probs=3.7
Q ss_pred cCCCccc
Q 026819 28 KCENCRA 34 (232)
Q Consensus 28 ~C~~C~~ 34 (232)
.|++||.
T Consensus 29 ~Cp~CG~ 35 (645)
T PRK14559 29 PCPQCGT 35 (645)
T ss_pred cCCCCCC
Confidence 4555554
No 125
>PRK04023 DNA polymerase II large subunit; Validated
Probab=26.94 E-value=36 Score=36.71 Aligned_cols=35 Identities=20% Similarity=0.481 Sum_probs=17.5
Q ss_pred CccccccCcccccceeeccC----CceEeecCCCcccccccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSP----GNIRLMKCENCRAVADEY 39 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~----~~i~l~~C~~C~~~~DkY 39 (232)
...|.+||+.... ..-| .+...-.|++|+.....|
T Consensus 626 ~RfCpsCG~~t~~---frCP~CG~~Te~i~fCP~CG~~~~~y 664 (1121)
T PRK04023 626 RRKCPSCGKETFY---RRCPFCGTHTEPVYRCPRCGIEVEED 664 (1121)
T ss_pred CccCCCCCCcCCc---ccCCCCCCCCCcceeCccccCcCCCC
Confidence 3578888877411 1111 122334566666655544
No 126
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=26.93 E-value=47 Score=24.47 Aligned_cols=29 Identities=24% Similarity=0.576 Sum_probs=17.5
Q ss_pred cccccCcccccceeeccCCceEeecCCCccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
.|. ||.....-=+ .+.+.++++.|++|+-
T Consensus 15 ~c~-~g~~f~~~ST-~~~~~i~vdi~s~~HP 43 (72)
T PRK00019 15 TCS-CGNVFETRST-LGKDEINVDVCSKCHP 43 (72)
T ss_pred EEC-CCCEEEEeec-CCCCcEEEEeCCCCCC
Confidence 455 6665322111 2345699999999983
No 127
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=26.82 E-value=27 Score=20.26 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=7.4
Q ss_pred eecCCCccc
Q 026819 26 LMKCENCRA 34 (232)
Q Consensus 26 l~~C~~C~~ 34 (232)
+.+|+.||+
T Consensus 2 l~~C~~CgR 10 (25)
T PF13913_consen 2 LVPCPICGR 10 (25)
T ss_pred CCcCCCCCC
Confidence 568999997
No 128
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=26.40 E-value=46 Score=28.01 Aligned_cols=30 Identities=30% Similarity=0.489 Sum_probs=19.5
Q ss_pred cccccCcccccceeecc-----CCceEeecCCCcc
Q 026819 4 RCVKCGFRIKTLFVQYS-----PGNIRLMKCENCR 33 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~-----~~~i~l~~C~~C~ 33 (232)
.|.+||++...-...++ .=-+--..|++||
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CG 36 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCG 36 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCC
Confidence 59999988654444332 2234457899999
No 129
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=26.39 E-value=40 Score=31.08 Aligned_cols=27 Identities=19% Similarity=0.366 Sum_probs=19.4
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.-|-.||++... .+.-.-..|++|++.
T Consensus 112 RFCg~CG~~~~~------~~~g~~~~C~~cg~~ 138 (279)
T COG2816 112 RFCGRCGTKTYP------REGGWARVCPKCGHE 138 (279)
T ss_pred cCCCCCCCcCcc------ccCceeeeCCCCCCc
Confidence 358999999733 334466689999975
No 130
>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=26.37 E-value=37 Score=28.49 Aligned_cols=31 Identities=26% Similarity=0.425 Sum_probs=17.0
Q ss_pred ccccccCcccccceeec-----cCCceEeecCCCcc
Q 026819 3 YRCVKCGFRIKTLFVQY-----SPGNIRLMKCENCR 33 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y-----~~~~i~l~~C~~C~ 33 (232)
-.|.+||++...-...| +.--|.-..|++||
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CG 37 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCG 37 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT-
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCC
Confidence 46999999854432222 22244555899999
No 131
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=26.08 E-value=50 Score=25.50 Aligned_cols=28 Identities=25% Similarity=0.778 Sum_probs=20.5
Q ss_pred CccccccCcc-cccceeeccCCceEeecCCCccccc
Q 026819 2 EYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAVA 36 (232)
Q Consensus 2 ~~~Ci~C~~~-v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (232)
.|.|..||.+ ++.. ..-+=+|.+|++..
T Consensus 36 ~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQ-------AVGIWRCKGCKKTV 64 (90)
T ss_pred CccCCCCCCCceeee-------eeEEEEcCCCCCEE
Confidence 5889999976 4443 44678999999753
No 132
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=26.01 E-value=15 Score=26.50 Aligned_cols=19 Identities=32% Similarity=0.684 Sum_probs=13.8
Q ss_pred ccccccCcccccceeeccC
Q 026819 3 YRCVKCGFRIKTLFVQYSP 21 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~ 21 (232)
-+|-.||+++.++|..|..
T Consensus 5 iRCFsCGkvi~~~w~~y~~ 23 (63)
T COG1644 5 VRCFSCGKVIGHKWEEYKR 23 (63)
T ss_pred eEeecCCCCHHHHHHHHHH
Confidence 3677888888887777743
No 133
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=25.96 E-value=24 Score=33.48 Aligned_cols=30 Identities=13% Similarity=0.516 Sum_probs=15.4
Q ss_pred ccccccCccccc--ceeeccCCceEeecCCCccc
Q 026819 3 YRCVKCGFRIKT--LFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 3 ~~Ci~C~~~v~~--l~~~y~~~~i~l~~C~~C~~ 34 (232)
.+|..|+++.+. .+.+..+ -+...|++|+.
T Consensus 148 ~~C~~C~~~~~~~~~~~~~~~--~~vP~C~~CgG 179 (349)
T PTZ00410 148 ASCIECHTPYDIEQAYLEARS--GKVPHCSTCGG 179 (349)
T ss_pred eEeCCCCCCcchhHHHHHhhc--CCCCCCCCCCC
Confidence 468888865331 1111111 13456888874
No 134
>KOG2682 consensus NAD-dependent histone deacetylases and class I sirtuins (SIR2 family) [Chromatin structure and dynamics; Transcription]
Probab=25.87 E-value=15 Score=33.57 Aligned_cols=37 Identities=16% Similarity=0.376 Sum_probs=25.0
Q ss_pred cccc-ccCcccccceeeccCCceEeecCCCcccccccc
Q 026819 3 YRCV-KCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (232)
Q Consensus 3 ~~Ci-~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY 39 (232)
-.|| +|+++.+.=|.+-.=-.-+.-+|+.|+..+.+=
T Consensus 153 s~Ci~~C~~~yp~e~~ka~i~~~~vpkC~vC~~lVKP~ 190 (314)
T KOG2682|consen 153 SHCISSCRHEYPLEWMKAKIMSEVVPKCEVCQGLVKPD 190 (314)
T ss_pred eeehhhhcCcCCHHHHHHHHHhccCCCCchhhcccccc
Confidence 4799 799997765544322223556999999876553
No 135
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=25.70 E-value=12 Score=27.15 Aligned_cols=34 Identities=15% Similarity=0.186 Sum_probs=20.5
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccccccccccchhHHHHH
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLI 49 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~i 49 (232)
..|.+|..-++. +.||.||.- |-==+++.+++.+
T Consensus 6 ~AC~~C~~i~~~------------~~Cp~Cgs~-~~S~~w~G~v~i~ 39 (64)
T PRK06393 6 RACKKCKRLTPE------------KTCPVHGDE-KTTTEWFGFLIIT 39 (64)
T ss_pred hhHhhCCcccCC------------CcCCCCCCC-cCCcCcceEEEEE
Confidence 468899877631 289999974 3233444444433
No 136
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=25.29 E-value=20 Score=25.64 Aligned_cols=16 Identities=38% Similarity=0.868 Sum_probs=8.8
Q ss_pred cccccCcccccceeec
Q 026819 4 RCVKCGFRIKTLFVQY 19 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y 19 (232)
+|-.||.++.+.|.+|
T Consensus 6 RCFTCGkvi~~~~e~y 21 (60)
T PF01194_consen 6 RCFTCGKVIGNKWEEY 21 (60)
T ss_dssp S-STTTSBTCGHHHHH
T ss_pred ecCCCCCChhHhHHHH
Confidence 4556666666555555
No 137
>PRK06260 threonine synthase; Validated
Probab=25.12 E-value=33 Score=32.41 Aligned_cols=28 Identities=21% Similarity=0.765 Sum_probs=19.3
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (232)
..+|+.||+.- +++. ....||.|+..-|
T Consensus 3 ~~~C~~cg~~~-------~~~~-~~~~Cp~cg~~l~ 30 (397)
T PRK06260 3 WLKCIECGKEY-------DPDE-IIYTCPECGGLLE 30 (397)
T ss_pred EEEECCCCCCC-------CCCC-ccccCCCCCCeEE
Confidence 46899999764 3322 2457999997655
No 138
>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=24.80 E-value=50 Score=24.71 Aligned_cols=33 Identities=15% Similarity=0.405 Sum_probs=16.4
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
+-|..|||.-.---+.-....+-.-.|..|+..
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGES 55 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEESSS--E
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCe
Confidence 579999977433333344456677789999853
No 139
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=24.69 E-value=18 Score=26.10 Aligned_cols=17 Identities=29% Similarity=0.769 Sum_probs=10.8
Q ss_pred cccccCcccccceeecc
Q 026819 4 RCVKCGFRIKTLFVQYS 20 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~ 20 (232)
+|-.||.++.+.|.+|.
T Consensus 6 RCFTCGkvi~~~we~y~ 22 (62)
T PRK04016 6 RCFTCGKVIAEKWEEFK 22 (62)
T ss_pred EecCCCCChHHHHHHHH
Confidence 56666666666666663
No 140
>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=24.40 E-value=33 Score=30.00 Aligned_cols=26 Identities=15% Similarity=0.369 Sum_probs=12.5
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
.+|..|++..+. .+..+.-.|++|+.
T Consensus 119 ~~C~~C~~~~~~------~~~~~~p~C~~Cgg 144 (225)
T cd01411 119 IYCTVCGKTVDW------EEYLKSPYHAKCGG 144 (225)
T ss_pred eEeCCCCCccch------hhcCCCCCCCCCCC
Confidence 356666654322 11123346777764
No 141
>PRK06424 transcription factor; Provisional
Probab=24.37 E-value=32 Score=28.51 Aligned_cols=37 Identities=24% Similarity=0.492 Sum_probs=27.4
Q ss_pred ccccCcccccceeeccCCceEeecCCCccccccccccc
Q 026819 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIEC 42 (232)
Q Consensus 5 Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~ 42 (232)
|-=||..++.+|+.-=.| -.+..|+.|.++--+=.++
T Consensus 3 CE~CG~~~~~~~~v~ieg-~~l~vC~~Ca~~G~~v~~~ 39 (144)
T PRK06424 3 CEMCGKKVPQTTKVMIDG-AILNVCDDCAKFGTPVIEH 39 (144)
T ss_pred ccccCcccCCceEEEEcC-eeeehhHHHHHcCCccccc
Confidence 888999999996554343 3699999998776544444
No 142
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.20 E-value=40 Score=34.49 Aligned_cols=14 Identities=29% Similarity=0.544 Sum_probs=10.0
Q ss_pred eecCCCcccccccc
Q 026819 26 LMKCENCRAVADEY 39 (232)
Q Consensus 26 l~~C~~C~~~~DkY 39 (232)
-..|++||...++-
T Consensus 41 ~~fC~~CG~~~~~~ 54 (645)
T PRK14559 41 EAHCPNCGAETGTI 54 (645)
T ss_pred cccccccCCcccch
Confidence 34799999876653
No 143
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.18 E-value=42 Score=24.57 Aligned_cols=9 Identities=44% Similarity=1.021 Sum_probs=6.6
Q ss_pred cccccCccc
Q 026819 4 RCVKCGFRI 12 (232)
Q Consensus 4 ~Ci~C~~~v 12 (232)
.|+.||...
T Consensus 6 kCpKCgn~~ 14 (68)
T COG3478 6 KCPKCGNTN 14 (68)
T ss_pred cCCCcCCcc
Confidence 488898763
No 144
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=24.03 E-value=39 Score=23.83 Aligned_cols=18 Identities=22% Similarity=0.429 Sum_probs=13.8
Q ss_pred cCCCccc-----------cccccccchhH
Q 026819 28 KCENCRA-----------VADEYIECEIM 45 (232)
Q Consensus 28 ~C~~C~~-----------~~DkYiE~d~~ 45 (232)
.||.||. +.|||-+|-..
T Consensus 19 ~CP~CG~~t~~~~P~rfSp~D~y~~yR~~ 47 (56)
T PRK13130 19 ICPVCGGKTKNPHPPRFSPEDKYGKYRRA 47 (56)
T ss_pred cCcCCCCCCCCCCCCCCCCCCccHHHHHH
Confidence 6999983 47999888743
No 145
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=23.79 E-value=55 Score=28.42 Aligned_cols=31 Identities=23% Similarity=0.399 Sum_probs=20.3
Q ss_pred cccccCcccccceeecc------CCceEeecCCCccc
Q 026819 4 RCVKCGFRIKTLFVQYS------PGNIRLMKCENCRA 34 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~------~~~i~l~~C~~C~~ 34 (232)
-|.+||.........+. .=-+--..|++||-
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGy 38 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGY 38 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCC
Confidence 39999987555444444 22444568999993
No 146
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=23.70 E-value=60 Score=22.30 Aligned_cols=33 Identities=24% Similarity=0.345 Sum_probs=17.2
Q ss_pred ccccccCcccccceeeccCCceEee---cCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLM---KCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~---~C~~C~~~ 35 (232)
..|.+|+...-...+.=.+..-||+ -||.|++-
T Consensus 8 L~C~~c~~rnY~t~KNk~~~~~rLelkKycp~c~kh 43 (50)
T PRK00504 8 LACTECKSRNYTTTKNKKNTPERLELKKFCPRCNKH 43 (50)
T ss_pred EEEcCCCCccEeEcCCCCCCCceEEEECcCCCCCCe
Confidence 3699999874222111111222444 39999864
No 147
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=23.49 E-value=48 Score=20.72 Aligned_cols=27 Identities=22% Similarity=0.452 Sum_probs=17.6
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.+|..||++. ++ ++.+ -...|+.|+..
T Consensus 4 ~~C~~C~~~~--i~--~~~~--~~~~C~~Cg~~ 30 (33)
T PF08792_consen 4 KKCSKCGGNG--IV--NKED--DYEVCIFCGSS 30 (33)
T ss_pred eEcCCCCCCe--EE--EecC--CeEEcccCCcE
Confidence 5789999986 22 1332 24579999875
No 148
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=23.09 E-value=39 Score=22.89 Aligned_cols=8 Identities=50% Similarity=1.414 Sum_probs=5.1
Q ss_pred cccccCcc
Q 026819 4 RCVKCGFR 11 (232)
Q Consensus 4 ~Ci~C~~~ 11 (232)
+|-+|||.
T Consensus 30 ~C~~Cgh~ 37 (55)
T PF14311_consen 30 KCPKCGHE 37 (55)
T ss_pred ECCCCCCe
Confidence 46666665
No 149
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.07 E-value=37 Score=34.58 Aligned_cols=22 Identities=23% Similarity=0.652 Sum_probs=14.9
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
-+|-+||+. ..+ ...||+||+-
T Consensus 560 ~~C~~CGy~-g~~----------~~~CP~CG~~ 581 (618)
T PRK14704 560 DRCKCCSYH-GVI----------GNECPSCGNE 581 (618)
T ss_pred eecCCCCCC-CCc----------CccCcCCCCC
Confidence 379999972 222 1689999963
No 150
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=22.92 E-value=61 Score=24.21 Aligned_cols=29 Identities=28% Similarity=0.598 Sum_probs=18.9
Q ss_pred cccccCcccccceeeccCCceEeecCCCcc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCR 33 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~ 33 (232)
.|..||..-..- ...+++.+++..|++|+
T Consensus 16 ~~~s~g~~f~~~-ST~~~~~i~vdV~s~~H 44 (75)
T COG0254 16 VCSSCGNEFTTR-STKGTDEINLDVCSKCH 44 (75)
T ss_pred EeCCCCCEEEEE-eccCCceEEEEeCCCCC
Confidence 466666653221 12344689999999998
No 151
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=22.76 E-value=55 Score=22.96 Aligned_cols=23 Identities=22% Similarity=0.473 Sum_probs=12.9
Q ss_pred cccccCcccccceeeccCCceEeecCCCcccccc
Q 026819 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (232)
.|-+||++.. ....|++||---+
T Consensus 29 ~C~~CG~~~~-----------~H~vC~~CG~Y~g 51 (57)
T PRK12286 29 ECPNCGEPKL-----------PHRVCPSCGYYKG 51 (57)
T ss_pred ECCCCCCccC-----------CeEECCCCCcCCC
Confidence 4666776532 2346777774433
No 152
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=22.75 E-value=42 Score=27.57 Aligned_cols=28 Identities=18% Similarity=0.479 Sum_probs=18.0
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (232)
+.|.+|+..+.. .+. ..-.|++|++..+
T Consensus 35 ~aC~~C~kkv~~----~~~---~~~~C~~C~~~~~ 62 (166)
T cd04476 35 PACPGCNKKVVE----EGN---GTYRCEKCNKSVP 62 (166)
T ss_pred ccccccCcccEe----CCC---CcEECCCCCCcCC
Confidence 468888887643 111 3457999987653
No 153
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=22.59 E-value=63 Score=19.14 Aligned_cols=29 Identities=21% Similarity=0.427 Sum_probs=15.3
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
-.|--|+++++..= .+.-...-|++|.++
T Consensus 2 ~~C~rC~~~~~~~~----~~~r~~~~C~rCq~v 30 (30)
T PF06827_consen 2 EKCPRCWNYIEDIG----INGRSTYLCPRCQKV 30 (30)
T ss_dssp SB-TTT--BBEEEE----ETTEEEEE-TTTCCH
T ss_pred CcCccCCCcceEeE----ecCCCCeECcCCcCC
Confidence 35888998876642 223345689999763
No 154
>PRK01397 50S ribosomal protein L31; Provisional
Probab=22.38 E-value=71 Score=23.95 Aligned_cols=15 Identities=13% Similarity=-0.015 Sum_probs=12.2
Q ss_pred cCCceEeecCCCccc
Q 026819 20 SPGNIRLMKCENCRA 34 (232)
Q Consensus 20 ~~~~i~l~~C~~C~~ 34 (232)
+++.|+++.|++|+-
T Consensus 28 ~~~~i~vdi~s~~HP 42 (78)
T PRK01397 28 PTGEILMDVDFRKHP 42 (78)
T ss_pred CCCcEEEEeCCCCCC
Confidence 346799999999973
No 155
>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]
Probab=22.10 E-value=44 Score=34.63 Aligned_cols=33 Identities=36% Similarity=0.818 Sum_probs=25.0
Q ss_pred CccccccCcccccceeeccCCceEeecCCCcccc
Q 026819 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.|.|..||.+ -.-|-+-++.-+|.+.|++|+..
T Consensus 292 ky~C~KC~~v-lgPF~qs~n~evkp~~C~~cqSk 324 (854)
T KOG0477|consen 292 KYDCLKCGFV-LGPFVQSSNSEVKPGSCPECQSK 324 (854)
T ss_pred hhhHHhhCCc-cCceeeccCceeCCCCCccccCC
Confidence 3789999954 34456667778899999999854
No 156
>PRK07218 replication factor A; Provisional
Probab=21.97 E-value=47 Score=32.28 Aligned_cols=20 Identities=20% Similarity=0.433 Sum_probs=14.1
Q ss_pred cCCceEeecCCCcccccccc
Q 026819 20 SPGNIRLMKCENCRAVADEY 39 (232)
Q Consensus 20 ~~~~i~l~~C~~C~~~~DkY 39 (232)
.++..=++.||.|+++.+++
T Consensus 291 ~~gsgli~rCP~C~r~v~~~ 310 (423)
T PRK07218 291 RDGSGLIERCPECGRVIQKG 310 (423)
T ss_pred ccCCcceecCcCccccccCC
Confidence 34444567888888888774
No 157
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=21.45 E-value=49 Score=32.13 Aligned_cols=26 Identities=19% Similarity=0.520 Sum_probs=18.6
Q ss_pred cccccCccc--ccceeeccCCceEeecCCCcccc
Q 026819 4 RCVKCGFRI--KTLFVQYSPGNIRLMKCENCRAV 35 (232)
Q Consensus 4 ~Ci~C~~~v--~~l~~~y~~~~i~l~~C~~C~~~ 35 (232)
.|-||+..+ +.| + .-+...||+||..
T Consensus 20 ~C~eCd~~~~~P~l----~--~~q~A~CPRC~~~ 47 (418)
T COG2995 20 LCPECDMLVSLPRL----D--SGQSAYCPRCGHT 47 (418)
T ss_pred cCCCCCceeccccC----C--CCCcccCCCCCCc
Confidence 699999985 444 1 2266799999964
No 158
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=21.30 E-value=57 Score=22.74 Aligned_cols=18 Identities=33% Similarity=0.671 Sum_probs=13.5
Q ss_pred ecCCCccc-----------cccccccchh
Q 026819 27 MKCENCRA-----------VADEYIECEI 44 (232)
Q Consensus 27 ~~C~~C~~-----------~~DkYiE~d~ 44 (232)
.+|+.||. +-|||-+|-.
T Consensus 18 ~~cp~cG~~T~~ahPaRFSPdDky~~yRi 46 (53)
T PF04135_consen 18 DKCPPCGGPTESAHPARFSPDDKYSKYRI 46 (53)
T ss_dssp SBBTTTSSBSEESSSSSS-TTTTTCHHHH
T ss_pred CccCCCCCCCcCCcCCCCCCCCccHHHHH
Confidence 37889984 4699988764
No 159
>PRK08402 replication factor A; Reviewed
Probab=21.24 E-value=43 Score=31.77 Aligned_cols=9 Identities=22% Similarity=0.866 Sum_probs=4.2
Q ss_pred cccccCccc
Q 026819 4 RCVKCGFRI 12 (232)
Q Consensus 4 ~Ci~C~~~v 12 (232)
.|.+|+..+
T Consensus 214 aCp~CnKkv 222 (355)
T PRK08402 214 ACPECRRKV 222 (355)
T ss_pred cCCCCCeEE
Confidence 444454443
No 160
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=20.99 E-value=24 Score=26.13 Aligned_cols=18 Identities=33% Similarity=0.671 Sum_probs=11.5
Q ss_pred cccccCcccccceeeccC
Q 026819 4 RCVKCGFRIKTLFVQYSP 21 (232)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~ 21 (232)
+|-.||+++.+.|.+|..
T Consensus 6 RCFTCGkvig~~we~y~~ 23 (71)
T PLN00032 6 RCFTCGKVIGNKWDTYLD 23 (71)
T ss_pred eecCCCCCcHHHHHHHHH
Confidence 566677776666666643
No 161
>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=20.85 E-value=45 Score=28.78 Aligned_cols=29 Identities=24% Similarity=0.559 Sum_probs=15.1
Q ss_pred ccccccCcccccceeeccCCceEeecCCCccc
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (232)
..|..|+.....- +.......-.|++|+.
T Consensus 110 ~~C~~C~~~~~~~---~~~~~~~~p~C~~Cgg 138 (224)
T cd01412 110 VRCSSCGYVGENN---EEIPEEELPRCPKCGG 138 (224)
T ss_pred cccCCCCCCCCcc---hhhhccCCCCCCCCCC
Confidence 4677777664321 1111123456888875
No 162
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.71 E-value=57 Score=24.86 Aligned_cols=37 Identities=27% Similarity=0.581 Sum_probs=25.3
Q ss_pred ccccccCcccccceeeccCCceEeecCCCcccc------ccccccch
Q 026819 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV------ADEYIECE 43 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~------~DkYiE~d 43 (232)
..|..||..... -...++.+..||+|..+ -||-+|-.
T Consensus 2 llCP~C~v~l~~----~~rs~vEiD~CPrCrGVWLDrGELdKli~r~ 44 (88)
T COG3809 2 LLCPICGVELVM----SVRSGVEIDYCPRCRGVWLDRGELDKLIERS 44 (88)
T ss_pred cccCcCCceeee----eeecCceeeeCCccccEeecchhHHHHHHHh
Confidence 368999987432 12347889999999975 45666555
No 163
>smart00507 HNHc HNH nucleases.
Probab=20.50 E-value=43 Score=20.87 Aligned_cols=11 Identities=27% Similarity=0.507 Sum_probs=7.8
Q ss_pred ccccccCcccc
Q 026819 3 YRCVKCGFRIK 13 (232)
Q Consensus 3 ~~Ci~C~~~v~ 13 (232)
+.|..||.+.+
T Consensus 11 ~~C~~C~~~~~ 21 (52)
T smart00507 11 GVCAYCGKPAS 21 (52)
T ss_pred CCCcCCcCCCC
Confidence 56777887764
No 164
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=20.29 E-value=15 Score=28.46 Aligned_cols=33 Identities=24% Similarity=0.556 Sum_probs=20.8
Q ss_pred ccccccCcc-cccceeec-cCCceEeecCCCcccc
Q 026819 3 YRCVKCGFR-IKTLFVQY-SPGNIRLMKCENCRAV 35 (232)
Q Consensus 3 ~~Ci~C~~~-v~~l~~~y-~~~~i~l~~C~~C~~~ 35 (232)
-.|+.|+.. |..-|..- .+....+..|++|++.
T Consensus 56 ~kC~~C~qktVk~AYh~iC~~Ca~~~~vCaKC~k~ 90 (92)
T PF10217_consen 56 KKCNKCQQKTVKHAYHVICDPCAKELKVCAKCGKP 90 (92)
T ss_pred ccccccccchHHHHHHHHHHHHHHhhccCcccCCC
Confidence 357777765 66665554 4445566777777764
No 165
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=20.14 E-value=34 Score=36.15 Aligned_cols=41 Identities=20% Similarity=0.460 Sum_probs=0.0
Q ss_pred ccccccCcccccceeecc-CCceEeecCCCccccccccccch
Q 026819 3 YRCVKCGFRIKTLFVQYS-PGNIRLMKCENCRAVADEYIECE 43 (232)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~-~~~i~l~~C~~C~~~~DkYiE~d 43 (232)
.+|-+||.+....|.=-. .....-..|++|+..+..|-..+
T Consensus 668 ~~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~~~~~~~ 709 (900)
T PF03833_consen 668 NRCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETTSYSKQK 709 (900)
T ss_dssp ------------------------------------------
T ss_pred hcCcccCCccccceeccccccccCccccccccccCcccceee
Confidence 355666665544432110 11112237888887777776544
Done!