Query 028469
Match_columns 208
No_of_seqs 134 out of 184
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 11:58:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028469.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028469hhsearch_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 9.4E-60 2E-64 401.3 12.0 194 3-196 1-208 (208)
2 KOG3134 Predicted membrane pro 100.0 1.8E-41 3.9E-46 289.2 10.3 197 3-202 1-209 (225)
3 COG5254 ARV1 Predicted membran 100.0 3.3E-39 7.1E-44 272.8 4.4 194 3-201 1-220 (239)
4 smart00834 CxxC_CXXC_SSSS Puta 93.6 0.027 5.8E-07 35.5 0.6 34 2-38 5-38 (41)
5 PF08271 TF_Zn_Ribbon: TFIIB z 93.3 0.057 1.2E-06 35.0 1.9 33 3-40 1-33 (43)
6 KOG3134 Predicted membrane pro 93.1 0.05 1.1E-06 47.5 1.6 84 113-201 101-189 (225)
7 PRK00398 rpoP DNA-directed RNA 93.0 0.047 1E-06 35.9 1.1 31 1-37 2-32 (46)
8 smart00659 RPOLCX RNA polymera 92.7 0.071 1.5E-06 35.3 1.6 28 1-35 1-28 (44)
9 PF09723 Zn-ribbon_8: Zinc rib 91.3 0.09 2E-06 34.1 0.8 34 2-38 5-39 (42)
10 TIGR02605 CxxC_CxxC_SSSS putat 90.6 0.11 2.4E-06 34.6 0.8 30 2-34 5-34 (52)
11 PF13248 zf-ribbon_3: zinc-rib 89.9 0.14 3E-06 30.0 0.7 24 1-34 1-24 (26)
12 COG1996 RPC10 DNA-directed RNA 89.7 0.12 2.6E-06 35.2 0.4 28 1-34 5-32 (49)
13 PF03604 DNA_RNApol_7kD: DNA d 89.7 0.21 4.5E-06 31.0 1.4 25 3-34 1-25 (32)
14 PF05180 zf-DNL: DNL zinc fing 88.3 0.25 5.5E-06 35.5 1.3 36 2-38 4-44 (66)
15 cd00729 rubredoxin_SM Rubredox 87.3 0.23 5.1E-06 30.9 0.6 32 2-41 2-33 (34)
16 COG5254 ARV1 Predicted membran 86.6 3.9 8.5E-05 35.7 7.8 46 151-196 142-188 (239)
17 PF14319 Zn_Tnp_IS91: Transpos 86.3 0.6 1.3E-05 36.4 2.5 52 2-67 42-95 (111)
18 PF07282 OrfB_Zn_ribbon: Putat 85.2 0.5 1.1E-05 33.0 1.4 30 3-38 29-58 (69)
19 PF01286 XPA_N: XPA protein N- 83.8 0.4 8.7E-06 30.2 0.3 28 1-33 2-31 (34)
20 PF04216 FdhE: Protein involve 82.0 1.1 2.5E-05 39.8 2.7 62 3-65 212-286 (290)
21 PRK00464 nrdR transcriptional 81.8 0.83 1.8E-05 37.8 1.6 44 3-46 1-48 (154)
22 PF12647 RNHCP: RNHCP domain; 81.8 0.72 1.6E-05 35.3 1.1 29 1-33 3-31 (92)
23 PF12773 DZR: Double zinc ribb 81.3 0.74 1.6E-05 30.2 0.9 30 3-39 13-42 (50)
24 PF01927 Mut7-C: Mut7-C RNAse 79.1 1 2.2E-05 36.4 1.2 33 3-35 92-133 (147)
25 PRK12495 hypothetical protein; 78.3 1.1 2.3E-05 39.4 1.2 29 2-38 42-70 (226)
26 PF13240 zinc_ribbon_2: zinc-r 78.0 0.84 1.8E-05 26.1 0.3 22 4-35 1-22 (23)
27 PF04981 NMD3: NMD3 family ; 76.5 1.3 2.8E-05 38.5 1.3 38 5-42 1-53 (236)
28 smart00401 ZnF_GATA zinc finge 76.1 1.5 3.3E-05 29.7 1.3 32 2-35 3-34 (52)
29 COG3364 Zn-ribbon containing p 74.7 1 2.3E-05 35.2 0.2 38 1-44 1-38 (112)
30 PF13453 zf-TFIIB: Transcripti 74.2 2.9 6.2E-05 26.7 2.1 27 5-35 2-28 (41)
31 COG2331 Uncharacterized protei 73.8 0.69 1.5E-05 34.4 -1.0 34 2-38 12-45 (82)
32 PF07754 DUF1610: Domain of un 73.6 2 4.4E-05 25.1 1.2 24 5-34 1-24 (24)
33 PF10571 UPF0547: Uncharacteri 73.4 1.5 3.3E-05 25.8 0.6 22 4-35 2-23 (26)
34 TIGR02098 MJ0042_CXXC MJ0042 f 72.7 1.7 3.7E-05 27.0 0.8 35 1-36 1-35 (38)
35 PF02591 DUF164: Putative zinc 71.7 1.1 2.3E-05 30.5 -0.4 33 2-35 22-55 (56)
36 cd00350 rubredoxin_like Rubred 71.5 1.9 4E-05 26.5 0.7 32 2-41 1-32 (33)
37 PF12760 Zn_Tnp_IS1595: Transp 70.6 2.9 6.3E-05 27.3 1.6 29 1-34 17-45 (46)
38 PRK00420 hypothetical protein; 70.2 2.5 5.3E-05 33.4 1.3 28 3-37 24-51 (112)
39 PRK03564 formate dehydrogenase 70.2 4.7 0.0001 37.0 3.3 63 3-66 227-301 (309)
40 PF14803 Nudix_N_2: Nudix N-te 70.1 2.3 4.9E-05 26.7 0.9 30 4-35 2-31 (34)
41 PF09082 DUF1922: Domain of un 70.0 1.7 3.7E-05 31.5 0.3 26 3-36 4-29 (68)
42 COG1656 Uncharacterized conser 69.2 2 4.3E-05 36.1 0.6 33 3-35 98-139 (165)
43 PF14446 Prok-RING_1: Prokaryo 69.0 2.9 6.2E-05 29.0 1.3 27 1-35 4-30 (54)
44 PF09538 FYDLN_acid: Protein o 68.1 2.2 4.8E-05 33.3 0.7 28 3-37 10-37 (108)
45 cd01121 Sms Sms (bacterial rad 67.4 2.7 5.8E-05 39.2 1.2 23 3-35 1-23 (372)
46 PF09845 DUF2072: Zn-ribbon co 64.4 2.4 5.2E-05 34.4 0.3 27 3-35 2-28 (131)
47 COG0846 SIR2 NAD-dependent pro 64.3 3 6.5E-05 37.1 0.8 34 2-35 122-155 (250)
48 PF14353 CpXC: CpXC protein 64.1 4.8 0.0001 31.4 1.9 56 3-68 2-70 (128)
49 PRK00423 tfb transcription ini 63.7 4.7 0.0001 36.4 2.0 32 2-38 11-42 (310)
50 PF14149 YhfH: YhfH-like prote 63.1 1.3 2.8E-05 28.5 -1.2 24 3-32 14-37 (37)
51 TIGR00416 sms DNA repair prote 62.9 3.7 8E-05 39.2 1.2 24 2-35 7-30 (454)
52 PF13719 zinc_ribbon_5: zinc-r 62.7 3.7 8.1E-05 25.8 0.8 34 1-35 1-34 (37)
53 smart00531 TFIIE Transcription 60.8 2.9 6.2E-05 33.8 0.1 35 2-37 99-134 (147)
54 PRK11823 DNA repair protein Ra 60.7 4.2 9.2E-05 38.6 1.2 29 2-41 7-35 (446)
55 PF13717 zinc_ribbon_4: zinc-r 59.9 4.9 0.00011 25.2 1.0 32 1-35 1-34 (36)
56 PHA02942 putative transposase; 59.4 5.2 0.00011 37.4 1.6 29 3-38 326-354 (383)
57 TIGR01562 FdhE formate dehydro 58.6 9.6 0.00021 34.9 3.1 61 3-65 225-300 (305)
58 COG1997 RPL43A Ribosomal prote 56.8 6.2 0.00013 30.0 1.3 28 1-35 34-62 (89)
59 PF14255 Cys_rich_CPXG: Cystei 56.7 8.8 0.00019 26.3 1.9 41 4-44 2-42 (52)
60 COG2260 Predicted Zn-ribbon RN 56.2 6.3 0.00014 27.8 1.1 19 27-45 18-47 (59)
61 PF11023 DUF2614: Protein of u 55.9 4.3 9.4E-05 32.2 0.3 25 3-35 70-94 (114)
62 COG2888 Predicted Zn-ribbon RN 55.5 7.5 0.00016 27.6 1.4 38 3-40 10-52 (61)
63 PRK07591 threonine synthase; V 53.4 7.3 0.00016 36.6 1.5 30 3-43 19-48 (421)
64 PF12156 ATPase-cat_bd: Putati 53.4 4.3 9.3E-05 30.3 -0.1 34 4-37 2-37 (88)
65 KOG1597 Transcription initiati 53.0 8.4 0.00018 35.3 1.7 29 4-35 2-30 (308)
66 PRK00564 hypA hydrogenase nick 52.7 6.5 0.00014 30.8 0.9 26 3-35 72-97 (117)
67 PRK12336 translation initiatio 51.8 12 0.00026 32.0 2.4 36 4-42 100-137 (201)
68 COG4031 Predicted metal-bindin 51.5 6.7 0.00014 34.0 0.8 30 3-44 1-34 (227)
69 PF00320 GATA: GATA zinc finge 51.4 4.8 0.0001 25.1 -0.0 31 5-37 1-31 (36)
70 COG1066 Sms Predicted ATP-depe 50.7 7.6 0.00017 37.4 1.1 23 2-34 7-29 (456)
71 TIGR02300 FYDLN_acid conserved 49.9 7.8 0.00017 31.4 0.9 28 2-36 9-36 (129)
72 PRK03681 hypA hydrogenase nick 49.6 8.7 0.00019 29.9 1.1 26 3-35 71-96 (114)
73 cd00202 ZnF_GATA Zinc finger D 49.3 5.1 0.00011 27.4 -0.2 34 4-39 1-34 (54)
74 PHA02768 hypothetical protein; 49.3 3.7 8E-05 28.5 -0.9 40 2-42 5-50 (55)
75 COG1499 NMD3 NMD protein affec 48.7 12 0.00026 35.0 2.1 32 2-33 6-50 (355)
76 PRK13130 H/ACA RNA-protein com 48.4 9.9 0.00021 26.5 1.1 19 28-46 19-48 (56)
77 smart00661 RPOL9 RNA polymeras 48.3 11 0.00023 24.6 1.2 28 4-35 2-29 (52)
78 COG1405 SUA7 Transcription ini 47.8 11 0.00024 34.1 1.7 38 2-44 1-39 (285)
79 PRK14890 putative Zn-ribbon RN 47.5 13 0.00029 26.2 1.6 38 2-39 7-49 (59)
80 PRK05978 hypothetical protein; 45.4 9.8 0.00021 31.4 0.9 28 3-35 34-61 (148)
81 PRK12380 hydrogenase nickel in 45.3 10 0.00022 29.5 0.9 25 3-35 71-95 (113)
82 PRK04136 rpl40e 50S ribosomal 45.2 11 0.00025 25.5 1.0 23 2-34 14-36 (48)
83 PRK03824 hypA hydrogenase nick 44.0 11 0.00024 30.3 0.9 34 2-35 70-116 (135)
84 PF09297 zf-NADH-PPase: NADH p 42.1 8.3 0.00018 23.2 -0.0 27 3-35 4-30 (32)
85 KOG3277 Uncharacterized conser 41.8 17 0.00037 30.5 1.8 36 2-38 79-119 (165)
86 PF02146 SIR2: Sir2 family; I 41.8 4.6 0.0001 33.1 -1.6 30 3-34 106-137 (178)
87 COG4888 Uncharacterized Zn rib 40.6 22 0.00048 27.7 2.1 32 3-34 23-54 (104)
88 PRK03976 rpl37ae 50S ribosomal 40.5 20 0.00044 27.3 1.8 28 2-36 36-64 (90)
89 COG1645 Uncharacterized Zn-fin 39.9 15 0.00033 29.8 1.2 24 3-34 29-52 (131)
90 PRK06260 threonine synthase; V 39.6 16 0.00035 33.9 1.4 32 2-43 3-34 (397)
91 PRK04023 DNA polymerase II lar 38.9 18 0.00038 38.4 1.7 16 27-42 664-679 (1121)
92 PRK02935 hypothetical protein; 38.8 16 0.00035 28.7 1.1 24 4-35 72-95 (110)
93 TIGR03829 YokU_near_AblA uncha 38.6 34 0.00074 26.0 2.8 50 5-54 2-60 (89)
94 TIGR01206 lysW lysine biosynth 38.2 22 0.00048 24.5 1.6 31 1-35 1-31 (54)
95 PF09567 RE_MamI: MamI restric 38.0 13 0.00028 33.7 0.5 47 4-68 84-143 (314)
96 PF07191 zinc-ribbons_6: zinc- 37.9 18 0.00038 26.4 1.1 35 3-37 2-41 (70)
97 COG1545 Predicted nucleic-acid 37.8 19 0.00042 29.0 1.5 31 3-43 30-61 (140)
98 PRK06266 transcription initiat 37.6 13 0.00027 31.3 0.4 32 2-38 117-148 (178)
99 PF09151 DUF1936: Domain of un 37.6 34 0.00073 21.4 2.2 27 3-31 2-29 (36)
100 PRK00019 rpmE 50S ribosomal pr 37.4 28 0.0006 25.3 2.1 29 4-34 15-43 (72)
101 PF05191 ADK_lid: Adenylate ki 36.9 21 0.00046 22.5 1.2 28 3-34 2-29 (36)
102 PF09332 Mcm10: Mcm10 replicat 36.3 15 0.00032 34.3 0.6 27 3-35 286-312 (344)
103 TIGR00100 hypA hydrogenase nic 36.3 16 0.00034 28.5 0.7 26 3-36 71-96 (115)
104 PF01155 HypA: Hydrogenase exp 35.6 14 0.0003 28.7 0.3 25 3-35 71-95 (113)
105 TIGR00280 L37a ribosomal prote 35.5 27 0.00058 26.7 1.8 28 2-36 35-63 (91)
106 COG1644 RPB10 DNA-directed RNA 35.2 8.5 0.00018 27.5 -0.9 19 3-21 5-23 (63)
107 PRK00762 hypA hydrogenase nick 35.2 20 0.00043 28.4 1.1 30 3-35 71-101 (124)
108 COG3357 Predicted transcriptio 34.9 17 0.00037 28.0 0.6 26 2-34 58-84 (97)
109 COG4830 RPS26B Ribosomal prote 34.8 22 0.00048 27.7 1.3 31 4-34 22-79 (108)
110 PF10122 Mu-like_Com: Mu-like 34.4 25 0.00053 24.2 1.3 30 2-35 4-33 (51)
111 PRK14714 DNA polymerase II lar 34.1 23 0.0005 38.4 1.7 15 27-41 710-724 (1337)
112 PF10083 DUF2321: Uncharacteri 33.7 17 0.00036 30.4 0.5 31 5-35 42-77 (158)
113 COG0375 HybF Zn finger protein 33.6 21 0.00046 28.3 1.1 29 3-39 71-99 (115)
114 PF04810 zf-Sec23_Sec24: Sec23 33.6 20 0.00044 22.7 0.8 18 27-44 3-20 (40)
115 PF03691 UPF0167: Uncharacteri 33.5 15 0.00032 31.2 0.2 37 2-39 24-65 (176)
116 COG1552 RPL40A Ribosomal prote 33.5 9.9 0.00021 26.0 -0.7 22 3-34 15-36 (50)
117 cd01407 SIR2-fam SIR2 family o 33.5 16 0.00034 31.1 0.3 32 2-35 109-142 (218)
118 COG3880 Modulator of heat shoc 33.4 29 0.00062 29.5 1.8 42 3-44 1-44 (176)
119 PRK06386 replication factor A; 33.3 20 0.00043 33.6 1.0 24 3-39 237-260 (358)
120 PRK14559 putative protein seri 33.3 19 0.00042 36.2 0.9 8 28-35 29-36 (645)
121 cd01408 SIRT1 SIRT1: Eukaryoti 33.1 12 0.00027 32.4 -0.4 14 22-35 112-125 (235)
122 PTZ00255 60S ribosomal protein 33.1 32 0.00068 26.2 1.9 28 2-36 36-64 (90)
123 PF10977 DUF2797: Protein of u 32.9 18 0.00039 31.9 0.6 29 4-32 13-43 (235)
124 PRK07218 replication factor A; 32.9 20 0.00044 34.2 1.0 21 46-66 323-343 (423)
125 PRK04016 DNA-directed RNA poly 32.8 11 0.00025 26.8 -0.5 19 3-21 5-23 (62)
126 PF03367 zf-ZPR1: ZPR1 zinc-fi 32.7 27 0.00058 28.9 1.6 32 3-34 2-38 (161)
127 COG1571 Predicted DNA-binding 32.5 23 0.0005 33.9 1.3 50 2-63 350-404 (421)
128 PF09889 DUF2116: Uncharacteri 32.4 19 0.0004 25.3 0.5 12 3-14 4-15 (59)
129 PF01194 RNA_pol_N: RNA polyme 32.1 13 0.00027 26.4 -0.4 17 4-20 6-22 (60)
130 PRK04023 DNA polymerase II lar 32.1 26 0.00057 37.2 1.7 35 2-39 626-664 (1121)
131 PF01197 Ribosomal_L31: Riboso 31.5 34 0.00075 24.4 1.8 30 4-34 15-44 (69)
132 COG0254 RpmE Ribosomal protein 31.2 39 0.00084 24.9 2.0 30 4-34 16-45 (75)
133 PTZ00410 NAD-dependent SIR2; P 31.2 18 0.00038 33.8 0.3 31 3-35 148-180 (349)
134 PF10058 DUF2296: Predicted in 31.0 37 0.0008 23.2 1.8 30 3-34 23-52 (54)
135 smart00709 Zpr1 Duplicated dom 30.8 35 0.00075 28.3 1.9 31 4-34 2-37 (160)
136 PF06542 PHA-1: Regulator prot 30.6 13 0.00028 35.2 -0.8 39 28-66 123-161 (390)
137 cd01411 SIR2H SIR2H: Uncharact 30.4 23 0.00051 30.4 0.9 26 3-34 119-144 (225)
138 TIGR00105 L31 ribosomal protei 30.2 45 0.00098 23.8 2.2 28 4-33 15-42 (68)
139 PRK14559 putative protein seri 30.2 26 0.00057 35.2 1.3 14 26-39 41-54 (645)
140 COG3478 Predicted nucleic-acid 29.9 28 0.00061 25.2 1.1 9 4-12 6-14 (68)
141 PRK01397 50S ribosomal protein 29.2 50 0.0011 24.4 2.3 15 20-34 28-42 (78)
142 COG2995 PqiA Uncharacterized p 28.4 29 0.00063 33.1 1.2 26 4-35 20-47 (418)
143 PLN00032 DNA-directed RNA poly 28.4 15 0.00033 26.9 -0.5 19 3-21 5-23 (71)
144 KOG2682 NAD-dependent histone 28.2 15 0.00032 33.2 -0.7 38 3-40 153-191 (314)
145 COG2816 NPY1 NTP pyrophosphohy 28.0 36 0.00078 30.9 1.7 27 3-35 112-138 (279)
146 TIGR00310 ZPR1_znf ZPR1 zinc f 28.0 41 0.0009 28.7 2.0 31 4-34 2-38 (192)
147 PRK00504 rpmG 50S ribosomal pr 27.7 50 0.0011 22.4 2.0 33 3-35 8-43 (50)
148 PF13913 zf-C2HC_2: zinc-finge 27.5 26 0.00056 20.1 0.5 9 26-34 2-10 (25)
149 KOG0477 DNA replication licens 27.4 29 0.00062 35.5 1.0 33 2-35 292-324 (854)
150 PRK14704 anaerobic ribonucleos 27.3 27 0.00059 34.9 0.9 22 3-35 560-581 (618)
151 PF04135 Nop10p: Nucleolar RNA 27.3 31 0.00066 23.8 0.8 19 27-45 18-47 (53)
152 PHA02637 TNF-alpha-receptor-li 27.1 37 0.00081 27.4 1.4 31 3-39 63-93 (127)
153 PRK06424 transcription factor; 27.0 27 0.00059 28.5 0.7 37 5-42 3-39 (144)
154 PRK08197 threonine synthase; V 26.7 35 0.00076 31.6 1.4 31 2-43 7-37 (394)
155 PF14311 DUF4379: Domain of un 26.5 32 0.00069 23.0 0.8 8 4-11 30-37 (55)
156 PF06827 zf-FPG_IleRS: Zinc fi 26.4 49 0.0011 19.4 1.5 29 3-35 2-30 (30)
157 PRK05638 threonine synthase; V 26.3 38 0.00083 31.9 1.6 30 2-43 1-30 (442)
158 PRK07218 replication factor A; 26.2 35 0.00076 32.6 1.3 20 20-39 291-310 (423)
159 PRK12286 rpmF 50S ribosomal pr 26.0 46 0.00099 23.0 1.6 23 4-37 29-51 (57)
160 cd04476 RPA1_DBD_C RPA1_DBD_C: 25.6 34 0.00073 27.6 1.0 28 3-37 35-62 (166)
161 PRK06450 threonine synthase; V 25.6 37 0.0008 31.1 1.3 33 2-43 3-35 (338)
162 smart00507 HNHc HNH nucleases. 25.2 30 0.00064 21.3 0.5 11 3-13 11-21 (52)
163 cd01412 SIRT5_Af1_CobB SIRT5_A 25.2 32 0.0007 29.2 0.8 29 3-34 110-138 (224)
164 PF03833 PolC_DP2: DNA polymer 25.1 24 0.00052 36.7 0.0 41 3-43 668-709 (900)
165 PRK08402 replication factor A; 25.0 32 0.00069 32.1 0.8 11 26-36 212-222 (355)
166 CHL00136 rpl31 ribosomal prote 24.5 56 0.0012 23.5 1.8 13 22-34 31-43 (68)
167 COG5257 GCD11 Translation init 24.4 17 0.00038 34.2 -1.0 25 3-36 58-82 (415)
168 PF01780 Ribosomal_L37ae: Ribo 24.2 31 0.00067 26.3 0.4 28 2-35 35-62 (90)
169 PRK00481 NAD-dependent deacety 23.5 40 0.00088 29.1 1.1 9 3-11 123-131 (242)
170 PRK12366 replication factor A; 23.4 36 0.00078 34.0 0.9 25 3-35 533-557 (637)
171 PF11781 RRN7: RNA polymerase 23.4 40 0.00088 21.1 0.8 25 5-36 11-35 (36)
172 smart00440 ZnF_C2C2 C2C2 Zinc 23.3 33 0.00072 21.8 0.4 9 3-11 29-37 (40)
173 TIGR03844 cysteate_syn cysteat 23.1 47 0.001 31.2 1.5 31 2-43 2-32 (398)
174 PRK00448 polC DNA polymerase I 23.1 40 0.00087 37.1 1.2 35 2-36 908-943 (1437)
175 TIGR00155 pqiA_fam integral me 23.0 40 0.00087 31.8 1.1 23 4-35 217-239 (403)
176 PF10217 DUF2039: Uncharacteri 23.0 11 0.00023 28.9 -2.3 33 3-35 56-90 (92)
177 PRK14714 DNA polymerase II lar 23.0 40 0.00088 36.6 1.2 30 3-35 668-701 (1337)
178 PRK14892 putative transcriptio 22.7 58 0.0013 25.1 1.7 29 3-34 22-50 (99)
179 PRK06393 rpoE DNA-directed RNA 22.6 14 0.00031 26.5 -1.6 21 3-35 6-26 (64)
180 TIGR00340 zpr1_rel ZPR1-relate 22.5 58 0.0013 27.1 1.8 30 5-34 1-36 (163)
181 PRK01678 rpmE2 50S ribosomal p 22.4 70 0.0015 24.2 2.1 12 23-34 45-56 (87)
182 PF12172 DUF35_N: Rubredoxin-l 22.1 52 0.0011 20.1 1.1 15 21-35 6-20 (37)
183 PF02132 RecR: RecR protein; 22.0 30 0.00065 22.1 0.0 14 25-38 16-29 (41)
184 TIGR01405 polC_Gram_pos DNA po 21.9 44 0.00095 36.1 1.2 35 2-36 683-718 (1213)
185 PF01412 ArfGap: Putative GTPa 21.8 15 0.00033 28.3 -1.7 28 3-34 14-41 (116)
186 PF09943 DUF2175: Uncharacteri 21.8 52 0.0011 25.6 1.3 26 2-27 2-29 (101)
187 KOG2462 C2H2-type Zn-finger pr 21.8 33 0.00072 31.2 0.2 36 3-38 188-228 (279)
188 PRK09263 anaerobic ribonucleos 21.3 49 0.0011 33.7 1.4 26 3-34 642-667 (711)
189 PF01529 zf-DHHC: DHHC palmito 21.3 50 0.0011 26.2 1.2 27 3-39 49-75 (174)
190 KOG3507 DNA-directed RNA polym 21.2 47 0.001 23.6 0.9 26 2-34 20-45 (62)
191 TIGR03830 CxxCG_CxxCG_HTH puta 21.1 78 0.0017 23.9 2.2 30 5-34 1-39 (127)
192 PF03833 PolC_DP2: DNA polymer 20.9 32 0.0007 35.8 0.0 35 3-37 656-691 (900)
193 PF13878 zf-C2H2_3: zinc-finge 20.5 59 0.0013 20.8 1.2 17 19-35 6-22 (41)
194 TIGR03831 YgiT_finger YgiT-typ 20.5 88 0.0019 19.3 2.0 30 5-34 1-40 (46)
195 PRK14138 NAD-dependent deacety 20.4 30 0.00064 30.2 -0.4 7 4-10 121-127 (244)
196 cd01413 SIR2_Af2 SIR2_Af2: Arc 20.4 43 0.00093 28.7 0.6 31 2-34 113-144 (222)
197 TIGR00515 accD acetyl-CoA carb 20.4 24 0.00053 31.9 -0.9 25 4-34 28-53 (285)
198 COG2093 DNA-directed RNA polym 20.2 44 0.00095 24.0 0.5 22 3-34 5-26 (64)
199 cd02336 ZZ_RSC8 Zinc finger, Z 20.2 54 0.0012 21.6 0.9 30 3-33 1-30 (45)
200 PF08646 Rep_fac-A_C: Replicat 20.1 52 0.0011 26.0 1.0 29 3-38 19-49 (146)
201 PF07975 C1_4: TFIIH C1-like d 20.0 50 0.0011 22.5 0.8 34 5-40 2-39 (51)
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=9.4e-60 Score=401.30 Aligned_cols=194 Identities=41% Similarity=0.643 Sum_probs=168.5
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccccccccceehhHHHHHHHHhcCcccceeeeccccccccc--------ch
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETV--------NL 74 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d~vil~IDllLlk~~ayRHllfN~~~~~~~--------~~ 74 (208)
++|||||+||++||++|||||||+|+|++||++||||||+|+|+++||++|+|||||||++||+.+++.. +.
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 34
Q ss_pred hhHHHHHHHHHHHHHHHHHHhhhcCCCCCCC---chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-CCCch
Q 028469 75 KGILWKSTVGFLLLDAYRSLLLSRSNEGQSS---SMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTS-AGASS 150 (208)
Q Consensus 75 ~~~~~kl~~~~ll~eay~~w~~~~~~~~~~~---s~~~~~~~~~~~~~l~~~~l~~~~f~~~~~~~~~~~l~~~-~~~~~ 150 (208)
.+.+||++++++++|||+.|..++++.+.+. .....+...++...+...++++++|+.++.+..+...+++ ....+
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 5679999999999999999987766643331 0101233555667778888899999998888888888887 55668
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhccCCCCccee--eeeeEEEeehhhhH
Q 028469 151 FKDFLLAVLISSYFKIFLVAMMVWNFPSSVIY--IIDLFVLSSNTVAL 196 (208)
Q Consensus 151 ~~~ll~alllSs~~KLF~ilmlIW~yd~s~~~--~i~~~vl~SN~~Al 196 (208)
++.+++|+++||+||+|+++|+||+||.++.. +++++|++||++||
T Consensus 161 ~~~l~~alllSs~~Klf~ilmlIW~~~~~~~~~~ii~~~v~~~~~~aL 208 (208)
T PF04161_consen 161 FRVLLTALLLSSYGKLFPILMLIWPYDSSPISLSIIDWFVLLSNIEAL 208 (208)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999977654 99999999999996
No 2
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=1.8e-41 Score=289.21 Aligned_cols=197 Identities=38% Similarity=0.587 Sum_probs=142.8
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccccccccceehhHHHHHHHHhcCcccceeeecccccccccchhhHHHHHH
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKST 82 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d~vil~IDllLlk~~ayRHllfN~~~~~~~~~~~~~~kl~ 82 (208)
++|||||+++++||++|||||||+|+||+|+++||||||+|+||++||++|+|||||||+|||+.++++.+..-.+||+.
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--------CCCchHHH
Q 028469 83 VGFLLLDAYRSLLLSRS-NEGQSSSMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTS--------AGASSFKD 153 (208)
Q Consensus 83 ~~~ll~eay~~w~~~~~-~~~~~~s~~~~~~~~~~~~~l~~~~l~~~~f~~~~~~~~~~~l~~~--------~~~~~~~~ 153 (208)
...++++.|.....+.+ ++|..+++++.-...... ......+++|.+.+...-..+.+.+ .....+..
T Consensus 81 ~~~~lL~~~~~~l~~~~~~~e~~~~~~~~~~~~~~~---~~~i~~~~l~~f~~~~~~~~~~~l~~~~lLl~~~~~~syi~ 157 (225)
T KOG3134|consen 81 FAWLLLQDFESLLLWLSEDDEWVFYRSFALPALEVL---SSLIERQYLFVFLWCNRETTFVQLSSALLLLKTLLLKSYIS 157 (225)
T ss_pred HHHHHHHHhHhhcccccCCCcchhhhhHHHHHHHHH---HHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHH
Confidence 88888877765555555 555665555321111111 1111113333332221111111111 01112333
Q ss_pred -HHHHHHHHhhhHHHhhhhhccCCCCc-c-eeeeeeEEEeehhhhHHHhhhh
Q 028469 154 -FLLAVLISSYFKIFLVAMMVWNFPSS-V-IYIIDLFVLSSNTVALKGKLLV 202 (208)
Q Consensus 154 -ll~alllSs~~KLF~ilmlIW~yd~s-~-~~~i~~~vl~SN~~Alr~~l~~ 202 (208)
+..+.+.|++.|.++|.|++|+||.+ + +..++|-...++..|+++....
T Consensus 158 ~i~~~~~~s~~~~v~~Ifml~~~~~~~~v~~~~v~~~~~~a~l~~l~i~s~~ 209 (225)
T KOG3134|consen 158 VISLLVILSSCVKVNPIFMLISCYQTSRVALGIVYWVSFLAVLLALKILSTS 209 (225)
T ss_pred HHHHHHHHHHhhhhhheeeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66677777777889999999999976 3 3678898899999999887643
No 3
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=100.00 E-value=3.3e-39 Score=272.79 Aligned_cols=194 Identities=21% Similarity=0.285 Sum_probs=132.7
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccccccccceehhHHHHHHHHhcCcccceeeecccccccccchhhHHHH--
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWK-- 80 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d~vil~IDllLlk~~ayRHllfN~~~~~~~~~~~~~~k-- 80 (208)
++|||||.||++||++||.++||+++||+|++.+|||+|.|.|+++||++|+|||+|||++||+++.++.+......+
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 589999999999999999999999999999999999999999999999999999999999999987553211111111
Q ss_pred ------HHHHHHHHHHHHHHhhhcCCCCCCCchhh------HHH----------H-HHHHHHHHHHHHHHHHHHHHHHHH
Q 028469 81 ------STVGFLLLDAYRSLLLSRSNEGQSSSMSF------SLL----------A-WIFQKMLKDVVLGNVMFLGVFLHA 137 (208)
Q Consensus 81 ------l~~~~ll~eay~~w~~~~~~~~~~~s~~~------~~~----------~-~~~~~~l~~~~l~~~~f~~~~~~~ 137 (208)
+..+...++.|+.|-..++.. +..+.+ -+. . .++.....-++++...|.....+.
T Consensus 81 ~~Fc~~~~~l~~~f~~~L~w~~~E~~~--~~~~a~~~~~~pes~~~~s~ilr~~~s~qyl~~~~vcl~~~~l~~~f~~lf 158 (239)
T COG5254 81 RMFCEPILQLHEAFGLLLSWGPGEGVS--IAEMATICRDVPESLMETSLILRLVFSMQYLHAGFVCLSSALLLSSFYYLF 158 (239)
T ss_pred HHHHHHHHHHHHHhhhheeeccccccc--hHHHHHhhhhhHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 223444555666665443321 000100 000 0 111122223333344444333332
Q ss_pred HHHHhhcCCCCchHHHHHHHHHHHhhhHHHhhhhhccCCCCcce-eeeeeEEEeehhhhHHHhhh
Q 028469 138 SRILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVI-YIIDLFVLSSNTVALKGKLL 201 (208)
Q Consensus 138 ~~~~l~~~~~~~~~~~ll~alllSs~~KLF~ilmlIW~yd~s~~-~~i~~~vl~SN~~Alr~~l~ 201 (208)
....++|.. ....-..++.+|+.+|.+|++|.||+||.+.+ .+|+|.++.+|.+|+|+++-
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 222333321 12233369999999999999999999998774 78999999999999999874
No 4
>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=93.60 E-value=0.027 Score=35.49 Aligned_cols=34 Identities=32% Similarity=0.632 Sum_probs=23.7
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~Dk 38 (208)
+|+|.+||+..+.+... +. -....||+||.-+.|
T Consensus 5 ~y~C~~Cg~~fe~~~~~-~~--~~~~~CP~Cg~~~~r 38 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI-SD--DPLATCPECGGDVRR 38 (41)
T ss_pred EEEcCCCCCEEEEEEec-CC--CCCCCCCCCCCccee
Confidence 58999999987665322 11 367789999985443
No 5
>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=93.34 E-value=0.057 Score=34.99 Aligned_cols=33 Identities=30% Similarity=0.729 Sum_probs=23.6
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccccccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYI 40 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYi 40 (208)
++|.+||... +..++..|.+ .|++||.+.|..+
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 8999999877654
No 6
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=93.05 E-value=0.05 Score=47.54 Aligned_cols=84 Identities=20% Similarity=0.132 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhhcC---CCCchHHHHHHHHHHHhhhH-HHhhhhhccCCCCcceeeeeeE
Q 028469 113 AWIFQKMLKDVVLGNVMFLGVFLHASRI-LLNTS---AGASSFKDFLLAVLISSYFK-IFLVAMMVWNFPSSVIYIIDLF 187 (208)
Q Consensus 113 ~~~~~~~l~~~~l~~~~f~~~~~~~~~~-~l~~~---~~~~~~~~ll~alllSs~~K-LF~ilmlIW~yd~s~~~~i~~~ 187 (208)
+|.+++.+.....+...+...-++...+ +.... .+.++...+++++.++||+| .+...+..|.... ...|
T Consensus 101 e~~~~~~~~~~~~~~~~~~i~~~~l~~f~~~~~~~~~~~l~~~~lLl~~~~~~syi~~i~~~~~~s~~~~v-----~~If 175 (225)
T KOG3134|consen 101 EWVFYRSFALPALEVLSSLIERQYLFVFLWCNRETTFVQLSSALLLLKTLLLKSYISVISLLVILSSCVKV-----NPIF 175 (225)
T ss_pred cchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh-----hhee
Confidence 6777887777777777776653333322 22222 34567778899999999999 6666666655544 4556
Q ss_pred EEeehhhhHHHhhh
Q 028469 188 VLSSNTVALKGKLL 201 (208)
Q Consensus 188 vl~SN~~Alr~~l~ 201 (208)
++.++.++.|+.+-
T Consensus 176 ml~~~~~~~~v~~~ 189 (225)
T KOG3134|consen 176 MLISCYQTSRVALG 189 (225)
T ss_pred eeehHHHHHHHHHH
Confidence 66666666666543
No 7
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=92.97 E-value=0.047 Score=35.86 Aligned_cols=31 Identities=23% Similarity=0.573 Sum_probs=22.6
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCcccccc
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~D 37 (208)
++|+|.+||..+.- .++. ....||+||...+
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=92.67 E-value=0.071 Score=35.28 Aligned_cols=28 Identities=29% Similarity=0.647 Sum_probs=20.4
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
+.|+|-+||+.++.- +.+ .-+|++||.-
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 222 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=91.25 E-value=0.09 Score=34.12 Aligned_cols=34 Identities=29% Similarity=0.641 Sum_probs=24.7
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccc-cccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA-VADE 38 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~-~~Dk 38 (208)
+|+|-+||+.-+.+-. .+. -....||+||. -+.|
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 5899999998777633 333 36779999998 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=90.61 E-value=0.11 Score=34.58 Aligned_cols=30 Identities=40% Similarity=0.877 Sum_probs=22.3
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
+|+|-+||+.-+.+ ...+. -....||+||.
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 33333 25678999997
No 11
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.90 E-value=0.14 Score=30.00 Aligned_cols=24 Identities=42% Similarity=0.796 Sum_probs=17.8
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCccc
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
|+..|.+||++++. .-.-|++||+
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
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=89.69 E-value=0.12 Score=35.19 Aligned_cols=28 Identities=32% Similarity=0.863 Sum_probs=19.9
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCccc
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
++|+|..||..++.+ . .-+--.||.||.
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 469999999999433 1 123348999985
No 13
>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=89.66 E-value=0.21 Score=31.03 Aligned_cols=25 Identities=28% Similarity=0.826 Sum_probs=16.9
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
|+|-+||+.++ + -..+. .+|++||.
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 78999999998 2 22333 38999985
No 14
>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=88.30 E-value=0.25 Score=35.54 Aligned_cols=36 Identities=33% Similarity=0.905 Sum_probs=24.7
Q ss_pred CceecccCcccccceee--ccCCceEeecCCCccc---cccc
Q 028469 2 EYRCVKCGFRIKTLFVQ--YSPGNIRLMKCENCRA---VADE 38 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~--ys~~~i~l~~C~~C~~---~~Dk 38 (208)
.+-|-.||++....+.+ |.+|. .+.+||+|++ +||.
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 46799999998887776 66654 8999999986 5664
No 15
>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=87.32 E-value=0.23 Score=30.93 Aligned_cols=32 Identities=25% Similarity=0.544 Sum_probs=23.6
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccccce
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE 41 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE 41 (208)
.++|..||+-.+. .-....||.|+...+++.+
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 4799999976432 1134599999999988765
No 16
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=86.64 E-value=3.9 Score=35.71 Aligned_cols=46 Identities=24% Similarity=0.595 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhccCCCCcc-eeeeeeEEEeehhhhH
Q 028469 151 FKDFLLAVLISSYFKIFLVAMMVWNFPSSV-IYIIDLFVLSSNTVAL 196 (208)
Q Consensus 151 ~~~ll~alllSs~~KLF~ilmlIW~yd~s~-~~~i~~~vl~SN~~Al 196 (208)
..-++.|.++|++..+|.+.|+.|+|..+. ...|++-..+.|.-.+
T Consensus 142 ~vcl~~~~l~~~f~~lf~~~~~~Wk~~~~~s~~~I~ls~~a~~~pV~ 188 (239)
T COG5254 142 FVCLSSALLLSSFYYLFMFIMTMWKYQCEESLLVIELSCVACNSPVI 188 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchheeeecchhcchhh
Confidence 446888999999999999999999999754 3577777777665443
No 17
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=86.31 E-value=0.6 Score=36.36 Aligned_cols=52 Identities=29% Similarity=0.617 Sum_probs=34.1
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccccceehhHHHHHHHHhcC--cccceeeecccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHK--PQAYRHLLYNVL 67 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d~vil~IDllLlk--~~ayRHllfN~~ 67 (208)
.+.|.+||+.-. .|.+..-| .||+|+..+- -.++|-...+ |-.|||++|=..
T Consensus 42 ~~~C~~Cg~~~~----~~~SCk~R--~CP~C~~~~~--------~~W~~~~~~~ll~~~y~HvVFTlP 95 (111)
T PF14319_consen 42 RYRCEDCGHEKI----VYNSCKNR--HCPSCQAKAT--------EQWIEKQREDLLPVPYFHVVFTLP 95 (111)
T ss_pred eeecCCCCceEE----ecCcccCc--CCCCCCChHH--------HHHHHHHHhhCCCCCeEEEEEcCc
Confidence 578999998752 24444334 8999998532 3444433333 578999999763
No 18
>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=85.23 E-value=0.5 Score=33.02 Aligned_cols=30 Identities=33% Similarity=0.688 Sum_probs=24.1
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~Dk 38 (208)
-.|-.||++.+. +.+-+.-.|++||...|.
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 345588899999998775
No 19
>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=83.76 E-value=0.4 Score=30.24 Aligned_cols=28 Identities=29% Similarity=0.681 Sum_probs=13.3
Q ss_pred CCceecccCccc--ccceeeccCCceEeecCCCcc
Q 028469 1 MEYRCVKCGFRI--KTLFVQYSPGNIRLMKCENCR 33 (208)
Q Consensus 1 ~~~~CI~C~~~v--~~Ly~~ys~~~i~l~~C~~C~ 33 (208)
+.+.|.|||.+- +-|++.| .+..|.+|.
T Consensus 2 ~~~~C~eC~~~f~dSyL~~~F-----~~~VCD~CR 31 (34)
T PF01286_consen 2 DYPKCDECGKPFMDSYLLNNF-----DLPVCDKCR 31 (34)
T ss_dssp S-EE-TTT--EES-SSCCCCT-----S-S--TTT-
T ss_pred CCchHhHhCCHHHHHHHHHhC-----Ccccccccc
Confidence 358999999993 4444444 556888885
No 20
>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=81.96 E-value=1.1 Score=39.84 Aligned_cols=62 Identities=23% Similarity=0.443 Sum_probs=29.2
Q ss_pred ceecccCcccccceeec---cCCceEeecCCCccc---cccccce-------ehhHHHHHHHHhcCcccceeeecc
Q 028469 3 YRCVKCGFRIKTLFVQY---SPGNIRLMKCENCRA---VADEYIE-------CEIMILLIDLILHKPQAYRHLLYN 65 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~y---s~~~i~l~~C~~C~~---~~DkYiE-------~d~vil~IDllLlk~~ayRHllfN 65 (208)
-.|..||+.-..-+.-+ ..+..|++.|++||. ..|.--. -|.-.+-+|++..+ +-|+..=+|
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd~~~~~~~~~~~dDl~tl~LD~~a~e-~Gy~r~~~n 286 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVDREKDPELDPVADDLATLHLDLLAQE-EGYRRAGPN 286 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEETTT-TT--HHHHHHTTHHHHHHHHH-TT-EE----
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHhhhhCcccchhhHHhhhhhHHHHHHh-CCCCCCCCC
Confidence 46999999876665555 456899999999994 5552221 12334556666543 335554444
No 21
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.84 E-value=0.83 Score=37.81 Aligned_cols=44 Identities=25% Similarity=0.462 Sum_probs=31.4
Q ss_pred ceecccCccc-ccceeec-cCCc-e-EeecCCCccccccccceehhHH
Q 028469 3 YRCVKCGFRI-KTLFVQY-SPGN-I-RLMKCENCRAVADEYIECEIMI 46 (208)
Q Consensus 3 ~~CI~C~~~v-~~Ly~~y-s~~~-i-~l~~C~~C~~~~DkYiE~d~vi 46 (208)
+.|.+||+|- .-.=.+| ++|| + |.-+|++||+-.--|=+.+.++
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 4689999999888887777664
No 22
>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=81.80 E-value=0.72 Score=35.29 Aligned_cols=29 Identities=24% Similarity=0.780 Sum_probs=23.0
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCcc
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCR 33 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~ 33 (208)
+.+.|.+||..|.- .++|+-.-..||+|=
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 46899999999876 356666677999995
No 23
>PF12773 DZR: Double zinc ribbon
Probab=81.25 E-value=0.74 Score=30.19 Aligned_cols=30 Identities=27% Similarity=0.507 Sum_probs=21.0
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkY 39 (208)
-.|.+||.+++ ........|++|++..++-
T Consensus 13 ~fC~~CG~~l~-------~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 13 KFCPHCGTPLP-------PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cCChhhcCChh-------hccCCCCCCcCCcCCCcCC
Confidence 46888999887 2222455799999876653
No 24
>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=79.07 E-value=1 Score=36.39 Aligned_cols=33 Identities=18% Similarity=0.479 Sum_probs=21.6
Q ss_pred ceecccCcccccceee-----cc----CCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQ-----YS----PGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~-----ys----~~~i~l~~C~~C~~~ 35 (208)
.+|..||.+....=++ -. ..+-+...|++||++
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 25
>PRK12495 hypothetical protein; Provisional
Probab=78.29 E-value=1.1 Score=39.43 Aligned_cols=29 Identities=28% Similarity=0.541 Sum_probs=22.4
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~Dk 38 (208)
...|-.||.|++ .| +| .+.|+.|+++++.
T Consensus 42 a~hC~~CG~PIp----a~-pG---~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 42 NAHCDECGDPIF----RH-DG---QEFCPTCQQPVTE 70 (226)
T ss_pred hhhcccccCccc----CC-CC---eeECCCCCCcccc
Confidence 357999999999 35 43 3579999998763
No 26
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=77.99 E-value=0.84 Score=26.11 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=15.2
Q ss_pred eecccCcccccceeeccCCceEeecCCCcccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.|.+||++++. .-..|++||..
T Consensus 1 ~Cp~CG~~~~~----------~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIED----------DAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCC----------cCcchhhhCCc
Confidence 38899998754 12259999863
No 27
>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=76.54 E-value=1.3 Score=38.46 Aligned_cols=38 Identities=24% Similarity=0.624 Sum_probs=25.2
Q ss_pred ecccCcccccceeec-------------cCCceEeecCCCccccc--ccccee
Q 028469 5 CVKCGFRIKTLFVQY-------------SPGNIRLMKCENCRAVA--DEYIEC 42 (208)
Q Consensus 5 CI~C~~~v~~Ly~~y-------------s~~~i~l~~C~~C~~~~--DkYiE~ 42 (208)
|..||.|.+.++... =|+.+.++.|+.||+.= .+.++.
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 777888776653221 24578999999999753 345544
No 28
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=76.13 E-value=1.5 Score=29.66 Aligned_cols=32 Identities=25% Similarity=0.537 Sum_probs=26.5
Q ss_pred CceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
+.+|.+||..-...+++...+. .+.|..|+-.
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 5789999999999999887775 5789999843
No 29
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=74.70 E-value=1 Score=35.22 Aligned_cols=38 Identities=24% Similarity=0.430 Sum_probs=26.0
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCccccccccceehh
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEI 44 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d~ 44 (208)
|..+|+.||+.-+. .+..-+.-||+||.--=+|+--|.
T Consensus 1 MpH~CtrCG~vf~~------g~~~il~GCp~CG~nkF~yv~~e~ 38 (112)
T COG3364 1 MPHQCTRCGEVFDD------GSEEILSGCPKCGCNKFLYVPEEK 38 (112)
T ss_pred CCceeccccccccc------ccHHHHccCccccchheEeccccc
Confidence 67899999986432 133456789999976556665443
No 30
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=74.17 E-value=2.9 Score=26.68 Aligned_cols=27 Identities=22% Similarity=0.859 Sum_probs=20.3
Q ss_pred ecccCcccccceeeccCCceEeecCCCcccc
Q 028469 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 5 CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
|..|++....... +.+.+..|++|+-+
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 7889887554322 56999999999974
No 31
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.79 E-value=0.69 Score=34.41 Aligned_cols=34 Identities=29% Similarity=0.717 Sum_probs=23.1
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~Dk 38 (208)
.|.|.|||+.-+-+ ...+.+ .+|.|+.|+....|
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 48999999984433 112332 68899999986554
No 32
>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=73.63 E-value=2 Score=25.07 Aligned_cols=24 Identities=29% Similarity=0.638 Sum_probs=14.1
Q ss_pred ecccCcccccceeeccCCceEeecCCCccc
Q 028469 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 5 CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
|+.||.++..- +.-..=.||+||.
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 77888875331 1112237999984
No 33
>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=73.36 E-value=1.5 Score=25.83 Aligned_cols=22 Identities=23% Similarity=0.618 Sum_probs=16.7
Q ss_pred eecccCcccccceeeccCCceEeecCCCcccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.|-+|++.|+. .-..||+||..
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 34579999863
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=72.75 E-value=1.7 Score=26.96 Aligned_cols=35 Identities=20% Similarity=0.481 Sum_probs=19.3
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCccccc
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~ 36 (208)
|...|-+||+...-==.+...+. ..-.|++|++..
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 45679999985211100111111 245699999864
No 35
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=71.69 E-value=1.1 Score=30.51 Aligned_cols=33 Identities=18% Similarity=0.486 Sum_probs=23.8
Q ss_pred CceecccCccc-ccceeeccCCceEeecCCCcccc
Q 028469 2 EYRCVKCGFRI-KTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 2 ~~~CI~C~~~v-~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
+-+|-.|+-.+ ++.+.+-..+ -++..||+||++
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 5555555444 478899999985
No 36
>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=71.52 E-value=1.9 Score=26.46 Aligned_cols=32 Identities=25% Similarity=0.584 Sum_probs=22.1
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccccce
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE 41 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE 41 (208)
.++|-.||.-.+.- . .-..||.|+...+.+..
T Consensus 1 ~~~C~~CGy~y~~~-------~-~~~~CP~Cg~~~~~F~~ 32 (33)
T cd00350 1 KYVCPVCGYIYDGE-------E-APWVCPVCGAPKDKFEK 32 (33)
T ss_pred CEECCCCCCEECCC-------c-CCCcCcCCCCcHHHcEE
Confidence 37899999763321 1 45589999987776543
No 37
>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=70.61 E-value=2.9 Score=27.30 Aligned_cols=29 Identities=24% Similarity=0.606 Sum_probs=18.8
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCccc
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
++++|..||+. .. |.-.+-+.-+|.+|++
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 21 2222246678988875
No 38
>PRK00420 hypothetical protein; Validated
Probab=70.25 E-value=2.5 Score=33.39 Aligned_cols=28 Identities=21% Similarity=0.317 Sum_probs=20.1
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~D 37 (208)
..|..||.|.-.+ +++ -..||+||++.+
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 4799999997554 333 348999998543
No 39
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=70.16 E-value=4.7 Score=36.97 Aligned_cols=63 Identities=16% Similarity=0.382 Sum_probs=40.9
Q ss_pred ceecccCcccccceeeccC--CceEeecCCCcccc---c----cccce---ehhHHHHHHHHhcCcccceeeeccc
Q 028469 3 YRCVKCGFRIKTLFVQYSP--GNIRLMKCENCRAV---A----DEYIE---CEIMILLIDLILHKPQAYRHLLYNV 66 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~--~~i~l~~C~~C~~~---~----DkYiE---~d~vil~IDllLlk~~ayRHllfN~ 66 (208)
-.|.+||+.-+--|-...+ ..+|.+.|++|+.- . |+.+| -|.--+.+|++..+ +-|++.=+|-
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 4699999863333332222 47899999999953 2 22221 14456788988855 5788887774
No 40
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=70.13 E-value=2.3 Score=26.67 Aligned_cols=30 Identities=17% Similarity=0.405 Sum_probs=14.7
Q ss_pred eecccCcccccceeeccCCceEeecCCCcccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
-|.+||+|++.- .-..++-.-..|+.|+.+
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 223344445579999865
No 41
>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=69.97 E-value=1.7 Score=31.52 Aligned_cols=26 Identities=31% Similarity=0.848 Sum_probs=19.0
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~ 36 (208)
++| .||... |++++-+-.+| .||+..
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 589 899876 88888899999 999753
No 42
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=69.21 E-value=2 Score=36.15 Aligned_cols=33 Identities=15% Similarity=0.460 Sum_probs=21.5
Q ss_pred ceecccCcccccceeeccC---------CceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSP---------GNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~---------~~i~l~~C~~C~~~ 35 (208)
-+|.+||.+...+.+.=-. ..-....|++||++
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 5899999987665332211 12246779999985
No 43
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=69.05 E-value=2.9 Score=29.01 Aligned_cols=27 Identities=26% Similarity=0.655 Sum_probs=19.7
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
++.+|..||.+++. ++ .+..|+.|+.+
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 36789999999842 12 46689999875
No 44
>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=68.09 E-value=2.2 Score=33.31 Aligned_cols=28 Identities=25% Similarity=0.561 Sum_probs=20.6
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~D 37 (208)
-+|.+||++---| |-.-..||+||..-+
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 5899999998555 224557999998644
No 45
>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=67.41 E-value=2.7 Score=39.19 Aligned_cols=23 Identities=35% Similarity=0.858 Sum_probs=18.2
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
|+|-+||+..+.- .-+||.|++.
T Consensus 1 ~~c~~cg~~~~~~----------~g~cp~c~~w 23 (372)
T cd01121 1 YVCSECGYVSPKW----------LGKCPECGEW 23 (372)
T ss_pred CCCCCCCCCCCCc----------cEECcCCCCc
Confidence 7899999987653 3489999864
No 46
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=64.44 E-value=2.4 Score=34.38 Aligned_cols=27 Identities=26% Similarity=0.566 Sum_probs=18.9
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.+|++||+--+. ....-|.-||+||.-
T Consensus 2 H~Ct~Cg~~f~d------gs~eil~GCP~CGg~ 28 (131)
T PF09845_consen 2 HQCTKCGRVFED------GSKEILSGCPECGGN 28 (131)
T ss_pred cccCcCCCCcCC------CcHHHHccCcccCCc
Confidence 689999986432 222367789999953
No 47
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=64.32 E-value=3 Score=37.05 Aligned_cols=34 Identities=24% Similarity=0.363 Sum_probs=21.6
Q ss_pred CceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
..+|+.||...+.-...-...+..+.+|++|+..
T Consensus 122 ~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 155 (250)
T COG0846 122 RVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP 155 (250)
T ss_pred eeEeCCCcCccchhhhhhhcccCCCCcCccCCCc
Confidence 3579999987753332112223356789999997
No 48
>PF14353 CpXC: CpXC protein
Probab=64.08 E-value=4.8 Score=31.36 Aligned_cols=56 Identities=18% Similarity=0.544 Sum_probs=36.8
Q ss_pred ceecccCcc-cccceeeccC------------CceEeecCCCccccccccceehhHHHHHHHHhcCcccceeeeccccc
Q 028469 3 YRCVKCGFR-IKTLFVQYSP------------GNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLN 68 (208)
Q Consensus 3 ~~CI~C~~~-v~~Ly~~ys~------------~~i~l~~C~~C~~~~DkYiE~d~vil~IDllLlk~~ayRHllfN~~~ 68 (208)
-.|-+||++ -..+|+.-.. |.+-.-.||+||+.. +++++. +-+.++. +-++++..+
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--RLEYPL-------LYHDPEK-KFMIYYFPD 70 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCce--ecCCCE-------EEEcCCC-CEEEEEcCC
Confidence 469999998 4666665542 566788999999876 466654 3344443 455556544
No 49
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=63.71 E-value=4.7 Score=36.42 Aligned_cols=32 Identities=31% Similarity=0.813 Sum_probs=23.0
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~Dk 38 (208)
+.+|.+||. +.+-.+|+.|. ..|.+||-+.++
T Consensus 11 ~~~Cp~Cg~--~~iv~d~~~Ge---~vC~~CG~Vl~e 42 (310)
T PRK00423 11 KLVCPECGS--DKLIYDYERGE---IVCADCGLVIEE 42 (310)
T ss_pred CCcCcCCCC--CCeeEECCCCe---EeecccCCcccc
Confidence 457999996 35556676653 589999986543
No 50
>PF14149 YhfH: YhfH-like protein
Probab=63.12 E-value=1.3 Score=28.50 Aligned_cols=24 Identities=29% Similarity=0.832 Sum_probs=16.6
Q ss_pred ceecccCcccccceeeccCCceEeecCCCc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENC 32 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C 32 (208)
..|.+||..+++-..-|++ .|++|
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 51
>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=62.86 E-value=3.7 Score=39.20 Aligned_cols=24 Identities=29% Similarity=0.668 Sum_probs=19.3
Q ss_pred CceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.|+|-+||+..+.. .-+||.|++.
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 3479999874
No 52
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=62.68 E-value=3.7 Score=25.80 Aligned_cols=34 Identities=24% Similarity=0.472 Sum_probs=19.5
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
|.-.|-+|++.-+-=-.+-.. .-+.-+|++|+++
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 345788998862111111222 2356789999975
No 53
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=60.80 E-value=2.9 Score=33.80 Aligned_cols=35 Identities=20% Similarity=0.390 Sum_probs=20.6
Q ss_pred CceecccCccccccee-eccCCceEeecCCCcccccc
Q 028469 2 EYRCVKCGFRIKTLFV-QYSPGNIRLMKCENCRAVAD 37 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~-~ys~~~i~l~~C~~C~~~~D 37 (208)
.|+|.+||.....+=- .+.. .-..-.||+||....
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d-~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLD-MDGTFTCPRCGEELE 134 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcC-CCCcEECCCCCCEEE
Confidence 5899999977543211 1100 112267999998654
No 54
>PRK11823 DNA repair protein RadA; Provisional
Probab=60.67 E-value=4.2 Score=38.62 Aligned_cols=29 Identities=31% Similarity=0.740 Sum_probs=21.1
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccccce
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE 41 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE 41 (208)
.|+|-+||+..+.. .-+||.|++. +.+.|
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 3379999764 34444
No 55
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=59.94 E-value=4.9 Score=25.18 Aligned_cols=32 Identities=28% Similarity=0.628 Sum_probs=19.9
Q ss_pred CCceecccCcc--cccceeeccCCceEeecCCCcccc
Q 028469 1 MEYRCVKCGFR--IKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 1 ~~~~CI~C~~~--v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
|.-.|.+|+.. ++. .+- ++.-+--+|++|++.
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 44578899876 221 111 334467789999974
No 56
>PHA02942 putative transposase; Provisional
Probab=59.43 E-value=5.2 Score=37.40 Aligned_cols=29 Identities=28% Similarity=0.728 Sum_probs=20.9
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~Dk 38 (208)
-.|-.||+..+.+ ..|.-.|++||...|.
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 4688999877543 2367789999987765
No 57
>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=58.58 E-value=9.6 Score=34.90 Aligned_cols=61 Identities=16% Similarity=0.405 Sum_probs=39.5
Q ss_pred ceecccCcccccc-eeecc----CCceEeecCCCcccc---cc----ccce---ehhHHHHHHHHhcCcccceeeecc
Q 028469 3 YRCVKCGFRIKTL-FVQYS----PGNIRLMKCENCRAV---AD----EYIE---CEIMILLIDLILHKPQAYRHLLYN 65 (208)
Q Consensus 3 ~~CI~C~~~v~~L-y~~ys----~~~i~l~~C~~C~~~---~D----kYiE---~d~vil~IDllLlk~~ayRHllfN 65 (208)
-.|.+||+. +.+ |-... .+.+|.+.|++|+.- .| .-+| -|.--+.+|++..+ +-|+..=+|
T Consensus 225 ~~C~~Cg~~-~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~~~adDlaSL~LD~~a~e-~Gy~r~~~n 300 (305)
T TIGR01562 225 VKCSHCEES-KHLAYLSLEHDAEKAVLKAETCDSCQGYLKILYQEKDPHADAVADDLASLALDMRMAE-DGYLRRSPN 300 (305)
T ss_pred ccCCCCCCC-CceeeEeecCCCCCcceEEeeccccccchhhhccccCCccCchHHHHhhhHhhHHHHh-cCCCCCCCC
Confidence 469999997 334 43332 246999999999953 22 1111 24556788888865 568876666
No 58
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=56.79 E-value=6.2 Score=30.02 Aligned_cols=28 Identities=29% Similarity=0.660 Sum_probs=20.3
Q ss_pred CCceecccCcc-cccceeeccCCceEeecCCCcccc
Q 028469 1 MEYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 1 ~~~~CI~C~~~-v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
+.|.|..||.+ |+.+ +. .+=+|++|+..
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 4432 33 46789999963
No 59
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=56.71 E-value=8.8 Score=26.28 Aligned_cols=41 Identities=17% Similarity=0.353 Sum_probs=31.9
Q ss_pred eecccCcccccceeeccCCceEeecCCCccccccccceehh
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEI 44 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d~ 44 (208)
.|-.||+++.-+-..-.++.--.+.|+.|.++-.=.++.|.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d~ 42 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVTVDE 42 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEEECC
Confidence 59999999887766666666788999999998766665553
No 60
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=56.17 E-value=6.3 Score=27.81 Aligned_cols=19 Identities=26% Similarity=0.441 Sum_probs=14.7
Q ss_pred ecCCCccc-----------cccccceehhH
Q 028469 27 MKCENCRA-----------VADEYIECEIM 45 (208)
Q Consensus 27 ~~C~~C~~-----------~~DkYiE~d~v 45 (208)
++|+.||. ..|||..|-.-
T Consensus 18 e~Cp~CG~~t~~~~PprFSPeD~y~kYR~~ 47 (59)
T COG2260 18 EKCPVCGGDTKVPHPPRFSPEDKYGKYRRE 47 (59)
T ss_pred ccCCCCCCccccCCCCCCCccchHHHHHHH
Confidence 68999994 47999887653
No 61
>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=55.87 E-value=4.3 Score=32.17 Aligned_cols=25 Identities=32% Similarity=0.708 Sum_probs=19.3
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
-+|.|||++.+-|= |...|.+|+++
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 36999999987762 33589999986
No 62
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.51 E-value=7.5 Score=27.59 Aligned_cols=38 Identities=26% Similarity=0.720 Sum_probs=23.9
Q ss_pred ceecccCccc--ccceeecc---CCceEeecCCCccccccccc
Q 028469 3 YRCVKCGFRI--KTLFVQYS---PGNIRLMKCENCRAVADEYI 40 (208)
Q Consensus 3 ~~CI~C~~~v--~~Ly~~ys---~~~i~l~~C~~C~~~~DkYi 40 (208)
++|+.||..+ .+-|.++. =|+..+..|.+|.+....|.
T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~ 52 (61)
T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKLGNPYR 52 (61)
T ss_pred ceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHHcCCceE
Confidence 6899999986 44455541 13456666666666666553
No 63
>PRK07591 threonine synthase; Validated
Probab=53.41 E-value=7.3 Score=36.62 Aligned_cols=30 Identities=23% Similarity=0.635 Sum_probs=21.3
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccccccccceeh
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d 43 (208)
.+|+.||+.- .++. . -.||+|+..-| ++||
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 4555
No 64
>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=53.37 E-value=4.3 Score=30.28 Aligned_cols=34 Identities=26% Similarity=0.619 Sum_probs=25.9
Q ss_pred eecccCcccc--cceeeccCCceEeecCCCcccccc
Q 028469 4 RCVKCGFRIK--TLFVQYSPGNIRLMKCENCRAVAD 37 (208)
Q Consensus 4 ~CI~C~~~v~--~Ly~~ys~~~i~l~~C~~C~~~~D 37 (208)
.|-|||.|++ .-++.--.|.-|.-=|+-|..++.
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 455555555667888999998874
No 65
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=53.04 E-value=8.4 Score=35.33 Aligned_cols=29 Identities=28% Similarity=0.528 Sum_probs=25.2
Q ss_pred eecccCcccccceeeccCCceEeecCCCcccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.|.+|..+-+.+-.+|+.| -|.|+.||.+
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 5999999888999999986 4799999974
No 66
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.70 E-value=6.5 Score=30.78 Aligned_cols=26 Identities=23% Similarity=0.636 Sum_probs=16.4
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.+|-+||+..+. +......||+||..
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 67
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=51.77 E-value=12 Score=31.98 Aligned_cols=36 Identities=19% Similarity=0.568 Sum_probs=27.2
Q ss_pred eecccCcccccceeeccCCceEeecCCCccc--ccccccee
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA--VADEYIEC 42 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~--~~DkYiE~ 42 (208)
.|-+|+.|=..|-++ +.+-..+|..||. .+|++-+.
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 699999998888654 4566789999997 46655443
No 68
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=51.47 E-value=6.7 Score=34.03 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=22.6
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc----ccccceehh
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV----ADEYIECEI 44 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~----~DkYiE~d~ 44 (208)
++| +||.+++. | ..|++|+.. ||-|.+--.
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 99999854 3 479999974 777776544
No 69
>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=51.39 E-value=4.8 Score=25.11 Aligned_cols=31 Identities=23% Similarity=0.491 Sum_probs=20.0
Q ss_pred ecccCcccccceeeccCCceEeecCCCcccccc
Q 028469 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (208)
Q Consensus 5 CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~D 37 (208)
|.+|+..-..++++-.+++ .+.|..|+-.-.
T Consensus 1 C~~C~tt~t~~WR~~~~g~--~~LCn~Cg~~~k 31 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGN--RTLCNACGLYYK 31 (36)
T ss_dssp -TTT--ST-SSEEEETTSE--E-EEHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCC--CHHHHHHHHHHH
Confidence 8899999999998887664 447988875433
No 70
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=50.71 E-value=7.6 Score=37.36 Aligned_cols=23 Identities=35% Similarity=0.853 Sum_probs=17.6
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
.|+|-|||..-+. =+-+||+|+.
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 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=49.86 E-value=7.8 Score=31.40 Aligned_cols=28 Identities=18% Similarity=0.129 Sum_probs=20.8
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~ 36 (208)
..+|.+||++---| |-.-..||+||...
T Consensus 9 Kr~Cp~cg~kFYDL-------nk~p~vcP~cg~~~ 36 (129)
T TIGR02300 9 KRICPNTGSKFYDL-------NRRPAVSPYTGEQF 36 (129)
T ss_pred cccCCCcCcccccc-------CCCCccCCCcCCcc
Confidence 35899999987555 22556899999863
No 72
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=49.61 E-value=8.7 Score=29.94 Aligned_cols=26 Identities=23% Similarity=0.604 Sum_probs=16.9
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.+|-+||+..+.. ......||+||..
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 73
>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=49.32 E-value=5.1 Score=27.37 Aligned_cols=34 Identities=21% Similarity=0.461 Sum_probs=26.4
Q ss_pred eecccCcccccceeeccCCceEeecCCCcccccccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkY 39 (208)
+|.+||..-..++++..++ .-+.|..|+-.--||
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 5999999999999997644 456899998655444
No 74
>PHA02768 hypothetical protein; Provisional
Probab=49.27 E-value=3.7 Score=28.53 Aligned_cols=40 Identities=33% Similarity=0.650 Sum_probs=23.6
Q ss_pred CceecccCccc---ccceeeccCCceEeecCCCcccc---cccccee
Q 028469 2 EYRCVKCGFRI---KTLFVQYSPGNIRLMKCENCRAV---ADEYIEC 42 (208)
Q Consensus 2 ~~~CI~C~~~v---~~Ly~~ys~~~i~l~~C~~C~~~---~DkYiE~ 42 (208)
+|.|-+||..- ++|.+--...+ +--+|.+|++. --+|||.
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 58899999873 33422111222 44578888774 3567764
No 75
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=48.73 E-value=12 Score=34.99 Aligned_cols=32 Identities=25% Similarity=0.702 Sum_probs=24.2
Q ss_pred CceecccCcccccc---------eeecc----CCceEeecCCCcc
Q 028469 2 EYRCVKCGFRIKTL---------FVQYS----PGNIRLMKCENCR 33 (208)
Q Consensus 2 ~~~CI~C~~~v~~L---------y~~ys----~~~i~l~~C~~C~ 33 (208)
.-.|..||.+++.+ +..++ |+++.+..|.+||
T Consensus 6 ~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cg 50 (355)
T COG1499 6 TILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCG 50 (355)
T ss_pred ccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCC
Confidence 35799999999643 23332 5689999999999
No 76
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=48.37 E-value=9.9 Score=26.47 Aligned_cols=19 Identities=21% Similarity=0.455 Sum_probs=14.3
Q ss_pred cCCCccc-----------cccccceehhHH
Q 028469 28 KCENCRA-----------VADEYIECEIMI 46 (208)
Q Consensus 28 ~C~~C~~-----------~~DkYiE~d~vi 46 (208)
.||.||. +.|||-+|-..+
T Consensus 19 ~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~ 48 (56)
T PRK13130 19 ICPVCGGKTKNPHPPRFSPEDKYGKYRRAL 48 (56)
T ss_pred cCcCCCCCCCCCCCCCCCCCCccHHHHHHH
Confidence 6888884 479998887643
No 77
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=48.28 E-value=11 Score=24.59 Aligned_cols=28 Identities=25% Similarity=0.538 Sum_probs=16.8
Q ss_pred eecccCcccccceeeccCCceEeecCCCcccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
-|.+||..+ +.+-..++ ..-.|++|+..
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 488999965 22222222 25579999953
No 78
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=47.84 E-value=11 Score=34.09 Aligned_cols=38 Identities=26% Similarity=0.655 Sum_probs=27.1
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccc-cccceehh
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA-DEYIECEI 44 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~-DkYiE~d~ 44 (208)
++.|-|||.. .+-++|..|. ..|..||-++ |++|..++
T Consensus 1 ~~~CpeCg~~--~~~~d~~~ge---~VC~~CG~Vi~~~~id~gp 39 (285)
T COG1405 1 VMSCPECGST--NIITDYERGE---IVCADCGLVLEDSLIDPGP 39 (285)
T ss_pred CCCCCCCCCc--cceeeccCCe---EEeccCCEEeccccccCCC
Confidence 3689999998 6666777653 5799999864 44655554
No 79
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=47.45 E-value=13 Score=26.21 Aligned_cols=38 Identities=32% Similarity=0.871 Sum_probs=21.2
Q ss_pred CceecccCccccc--ceeecc-C--CceEeecCCCcccccccc
Q 028469 2 EYRCVKCGFRIKT--LFVQYS-P--GNIRLMKCENCRAVADEY 39 (208)
Q Consensus 2 ~~~CI~C~~~v~~--Ly~~ys-~--~~i~l~~C~~C~~~~DkY 39 (208)
.+.|+-||.++.. =+.++. | |..-+..|++|.+..-.|
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~~~Y 49 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPY 49 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcCCce
Confidence 4679999988642 134441 1 233355566666655555
No 80
>PRK05978 hypothetical protein; Provisional
Probab=45.45 E-value=9.8 Score=31.39 Aligned_cols=28 Identities=29% Similarity=0.617 Sum_probs=20.2
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
-+|-+||+. .+|+.|-+ --..|+.||.-
T Consensus 34 grCP~CG~G--~LF~g~Lk---v~~~C~~CG~~ 61 (148)
T PRK05978 34 GRCPACGEG--KLFRAFLK---PVDHCAACGED 61 (148)
T ss_pred CcCCCCCCC--cccccccc---cCCCccccCCc
Confidence 479999985 56777744 33579999963
No 81
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=45.31 E-value=10 Score=29.49 Aligned_cols=25 Identities=16% Similarity=0.484 Sum_probs=15.6
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.+|-+||+..+. +. ....||+||..
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 82
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=45.21 E-value=11 Score=25.49 Aligned_cols=23 Identities=30% Similarity=0.681 Sum_probs=17.9
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
..||-.|+.+.+- +-+.|.+||.
T Consensus 14 k~ICrkC~ARnp~----------~A~~CRKCg~ 36 (48)
T PRK04136 14 KKICMRCNARNPW----------RATKCRKCGY 36 (48)
T ss_pred ccchhcccCCCCc----------cccccccCCC
Confidence 4689999887643 6788999986
No 83
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.01 E-value=11 Score=30.27 Aligned_cols=34 Identities=21% Similarity=0.553 Sum_probs=18.7
Q ss_pred CceecccCcccccce------------eeccCCc-eEeecCCCcccc
Q 028469 2 EYRCVKCGFRIKTLF------------VQYSPGN-IRLMKCENCRAV 35 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly------------~~ys~~~-i~l~~C~~C~~~ 35 (208)
..+|-+||+..+.-= ..|.|+. -....||+||..
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 368999996532210 0122321 133569999975
No 84
>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=42.15 E-value=8.3 Score=23.22 Aligned_cols=27 Identities=26% Similarity=0.540 Sum_probs=13.6
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.-|-.||.|.... + .-.-.+|++|+..
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 3588899997543 2 1245579999863
No 85
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.84 E-value=17 Score=30.47 Aligned_cols=36 Identities=28% Similarity=0.748 Sum_probs=25.8
Q ss_pred CceecccCcccccceee--ccCCceEeecCCCccc---cccc
Q 028469 2 EYRCVKCGFRIKTLFVQ--YSPGNIRLMKCENCRA---VADE 38 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~--ys~~~i~l~~C~~C~~---~~Dk 38 (208)
.|.|--||++...-+.+ |.+|. .+-+|+.|+. +||-
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 5553
No 86
>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=41.77 E-value=4.6 Score=33.09 Aligned_cols=30 Identities=23% Similarity=0.477 Sum_probs=15.8
Q ss_pred ceecccCcccccce--eeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLF--VQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly--~~ys~~~i~l~~C~~C~~ 34 (208)
.+|.+|++..+.-. .....+ ...+|+.|+.
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 46888887653321 111222 2237888877
No 87
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=40.62 E-value=22 Score=27.73 Aligned_cols=32 Identities=25% Similarity=0.529 Sum_probs=23.9
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
+-|..|||...+--+.=..+++-...|++|+.
T Consensus 23 FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGl 54 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGL 54 (104)
T ss_pred EecCccCCeeeeEEEEEecCceeEEEcccCcc
Confidence 56999999854433344566888899999996
No 88
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=40.52 E-value=20 Score=27.30 Aligned_cols=28 Identities=25% Similarity=0.599 Sum_probs=21.4
Q ss_pred CceecccCcc-cccceeeccCCceEeecCCCccccc
Q 028469 2 EYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAVA 36 (208)
Q Consensus 2 ~~~CI~C~~~-v~~Ly~~ys~~~i~l~~C~~C~~~~ 36 (208)
.|.|..||.+ ++.. ..-+=+|.+|++..
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 5889999887 5543 55778999999853
No 89
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=39.85 E-value=15 Score=29.77 Aligned_cols=24 Identities=29% Similarity=0.634 Sum_probs=17.3
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
..|-.||.|. |+ +.+. ..||.|+.
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 5699999995 55 3332 37999994
No 90
>PRK06260 threonine synthase; Validated
Probab=39.59 E-value=16 Score=33.90 Aligned_cols=32 Identities=19% Similarity=0.697 Sum_probs=21.3
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccccceeh
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d 43 (208)
..+|+.||+.- +++. ....||.|+..-| ++||
T Consensus 3 ~~~C~~cg~~~-------~~~~-~~~~Cp~cg~~l~--~~y~ 34 (397)
T PRK06260 3 WLKCIECGKEY-------DPDE-IIYTCPECGGLLE--VIYD 34 (397)
T ss_pred EEEECCCCCCC-------CCCC-ccccCCCCCCeEE--EEec
Confidence 46899999763 3332 2457999997655 4454
No 91
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.93 E-value=18 Score=38.39 Aligned_cols=16 Identities=25% Similarity=0.561 Sum_probs=9.4
Q ss_pred ecCCCcccccccccee
Q 028469 27 MKCENCRAVADEYIEC 42 (208)
Q Consensus 27 ~~C~~C~~~~DkYiE~ 42 (208)
..||+|+.....+-..
T Consensus 664 y~CPKCG~El~~~s~~ 679 (1121)
T PRK04023 664 DECEKCGREPTPYSKR 679 (1121)
T ss_pred CcCCCCCCCCCccceE
Confidence 3577777765554433
No 92
>PRK02935 hypothetical protein; Provisional
Probab=38.79 E-value=16 Score=28.72 Aligned_cols=24 Identities=29% Similarity=0.533 Sum_probs=18.0
Q ss_pred eecccCcccccceeeccCCceEeecCCCcccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.|.+|+++.+-|= |...|..|+++
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 6888888887761 55578888875
No 93
>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=38.58 E-value=34 Score=25.98 Aligned_cols=50 Identities=20% Similarity=0.320 Sum_probs=32.7
Q ss_pred ecccCc--ccccc---eeeccCC----ceEeecCCCccccccccceehhHHHHHHHHhc
Q 028469 5 CVKCGF--RIKTL---FVQYSPG----NIRLMKCENCRAVADEYIECEIMILLIDLILH 54 (208)
Q Consensus 5 CI~C~~--~v~~L---y~~ys~~----~i~l~~C~~C~~~~DkYiE~d~vil~IDllLl 54 (208)
|.-|+. ..++. +.+|.+| .||-..|-.|.+--..|++-|.+--+=|.+++
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 24444 3444443 45566677777777889999888777775554
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=38.21 E-value=22 Score=24.46 Aligned_cols=31 Identities=32% Similarity=0.724 Sum_probs=19.1
Q ss_pred CCceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 1 ~~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
|...|.+||..+.- =.... | .+-.|+.||.-
T Consensus 1 ~~~~CP~CG~~iev-~~~~~-G--eiV~Cp~CGae 31 (54)
T TIGR01206 1 MQFECPDCGAEIEL-ENPEL-G--ELVICDECGAE 31 (54)
T ss_pred CccCCCCCCCEEec-CCCcc-C--CEEeCCCCCCE
Confidence 34689999998522 11122 2 24489999963
No 95
>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=38.03 E-value=13 Score=33.65 Aligned_cols=47 Identities=23% Similarity=0.545 Sum_probs=29.5
Q ss_pred eecccCcccccceeeccCCceEeecCCCcccc----cc--cc-------ceehhHHHHHHHHhcCcccceeeeccccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV----AD--EY-------IECEIMILLIDLILHKPQAYRHLLYNVLN 68 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~----~D--kY-------iE~d~vil~IDllLlk~~ayRHllfN~~~ 68 (208)
.|-+||..|..+ -+.||+|+.- -| |. -|+ ..+++|.-|--+||-..+
T Consensus 84 ~C~~CGa~V~~~----------e~~Cp~C~StnI~r~DdSkWl~~ir~d~E~--------~e~L~P~~~ylvlfd~~d 143 (314)
T PF09567_consen 84 KCNNCGANVSRL----------EESCPNCGSTNIKRKDDSKWLFGIRSDDEF--------EEYLNPRMIYLVLFDFPD 143 (314)
T ss_pred hhccccceeeeh----------hhcCCCCCcccccccCCcceecccccHHHH--------HHhcCccEEEEEEecccC
Confidence 599999999874 2369999953 11 11 122 223457777778776644
No 96
>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=37.90 E-value=18 Score=26.40 Aligned_cols=35 Identities=17% Similarity=0.328 Sum_probs=16.4
Q ss_pred ceecccCcccccceeec-----cCCceEeecCCCcccccc
Q 028469 3 YRCVKCGFRIKTLFVQY-----SPGNIRLMKCENCRAVAD 37 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~y-----s~~~i~l~~C~~C~~~~D 37 (208)
-.|..|+++.+.-..+| ..+..+...||.|++.-.
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHH
Confidence 35666776654433333 234567778888887643
No 97
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=37.79 E-value=19 Score=29.01 Aligned_cols=31 Identities=29% Similarity=0.787 Sum_probs=19.6
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccccc-ccceeh
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD-EYIECE 43 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~D-kYiE~d 43 (208)
-+|-+||+-- |-|. ..|++|+.-.| +.+|..
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 3677777642 2332 36888888777 777754
No 98
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=37.63 E-value=13 Score=31.32 Aligned_cols=32 Identities=19% Similarity=0.429 Sum_probs=20.1
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~Dk 38 (208)
.|+|.+||.+.+.+=- .+. -=.||.||..--.
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 5899999977433210 111 2379999986543
No 99
>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=37.57 E-value=34 Score=21.42 Aligned_cols=27 Identities=37% Similarity=0.849 Sum_probs=16.2
Q ss_pred ceecccCcccccceeec-cCCceEeecCCC
Q 028469 3 YRCVKCGFRIKTLFVQY-SPGNIRLMKCEN 31 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~y-s~~~i~l~~C~~ 31 (208)
..|..||..| |--.| .+|.|+.-+|+|
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 100
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=37.41 E-value=28 Score=25.35 Aligned_cols=29 Identities=24% Similarity=0.576 Sum_probs=17.7
Q ss_pred eecccCcccccceeeccCCceEeecCCCccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
.|. ||......=+ .+.+.+++..|++|+-
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 466 6665322111 2344699999999983
No 101
>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=36.85 E-value=21 Score=22.45 Aligned_cols=28 Identities=29% Similarity=0.457 Sum_probs=16.9
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
.+|..||+.-.-.|..-. .-.+|++||.
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 478899976433322222 3348999986
No 102
>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=36.27 E-value=15 Score=34.29 Aligned_cols=27 Identities=30% Similarity=0.781 Sum_probs=13.5
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
+.|-+||.+.-++. +|.+ ..|++||..
T Consensus 286 FkC~~C~~Rt~sl~-r~P~-----~~C~~Cg~~ 312 (344)
T PF09332_consen 286 FKCKDCGNRTISLE-RLPK-----KHCSNCGSS 312 (344)
T ss_dssp EE-T-TS-EEEESS-SS-------S--TTT-S-
T ss_pred EECCCCCCeeeecc-cCCC-----CCCCcCCcC
Confidence 46999999977773 4633 389999974
No 103
>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=36.25 E-value=16 Score=28.48 Aligned_cols=26 Identities=19% Similarity=0.630 Sum_probs=16.7
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~ 36 (208)
-+|-+||+..+.- . ....||+||..-
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 104
>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=35.62 E-value=14 Score=28.68 Aligned_cols=25 Identities=24% Similarity=0.769 Sum_probs=14.6
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
-+|-+||+.-+- +..+ ..||+||..
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 479999986422 1112 459999986
No 105
>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=35.50 E-value=27 Score=26.69 Aligned_cols=28 Identities=29% Similarity=0.660 Sum_probs=21.0
Q ss_pred CceecccCcc-cccceeeccCCceEeecCCCccccc
Q 028469 2 EYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAVA 36 (208)
Q Consensus 2 ~~~CI~C~~~-v~~Ly~~ys~~~i~l~~C~~C~~~~ 36 (208)
.|.|..||.+ ++.. ..-+=+|.+|++..
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 5889999976 4443 45678999999853
No 106
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=35.24 E-value=8.5 Score=27.48 Aligned_cols=19 Identities=32% Similarity=0.684 Sum_probs=15.2
Q ss_pred ceecccCcccccceeeccC
Q 028469 3 YRCVKCGFRIKTLFVQYSP 21 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~ 21 (208)
-+|-.||+++.++|.+|..
T Consensus 5 iRCFsCGkvi~~~w~~y~~ 23 (63)
T COG1644 5 VRCFSCGKVIGHKWEEYKR 23 (63)
T ss_pred eEeecCCCCHHHHHHHHHH
Confidence 3788899998888888854
No 107
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.19 E-value=20 Score=28.36 Aligned_cols=30 Identities=17% Similarity=0.440 Sum_probs=15.0
Q ss_pred ceecccCcccccceeeccCCceE-eecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIR-LMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~-l~~C~~C~~~ 35 (208)
-+| +||+..+.-- ....... ...||+||..
T Consensus 71 ~~C-~Cg~~~~~~~--~~~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 71 IEC-ECGYEGVVDE--DEIDHYAAVIECPVCGNK 101 (124)
T ss_pred EEe-eCcCcccccc--cchhccccCCcCcCCCCC
Confidence 579 9996532110 0000000 1369999954
No 108
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=34.92 E-value=17 Score=27.98 Aligned_cols=26 Identities=35% Similarity=0.998 Sum_probs=18.8
Q ss_pred CceecccCcccccceeeccCCceE-eecCCCccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIR-LMKCENCRA 34 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~-l~~C~~C~~ 34 (208)
.++|-.||..-.. +.|+ -+.||+|+.
T Consensus 58 Pa~CkkCGfef~~-------~~ik~pSRCP~CKS 84 (97)
T COG3357 58 PARCKKCGFEFRD-------DKIKKPSRCPKCKS 84 (97)
T ss_pred ChhhcccCccccc-------cccCCcccCCcchh
Confidence 4789999986433 3444 679999985
No 109
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=34.79 E-value=22 Score=27.71 Aligned_cols=31 Identities=26% Similarity=0.725 Sum_probs=20.4
Q ss_pred eecccCcccc-------------------------cceeec--cCCceEeecCCCccc
Q 028469 4 RCVKCGFRIK-------------------------TLFVQY--SPGNIRLMKCENCRA 34 (208)
Q Consensus 4 ~CI~C~~~v~-------------------------~Ly~~y--s~~~i~l~~C~~C~~ 34 (208)
.|++||..++ ++|.+| .....++.-|-+|--
T Consensus 22 ~CdnCg~~vPkdKAikr~~i~s~Ve~a~~rdL~~asIy~~y~vpk~~~k~qyCVsCAi 79 (108)
T COG4830 22 RCDNCGKAVPKDKAIKRTAIRSPVEAAAARDLSEASIYSEYAVPKTYNKLQYCVSCAI 79 (108)
T ss_pred eeccccccCCccceeeEeeccCcccHHHHHHHhhceeeeeeeccccccceeeeeeeee
Confidence 6999998765 244444 234567778888864
No 110
>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=34.38 E-value=25 Score=24.18 Aligned_cols=30 Identities=23% Similarity=0.545 Sum_probs=16.9
Q ss_pred CceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
+.+|-+|++-.-.- ..|.. ---+||+|+.+
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 56888888764221 01221 12379999864
No 111
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=34.13 E-value=23 Score=38.36 Aligned_cols=15 Identities=20% Similarity=0.625 Sum_probs=8.7
Q ss_pred ecCCCccccccccce
Q 028469 27 MKCENCRAVADEYIE 41 (208)
Q Consensus 27 ~~C~~C~~~~DkYiE 41 (208)
+.||+|+...-.|-.
T Consensus 710 ~~CP~CGtplv~~~~ 724 (1337)
T PRK14714 710 VECPRCDVELTPYQR 724 (1337)
T ss_pred ccCCCCCCcccccce
Confidence 367777765544433
No 112
>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=33.70 E-value=17 Score=30.44 Aligned_cols=31 Identities=19% Similarity=0.360 Sum_probs=15.4
Q ss_pred ecccCcccccceee-----ccCCceEeecCCCcccc
Q 028469 5 CVKCGFRIKTLFVQ-----YSPGNIRLMKCENCRAV 35 (208)
Q Consensus 5 CI~C~~~v~~Ly~~-----ys~~~i~l~~C~~C~~~ 35 (208)
|-+|++|+..=|.. +++++-.-.-|.+||+.
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 66666666543321 12233344556666653
No 113
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=33.65 E-value=21 Score=28.29 Aligned_cols=29 Identities=21% Similarity=0.678 Sum_probs=18.6
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkY 39 (208)
-.|-.|+++++..-..| .||+||..-.+=
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 36889988865432222 299999765543
No 114
>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=33.58 E-value=20 Score=22.72 Aligned_cols=18 Identities=22% Similarity=0.709 Sum_probs=11.6
Q ss_pred ecCCCccccccccceehh
Q 028469 27 MKCENCRAVADEYIECEI 44 (208)
Q Consensus 27 ~~C~~C~~~~DkYiE~d~ 44 (208)
-+|++|+...-+|.++|.
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 479999999999999886
No 115
>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=33.48 E-value=15 Score=31.16 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=29.2
Q ss_pred CceecccCcccccceee--ccCCceEeecCCCc---ccccccc
Q 028469 2 EYRCVKCGFRIKTLFVQ--YSPGNIRLMKCENC---RAVADEY 39 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~--ys~~~i~l~~C~~C---~~~~DkY 39 (208)
+-+|.=||++..-.|+- |+.+++. ..||-| |+-|+||
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 34799999998887775 7888888 899999 4566664
No 116
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=33.47 E-value=9.9 Score=25.95 Aligned_cols=22 Identities=32% Similarity=0.587 Sum_probs=17.0
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
.||-.||.+.+ .+-|+|.+|+-
T Consensus 15 kIC~rC~Arnp----------~~A~kCRkC~~ 36 (50)
T COG1552 15 KICRRCYARNP----------PRATKCRKCGY 36 (50)
T ss_pred HHHHHhcCCCC----------cchhHHhhccC
Confidence 57899988764 37788999973
No 117
>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=33.46 E-value=16 Score=31.10 Aligned_cols=32 Identities=22% Similarity=0.521 Sum_probs=17.8
Q ss_pred CceecccCcccccce--eeccCCceEeecCCCcccc
Q 028469 2 EYRCVKCGFRIKTLF--VQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly--~~ys~~~i~l~~C~~C~~~ 35 (208)
..+|..|++..+.-. .... .-.+..|++|+..
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~--~~~~p~C~~Cg~~ 142 (218)
T cd01407 109 RVRCTKCGKEYPRDELQADID--REEVPRCPKCGGL 142 (218)
T ss_pred cceeCCCcCCCcHHHHhHhhc--cCCCCcCCCCCCc
Confidence 357888888653211 1111 1235679999865
No 118
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=33.39 E-value=29 Score=29.50 Aligned_cols=42 Identities=24% Similarity=0.424 Sum_probs=31.7
Q ss_pred ceecccCc-ccccceeec-cCCceEeecCCCccccccccceehh
Q 028469 3 YRCVKCGF-RIKTLFVQY-SPGNIRLMKCENCRAVADEYIECEI 44 (208)
Q Consensus 3 ~~CI~C~~-~v~~Ly~~y-s~~~i~l~~C~~C~~~~DkYiE~d~ 44 (208)
.+|-+|+. |+.-=|++- +++.+++..|.+|-+.-..|.+-|.
T Consensus 1 miCq~CqqnpAti~~tkI~~~~k~e~~vCe~Ca~~~s~a~~~e~ 44 (176)
T COG3880 1 MICQNCQQNPATIHFTKIINGEKIELYVCETCAKPHSEAYDIEH 44 (176)
T ss_pred CcchhhcCCcceEEEEEeecCCeeEeehhhcCCCchhhhccchh
Confidence 37999999 777777665 5678999999999887555554443
No 119
>PRK06386 replication factor A; Reviewed
Probab=33.31 E-value=20 Score=33.59 Aligned_cols=24 Identities=25% Similarity=0.498 Sum_probs=0.0
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkY 39 (208)
.+|.+|+..++. ..|+.|++ ++.|
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
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=33.28 E-value=19 Score=36.16 Aligned_cols=8 Identities=25% Similarity=0.845 Sum_probs=4.0
Q ss_pred cCCCcccc
Q 028469 28 KCENCRAV 35 (208)
Q Consensus 28 ~C~~C~~~ 35 (208)
.|++||+.
T Consensus 29 ~Cp~CG~~ 36 (645)
T PRK14559 29 PCPQCGTE 36 (645)
T ss_pred cCCCCCCC
Confidence 45555543
No 121
>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=33.13 E-value=12 Score=32.36 Aligned_cols=14 Identities=21% Similarity=0.662 Sum_probs=6.6
Q ss_pred CceEeecCCCcccc
Q 028469 22 GNIRLMKCENCRAV 35 (208)
Q Consensus 22 ~~i~l~~C~~C~~~ 35 (208)
|++...+|.+|++.
T Consensus 112 G~l~~~~C~~C~~~ 125 (235)
T cd01408 112 GSFATAHCIKCKHK 125 (235)
T ss_pred cCCCccccccCCCc
Confidence 34444455555543
No 122
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=33.07 E-value=32 Score=26.24 Aligned_cols=28 Identities=25% Similarity=0.778 Sum_probs=20.8
Q ss_pred CceecccCcc-cccceeeccCCceEeecCCCccccc
Q 028469 2 EYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAVA 36 (208)
Q Consensus 2 ~~~CI~C~~~-v~~Ly~~ys~~~i~l~~C~~C~~~~ 36 (208)
.|.|..||.+ ++.. ..-+=+|.+|++..
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 4442 44778999999853
No 123
>PF10977 DUF2797: Protein of unknown function (DUF2797); InterPro: IPR021246 This family of proteins has no known function.
Probab=32.94 E-value=18 Score=31.88 Aligned_cols=29 Identities=38% Similarity=0.910 Sum_probs=20.4
Q ss_pred eecccCcccccceee-c-cCCceEeecCCCc
Q 028469 4 RCVKCGFRIKTLFVQ-Y-SPGNIRLMKCENC 32 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~-y-s~~~i~l~~C~~C 32 (208)
.|++||...+.-|.+ | -+.--++.+|+.|
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 699999998777776 2 1223366688887
No 124
>PRK07218 replication factor A; Provisional
Probab=32.86 E-value=20 Score=34.18 Aligned_cols=21 Identities=19% Similarity=0.156 Sum_probs=12.5
Q ss_pred HHHHHHHhcCcccceeeeccc
Q 028469 46 ILLIDLILHKPQAYRHLLYNV 66 (208)
Q Consensus 46 il~IDllLlk~~ayRHllfN~ 66 (208)
.+.|+.+|-.=--+.-.+||+
T Consensus 323 dlrik~vLDDGtg~~~~~~~~ 343 (423)
T PRK07218 323 DLRIKAILDDGTGSVTVILDR 343 (423)
T ss_pred eeEEEEEEECCCCeEEEEECh
Confidence 345556666655566666666
No 125
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=32.82 E-value=11 Score=26.80 Aligned_cols=19 Identities=26% Similarity=0.660 Sum_probs=13.1
Q ss_pred ceecccCcccccceeeccC
Q 028469 3 YRCVKCGFRIKTLFVQYSP 21 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~ 21 (208)
-+|-.||.++.+.|.+|..
T Consensus 5 vRCFTCGkvi~~~we~y~~ 23 (62)
T PRK04016 5 VRCFTCGKVIAEKWEEFKE 23 (62)
T ss_pred eEecCCCCChHHHHHHHHH
Confidence 3677777777777777743
No 126
>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=32.72 E-value=27 Score=28.92 Aligned_cols=32 Identities=25% Similarity=0.389 Sum_probs=17.2
Q ss_pred ceecccCcccccceeec-----cCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQY-----SPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~y-----s~~~i~l~~C~~C~~ 34 (208)
-.|.+||++...-...| +.--|.-..|++||-
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGy 38 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGY 38 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCC
Confidence 46999999854432332 233445558999993
No 127
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=32.48 E-value=23 Score=33.93 Aligned_cols=50 Identities=34% Similarity=0.479 Sum_probs=31.7
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccc--cceehhHHHHHHHHh---cCcccceeee
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE--YIECEIMILLIDLIL---HKPQAYRHLL 63 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~Dk--YiE~d~vil~IDllL---lk~~ayRHll 63 (208)
.|+|-.||...++.=+. =-+|++|+..+.+ +.|.+. ||-- --|.|.|||.
T Consensus 350 ~p~Cp~Cg~~m~S~G~~-------g~rC~kCg~~~~~~~~~~v~r-----~l~~g~evp~~arRHLs 404 (421)
T COG1571 350 NPVCPRCGGRMKSAGRN-------GFRCKKCGTRARETLIKEVPR-----DLEPGVEVPPVARRHLS 404 (421)
T ss_pred CCCCCccCCchhhcCCC-------CcccccccccCCccccccccc-----ccCCCCcCCchhhhhcc
Confidence 58999999998875221 3489999986543 234333 2222 2266788874
No 128
>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=32.41 E-value=19 Score=25.35 Aligned_cols=12 Identities=33% Similarity=0.664 Sum_probs=9.9
Q ss_pred ceecccCccccc
Q 028469 3 YRCVKCGFRIKT 14 (208)
Q Consensus 3 ~~CI~C~~~v~~ 14 (208)
..|+.||.|++.
T Consensus 4 kHC~~CG~~Ip~ 15 (59)
T PF09889_consen 4 KHCPVCGKPIPP 15 (59)
T ss_pred CcCCcCCCcCCc
Confidence 469999999874
No 129
>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=32.13 E-value=13 Score=26.36 Aligned_cols=17 Identities=35% Similarity=0.776 Sum_probs=10.4
Q ss_pred eecccCcccccceeecc
Q 028469 4 RCVKCGFRIKTLFVQYS 20 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys 20 (208)
+|-.||.++.+.|.+|.
T Consensus 6 RCFTCGkvi~~~~e~y~ 22 (60)
T PF01194_consen 6 RCFTCGKVIGNKWEEYL 22 (60)
T ss_dssp S-STTTSBTCGHHHHHH
T ss_pred ecCCCCCChhHhHHHHH
Confidence 56667776666666663
No 130
>PRK04023 DNA polymerase II large subunit; Validated
Probab=32.06 E-value=26 Score=37.19 Aligned_cols=35 Identities=20% Similarity=0.481 Sum_probs=17.4
Q ss_pred CceecccCcccccceeeccC----CceEeecCCCcccccccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSP----GNIRLMKCENCRAVADEY 39 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~----~~i~l~~C~~C~~~~DkY 39 (208)
...|.+||+.... ..-| .+-..-.|++|++.+..|
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 112333566666655544
No 131
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=31.53 E-value=34 Score=24.43 Aligned_cols=30 Identities=27% Similarity=0.527 Sum_probs=16.6
Q ss_pred eecccCcccccceeeccCCceEeecCCCccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
.|..||......=+ ...+.+++..|++|+=
T Consensus 15 ~c~s~g~~~~~~St-~~~~~~~vdi~s~~HP 44 (69)
T PF01197_consen 15 TCSSCGNTFETRST-KEYPVIKVDICSNCHP 44 (69)
T ss_dssp EES-SSSCECECSS-SSES-EEECSCSSSSC
T ss_pred EEcCCCCEEEEEEC-CcceEEEEeecCCCCE
Confidence 46666654322211 1234599999999983
No 132
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=31.24 E-value=39 Score=24.92 Aligned_cols=30 Identities=27% Similarity=0.582 Sum_probs=19.5
Q ss_pred eecccCcccccceeeccCCceEeecCCCccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
.|..||..-..- ...+.+.|++..|++|+-
T Consensus 16 ~~~s~g~~f~~~-ST~~~~~i~vdV~s~~HP 45 (75)
T COG0254 16 VCSSCGNEFTTR-STKGTDEINLDVCSKCHP 45 (75)
T ss_pred EeCCCCCEEEEE-eccCCceEEEEeCCCCCC
Confidence 466677653221 123446899999999983
No 133
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=31.15 E-value=18 Score=33.82 Aligned_cols=31 Identities=16% Similarity=0.652 Sum_probs=16.9
Q ss_pred ceecccCccccc--ceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKT--LFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~--Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.+|..|+++.+. .+.+..++ +..+|++|+.+
T Consensus 148 ~~C~~C~~~~~~~~~~~~~~~~--~vP~C~~CgG~ 180 (349)
T PTZ00410 148 ASCIECHTPYDIEQAYLEARSG--KVPHCSTCGGI 180 (349)
T ss_pred eEeCCCCCCcchhHHHHHhhcC--CCCCCCCCCCc
Confidence 478899865431 11111111 34678888753
No 134
>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=30.99 E-value=37 Score=23.22 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=17.8
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
-||-+|....... .+-..+.+ --+|++||.
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 3788887764332 23333344 557888885
No 135
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=30.82 E-value=35 Score=28.31 Aligned_cols=31 Identities=29% Similarity=0.449 Sum_probs=20.0
Q ss_pred eecccCcccccceeecc-----CCceEeecCCCccc
Q 028469 4 RCVKCGFRIKTLFVQYS-----PGNIRLMKCENCRA 34 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys-----~~~i~l~~C~~C~~ 34 (208)
.|.+||++...-...++ .=-|--..|++||-
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGy 37 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGY 37 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCC
Confidence 59999988654444432 22444578999983
No 136
>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=30.55 E-value=13 Score=35.16 Aligned_cols=39 Identities=21% Similarity=0.439 Sum_probs=35.7
Q ss_pred cCCCccccccccceehhHHHHHHHHhcCcccceeeeccc
Q 028469 28 KCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNV 66 (208)
Q Consensus 28 ~C~~C~~~~DkYiE~d~vil~IDllLlk~~ayRHllfN~ 66 (208)
-|+.|.++|++-.||.++..=.+.-+-+|.-|++|..+-
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 489999999999999999998888899999999998875
No 137
>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=30.37 E-value=23 Score=30.42 Aligned_cols=26 Identities=15% Similarity=0.369 Sum_probs=12.9
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
.+|..|++..+. .+..+.-.|++|+.
T Consensus 119 ~~C~~C~~~~~~------~~~~~~p~C~~Cgg 144 (225)
T cd01411 119 IYCTVCGKTVDW------EEYLKSPYHAKCGG 144 (225)
T ss_pred eEeCCCCCccch------hhcCCCCCCCCCCC
Confidence 457777654322 11123356777764
No 138
>TIGR00105 L31 ribosomal protein L31. This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc.
Probab=30.20 E-value=45 Score=23.81 Aligned_cols=28 Identities=25% Similarity=0.634 Sum_probs=17.2
Q ss_pred eecccCcccccceeeccCCceEeecCCCcc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCR 33 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~ 33 (208)
.| .||......-+ +.++.++++.|++|+
T Consensus 15 ~~-s~g~~f~~~ST-~~~~~i~vdi~s~~H 42 (68)
T TIGR00105 15 TC-TCGNVFTTRST-WGKETLNLDICSKCH 42 (68)
T ss_pred EE-CCCCEEEEeee-cCCceEEEEECCCCc
Confidence 35 36665443222 333349999999997
No 139
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.17 E-value=26 Score=35.20 Aligned_cols=14 Identities=29% Similarity=0.544 Sum_probs=10.1
Q ss_pred eecCCCcccccccc
Q 028469 26 LMKCENCRAVADEY 39 (208)
Q Consensus 26 l~~C~~C~~~~DkY 39 (208)
-..|++||...++-
T Consensus 41 ~~fC~~CG~~~~~~ 54 (645)
T PRK14559 41 EAHCPNCGAETGTI 54 (645)
T ss_pred cccccccCCcccch
Confidence 34799999876653
No 140
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=29.93 E-value=28 Score=25.16 Aligned_cols=9 Identities=44% Similarity=1.021 Sum_probs=6.7
Q ss_pred eecccCccc
Q 028469 4 RCVKCGFRI 12 (208)
Q Consensus 4 ~CI~C~~~v 12 (208)
.|+.||...
T Consensus 6 kCpKCgn~~ 14 (68)
T COG3478 6 KCPKCGNTN 14 (68)
T ss_pred cCCCcCCcc
Confidence 488998763
No 141
>PRK01397 50S ribosomal protein L31; Provisional
Probab=29.16 E-value=50 Score=24.42 Aligned_cols=15 Identities=13% Similarity=-0.015 Sum_probs=12.2
Q ss_pred cCCceEeecCCCccc
Q 028469 20 SPGNIRLMKCENCRA 34 (208)
Q Consensus 20 s~~~i~l~~C~~C~~ 34 (208)
+++.|+++.|++|+-
T Consensus 28 ~~~~i~vdi~s~~HP 42 (78)
T PRK01397 28 PTGEILMDVDFRKHP 42 (78)
T ss_pred CCCcEEEEeCCCCCC
Confidence 346799999999983
No 142
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=28.40 E-value=29 Score=33.13 Aligned_cols=26 Identities=19% Similarity=0.514 Sum_probs=18.6
Q ss_pred eecccCccc--ccceeeccCCceEeecCCCcccc
Q 028469 4 RCVKCGFRI--KTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 4 ~CI~C~~~v--~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.|-||+..+ +.| ++ -+...||+||+.
T Consensus 20 ~C~eCd~~~~~P~l----~~--~q~A~CPRC~~~ 47 (418)
T COG2995 20 LCPECDMLVSLPRL----DS--GQSAYCPRCGHT 47 (418)
T ss_pred cCCCCCceeccccC----CC--CCcccCCCCCCc
Confidence 699999985 444 11 256799999964
No 143
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=28.38 E-value=15 Score=26.85 Aligned_cols=19 Identities=32% Similarity=0.616 Sum_probs=13.5
Q ss_pred ceecccCcccccceeeccC
Q 028469 3 YRCVKCGFRIKTLFVQYSP 21 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~ 21 (208)
-+|-.||+++.+.|.+|..
T Consensus 5 VRCFTCGkvig~~we~y~~ 23 (71)
T PLN00032 5 VRCFTCGKVIGNKWDTYLD 23 (71)
T ss_pred eeecCCCCCcHHHHHHHHH
Confidence 3677777777777777754
No 144
>KOG2682 consensus NAD-dependent histone deacetylases and class I sirtuins (SIR2 family) [Chromatin structure and dynamics; Transcription]
Probab=28.24 E-value=15 Score=33.24 Aligned_cols=38 Identities=18% Similarity=0.401 Sum_probs=25.2
Q ss_pred ceec-ccCcccccceeeccCCceEeecCCCccccccccc
Q 028469 3 YRCV-KCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYI 40 (208)
Q Consensus 3 ~~CI-~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYi 40 (208)
-.|| +|+++.+.=|.+-.=-.-+.-+|+.|+..+.+=|
T Consensus 153 s~Ci~~C~~~yp~e~~ka~i~~~~vpkC~vC~~lVKP~I 191 (314)
T KOG2682|consen 153 SHCISSCRHEYPLEWMKAKIMSEVVPKCEVCQGLVKPDI 191 (314)
T ss_pred eeehhhhcCcCCHHHHHHHHHhccCCCCchhhccccccE
Confidence 4799 7999977655443222225559999998765543
No 145
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=27.99 E-value=36 Score=30.94 Aligned_cols=27 Identities=19% Similarity=0.366 Sum_probs=19.1
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.-|-.||++... ...-.-..|++|++.
T Consensus 112 RFCg~CG~~~~~------~~~g~~~~C~~cg~~ 138 (279)
T COG2816 112 RFCGRCGTKTYP------REGGWARVCPKCGHE 138 (279)
T ss_pred cCCCCCCCcCcc------ccCceeeeCCCCCCc
Confidence 358999999733 333356689999975
No 146
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=27.96 E-value=41 Score=28.73 Aligned_cols=31 Identities=23% Similarity=0.399 Sum_probs=20.4
Q ss_pred eecccCcccccceeecc------CCceEeecCCCccc
Q 028469 4 RCVKCGFRIKTLFVQYS------PGNIRLMKCENCRA 34 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys------~~~i~l~~C~~C~~ 34 (208)
-|.+||.+.......+. .=-|--..|++||-
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 22445578999994
No 147
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=27.74 E-value=50 Score=22.38 Aligned_cols=33 Identities=24% Similarity=0.485 Sum_probs=17.4
Q ss_pred ceecccCcccccceee--ccCCceEee-cCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQ--YSPGNIRLM-KCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~--ys~~~i~l~-~C~~C~~~ 35 (208)
..|.+||...-...+. -.|+.+.+- -||.|++-
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 3699999874222111 123323332 39999874
No 148
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=27.51 E-value=26 Score=20.10 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=7.3
Q ss_pred eecCCCccc
Q 028469 26 LMKCENCRA 34 (208)
Q Consensus 26 l~~C~~C~~ 34 (208)
+.+|+.||+
T Consensus 2 l~~C~~CgR 10 (25)
T PF13913_consen 2 LVPCPICGR 10 (25)
T ss_pred CCcCCCCCC
Confidence 468999997
No 149
>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]
Probab=27.36 E-value=29 Score=35.46 Aligned_cols=33 Identities=36% Similarity=0.818 Sum_probs=25.7
Q ss_pred CceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.|.|..||.+ -.-|-|-++.-+|.+.|++|+..
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 34456667778899999999976
No 150
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.33 E-value=27 Score=34.90 Aligned_cols=22 Identities=23% Similarity=0.652 Sum_probs=15.0
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
-+|-+||+. ..+ ...||+||+-
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 151
>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=27.30 E-value=31 Score=23.80 Aligned_cols=19 Identities=32% Similarity=0.623 Sum_probs=13.7
Q ss_pred ecCCCccc-----------cccccceehhH
Q 028469 27 MKCENCRA-----------VADEYIECEIM 45 (208)
Q Consensus 27 ~~C~~C~~-----------~~DkYiE~d~v 45 (208)
.+|+.||. +-|||-+|-..
T Consensus 18 ~~cp~cG~~T~~ahPaRFSPdDky~~yRi~ 47 (53)
T PF04135_consen 18 DKCPPCGGPTESAHPARFSPDDKYSKYRIA 47 (53)
T ss_dssp SBBTTTSSBSEESSSSSS-TTTTTCHHHHH
T ss_pred CccCCCCCCCcCCcCCCCCCCCccHHHHHH
Confidence 37888884 36899887654
No 152
>PHA02637 TNF-alpha-receptor-like protein; Provisional
Probab=27.06 E-value=37 Score=27.43 Aligned_cols=31 Identities=26% Similarity=0.596 Sum_probs=23.0
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkY 39 (208)
..|.-|.... |++..+ .+++|-.|+..|||=
T Consensus 63 T~C~PCp~GT---YTe~~N---~~~~C~~C~~~Cd~~ 93 (127)
T PHA02637 63 TQCTPCGSGT---FTSHNN---HLPACLSCNGRCDRV 93 (127)
T ss_pred cccccCCCCC---eeccCC---CCCcccccCCccCcc
Confidence 4677777663 666554 567999999999984
No 153
>PRK06424 transcription factor; Provisional
Probab=27.01 E-value=27 Score=28.47 Aligned_cols=37 Identities=24% Similarity=0.496 Sum_probs=27.3
Q ss_pred ecccCcccccceeeccCCceEeecCCCcccccccccee
Q 028469 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIEC 42 (208)
Q Consensus 5 CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~ 42 (208)
|==||..++.+|+.-=.|. .+..|+.|.++--+=.++
T Consensus 3 CE~CG~~~~~~~~v~ieg~-~l~vC~~Ca~~G~~v~~~ 39 (144)
T PRK06424 3 CEMCGKKVPQTTKVMIDGA-ILNVCDDCAKFGTPVIEH 39 (144)
T ss_pred ccccCcccCCceEEEEcCe-eeehhHHHHHcCCccccc
Confidence 8889999999965543443 699999998766544444
No 154
>PRK08197 threonine synthase; Validated
Probab=26.67 E-value=35 Score=31.62 Aligned_cols=31 Identities=19% Similarity=0.456 Sum_probs=20.3
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccccceeh
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d 43 (208)
.++|+.||+.- +++. ....| .|+..-| ++||
T Consensus 7 ~~~C~~Cg~~~-------~~~~-~~~~C-~cg~~l~--~~~d 37 (394)
T PRK08197 7 HLECSKCGETY-------DADQ-VHNLC-KCGKPLL--VRYD 37 (394)
T ss_pred EEEECCCCCCC-------CCCC-cceec-CCCCeeE--EEec
Confidence 36899999763 3322 23469 8998877 4444
No 155
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=26.49 E-value=32 Score=22.99 Aligned_cols=8 Identities=50% Similarity=1.414 Sum_probs=5.1
Q ss_pred eecccCcc
Q 028469 4 RCVKCGFR 11 (208)
Q Consensus 4 ~CI~C~~~ 11 (208)
+|-+|||.
T Consensus 30 ~C~~Cgh~ 37 (55)
T PF14311_consen 30 KCPKCGHE 37 (55)
T ss_pred ECCCCCCe
Confidence 46667665
No 156
>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=26.35 E-value=49 Score=19.37 Aligned_cols=29 Identities=21% Similarity=0.493 Sum_probs=15.3
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
-.|--|+++++..=. +.-...-|++|.++
T Consensus 2 ~~C~rC~~~~~~~~~----~~r~~~~C~rCq~v 30 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGI----NGRSTYLCPRCQKV 30 (30)
T ss_dssp SB-TTT--BBEEEEE----TTEEEEE-TTTCCH
T ss_pred CcCccCCCcceEeEe----cCCCCeECcCCcCC
Confidence 358889988766421 23345689999763
No 157
>PRK05638 threonine synthase; Validated
Probab=26.29 E-value=38 Score=31.92 Aligned_cols=30 Identities=23% Similarity=0.482 Sum_probs=19.2
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccccceeh
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d 43 (208)
..+|+.||+.-+ ++.. ..| .|+..-| ++||
T Consensus 1 ~l~C~~Cg~~~~-------~~~~--~~C-~c~~~l~--~~y~ 30 (442)
T PRK05638 1 KMKCPKCGREYN-------SYIP--PFC-ICGELLE--IIYD 30 (442)
T ss_pred CeEeCCCCCCCC-------CCCc--eec-CCCCcEE--EEec
Confidence 368999997743 2221 569 7987765 4444
No 158
>PRK07218 replication factor A; Provisional
Probab=26.19 E-value=35 Score=32.63 Aligned_cols=20 Identities=20% Similarity=0.433 Sum_probs=14.1
Q ss_pred cCCceEeecCCCcccccccc
Q 028469 20 SPGNIRLMKCENCRAVADEY 39 (208)
Q Consensus 20 s~~~i~l~~C~~C~~~~DkY 39 (208)
.++..=++.||.|+++.+++
T Consensus 291 ~~gsgli~rCP~C~r~v~~~ 310 (423)
T PRK07218 291 RDGSGLIERCPECGRVIQKG 310 (423)
T ss_pred ccCCcceecCcCccccccCC
Confidence 34444567888888888774
No 159
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=26.02 E-value=46 Score=23.04 Aligned_cols=23 Identities=22% Similarity=0.473 Sum_probs=13.2
Q ss_pred eecccCcccccceeeccCCceEeecCCCcccccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~D 37 (208)
.|-+||++.. ....|++||---+
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 4667776632 2446777774433
No 160
>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=25.62 E-value=34 Score=27.61 Aligned_cols=28 Identities=18% Similarity=0.479 Sum_probs=18.1
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~D 37 (208)
+.|..|+..+.. .+. ..-.|++|++..+
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 3457999988653
No 161
>PRK06450 threonine synthase; Validated
Probab=25.56 E-value=37 Score=31.05 Aligned_cols=33 Identities=24% Similarity=0.528 Sum_probs=22.0
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccccceeh
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d 43 (208)
.++|..||+.- ++. ....|+.|+..-|--.+++
T Consensus 3 ~~~C~~Cg~~~-------~~~--~~~~C~~cg~~l~~~~d~~ 35 (338)
T PRK06450 3 KEVCMKCGKER-------ESI--YEIRCKKCGGPFEILIDFE 35 (338)
T ss_pred eeEECCcCCcC-------CCc--ccccCCcCCCEeEEeeccc
Confidence 36899999763 221 1358999998777444444
No 162
>smart00507 HNHc HNH nucleases.
Probab=25.23 E-value=30 Score=21.30 Aligned_cols=11 Identities=27% Similarity=0.507 Sum_probs=7.6
Q ss_pred ceecccCcccc
Q 028469 3 YRCVKCGFRIK 13 (208)
Q Consensus 3 ~~CI~C~~~v~ 13 (208)
+.|..||.+.+
T Consensus 11 ~~C~~C~~~~~ 21 (52)
T smart00507 11 GVCAYCGKPAS 21 (52)
T ss_pred CCCcCCcCCCC
Confidence 56777777754
No 163
>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=25.20 E-value=32 Score=29.19 Aligned_cols=29 Identities=24% Similarity=0.559 Sum_probs=15.1
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
.+|..|+.....- +.......-.|++|+.
T Consensus 110 ~~C~~C~~~~~~~---~~~~~~~~p~C~~Cgg 138 (224)
T cd01412 110 VRCSSCGYVGENN---EEIPEEELPRCPKCGG 138 (224)
T ss_pred cccCCCCCCCCcc---hhhhccCCCCCCCCCC
Confidence 4677787764321 1111123456888875
No 164
>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=25.07 E-value=24 Score=36.74 Aligned_cols=41 Identities=20% Similarity=0.460 Sum_probs=0.0
Q ss_pred ceecccCcccccceeecc-CCceEeecCCCccccccccceeh
Q 028469 3 YRCVKCGFRIKTLFVQYS-PGNIRLMKCENCRAVADEYIECE 43 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys-~~~i~l~~C~~C~~~~DkYiE~d 43 (208)
.+|-+||.+....|.=-. .....-..|++|+..+..|-...
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 356666666544432110 11112237888888777766543
No 165
>PRK08402 replication factor A; Reviewed
Probab=25.02 E-value=32 Score=32.08 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=5.1
Q ss_pred eecCCCccccc
Q 028469 26 LMKCENCRAVA 36 (208)
Q Consensus 26 l~~C~~C~~~~ 36 (208)
...||+|++.+
T Consensus 212 y~aCp~CnKkv 222 (355)
T PRK08402 212 YDACPECRRKV 222 (355)
T ss_pred EecCCCCCeEE
Confidence 34455555443
No 166
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=24.47 E-value=56 Score=23.48 Aligned_cols=13 Identities=0% Similarity=-0.054 Sum_probs=11.2
Q ss_pred CceEeecCCCccc
Q 028469 22 GNIRLMKCENCRA 34 (208)
Q Consensus 22 ~~i~l~~C~~C~~ 34 (208)
+.+++..|++|+-
T Consensus 31 ~~i~vdv~s~~HP 43 (68)
T CHL00136 31 PELNVDIWSGNHP 43 (68)
T ss_pred CCEEEEeCCCCCc
Confidence 5699999999984
No 167
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=24.37 E-value=17 Score=34.24 Aligned_cols=25 Identities=36% Similarity=0.765 Sum_probs=16.6
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~ 36 (208)
|+|-+|..| + .|.. -.+|++|+...
T Consensus 58 ~kC~~c~~~-~----~y~~----~~~C~~cg~~~ 82 (415)
T COG5257 58 YKCPECYRP-E----CYTT----EPKCPNCGAET 82 (415)
T ss_pred EeCCCCCCC-c----cccc----CCCCCCCCCCc
Confidence 679999887 1 1322 23799998754
No 168
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=24.15 E-value=31 Score=26.29 Aligned_cols=28 Identities=25% Similarity=0.642 Sum_probs=18.6
Q ss_pred CceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.|.|..||... .++-+- -+=+|.+|++.
T Consensus 35 ky~Cp~Cgk~~---vkR~a~---GIW~C~~C~~~ 62 (90)
T PF01780_consen 35 KYTCPFCGKTS---VKRVAT---GIWKCKKCGKK 62 (90)
T ss_dssp -BEESSSSSSE---EEEEET---TEEEETTTTEE
T ss_pred CCcCCCCCCce---eEEeee---EEeecCCCCCE
Confidence 58899999974 222233 34789999974
No 169
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=23.50 E-value=40 Score=29.08 Aligned_cols=9 Identities=56% Similarity=1.202 Sum_probs=6.1
Q ss_pred ceecccCcc
Q 028469 3 YRCVKCGFR 11 (208)
Q Consensus 3 ~~CI~C~~~ 11 (208)
.+|..|+..
T Consensus 123 ~~C~~C~~~ 131 (242)
T PRK00481 123 ARCTKCGQT 131 (242)
T ss_pred eeeCCCCCC
Confidence 467888654
No 170
>PRK12366 replication factor A; Reviewed
Probab=23.39 E-value=36 Score=34.03 Aligned_cols=25 Identities=32% Similarity=0.671 Sum_probs=15.3
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
+.|.+|+..+.. ++ ..-.|++|++.
T Consensus 533 ~aCp~CnkKv~~-----~~---g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPNCRKRVEE-----VD---GEYICEFCGEV 557 (637)
T ss_pred ecccccCeEeEc-----CC---CcEECCCCCCC
Confidence 568888777642 11 22368888876
No 171
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=23.36 E-value=40 Score=21.14 Aligned_cols=25 Identities=36% Similarity=0.882 Sum_probs=14.5
Q ss_pred ecccCcccccceeeccCCceEeecCCCccccc
Q 028469 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (208)
Q Consensus 5 CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~ 36 (208)
|-+||.. .| ++.+ -..-|.+||.+.
T Consensus 11 C~~C~~~---~~--~~~d--G~~yC~~cG~~~ 35 (36)
T PF11781_consen 11 CPVCGSR---WF--YSDD--GFYYCDRCGHQS 35 (36)
T ss_pred CCCCCCe---Ee--EccC--CEEEhhhCceEc
Confidence 8888877 21 1222 234688888765
No 172
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.33 E-value=33 Score=21.84 Aligned_cols=9 Identities=67% Similarity=1.597 Sum_probs=6.6
Q ss_pred ceecccCcc
Q 028469 3 YRCVKCGFR 11 (208)
Q Consensus 3 ~~CI~C~~~ 11 (208)
|+|.+||+.
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 578888864
No 173
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=23.15 E-value=47 Score=31.20 Aligned_cols=31 Identities=19% Similarity=0.383 Sum_probs=20.0
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccccccccceeh
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkYiE~d 43 (208)
..+|+.||+..+ +.. ...|++|+..-| ++||
T Consensus 2 ~l~C~~Cg~~~~--------~~~-~~~C~~c~g~l~--~~y~ 32 (398)
T TIGR03844 2 TLRCPGCGEVLP--------DHY-TLSCPLDCGLLR--AEYA 32 (398)
T ss_pred EEEeCCCCCccC--------Ccc-ccCCCCCCCceE--Eeec
Confidence 368999997643 121 357999886555 4444
No 174
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=23.12 E-value=40 Score=37.08 Aligned_cols=35 Identities=17% Similarity=0.386 Sum_probs=20.9
Q ss_pred CceecccCcccccceeeccCC-ceEeecCCCccccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPG-NIRLMKCENCRAVA 36 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~-~i~l~~C~~C~~~~ 36 (208)
.|+|.+|.+.-=..--.+++| .+.--.||+||...
T Consensus 908 hy~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~ 943 (1437)
T PRK00448 908 HYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTKL 943 (1437)
T ss_pred cccCcccccccccccccccccccCccccCccccccc
Confidence 589999986421111123332 45566899999753
No 175
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=23.01 E-value=40 Score=31.82 Aligned_cols=23 Identities=26% Similarity=0.632 Sum_probs=14.7
Q ss_pred eecccCcccccceeeccCCceEeecCCCcccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
.|-+|+..++ ++ +-..||+||..
T Consensus 217 ~C~~Cd~~~~-------~~--~~a~CpRC~~~ 239 (403)
T TIGR00155 217 SCSACHTTIL-------PA--QEPVCPRCSTP 239 (403)
T ss_pred cCCCCCCccC-------CC--CCcCCcCCCCc
Confidence 3888888652 12 23578888864
No 176
>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=22.97 E-value=11 Score=28.94 Aligned_cols=33 Identities=24% Similarity=0.556 Sum_probs=20.0
Q ss_pred ceecccCcc-cccceeec-cCCceEeecCCCcccc
Q 028469 3 YRCVKCGFR-IKTLFVQY-SPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~-v~~Ly~~y-s~~~i~l~~C~~C~~~ 35 (208)
-.|+.|+.. |..-|..- .+....+..|++|++.
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 357777755 56655544 3445566677777764
No 177
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.95 E-value=40 Score=36.61 Aligned_cols=30 Identities=27% Similarity=0.542 Sum_probs=17.3
Q ss_pred ceecccCcccccceeeccC----CceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSP----GNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~----~~i~l~~C~~C~~~ 35 (208)
.+|.+||+++... +-| ..-....|++||..
T Consensus 668 rkCPkCG~~t~~~---fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 668 RRCPSCGTETYEN---RCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EECCCCCCccccc---cCcccCCcCCCceeCccCCCc
Confidence 5788888876442 322 11123478888874
No 178
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.70 E-value=58 Score=25.09 Aligned_cols=29 Identities=31% Similarity=0.831 Sum_probs=16.2
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
..|-+||+. .+=-.-+. ++-...|++||.
T Consensus 22 f~CP~Cge~--~v~v~~~k-~~~h~~C~~CG~ 50 (99)
T PRK14892 22 FECPRCGKV--SISVKIKK-NIAIITCGNCGL 50 (99)
T ss_pred eECCCCCCe--EeeeecCC-CcceEECCCCCC
Confidence 358888853 22111222 455677888874
No 179
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=22.58 E-value=14 Score=26.45 Aligned_cols=21 Identities=19% Similarity=0.276 Sum_probs=15.2
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~ 35 (208)
..|.+|..-++. +.||.||.-
T Consensus 6 ~AC~~C~~i~~~------------~~Cp~Cgs~ 26 (64)
T PRK06393 6 RACKKCKRLTPE------------KTCPVHGDE 26 (64)
T ss_pred hhHhhCCcccCC------------CcCCCCCCC
Confidence 468888877631 289999974
No 180
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=22.45 E-value=58 Score=27.12 Aligned_cols=30 Identities=30% Similarity=0.646 Sum_probs=18.3
Q ss_pred ecccCcc-cccceeec-----cCCceEeecCCCccc
Q 028469 5 CVKCGFR-IKTLFVQY-----SPGNIRLMKCENCRA 34 (208)
Q Consensus 5 CI~C~~~-v~~Ly~~y-----s~~~i~l~~C~~C~~ 34 (208)
|-.||++ .......+ +.=-|--..|++||-
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGy 36 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGY 36 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCC
Confidence 7889987 33322222 333455678999994
No 181
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Probab=22.41 E-value=70 Score=24.15 Aligned_cols=12 Identities=0% Similarity=0.044 Sum_probs=10.4
Q ss_pred ceEeecCCCccc
Q 028469 23 NIRLMKCENCRA 34 (208)
Q Consensus 23 ~i~l~~C~~C~~ 34 (208)
.+++..|++|+-
T Consensus 45 ~i~vdi~S~~HP 56 (87)
T PRK01678 45 LVKVEISSASHP 56 (87)
T ss_pred eEEEEeCCCCCC
Confidence 399999999983
No 182
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=22.05 E-value=52 Score=20.15 Aligned_cols=15 Identities=27% Similarity=0.704 Sum_probs=7.9
Q ss_pred CCceEeecCCCcccc
Q 028469 21 PGNIRLMKCENCRAV 35 (208)
Q Consensus 21 ~~~i~l~~C~~C~~~ 35 (208)
.+.+...+|++|+++
T Consensus 6 ~~~l~~~rC~~Cg~~ 20 (37)
T PF12172_consen 6 EGRLLGQRCRDCGRV 20 (37)
T ss_dssp TT-EEEEE-TTT--E
T ss_pred CCEEEEEEcCCCCCE
Confidence 356777888888865
No 183
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=22.00 E-value=30 Score=22.06 Aligned_cols=14 Identities=21% Similarity=0.636 Sum_probs=7.8
Q ss_pred EeecCCCccccccc
Q 028469 25 RLMKCENCRAVADE 38 (208)
Q Consensus 25 ~l~~C~~C~~~~Dk 38 (208)
++..|+.|+.+.|.
T Consensus 16 ~i~~C~~C~nlse~ 29 (41)
T PF02132_consen 16 NIKFCSICGNLSEE 29 (41)
T ss_dssp H-EE-SSS--EESS
T ss_pred cCCccCCCCCcCCC
Confidence 46689999998874
No 184
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=21.93 E-value=44 Score=36.12 Aligned_cols=35 Identities=20% Similarity=0.415 Sum_probs=20.6
Q ss_pred CceecccCcccccceeeccCC-ceEeecCCCccccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPG-NIRLMKCENCRAVA 36 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~-~i~l~~C~~C~~~~ 36 (208)
.|+|.+|.+.-=..=-.+++| .+.--.||+||..-
T Consensus 683 hy~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~~~ 718 (1213)
T TIGR01405 683 HYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPL 718 (1213)
T ss_pred cccCcccccccccccccccccccCccccCccccccc
Confidence 589999986411000123332 45566899999753
No 185
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=21.78 E-value=15 Score=28.34 Aligned_cols=28 Identities=25% Similarity=0.579 Sum_probs=15.9
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
.+|.+||.+-++ |-+-+.-.-.|.+|..
T Consensus 14 ~~CaDCg~~~p~----w~s~~~GiflC~~Cag 41 (116)
T PF01412_consen 14 KVCADCGAPNPT----WASLNYGIFLCLECAG 41 (116)
T ss_dssp TB-TTT-SBS------EEETTTTEEE-HHHHH
T ss_pred CcCCCCCCCCCC----EEEeecChhhhHHHHH
Confidence 579999988773 5444455677888864
No 186
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=21.77 E-value=52 Score=25.62 Aligned_cols=26 Identities=27% Similarity=0.597 Sum_probs=21.5
Q ss_pred CceecccCccc--ccceeeccCCceEee
Q 028469 2 EYRCVKCGFRI--KTLFVQYSPGNIRLM 27 (208)
Q Consensus 2 ~~~CI~C~~~v--~~Ly~~ys~~~i~l~ 27 (208)
+..|.=||.++ .++||=+++|.+-.+
T Consensus 2 kWkC~iCg~~I~~gqlFTF~~kG~VH~~ 29 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQLFTFTKKGPVHYE 29 (101)
T ss_pred ceEEEecCCeeeecceEEEecCCcEeHH
Confidence 57899999996 899999999765544
No 187
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=21.76 E-value=33 Score=31.15 Aligned_cols=36 Identities=19% Similarity=0.463 Sum_probs=24.7
Q ss_pred ceecccCcccccceeec----cCCceEeecCCCccc-cccc
Q 028469 3 YRCVKCGFRIKTLFVQY----SPGNIRLMKCENCRA-VADE 38 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~y----s~~~i~l~~C~~C~~-~~Dk 38 (208)
-.|.-||..-.+-|--= +....|-=.|+.|++ +||+
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADR 228 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADR 228 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccchhcch
Confidence 46888888766544321 234557788999998 8886
No 188
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.33 E-value=49 Score=33.65 Aligned_cols=26 Identities=23% Similarity=0.539 Sum_probs=15.2
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
-+|-+||+.=..-. -+. -..||+||+
T Consensus 642 ~~C~~CG~~Ge~~~--~~~----~~~CP~CG~ 667 (711)
T PRK09263 642 DECYECGFTGEFEC--TEK----GFTCPKCGN 667 (711)
T ss_pred cccCCCCCCccccC--CCC----CCcCcCCCC
Confidence 37999997311100 111 158999996
No 189
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=21.28 E-value=50 Score=26.24 Aligned_cols=27 Identities=19% Similarity=0.464 Sum_probs=16.3
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcccccccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~DkY 39 (208)
..|..|..+-+. |--.|+.|++.+.+|
T Consensus 49 ~~C~~C~~~kp~----------Rs~HC~~C~~CV~~~ 75 (174)
T PF01529_consen 49 KYCSTCKIIKPP----------RSHHCRVCNRCVLRF 75 (174)
T ss_pred EECcccCCcCCC----------cceeccccccccccc
Confidence 456666654322 555788887776654
No 190
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=21.25 E-value=47 Score=23.59 Aligned_cols=26 Identities=27% Similarity=0.579 Sum_probs=17.0
Q ss_pred CceecccCcccccceeeccCCceEeecCCCccc
Q 028469 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
-|+|-+||....- -+.+.| +|..||.
T Consensus 20 iYiCgdC~~en~l----k~~D~i---rCReCG~ 45 (62)
T KOG3507|consen 20 IYICGDCGQENTL----KRGDVI---RCRECGY 45 (62)
T ss_pred EEEeccccccccc----cCCCcE---ehhhcch
Confidence 4899999988532 234444 5777773
No 191
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=21.08 E-value=78 Score=23.89 Aligned_cols=30 Identities=23% Similarity=0.473 Sum_probs=15.9
Q ss_pred ecccCcc-c----ccceeeccCCc----eEeecCCCccc
Q 028469 5 CVKCGFR-I----KTLFVQYSPGN----IRLMKCENCRA 34 (208)
Q Consensus 5 CI~C~~~-v----~~Ly~~ys~~~----i~l~~C~~C~~ 34 (208)
|..||.. . ..--..|++.. +.-..|+.||.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe 39 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGE 39 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCC
Confidence 8889853 2 22222344432 23456888875
No 192
>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=20.92 E-value=32 Score=35.82 Aligned_cols=35 Identities=20% Similarity=0.390 Sum_probs=0.0
Q ss_pred ceecccCcccccc-eeeccCCceEeecCCCcccccc
Q 028469 3 YRCVKCGFRIKTL-FVQYSPGNIRLMKCENCRAVAD 37 (208)
Q Consensus 3 ~~CI~C~~~v~~L-y~~ys~~~i~l~~C~~C~~~~D 37 (208)
.+|.+||...-.. -..=+..+...-.|++|++.++
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~ 691 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVE 691 (900)
T ss_dssp ------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCccccceeccccccccC
Confidence 5799999984322 1122334556667777777554
No 193
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=20.51 E-value=59 Score=20.83 Aligned_cols=17 Identities=12% Similarity=0.421 Sum_probs=10.9
Q ss_pred ccCCceEeecCCCcccc
Q 028469 19 YSPGNIRLMKCENCRAV 35 (208)
Q Consensus 19 ys~~~i~l~~C~~C~~~ 35 (208)
.+......+.|+.||-.
T Consensus 6 ~gq~~~~~~~C~~CgM~ 22 (41)
T PF13878_consen 6 LGQKSFGATTCPTCGML 22 (41)
T ss_pred CCCCccCCcCCCCCCCE
Confidence 33334446799999853
No 194
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=20.51 E-value=88 Score=19.32 Aligned_cols=30 Identities=23% Similarity=0.535 Sum_probs=16.0
Q ss_pred ecccCcc-cccce----eeccCCce-----EeecCCCccc
Q 028469 5 CVKCGFR-IKTLF----VQYSPGNI-----RLMKCENCRA 34 (208)
Q Consensus 5 CI~C~~~-v~~Ly----~~ys~~~i-----~l~~C~~C~~ 34 (208)
|..||.. ++.-- ..|+...+ .-..|++||.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE 40 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGE 40 (46)
T ss_pred CCCCCCceecceEEEEEEEeCCEEEEEeCCCccccccCCC
Confidence 6678533 33322 34544433 3345999986
No 195
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=20.38 E-value=30 Score=30.22 Aligned_cols=7 Identities=57% Similarity=1.454 Sum_probs=3.4
Q ss_pred eecccCc
Q 028469 4 RCVKCGF 10 (208)
Q Consensus 4 ~CI~C~~ 10 (208)
.|..|++
T Consensus 121 ~C~~C~~ 127 (244)
T PRK14138 121 YCVRCGK 127 (244)
T ss_pred EECCCCC
Confidence 3555554
No 196
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=20.37 E-value=43 Score=28.66 Aligned_cols=31 Identities=19% Similarity=0.422 Sum_probs=15.8
Q ss_pred CceecccCcccccce-eeccCCceEeecCCCccc
Q 028469 2 EYRCVKCGFRIKTLF-VQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 2 ~~~CI~C~~~v~~Ly-~~ys~~~i~l~~C~~C~~ 34 (208)
..+|..|++..+.-. .+...+ ..-+|++|+.
T Consensus 113 ~~~C~~C~~~~~~~~~~~~~~~--~~p~C~~Cgg 144 (222)
T cd01413 113 TAYCVNCGSKYDLEEVKYAKKH--EVPRCPKCGG 144 (222)
T ss_pred cceECCCCCCcchhHHHHhccC--CCCcCCCCCC
Confidence 357888887533211 111111 2456888874
No 197
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=20.36 E-value=24 Score=31.87 Aligned_cols=25 Identities=32% Similarity=0.763 Sum_probs=15.2
Q ss_pred eecccCcccccceeeccCCc-eEeecCCCccc
Q 028469 4 RCVKCGFRIKTLFVQYSPGN-IRLMKCENCRA 34 (208)
Q Consensus 4 ~CI~C~~~v~~Ly~~ys~~~-i~l~~C~~C~~ 34 (208)
.|-+|+..+ |.++- -.+..||+|+.
T Consensus 28 ~c~~c~~~~------~~~~l~~~~~vc~~c~~ 53 (285)
T TIGR00515 28 KCPKCGQVL------YTKELERNLEVCPKCDH 53 (285)
T ss_pred ECCCCcchh------hHHHHHhhCCCCCCCCC
Confidence 588888875 22211 02358999985
No 198
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=20.22 E-value=44 Score=23.97 Aligned_cols=22 Identities=18% Similarity=0.400 Sum_probs=15.5
Q ss_pred ceecccCcccccceeeccCCceEeecCCCccc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~ 34 (208)
..|.+|..-++. .-+.||.||.
T Consensus 5 kAC~~Ck~l~~~----------d~e~CP~Cgs 26 (64)
T COG2093 5 KACKNCKRLTPE----------DTEICPVCGS 26 (64)
T ss_pred HHHhhccccCCC----------CCccCCCCCC
Confidence 468888776644 3457999996
No 199
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=20.19 E-value=54 Score=21.64 Aligned_cols=30 Identities=20% Similarity=0.510 Sum_probs=19.1
Q ss_pred ceecccCcccccceeeccCCceEeecCCCcc
Q 028469 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCR 33 (208)
Q Consensus 3 ~~CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~ 33 (208)
|.|=.||....+++-+..+. -+-..|+.|=
T Consensus 1 y~C~~Cg~D~t~vryh~~~~-~~~dLC~~CF 30 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLKA-KKYDLCPSCY 30 (45)
T ss_pred CcccCCCCccCceEEEecCC-CccccChHHH
Confidence 57889999988743333322 2466777773
No 200
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=20.11 E-value=52 Score=25.96 Aligned_cols=29 Identities=24% Similarity=0.689 Sum_probs=16.9
Q ss_pred ceec--ccCcccccceeeccCCceEeecCCCccccccc
Q 028469 3 YRCV--KCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (208)
Q Consensus 3 ~~CI--~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~~Dk 38 (208)
+.|. .|+..+.. .+.| .-.|++|++..++
T Consensus 19 ~aC~~~~C~kKv~~----~~~~---~y~C~~C~~~~~~ 49 (146)
T PF08646_consen 19 PACPNEKCNKKVTE----NGDG---SYRCEKCNKTVEN 49 (146)
T ss_dssp EE-TSTTTS-B-EE----ETTT---EEEETTTTEEESS
T ss_pred CCCCCccCCCEeec----CCCc---EEECCCCCCcCCC
Confidence 4688 99987644 1222 2479999987654
No 201
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=20.02 E-value=50 Score=22.53 Aligned_cols=34 Identities=18% Similarity=0.443 Sum_probs=14.3
Q ss_pred ecccCcccccceeeccCCceEeecCCCcccc----ccccc
Q 028469 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAV----ADEYI 40 (208)
Q Consensus 5 CI~C~~~v~~Ly~~ys~~~i~l~~C~~C~~~----~DkYi 40 (208)
|-.|..+.+..=.+ +++-..-+|++|++. +|-||
T Consensus 2 CfgC~~~~~~~~~~--~~~~~~y~C~~C~~~FC~dCD~fi 39 (51)
T PF07975_consen 2 CFGCQKPFPDGPEK--KADSSRYRCPKCKNHFCIDCDVFI 39 (51)
T ss_dssp ETTTTEE-TTS---------EEE--TTTT--B-HHHHHTT
T ss_pred CccCCCCCCCcccc--cccCCeEECCCCCCccccCcChhh
Confidence 56677776553111 111345589999984 55554
Done!