Query 029119
Match_columns 198
No_of_seqs 136 out of 182
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 07:48:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029119.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029119hhsearch_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 6.1E-60 1.3E-64 399.2 13.4 194 3-196 1-208 (208)
2 KOG3134 Predicted membrane pro 100.0 2.5E-43 5.4E-48 298.2 6.0 192 3-197 1-204 (225)
3 COG5254 ARV1 Predicted membran 100.0 1.5E-38 3.3E-43 266.7 4.5 192 3-197 1-216 (239)
4 smart00834 CxxC_CXXC_SSSS Puta 93.5 0.029 6.3E-07 35.0 0.7 34 2-38 5-38 (41)
5 PF08271 TF_Zn_Ribbon: TFIIB z 93.2 0.059 1.3E-06 34.6 1.8 33 3-40 1-33 (43)
6 PRK00398 rpoP DNA-directed RNA 92.8 0.051 1.1E-06 35.4 1.0 31 1-37 2-32 (46)
7 smart00659 RPOLCX RNA polymera 91.6 0.11 2.3E-06 34.1 1.5 28 1-35 1-28 (44)
8 PF09723 Zn-ribbon_8: Zinc rib 91.2 0.086 1.9E-06 33.9 0.7 34 2-38 5-39 (42)
9 KOG3134 Predicted membrane pro 90.6 0.68 1.5E-05 40.2 5.8 83 111-193 99-186 (225)
10 TIGR02605 CxxC_CxxC_SSSS putat 90.3 0.12 2.5E-06 34.2 0.7 30 2-34 5-34 (52)
11 COG5254 ARV1 Predicted membran 90.2 1.6 3.4E-05 37.8 7.6 46 151-196 142-188 (239)
12 PF14319 Zn_Tnp_IS91: Transpos 89.6 0.29 6.4E-06 37.8 2.6 52 2-67 42-95 (111)
13 PF13248 zf-ribbon_3: zinc-rib 89.5 0.16 3.5E-06 29.4 0.8 24 1-34 1-24 (26)
14 PF03604 DNA_RNApol_7kD: DNA d 88.6 0.26 5.6E-06 30.3 1.3 25 3-34 1-25 (32)
15 COG1996 RPC10 DNA-directed RNA 88.4 0.16 3.4E-06 34.3 0.2 28 1-34 5-32 (49)
16 PF05180 zf-DNL: DNL zinc fing 87.5 0.25 5.4E-06 35.3 0.9 36 2-38 4-44 (66)
17 cd00729 rubredoxin_SM Rubredox 86.5 0.26 5.6E-06 30.5 0.4 32 2-41 2-33 (34)
18 PF07282 OrfB_Zn_ribbon: Putat 84.1 0.62 1.3E-05 32.3 1.5 30 3-38 29-58 (69)
19 PF04216 FdhE: Protein involve 83.3 1 2.2E-05 39.8 2.9 62 3-65 212-286 (290)
20 PF01286 XPA_N: XPA protein N- 82.1 0.48 1E-05 29.6 0.2 28 1-33 2-31 (34)
21 PF12773 DZR: Double zinc ribb 82.0 0.71 1.5E-05 30.0 1.1 30 3-39 13-42 (50)
22 PRK00464 nrdR transcriptional 81.3 0.89 1.9E-05 37.3 1.6 44 3-46 1-48 (154)
23 PF12647 RNHCP: RNHCP domain; 81.1 0.8 1.7E-05 34.7 1.2 29 1-33 3-31 (92)
24 PF01927 Mut7-C: Mut7-C RNAse 80.2 0.91 2E-05 36.4 1.3 33 3-35 92-133 (147)
25 PF13240 zinc_ribbon_2: zinc-r 77.4 0.92 2E-05 25.7 0.4 22 4-35 1-22 (23)
26 PRK12495 hypothetical protein; 76.9 1.3 2.7E-05 38.7 1.2 29 2-38 42-70 (226)
27 smart00401 ZnF_GATA zinc finge 76.8 1.4 3.1E-05 29.5 1.3 32 2-35 3-34 (52)
28 PF04981 NMD3: NMD3 family ; 75.9 1.4 3.1E-05 37.9 1.3 38 5-42 1-53 (236)
29 PF13453 zf-TFIIB: Transcripti 75.8 2.5 5.4E-05 26.7 2.2 27 5-35 2-28 (41)
30 COG3364 Zn-ribbon containing p 74.1 1.1 2.3E-05 34.9 0.1 37 1-43 1-37 (112)
31 PF10571 UPF0547: Uncharacteri 73.1 1.6 3.5E-05 25.5 0.7 22 4-35 2-23 (26)
32 PRK03564 formate dehydrogenase 72.0 4.4 9.5E-05 36.9 3.5 63 3-66 227-301 (309)
33 PF12760 Zn_Tnp_IS1595: Transp 71.1 3.2 6.9E-05 26.9 1.8 29 1-34 17-45 (46)
34 TIGR02098 MJ0042_CXXC MJ0042 f 70.8 1.9 4.1E-05 26.5 0.6 35 1-36 1-35 (38)
35 PF14803 Nudix_N_2: Nudix N-te 70.7 2.2 4.8E-05 26.5 1.0 30 4-35 2-31 (34)
36 PF02591 DUF164: Putative zinc 70.3 1.1 2.5E-05 30.1 -0.5 33 2-35 22-55 (56)
37 COG2331 Uncharacterized protei 70.3 0.86 1.9E-05 33.6 -1.1 34 2-38 12-45 (82)
38 PRK00420 hypothetical protein; 69.6 2.6 5.7E-05 32.9 1.4 28 3-37 24-51 (112)
39 cd00350 rubredoxin_like Rubred 68.4 2.2 4.8E-05 25.9 0.6 32 2-41 1-32 (33)
40 PF09538 FYDLN_acid: Protein o 68.4 2.3 4.9E-05 33.0 0.8 28 3-37 10-37 (108)
41 COG1656 Uncharacterized conser 67.9 2 4.4E-05 35.8 0.4 33 3-35 98-139 (165)
42 PF14446 Prok-RING_1: Prokaryo 66.4 3.7 8.1E-05 28.2 1.4 27 1-35 4-30 (54)
43 cd01121 Sms Sms (bacterial rad 66.2 3 6.5E-05 38.5 1.3 23 3-35 1-23 (372)
44 PF09845 DUF2072: Zn-ribbon co 66.0 2.2 4.8E-05 34.3 0.3 27 3-35 2-28 (131)
45 PF09082 DUF1922: Domain of un 66.0 2.2 4.9E-05 30.6 0.3 25 3-35 4-28 (68)
46 PF14353 CpXC: CpXC protein 64.3 5.3 0.00012 30.8 2.2 56 3-68 2-70 (128)
47 PF14149 YhfH: YhfH-like prote 63.9 1.1 2.5E-05 28.5 -1.4 24 3-32 14-37 (37)
48 PRK00423 tfb transcription ini 63.3 5 0.00011 35.9 2.1 32 2-38 11-42 (310)
49 COG2260 Predicted Zn-ribbon RN 62.2 3.8 8.2E-05 28.7 0.9 20 24-44 16-46 (59)
50 TIGR01562 FdhE formate dehydro 61.3 8.8 0.00019 34.8 3.3 62 3-66 225-301 (305)
51 COG4888 Uncharacterized Zn rib 61.3 4.7 0.0001 31.1 1.3 53 3-55 23-80 (104)
52 COG0846 SIR2 NAD-dependent pro 60.9 3.4 7.3E-05 36.4 0.5 33 3-35 123-155 (250)
53 TIGR00416 sms DNA repair prote 60.7 4.1 8.9E-05 38.5 1.1 24 2-35 7-30 (454)
54 PF07754 DUF1610: Domain of un 60.6 6.1 0.00013 22.8 1.4 24 5-34 1-24 (24)
55 PF13719 zinc_ribbon_5: zinc-r 59.9 4.1 9E-05 25.4 0.7 34 1-35 1-34 (37)
56 PRK11823 DNA repair protein Ra 58.5 4.7 0.0001 38.0 1.1 29 2-41 7-35 (446)
57 smart00531 TFIIE Transcription 58.0 3.2 6.9E-05 33.2 -0.1 36 2-38 99-135 (147)
58 PF14255 Cys_rich_CPXG: Cystei 57.3 7.8 0.00017 26.3 1.7 40 4-43 2-41 (52)
59 PHA02942 putative transposase; 57.2 5.8 0.00013 36.8 1.4 29 3-38 326-354 (383)
60 COG2888 Predicted Zn-ribbon RN 56.3 7 0.00015 27.5 1.4 38 3-40 10-52 (61)
61 PF13717 zinc_ribbon_4: zinc-r 56.1 6.1 0.00013 24.5 1.0 32 1-35 1-34 (36)
62 COG1997 RPL43A Ribosomal prote 53.9 7.8 0.00017 29.2 1.4 28 1-35 34-62 (89)
63 PF12156 ATPase-cat_bd: Putati 53.8 4.3 9.3E-05 30.0 -0.0 34 4-37 2-37 (88)
64 PF11023 DUF2614: Protein of u 53.3 5 0.00011 31.5 0.3 25 3-35 70-94 (114)
65 PF00320 GATA: GATA zinc finge 53.3 4.4 9.6E-05 25.1 -0.0 31 5-37 1-31 (36)
66 KOG1597 Transcription initiati 51.4 9.5 0.00021 34.7 1.8 29 4-35 2-30 (308)
67 cd00202 ZnF_GATA Zinc finger D 50.6 4.8 0.0001 27.3 -0.2 34 4-39 1-34 (54)
68 PRK00564 hypA hydrogenase nick 50.6 7.3 0.00016 30.2 0.8 26 3-35 72-97 (117)
69 TIGR02300 FYDLN_acid conserved 49.6 8.2 0.00018 31.0 1.0 28 2-36 9-36 (129)
70 PRK14890 putative Zn-ribbon RN 49.0 12 0.00027 26.1 1.7 38 2-39 7-49 (59)
71 PRK03681 hypA hydrogenase nick 48.9 9.2 0.0002 29.6 1.2 26 3-35 71-96 (114)
72 COG1405 SUA7 Transcription ini 47.8 11 0.00025 33.7 1.8 37 2-43 1-38 (285)
73 COG1066 Sms Predicted ATP-depe 47.2 9 0.0002 36.6 1.0 23 2-34 7-29 (456)
74 PRK12336 translation initiatio 47.2 16 0.00034 31.0 2.4 35 4-41 100-136 (201)
75 PRK07591 threonine synthase; V 46.8 9.3 0.0002 35.6 1.0 30 3-43 19-48 (421)
76 smart00661 RPOL9 RNA polymeras 46.7 12 0.00027 24.1 1.3 28 4-35 2-29 (52)
77 PRK05978 hypothetical protein; 45.8 9.8 0.00021 31.1 0.9 27 3-34 34-60 (148)
78 COG4031 Predicted metal-bindin 45.5 9.7 0.00021 32.8 0.9 30 3-44 1-34 (227)
79 PRK12380 hydrogenase nickel in 44.6 11 0.00024 29.1 1.0 25 3-35 71-95 (113)
80 PHA02768 hypothetical protein; 43.2 5.2 0.00011 27.6 -0.9 40 2-42 5-50 (55)
81 COG1499 NMD3 NMD protein affec 42.0 17 0.00036 33.7 1.9 32 2-33 6-50 (355)
82 PRK03824 hypA hydrogenase nick 41.6 13 0.00027 29.6 0.9 34 2-35 70-116 (135)
83 KOG3277 Uncharacterized conser 41.3 16 0.00034 30.5 1.4 35 3-38 80-119 (165)
84 PRK04136 rpl40e 50S ribosomal 40.8 15 0.00033 24.7 1.1 23 2-34 14-36 (48)
85 PF01155 HypA: Hydrogenase exp 40.6 8.2 0.00018 29.7 -0.3 25 3-35 71-95 (113)
86 PF07191 zinc-ribbons_6: zinc- 40.0 17 0.00036 26.3 1.3 34 3-36 2-40 (70)
87 PF09297 zf-NADH-PPase: NADH p 39.8 9.2 0.0002 22.8 -0.1 27 3-35 4-30 (32)
88 TIGR03829 YokU_near_AblA uncha 39.2 38 0.00083 25.5 3.1 50 5-54 2-60 (89)
89 COG1645 Uncharacterized Zn-fin 38.8 17 0.00037 29.2 1.3 24 3-34 29-52 (131)
90 PF09151 DUF1936: Domain of un 37.9 38 0.00083 21.0 2.4 27 3-31 2-29 (36)
91 PF02146 SIR2: Sir2 family; I 37.8 5.2 0.00011 32.5 -1.9 30 3-34 106-137 (178)
92 COG3880 Modulator of heat shoc 37.6 24 0.00053 29.7 2.0 41 3-43 1-43 (176)
93 TIGR01206 lysW lysine biosynth 37.6 24 0.00051 24.1 1.6 30 2-35 2-31 (54)
94 PRK04023 DNA polymerase II lar 37.4 20 0.00043 37.7 1.8 40 3-42 639-679 (1121)
95 PF10122 Mu-like_Com: Mu-like 37.1 20 0.00043 24.4 1.2 30 2-35 4-33 (51)
96 PRK03976 rpl37ae 50S ribosomal 36.9 26 0.00056 26.5 1.9 28 2-36 36-64 (90)
97 PRK02935 hypothetical protein; 36.6 18 0.00039 28.2 1.1 24 4-35 72-95 (110)
98 TIGR00100 hypA hydrogenase nic 36.3 16 0.00034 28.2 0.7 26 3-36 71-96 (115)
99 PF09567 RE_MamI: MamI restric 35.0 16 0.00035 32.8 0.6 21 4-34 84-104 (314)
100 PF10083 DUF2321: Uncharacteri 34.9 17 0.00036 30.2 0.7 32 4-35 41-77 (158)
101 COG3357 Predicted transcriptio 34.7 18 0.00039 27.6 0.8 26 2-34 58-84 (97)
102 PF05191 ADK_lid: Adenylate ki 34.1 22 0.00048 22.2 1.0 28 3-34 2-29 (36)
103 COG1545 Predicted nucleic-acid 34.0 22 0.00048 28.4 1.2 30 4-43 31-61 (140)
104 PF09332 Mcm10: Mcm10 replicat 33.6 16 0.00035 33.8 0.4 27 3-35 286-312 (344)
105 COG0375 HybF Zn finger protein 33.4 21 0.00045 28.1 1.0 29 3-39 71-99 (115)
106 PRK06266 transcription initiat 33.2 15 0.00033 30.6 0.2 32 2-38 117-148 (178)
107 PRK00019 rpmE 50S ribosomal pr 32.6 34 0.00073 24.7 1.9 29 4-34 15-43 (72)
108 PF06542 PHA-1: Regulator prot 32.3 11 0.00024 35.2 -0.9 39 28-66 123-161 (390)
109 PF09889 DUF2116: Uncharacteri 32.1 19 0.00042 25.0 0.5 12 3-14 4-15 (59)
110 PF03367 zf-ZPR1: ZPR1 zinc-fi 32.0 28 0.00061 28.5 1.6 31 3-33 2-37 (161)
111 TIGR00280 L37a ribosomal prote 31.9 34 0.00074 25.9 1.9 28 2-36 35-63 (91)
112 COG1571 Predicted DNA-binding 31.6 25 0.00054 33.4 1.3 29 2-37 350-378 (421)
113 PRK14714 DNA polymerase II lar 31.6 27 0.00058 37.6 1.7 15 27-41 710-724 (1337)
114 PRK06386 replication factor A; 31.5 22 0.00049 33.0 1.0 24 3-39 237-260 (358)
115 smart00709 Zpr1 Duplicated dom 31.4 36 0.00078 28.0 2.1 30 4-33 2-36 (160)
116 PRK00762 hypA hydrogenase nick 31.4 23 0.0005 27.7 0.9 30 3-35 71-101 (124)
117 PRK07218 replication factor A; 31.3 23 0.0005 33.6 1.0 20 47-66 324-343 (423)
118 COG1552 RPL40A Ribosomal prote 31.3 13 0.00028 25.1 -0.4 22 3-34 15-36 (50)
119 PF03691 UPF0167: Uncharacteri 31.2 18 0.00039 30.4 0.3 37 2-39 24-65 (176)
120 PRK14559 putative protein seri 30.5 23 0.0005 35.3 1.0 7 28-34 29-35 (645)
121 PF04810 zf-Sec23_Sec24: Sec23 30.5 22 0.00048 22.4 0.5 18 27-44 3-20 (40)
122 cd01408 SIRT1 SIRT1: Eukaryoti 30.5 14 0.00031 31.7 -0.4 14 22-35 112-125 (235)
123 cd01407 SIR2-fam SIR2 family o 30.4 17 0.00037 30.6 0.1 31 3-35 110-142 (218)
124 COG1644 RPB10 DNA-directed RNA 30.4 10 0.00023 26.8 -1.0 19 3-21 5-23 (63)
125 PTZ00255 60S ribosomal protein 29.9 40 0.00086 25.5 1.9 27 2-35 36-63 (90)
126 PRK04023 DNA polymerase II lar 29.8 31 0.00066 36.4 1.7 11 2-12 626-636 (1121)
127 PF10977 DUF2797: Protein of u 29.7 21 0.00045 31.2 0.5 29 4-32 13-43 (235)
128 PF01194 RNA_pol_N: RNA polyme 28.8 15 0.00032 25.8 -0.5 16 4-19 6-21 (60)
129 PRK06424 transcription factor; 28.6 26 0.00056 28.4 0.8 37 5-42 3-39 (144)
130 PRK06260 threonine synthase; V 28.3 26 0.00057 32.2 0.9 28 2-37 3-30 (397)
131 PRK04016 DNA-directed RNA poly 28.3 13 0.00028 26.3 -0.9 17 4-20 6-22 (62)
132 PTZ00410 NAD-dependent SIR2; P 28.2 19 0.00042 33.3 -0.0 31 3-35 148-180 (349)
133 PF06827 zf-FPG_IleRS: Zinc fi 28.2 48 0.001 19.2 1.7 29 3-35 2-30 (30)
134 TIGR00310 ZPR1_znf ZPR1 zinc f 27.7 45 0.00099 28.2 2.2 30 4-33 2-37 (192)
135 cd01411 SIR2H SIR2H: Uncharact 27.4 27 0.00058 29.8 0.7 9 26-34 136-144 (225)
136 PF14800 DUF4481: Domain of un 27.3 4.2E+02 0.009 24.3 8.2 24 43-66 39-62 (308)
137 COG0254 RpmE Ribosomal protein 27.1 45 0.00099 24.3 1.8 29 4-33 16-44 (75)
138 PRK14892 putative transcriptio 27.1 39 0.00085 25.8 1.5 50 3-55 22-76 (99)
139 PF10058 DUF2296: Predicted in 27.1 46 0.001 22.5 1.7 30 3-34 23-52 (54)
140 KOG2682 NAD-dependent histone 27.0 13 0.00028 33.3 -1.3 38 3-40 153-191 (314)
141 PRK14559 putative protein seri 26.8 34 0.00073 34.2 1.4 14 26-39 41-54 (645)
142 KOG0477 DNA replication licens 26.8 32 0.0007 34.9 1.2 33 2-35 292-324 (854)
143 PF13913 zf-C2HC_2: zinc-finge 26.7 28 0.0006 19.8 0.5 9 26-34 2-10 (25)
144 PRK13130 H/ACA RNA-protein com 26.6 33 0.00072 23.6 0.9 19 28-46 19-48 (56)
145 PF05129 Elf1: Transcription e 26.6 49 0.0011 24.2 1.9 50 3-52 23-77 (81)
146 PRK06393 rpoE DNA-directed RNA 26.5 11 0.00024 26.7 -1.4 34 3-49 6-39 (64)
147 CHL00174 accD acetyl-CoA carbo 26.5 14 0.0003 33.5 -1.2 25 4-34 40-65 (296)
148 COG2816 NPY1 NTP pyrophosphohy 26.4 41 0.00088 30.3 1.7 27 3-35 112-138 (279)
149 PRK12286 rpmF 50S ribosomal pr 25.8 46 0.00099 22.9 1.5 23 4-37 29-51 (57)
150 PF04135 Nop10p: Nucleolar RNA 25.7 39 0.00085 23.1 1.1 19 27-45 18-47 (53)
151 PF14311 DUF4379: Domain of un 25.5 33 0.00071 22.7 0.7 8 4-11 30-37 (55)
152 cd04476 RPA1_DBD_C RPA1_DBD_C: 25.5 36 0.00078 27.2 1.1 28 3-37 35-62 (166)
153 PRK01397 50S ribosomal protein 25.3 58 0.0013 23.9 2.1 14 21-34 29-42 (78)
154 PRK07218 replication factor A; 25.3 39 0.00085 32.0 1.5 20 20-39 291-310 (423)
155 PRK00504 rpmG 50S ribosomal pr 25.0 54 0.0012 22.0 1.7 33 3-35 8-43 (50)
156 PHA02637 TNF-alpha-receptor-li 24.8 45 0.00098 26.7 1.5 31 3-39 63-93 (127)
157 PRK08402 replication factor A; 24.8 34 0.00074 31.6 1.0 9 4-12 214-222 (355)
158 PRK14704 anaerobic ribonucleos 24.4 33 0.00071 34.1 0.8 22 3-35 560-581 (618)
159 PLN00032 DNA-directed RNA poly 24.3 17 0.00037 26.3 -0.9 18 4-21 6-23 (71)
160 COG3478 Predicted nucleic-acid 23.9 42 0.00091 24.1 1.0 9 4-12 6-14 (68)
161 PF03833 PolC_DP2: DNA polymer 23.6 27 0.00058 36.1 0.0 41 3-43 668-709 (900)
162 PRK12366 replication factor A; 23.4 37 0.00081 33.6 1.0 25 3-35 533-557 (637)
163 cd01412 SIRT5_Af1_CobB SIRT5_A 23.4 37 0.0008 28.6 0.8 29 3-34 110-138 (224)
164 COG2995 PqiA Uncharacterized p 23.3 43 0.00092 31.8 1.3 26 4-35 20-47 (418)
165 TIGR00340 zpr1_rel ZPR1-relate 23.2 57 0.0012 26.9 1.9 29 5-33 1-35 (163)
166 smart00507 HNHc HNH nucleases. 23.1 35 0.00075 20.8 0.5 11 3-13 11-21 (52)
167 PRK06450 threonine synthase; V 22.9 41 0.00089 30.5 1.1 32 3-43 4-35 (338)
168 PF02132 RecR: RecR protein; 22.4 31 0.00067 21.8 0.1 14 25-38 16-29 (41)
169 smart00440 ZnF_C2C2 C2C2 Zinc 22.3 32 0.0007 21.7 0.2 9 3-11 29-37 (40)
170 CHL00136 rpl31 ribosomal prote 22.0 65 0.0014 22.9 1.7 13 22-34 31-43 (68)
171 PF10217 DUF2039: Uncharacteri 22.0 11 0.00023 28.6 -2.4 33 3-35 56-90 (92)
172 PRK05638 threonine synthase; V 21.9 50 0.0011 30.9 1.4 25 3-37 2-26 (442)
173 PF12172 DUF35_N: Rubredoxin-l 21.7 59 0.0013 19.7 1.3 15 21-35 6-20 (37)
174 PRK14714 DNA polymerase II lar 21.5 44 0.00096 36.0 1.1 30 3-35 668-701 (1337)
175 PRK00481 NAD-dependent deacety 21.3 46 0.00099 28.5 1.0 9 3-11 123-131 (242)
176 COG3809 Uncharacterized protei 21.2 57 0.0012 24.3 1.3 37 3-43 2-44 (88)
177 PRK00448 polC DNA polymerase I 21.0 48 0.001 36.2 1.2 34 2-35 908-942 (1437)
178 TIGR03831 YgiT_finger YgiT-typ 20.7 95 0.002 19.0 2.2 30 5-34 1-40 (46)
179 COG4416 Com Mu-like prophage p 20.7 35 0.00076 23.7 0.1 35 3-41 5-39 (60)
180 PF01412 ArfGap: Putative GTPa 20.7 18 0.00038 27.8 -1.5 29 3-35 14-42 (116)
181 PF13878 zf-C2H2_3: zinc-finge 20.4 60 0.0013 20.6 1.2 17 19-35 6-22 (41)
182 cd02336 ZZ_RSC8 Zinc finger, Z 20.2 57 0.0012 21.3 1.1 30 3-33 1-30 (45)
183 KOG2462 C2H2-type Zn-finger pr 20.1 37 0.00081 30.6 0.2 36 3-38 188-228 (279)
184 PF07975 C1_4: TFIIH C1-like d 20.0 51 0.0011 22.3 0.8 34 5-40 2-39 (51)
185 COG2093 DNA-directed RNA polym 20.0 48 0.001 23.6 0.7 22 3-34 5-26 (64)
186 TIGR01405 polC_Gram_pos DNA po 20.0 52 0.0011 35.3 1.3 34 2-35 683-717 (1213)
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=6.1e-60 Score=399.15 Aligned_cols=194 Identities=41% Similarity=0.643 Sum_probs=169.3
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccccccchhHHHHHHHHhcCcchheeeeccccccccc--------ch
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETV--------NL 74 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayRHllfN~~~~~~~--------~~ 74 (198)
++|||||+||++||++|||||||+|+|++||++||||||+|+++++||++|+|||||||++||+.+++.. +.
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDkYiE~d~vil~IDLlLlK~~AYRHllfN~~~~~~~~~~~~~~~~~ 80 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADKYIEYDNVILFIDLLLLKPQAYRHLLFNRLEPELSKFQVKNWFSK 80 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCcccceeccccHHHHHHHHHcchhhHHHhhccCCccccccchhhhhhhh
Confidence 5899999999999999999999999999999999999999999999999999999999999999887765 44
Q ss_pred hhHHHHHHHHHHHHHHHHHHhhhccCCCCCC---cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCch
Q 029119 75 KGILWKSTVGFLLLDAYRSLLLSRSNEGQSS---SMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTS-AGASS 150 (198)
Q Consensus 75 ~~~l~kl~~~~ll~eay~~w~~~~~~~~~~~---s~~~~~~~~~~~~~l~~~~l~~~~f~~~~~l~~~~~l~~~-~~~~~ 150 (198)
.+.+||++++++++|||+.|...+.+.+.+. .....+...++..++...++++++|+.++.+..+..++++ ....+
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 5689999999999999999987665543321 1111233555667778888899999999999999888887 55668
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhccCCCCchhh--hhheeEEeeccccc
Q 029119 151 FKDFLLAVLISSYFKIFLVAMMVWNFPSSVIY--IIDLFVLSSNTVAL 196 (198)
Q Consensus 151 ~~~ll~alllSs~~KLF~ilmlIW~yd~s~~~--~i~~~vl~sN~~Al 196 (198)
++.+++|+++||++|+|+++|+||+||.++.. +++++|++||++||
T Consensus 161 ~~~l~~alllSs~~Klf~ilmlIW~~~~~~~~~~ii~~~v~~~~~~aL 208 (208)
T PF04161_consen 161 FRVLLTALLLSSYGKLFPILMLIWPYDSSPISLSIIDWFVLLSNIEAL 208 (208)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999987766 99999999999997
No 2
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=2.5e-43 Score=298.22 Aligned_cols=192 Identities=38% Similarity=0.616 Sum_probs=140.5
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccccccchhHHHHHHHHhcCcchheeeecccccccccchhhHHHHHH
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWKST 82 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayRHllfN~~~~~~~~~~~~l~kl~ 82 (198)
++|||||+++++||++||+||||+|+||+|+++||||||+|+||++||++|+|+|||||+|||..++++.+..-.+||+.
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-CCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--------CCCchHHH
Q 029119 83 VGFLLLDAYRSLLLSRS-NEGQSSSMSFSLLAWIFQKMLKDVVLGNVMFLGVFLHASRILLNTS--------AGASSFKD 153 (198)
Q Consensus 83 ~~~ll~eay~~w~~~~~-~~~~~~s~~~~~~~~~~~~~l~~~~l~~~~f~~~~~l~~~~~l~~~--------~~~~~~~~ 153 (198)
...++++.+.....+.+ ++|+.+.++.. ....+.+......++.|.+.+...-..+.+.. .....+..
T Consensus 81 ~~~~lL~~~~~~l~~~~~~~e~~~~~~~~---~~~~~~~~~~i~~~~l~~f~~~~~~~~~~~l~~~~lLl~~~~~~syi~ 157 (225)
T KOG3134|consen 81 FAWLLLQDFESLLLWLSEDDEWVFYRSFA---LPALEVLSSLIERQYLFVFLWCNRETTFVQLSSALLLLKTLLLKSYIS 157 (225)
T ss_pred HHHHHHHHhHhhcccccCCCcchhhhhHH---HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHH
Confidence 88888887766666555 55665555431 11112222222223333332222211111111 01123333
Q ss_pred -HHHHHHHHhhhHHHhhhhhccCCCCc-hh-hhhheeEEeecccccc
Q 029119 154 -FLLAVLISSYFKIFLVAMMVWNFPSS-VI-YIIDLFVLSSNTVALK 197 (198)
Q Consensus 154 -ll~alllSs~~KLF~ilmlIW~yd~s-~~-~~i~~~vl~sN~~Al~ 197 (198)
+..+.+.|++.|+++|.|++|+||.+ +. -.++|...+++..|+|
T Consensus 158 ~i~~~~~~s~~~~v~~Ifml~~~~~~~~v~~~~v~~~~~~a~l~~l~ 204 (225)
T KOG3134|consen 158 VISLLVILSSCVKVNPIFMLISCYQTSRVALGIVYWVSFLAVLLALK 204 (225)
T ss_pred HHHHHHHHHHhhhhhheeeeehHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67777788888899999999999987 43 3888888888877764
No 3
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=100.00 E-value=1.5e-38 Score=266.71 Aligned_cols=192 Identities=21% Similarity=0.305 Sum_probs=128.0
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccccccchhHHHHHHHHhcCcchheeeecccccccccchhhHHHH--
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLNSETVNLKGILWK-- 80 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayRHllfN~~~~~~~~~~~~l~k-- 80 (198)
++|||||.||++||++||.++||+++||+|++.+|||+|.|+|+++||++|+|||+|||++||+.+.++....-...+
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 589999999999999999999999999999999999999999999999999999999999999988554322211111
Q ss_pred ------HHHHHHHHHHHHHHhhhccCCCCC--------------Ccc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029119 81 ------STVGFLLLDAYRSLLLSRSNEGQS--------------SSM-SFSLLAWIFQKMLKDVVLGNVMFLGVFLHASR 139 (198)
Q Consensus 81 ------l~~~~ll~eay~~w~~~~~~~~~~--------------~s~-~~~~~~~~~~~~l~~~~l~~~~f~~~~~l~~~ 139 (198)
+..+...++.|+.|-..++...+. .+. .+.-...++.....-++++...|.....+...
T Consensus 81 ~~Fc~~~~~l~~~f~~~L~w~~~E~~~~~~~a~~~~~~pes~~~~s~ilr~~~s~qyl~~~~vcl~~~~l~~~f~~lf~~ 160 (239)
T COG5254 81 RMFCEPILQLHEAFGLLLSWGPGEGVSIAEMATICRDVPESLMETSLILRLVFSMQYLHAGFVCLSSALLLSSFYYLFMF 160 (239)
T ss_pred HHHHHHHHHHHHHhhhheeeccccccchHHHHHhhhhhHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 113334444555554332210000 000 00000011112222333344444443333333
Q ss_pred HHHhccCCCchHHHHHHHHHHHhhhHHHhhhhhccCCCCchhh-hhheeEEeecccccc
Q 029119 140 ILLNTSAGASSFKDFLLAVLISSYFKIFLVAMMVWNFPSSVIY-IIDLFVLSSNTVALK 197 (198)
Q Consensus 140 ~~l~~~~~~~~~~~ll~alllSs~~KLF~ilmlIW~yd~s~~~-~i~~~vl~sN~~Al~ 197 (198)
..++|.. ....-..++.+|+.+|.+|++|+||+||.+... +|+|.++.+|.+|+|
T Consensus 161 ~~~~Wk~---~~~~s~~~I~ls~~a~~~pV~m~Iw~yd~~Ia~~~I~wv~~~~~~~~l~ 216 (239)
T COG5254 161 IMTMWKY---QCEESLLVIELSCVACNSPVIMEIWLYDNEIALGCIYWVKFAAGLVCLR 216 (239)
T ss_pred HHHHHHH---HhhhcchheeeecchhcchhheeehhcchHHHHHHHHHHHHHHhHHHHH
Confidence 3333321 122333699999999999999999999998654 999999999999986
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=93.53 E-value=0.029 Score=35.02 Aligned_cols=34 Identities=32% Similarity=0.632 Sum_probs=23.8
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (198)
+|+|.+||+..+.+... +. -....||+||.-+.|
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 48999999987765322 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=93.24 E-value=0.059 Score=34.64 Aligned_cols=33 Identities=30% Similarity=0.729 Sum_probs=23.5
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYI 40 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYi 40 (198)
++|.+||... +..++..|.+ .|++||.+.|..+
T Consensus 1 m~Cp~Cg~~~--~~~D~~~g~~---vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 1 MKCPNCGSKE--IVFDPERGEL---VCPNCGLVLEENI 33 (43)
T ss_dssp ESBTTTSSSE--EEEETTTTEE---EETTT-BBEE-TT
T ss_pred CCCcCCcCCc--eEEcCCCCeE---ECCCCCCEeeccc
Confidence 5799999965 6666766653 8999998877554
No 6
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=92.75 E-value=0.051 Score=35.37 Aligned_cols=31 Identities=23% Similarity=0.573 Sum_probs=22.7
Q ss_pred CCccccccCcccccceeeecCCceEeecCCCcccccc
Q 029119 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (198)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (198)
++|+|.+||..+.- .++. ....||+||...+
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 7
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=91.57 E-value=0.11 Score=34.11 Aligned_cols=28 Identities=29% Similarity=0.642 Sum_probs=20.3
Q ss_pred CCccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
+.|+|-+||+.++.- +. ..-+|++||.-
T Consensus 1 ~~Y~C~~Cg~~~~~~----~~---~~irC~~CG~r 28 (44)
T smart00659 1 MIYICGECGRENEIK----SK---DVVRCRECGYR 28 (44)
T ss_pred CEEECCCCCCEeecC----CC---CceECCCCCce
Confidence 579999999987642 22 23479999963
No 8
>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=91.20 E-value=0.086 Score=33.93 Aligned_cols=34 Identities=29% Similarity=0.641 Sum_probs=24.8
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccc-cccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA-VADE 38 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~-~~Dk 38 (198)
+|+|-+||+.-+.+.. .+. -....||+||. -+.|
T Consensus 5 ey~C~~Cg~~fe~~~~-~~~--~~~~~CP~Cg~~~~~r 39 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQS-ISE--DDPVPCPECGSTEVRR 39 (42)
T ss_pred EEEeCCCCCEEEEEEE-cCC--CCCCcCCCCCCCceEE
Confidence 5899999998877643 222 46779999998 4443
No 9
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=90.55 E-value=0.68 Score=40.23 Aligned_cols=83 Identities=19% Similarity=0.136 Sum_probs=52.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-Hhcc---CCCchHHHHHHHHHHHhhhH-HHhhhhhccCCCCchhhhhh
Q 029119 111 LLAWIFQKMLKDVVLGNVMFLGVFLHASRIL-LNTS---AGASSFKDFLLAVLISSYFK-IFLVAMMVWNFPSSVIYIID 185 (198)
Q Consensus 111 ~~~~~~~~~l~~~~l~~~~f~~~~~l~~~~~-l~~~---~~~~~~~~ll~alllSs~~K-LF~ilmlIW~yd~s~~~~i~ 185 (198)
..+|.+++.......+...+.++-++.+... .... .+.++...+++++.++||+| .+...+..|.....++++++
T Consensus 99 ~~e~~~~~~~~~~~~~~~~~~i~~~~l~~f~~~~~~~~~~~l~~~~lLl~~~~~~syi~~i~~~~~~s~~~~v~~Ifml~ 178 (225)
T KOG3134|consen 99 DDEWVFYRSFALPALEVLSSLIERQYLFVFLWCNRETTFVQLSSALLLLKTLLLKSYISVISLLVILSSCVKVNPIFMLI 178 (225)
T ss_pred CCcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhheeeee
Confidence 4478888888888888877777544444322 1222 23567778889999999999 66666666665555554444
Q ss_pred eeEEeecc
Q 029119 186 LFVLSSNT 193 (198)
Q Consensus 186 ~~vl~sN~ 193 (198)
|-+.+||+
T Consensus 179 ~~~~~~~v 186 (225)
T KOG3134|consen 179 SCYQTSRV 186 (225)
T ss_pred hHHHHHHH
Confidence 44444443
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=90.29 E-value=0.12 Score=34.15 Aligned_cols=30 Identities=40% Similarity=0.877 Sum_probs=22.3
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
+|+|-+||+..+.+ ...+. -....||+|+.
T Consensus 5 ey~C~~Cg~~fe~~-~~~~~--~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVL-QKMSD--DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEE-EecCC--CCCCCCCCCCC
Confidence 58999999987765 33332 25678999997
No 11
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=90.18 E-value=1.6 Score=37.84 Aligned_cols=46 Identities=24% Similarity=0.595 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhccCCCCch-hhhhheeEEeeccccc
Q 029119 151 FKDFLLAVLISSYFKIFLVAMMVWNFPSSV-IYIIDLFVLSSNTVAL 196 (198)
Q Consensus 151 ~~~ll~alllSs~~KLF~ilmlIW~yd~s~-~~~i~~~vl~sN~~Al 196 (198)
..-++.|.++|++..+|.+.|+.|+|..+. ...|++...+.|...+
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 446889999999999999999999998654 4588888888876543
No 12
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=89.63 E-value=0.29 Score=37.80 Aligned_cols=52 Identities=29% Similarity=0.613 Sum_probs=34.1
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccccccccccchhHHHHHHHHhcC--cchheeeecccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLIDLILHK--PQAYRHLLYNVL 67 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k--~~ayRHllfN~~ 67 (198)
.++|.+||+.-. .|.+..-| .||+|+..+ .-.+++-...+ |-.|||++|=..
T Consensus 42 ~~~C~~Cg~~~~----~~~SCk~R--~CP~C~~~~--------~~~W~~~~~~~ll~~~y~HvVFTlP 95 (111)
T PF14319_consen 42 RYRCEDCGHEKI----VYNSCKNR--HCPSCQAKA--------TEQWIEKQREDLLPVPYFHVVFTLP 95 (111)
T ss_pred eeecCCCCceEE----ecCcccCc--CCCCCCChH--------HHHHHHHHHhhCCCCCeEEEEEcCc
Confidence 578999998752 25444334 899999753 23444433333 578999999763
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.46 E-value=0.16 Score=29.44 Aligned_cols=24 Identities=42% Similarity=0.796 Sum_probs=17.8
Q ss_pred CCccccccCcccccceeeecCCceEeecCCCccc
Q 029119 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
|+..|.+||++++. .-.-|++||+
T Consensus 1 m~~~Cp~Cg~~~~~----------~~~fC~~CG~ 24 (26)
T PF13248_consen 1 MEMFCPNCGAEIDP----------DAKFCPNCGA 24 (26)
T ss_pred CcCCCcccCCcCCc----------ccccChhhCC
Confidence 56789999997644 2347999986
No 14
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=88.57 E-value=0.26 Score=30.33 Aligned_cols=25 Identities=28% Similarity=0.826 Sum_probs=16.8
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
|+|-+||+.++ + -..+. .+|++||.
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 68999999988 2 22333 38999985
No 15
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=88.42 E-value=0.16 Score=34.33 Aligned_cols=28 Identities=32% Similarity=0.863 Sum_probs=19.9
Q ss_pred CCccccccCcccccceeeecCCceEeecCCCccc
Q 029119 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
++|+|..||..++.+ . .-+--.||.||.
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 16
>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=87.52 E-value=0.25 Score=35.25 Aligned_cols=36 Identities=33% Similarity=0.905 Sum_probs=24.6
Q ss_pred CccccccCcccccceee--ecCCceEeecCCCccc---cccc
Q 029119 2 EYRCVKCGFRIKTLFVQ--YSPGNIRLMKCENCRA---VADE 38 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~--y~~~~i~l~~C~~C~~---~~Dk 38 (198)
.+-|-.|+++....+.+ |.+|. .+.+||+|++ +||.
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 46799999998887765 56654 8999999986 5664
No 17
>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=86.46 E-value=0.26 Score=30.46 Aligned_cols=32 Identities=25% Similarity=0.544 Sum_probs=23.6
Q ss_pred CccccccCcccccceeeecCCceEeecCCCcccccccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE 41 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE 41 (198)
.++|..||+-.+. .-....||.|+...+++.+
T Consensus 2 ~~~C~~CG~i~~g--------~~~p~~CP~Cg~~~~~F~~ 33 (34)
T cd00729 2 VWVCPVCGYIHEG--------EEAPEKCPICGAPKEKFEE 33 (34)
T ss_pred eEECCCCCCEeEC--------CcCCCcCcCCCCchHHcEE
Confidence 4789999976432 1134599999999888765
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=84.09 E-value=0.62 Score=32.25 Aligned_cols=30 Identities=33% Similarity=0.688 Sum_probs=24.0
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (198)
-.|-.||++.+. +.+-+.-.|++||...|.
T Consensus 29 q~C~~CG~~~~~------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 29 QTCPRCGHRNKK------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred cCccCccccccc------ccccceEEcCCCCCEECc
Confidence 469999999877 335588899999988775
No 19
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=83.31 E-value=1 Score=39.82 Aligned_cols=62 Identities=23% Similarity=0.444 Sum_probs=29.0
Q ss_pred ccccccCcccccceeee---cCCceEeecCCCccc---cccccccc-------hhHHHHHHHHhcCcchheeeecc
Q 029119 3 YRCVKCGFRIKTLFVQY---SPGNIRLMKCENCRA---VADEYIEC-------EIMILLIDLILHKPQAYRHLLYN 65 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y---~~~~i~l~~C~~C~~---~~DkYiE~-------d~~i~~iDl~L~k~~ayRHllfN 65 (198)
-.|..||+.-..-+.-+ ..+..|+..|++|+. ..|.-..- |.-.+-+|++..+ +-|+..=+|
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 46999999876666555 456899999999994 55522221 2334555665533 335554444
No 20
>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=82.09 E-value=0.48 Score=29.62 Aligned_cols=28 Identities=32% Similarity=0.669 Sum_probs=13.1
Q ss_pred CCccccccCccc--ccceeeecCCceEeecCCCcc
Q 029119 1 MEYRCVKCGFRI--KTLFVQYSPGNIRLMKCENCR 33 (198)
Q Consensus 1 ~~~~Ci~C~~~v--~~l~~~y~~~~i~l~~C~~C~ 33 (198)
+.+.|.|||.+- +-|++ +..+..|.+|.
T Consensus 2 ~~~~C~eC~~~f~dSyL~~-----~F~~~VCD~CR 31 (34)
T PF01286_consen 2 DYPKCDECGKPFMDSYLLN-----NFDLPVCDKCR 31 (34)
T ss_dssp S-EE-TTT--EES-SSCCC-----CTS-S--TTT-
T ss_pred CCchHhHhCCHHHHHHHHH-----hCCcccccccc
Confidence 358999999984 33433 44566888885
No 21
>PF12773 DZR: Double zinc ribbon
Probab=82.03 E-value=0.71 Score=30.01 Aligned_cols=30 Identities=27% Similarity=0.507 Sum_probs=21.0
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY 39 (198)
-.|.+||++++ ........|++|+...++-
T Consensus 13 ~fC~~CG~~l~-------~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 13 KFCPHCGTPLP-------PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cCChhhcCChh-------hccCCCCCCcCCcCCCcCC
Confidence 46889999887 2222455799999876654
No 22
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.25 E-value=0.89 Score=37.31 Aligned_cols=44 Identities=25% Similarity=0.462 Sum_probs=31.1
Q ss_pred ccccccCccc-ccceeee-cCCc-e-EeecCCCccccccccccchhHH
Q 029119 3 YRCVKCGFRI-KTLFVQY-SPGN-I-RLMKCENCRAVADEYIECEIMI 46 (198)
Q Consensus 3 ~~Ci~C~~~v-~~l~~~y-~~~~-i-~l~~C~~C~~~~DkYiE~d~~i 46 (198)
+.|.+||+|- .-.=.+| ++|| + |.-+|++||.-.--|=+.+.++
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 4689999999888887777654
No 23
>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=81.11 E-value=0.8 Score=34.73 Aligned_cols=29 Identities=24% Similarity=0.780 Sum_probs=22.8
Q ss_pred CCccccccCcccccceeeecCCceEeecCCCcc
Q 029119 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCR 33 (198)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~ 33 (198)
+.+.|.+||..|.- .++|+-.-..||+|-
T Consensus 3 ~~F~C~~CG~~V~p----~~~g~~~RNHCP~CL 31 (92)
T PF12647_consen 3 ESFTCVHCGLTVSP----LAAGSAHRNHCPSCL 31 (92)
T ss_pred cccCccccCCCccc----CCCCCCccCcCcccc
Confidence 46899999999976 356666667999995
No 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=80.20 E-value=0.91 Score=36.36 Aligned_cols=33 Identities=18% Similarity=0.463 Sum_probs=21.9
Q ss_pred ccccccCcccccceeee-----c----CCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQY-----S----PGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y-----~----~~~i~l~~C~~C~~~ 35 (198)
-+|+.||.+...+=++- . ..+-+...|++||++
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 48999999865543220 0 113358899999986
No 25
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=77.38 E-value=0.92 Score=25.72 Aligned_cols=22 Identities=32% Similarity=0.721 Sum_probs=15.2
Q ss_pred cccccCcccccceeeecCCceEeecCCCcccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.|.+||++++. . -..|++||..
T Consensus 1 ~Cp~CG~~~~~------~----~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIED------D----AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCC------c----CcchhhhCCc
Confidence 38899998854 1 2259999863
No 26
>PRK12495 hypothetical protein; Provisional
Probab=76.86 E-value=1.3 Score=38.66 Aligned_cols=29 Identities=28% Similarity=0.521 Sum_probs=22.4
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (198)
...|-.||.|++. | +| .+.|+.|+++++.
T Consensus 42 a~hC~~CG~PIpa----~-pG---~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 42 NAHCDECGDPIFR----H-DG---QEFCPTCQQPVTE 70 (226)
T ss_pred hhhcccccCcccC----C-CC---eeECCCCCCcccc
Confidence 3579999999993 4 44 3579999998773
No 27
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=76.75 E-value=1.4 Score=29.52 Aligned_cols=32 Identities=25% Similarity=0.537 Sum_probs=26.5
Q ss_pred CccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
..+|.+|+..-...+++...+. .+.|..|+-.
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 5789999999999999887765 5789999853
No 28
>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=75.86 E-value=1.4 Score=37.89 Aligned_cols=38 Identities=24% Similarity=0.624 Sum_probs=25.0
Q ss_pred ccccCcccccceeee-------------cCCceEeecCCCccccc--cccccc
Q 029119 5 CVKCGFRIKTLFVQY-------------SPGNIRLMKCENCRAVA--DEYIEC 42 (198)
Q Consensus 5 Ci~C~~~v~~l~~~y-------------~~~~i~l~~C~~C~~~~--DkYiE~ 42 (198)
|..||.|.+.++... =|+.+.++.|+.||+.= .+.++.
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 344444
No 29
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=75.84 E-value=2.5 Score=26.71 Aligned_cols=27 Identities=22% Similarity=0.859 Sum_probs=20.5
Q ss_pred ccccCcccccceeeecCCceEeecCCCcccc
Q 029119 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 5 Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
|..|++....... +.+.+..|++|+.+
T Consensus 2 CP~C~~~l~~~~~----~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 2 CPRCGTELEPVRL----GDVEIDVCPSCGGI 28 (41)
T ss_pred cCCCCcccceEEE----CCEEEEECCCCCeE
Confidence 8889987554322 56999999999974
No 30
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=74.13 E-value=1.1 Score=34.89 Aligned_cols=37 Identities=24% Similarity=0.460 Sum_probs=25.8
Q ss_pred CCccccccCcccccceeeecCCceEeecCCCccccccccccch
Q 029119 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (198)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d 43 (198)
|..+|+.||+.-+. .+..-+.-||+||.--=+|+--|
T Consensus 1 MpH~CtrCG~vf~~------g~~~il~GCp~CG~nkF~yv~~e 37 (112)
T COG3364 1 MPHQCTRCGEVFDD------GSEEILSGCPKCGCNKFLYVPEE 37 (112)
T ss_pred CCceeccccccccc------ccHHHHccCccccchheEecccc
Confidence 67899999986433 13445678999997655666554
No 31
>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=73.14 E-value=1.6 Score=25.50 Aligned_cols=22 Identities=23% Similarity=0.618 Sum_probs=16.6
Q ss_pred cccccCcccccceeeecCCceEeecCCCcccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.|-+|++.|+. .-..||+||..
T Consensus 2 ~CP~C~~~V~~----------~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPE----------SAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchh----------hcCcCCCCCCC
Confidence 58999999855 34479999853
No 32
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=71.99 E-value=4.4 Score=36.87 Aligned_cols=63 Identities=16% Similarity=0.382 Sum_probs=40.6
Q ss_pred ccccccCcccccceeeecC--CceEeecCCCcccc---c----ccccc---chhHHHHHHHHhcCcchheeeeccc
Q 029119 3 YRCVKCGFRIKTLFVQYSP--GNIRLMKCENCRAV---A----DEYIE---CEIMILLIDLILHKPQAYRHLLYNV 66 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~--~~i~l~~C~~C~~~---~----DkYiE---~d~~i~~iDl~L~k~~ayRHllfN~ 66 (198)
-.|.+||..-+--|-...+ ..+|.+.|++|+.- . |+.+| -|.--+.+|++..+ +-|++.=+|-
T Consensus 227 ~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~p~adDlatL~LDl~a~e-~Gy~r~~~Np 301 (309)
T PRK03564 227 VKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQEKDPKVEAVADDLASLVLDARMEQ-EGFARSSINP 301 (309)
T ss_pred ccCCCCCCCCceeeeeecCCCcceEeeecccccccceecccccCCCCCcchhHHhhhHhHHHHHh-cCCCCCCCCc
Confidence 4699999863333332322 47899999999953 2 22221 14456788888855 5788887775
No 33
>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=71.15 E-value=3.2 Score=26.89 Aligned_cols=29 Identities=24% Similarity=0.606 Sum_probs=18.9
Q ss_pred CCccccccCcccccceeeecCCceEeecCCCccc
Q 029119 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
++++|..||+. .. |.-.+-+.-+|.+|++
T Consensus 17 ~g~~CP~Cg~~--~~---~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGST--KH---YRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCe--ee---EEeCCCCeEECCCCCC
Confidence 46789999987 22 2222246678988875
No 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=70.76 E-value=1.9 Score=26.54 Aligned_cols=35 Identities=20% Similarity=0.481 Sum_probs=19.1
Q ss_pred CCccccccCcccccceeeecCCceEeecCCCccccc
Q 029119 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (198)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (198)
|...|.+||+...-==.+...+. ..-.|++|+...
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
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=70.68 E-value=2.2 Score=26.48 Aligned_cols=30 Identities=17% Similarity=0.405 Sum_probs=14.7
Q ss_pred cccccCcccccceeeecCCceEeecCCCcccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
-|.+||+|++.- .-..++-.-..|++|+.+
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 36
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=70.29 E-value=1.1 Score=30.07 Aligned_cols=33 Identities=18% Similarity=0.486 Sum_probs=23.5
Q ss_pred CccccccCccc-ccceeeecCCceEeecCCCcccc
Q 029119 2 EYRCVKCGFRI-KTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 2 ~~~Ci~C~~~v-~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.-+|-.|+..+ ++.+.+-..+ -++..||+||++
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~-~~i~~Cp~CgRi 55 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKG-DEIVFCPNCGRI 55 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcC-CCeEECcCCCcc
Confidence 34788899885 4555555444 478899999985
No 37
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.28 E-value=0.86 Score=33.61 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=23.0
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (198)
.|+|.|||+.-+-+- ..+.+ -+|.|+.|+....|
T Consensus 12 ~Y~c~~cg~~~dvvq-~~~dd--plt~ce~c~a~~kk 45 (82)
T COG2331 12 SYECTECGNRFDVVQ-AMTDD--PLTTCEECGARLKK 45 (82)
T ss_pred EEeecccchHHHHHH-hcccC--ccccChhhChHHHH
Confidence 489999999844331 12222 68899999976544
No 38
>PRK00420 hypothetical protein; Validated
Probab=69.57 E-value=2.6 Score=32.94 Aligned_cols=28 Identities=21% Similarity=0.317 Sum_probs=20.2
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (198)
..|..||.|.-.+ +++ -..||+||++.+
T Consensus 24 ~~CP~Cg~pLf~l---k~g----~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFEL---KDG----EVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceec---CCC----ceECCCCCCeee
Confidence 4799999997655 333 348999998543
No 39
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=68.43 E-value=2.2 Score=25.91 Aligned_cols=32 Identities=25% Similarity=0.546 Sum_probs=22.0
Q ss_pred CccccccCcccccceeeecCCceEeecCCCcccccccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE 41 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE 41 (198)
.++|-.||.-.+.- ..-..||.|+...+.+..
T Consensus 1 ~~~C~~CGy~y~~~--------~~~~~CP~Cg~~~~~F~~ 32 (33)
T cd00350 1 KYVCPVCGYIYDGE--------EAPWVCPVCGAPKDKFEK 32 (33)
T ss_pred CEECCCCCCEECCC--------cCCCcCcCCCCcHHHcEE
Confidence 37899999763321 145589999987776543
No 40
>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=68.39 E-value=2.3 Score=32.98 Aligned_cols=28 Identities=25% Similarity=0.561 Sum_probs=20.7
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (198)
-+|.+||++---| |-.-..||+||...+
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 41
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=67.91 E-value=2 Score=35.79 Aligned_cols=33 Identities=15% Similarity=0.460 Sum_probs=21.7
Q ss_pred ccccccCcccccceeeecC---------CceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSP---------GNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~---------~~i~l~~C~~C~~~ 35 (198)
-+|.+||.+...+.+.=-. ..-....|++|+++
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 5899999997665332100 12246779999985
No 42
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=66.39 E-value=3.7 Score=28.22 Aligned_cols=27 Identities=26% Similarity=0.655 Sum_probs=19.7
Q ss_pred CCccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
++.+|..||.+++. ++ -+..|+.|+.+
T Consensus 4 ~~~~C~~Cg~~~~~------~d--DiVvCp~Cgap 30 (54)
T PF14446_consen 4 EGCKCPVCGKKFKD------GD--DIVVCPECGAP 30 (54)
T ss_pred cCccChhhCCcccC------CC--CEEECCCCCCc
Confidence 35789999999843 12 45689999865
No 43
>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=66.19 E-value=3 Score=38.50 Aligned_cols=23 Identities=35% Similarity=0.858 Sum_probs=18.2
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
|+|-+||+..+.- +-+||.|++.
T Consensus 1 ~~c~~cg~~~~~~----------~g~cp~c~~w 23 (372)
T cd01121 1 YVCSECGYVSPKW----------LGKCPECGEW 23 (372)
T ss_pred CCCCCCCCCCCCc----------cEECcCCCCc
Confidence 7899999987663 3479999864
No 44
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=66.05 E-value=2.2 Score=34.30 Aligned_cols=27 Identities=26% Similarity=0.566 Sum_probs=19.0
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
++|++||+--+. ....-|.-||+||.-
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 45
>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=66.03 E-value=2.2 Score=30.63 Aligned_cols=25 Identities=32% Similarity=0.898 Sum_probs=18.5
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
++| .||... |++++-+-.+| .||+.
T Consensus 4 frC-~Cgr~l------ya~e~~kTkkC-~CG~~ 28 (68)
T PF09082_consen 4 FRC-DCGRYL------YAKEGAKTKKC-VCGKT 28 (68)
T ss_dssp EEE-TTS--E------EEETT-SEEEE-TTTEE
T ss_pred EEe-cCCCEE------EecCCcceeEe-cCCCe
Confidence 578 799876 88888899999 99975
No 46
>PF14353 CpXC: CpXC protein
Probab=64.34 E-value=5.3 Score=30.84 Aligned_cols=56 Identities=20% Similarity=0.551 Sum_probs=36.7
Q ss_pred ccccccCcc-cccceeeecC------------CceEeecCCCccccccccccchhHHHHHHHHhcCcchheeeeccccc
Q 029119 3 YRCVKCGFR-IKTLFVQYSP------------GNIRLMKCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNVLN 68 (198)
Q Consensus 3 ~~Ci~C~~~-v~~l~~~y~~------------~~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayRHllfN~~~ 68 (198)
-.|.+||++ -..+|+.... |.+-.-.||+||+.. ++++. ++-+.++. +-++++..+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~--~~~~p-------~lY~D~~~-~~~i~~~P~ 70 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKF--RLEYP-------LLYHDPEK-KFMIYYFPD 70 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCce--ecCCC-------EEEEcCCC-CEEEEEcCC
Confidence 469999998 4566665542 566788999999876 46665 23344443 455556644
No 47
>PF14149 YhfH: YhfH-like protein
Probab=63.91 E-value=1.1 Score=28.51 Aligned_cols=24 Identities=29% Similarity=0.832 Sum_probs=16.7
Q ss_pred ccccccCcccccceeeecCCceEeecCCCc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENC 32 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C 32 (198)
..|.+||..+++-..-|++ .|++|
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 4688888887777666665 46665
No 48
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=63.29 E-value=5 Score=35.94 Aligned_cols=32 Identities=31% Similarity=0.813 Sum_probs=23.0
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (198)
+.+|.+||. +.+-.+|+.|. ..|.+||-+.++
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 35656676653 589999986543
No 49
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=62.18 E-value=3.8 Score=28.67 Aligned_cols=20 Identities=25% Similarity=0.544 Sum_probs=15.2
Q ss_pred eEeecCCCccc-----------cccccccchh
Q 029119 24 IRLMKCENCRA-----------VADEYIECEI 44 (198)
Q Consensus 24 i~l~~C~~C~~-----------~~DkYiE~d~ 44 (198)
++ ++|+.||. +.|||..|-.
T Consensus 16 Lk-e~Cp~CG~~t~~~~PprFSPeD~y~kYR~ 46 (59)
T COG2260 16 LK-EKCPVCGGDTKVPHPPRFSPEDKYGKYRR 46 (59)
T ss_pred ec-ccCCCCCCccccCCCCCCCccchHHHHHH
Confidence 34 68999993 5799988764
No 50
>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=61.33 E-value=8.8 Score=34.84 Aligned_cols=62 Identities=16% Similarity=0.401 Sum_probs=39.6
Q ss_pred ccccccCcccccc-eeeec----CCceEeecCCCcccc---ccc----ccc---chhHHHHHHHHhcCcchheeeeccc
Q 029119 3 YRCVKCGFRIKTL-FVQYS----PGNIRLMKCENCRAV---ADE----YIE---CEIMILLIDLILHKPQAYRHLLYNV 66 (198)
Q Consensus 3 ~~Ci~C~~~v~~l-~~~y~----~~~i~l~~C~~C~~~---~Dk----YiE---~d~~i~~iDl~L~k~~ayRHllfN~ 66 (198)
-.|.+||+. +.+ |-... .+.+|.+.|++|+.. .|. -+| -|.--+.+|++..+ +-|+..=+|-
T Consensus 225 ~~C~~Cg~~-~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~~~adDlaSL~LD~~a~e-~Gy~r~~~np 301 (305)
T TIGR01562 225 VKCSHCEES-KHLAYLSLEHDAEKAVLKAETCDSCQGYLKILYQEKDPHADAVADDLASLALDMRMAE-DGYLRRSPNP 301 (305)
T ss_pred ccCCCCCCC-CceeeEeecCCCCCcceEEeeccccccchhhhccccCCccCchHHHHhhhHhhHHHHh-cCCCCCCCCc
Confidence 469999997 334 43332 246899999999953 221 111 24556788888865 5688766663
No 51
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=61.26 E-value=4.7 Score=31.15 Aligned_cols=53 Identities=19% Similarity=0.337 Sum_probs=34.3
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccc-----cccccchhHHHHHHHHhcC
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA-----DEYIECEIMILLIDLILHK 55 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~-----DkYiE~d~~i~~iDl~L~k 55 (198)
+-|..|||..-+.-+.=...++-...|++|+.-. .=.-+.|..-.|+|+-+--
T Consensus 23 FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wvDay~eg 80 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVYSAWVDAYLEG 80 (104)
T ss_pred EecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHHHHHHHHHHhc
Confidence 5699999985543333455678889999999521 1122345556778876643
No 52
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=60.86 E-value=3.4 Score=36.39 Aligned_cols=33 Identities=24% Similarity=0.370 Sum_probs=21.1
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.+|+.||...+.-...-...+..+.+|++|+..
T Consensus 123 ~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 155 (250)
T COG0846 123 VRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP 155 (250)
T ss_pred eEeCCCcCccchhhhhhhcccCCCCcCccCCCc
Confidence 579999987653332112223356789999986
No 53
>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=60.67 E-value=4.1 Score=38.52 Aligned_cols=24 Identities=29% Similarity=0.668 Sum_probs=19.2
Q ss_pred CccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.|+|-+||...+.. .-+||.|++.
T Consensus 7 ~y~C~~Cg~~~~~~----------~g~Cp~C~~w 30 (454)
T TIGR00416 7 KFVCQHCGADSPKW----------QGKCPACHAW 30 (454)
T ss_pred eEECCcCCCCCccc----------cEECcCCCCc
Confidence 48999999987764 3479999864
No 54
>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=60.62 E-value=6.1 Score=22.84 Aligned_cols=24 Identities=29% Similarity=0.638 Sum_probs=14.1
Q ss_pred ccccCcccccceeeecCCceEeecCCCccc
Q 029119 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 5 Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
|+.||.++..- +.-..-.||+||.
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 77788775431 1112337999984
No 55
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=59.91 E-value=4.1 Score=25.36 Aligned_cols=34 Identities=24% Similarity=0.472 Sum_probs=19.2
Q ss_pred CCccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 1 MEYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 1 ~~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
|.-.|.+|++.-+-=-.+-.. .-+.-+|++|+++
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 56
>PRK11823 DNA repair protein RadA; Provisional
Probab=58.47 E-value=4.7 Score=37.97 Aligned_cols=29 Identities=31% Similarity=0.740 Sum_probs=20.9
Q ss_pred CccccccCcccccceeeecCCceEeecCCCcccccccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE 41 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE 41 (198)
.|+|-+||+..+.. .-+||.|++. +.+.|
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 58999999987764 2379999863 33444
No 57
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.04 E-value=3.2 Score=33.24 Aligned_cols=36 Identities=22% Similarity=0.412 Sum_probs=20.9
Q ss_pred CccccccCccccccee-eecCCceEeecCCCccccccc
Q 029119 2 EYRCVKCGFRIKTLFV-QYSPGNIRLMKCENCRAVADE 38 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~-~y~~~~i~l~~C~~C~~~~Dk 38 (198)
.|+|.+||.....+=- .+.. .-..-.||+||.....
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d-~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLD-MDGTFTCPRCGEELEE 135 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcC-CCCcEECCCCCCEEEE
Confidence 5899999977543210 1101 1122679999986543
No 58
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=57.26 E-value=7.8 Score=26.30 Aligned_cols=40 Identities=18% Similarity=0.385 Sum_probs=31.4
Q ss_pred cccccCcccccceeeecCCceEeecCCCccccccccccch
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d 43 (198)
.|..||+++.-+-..-.++.--.+.|+.|.++-.=.++.|
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d 41 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVTVD 41 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEEEC
Confidence 5999999998876666666678899999999866555554
No 59
>PHA02942 putative transposase; Provisional
Probab=57.19 E-value=5.8 Score=36.77 Aligned_cols=29 Identities=28% Similarity=0.728 Sum_probs=21.0
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (198)
-.|-.||+..+.+ ..|.-.|++||...|.
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 60
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=56.31 E-value=7 Score=27.51 Aligned_cols=38 Identities=26% Similarity=0.724 Sum_probs=23.8
Q ss_pred ccccccCccc--ccceeee---cCCceEeecCCCccccccccc
Q 029119 3 YRCVKCGFRI--KTLFVQY---SPGNIRLMKCENCRAVADEYI 40 (198)
Q Consensus 3 ~~Ci~C~~~v--~~l~~~y---~~~~i~l~~C~~C~~~~DkYi 40 (198)
++|+.||..+ .+-|.++ .=|+..+..|.+|.+....|.
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 4444444 124456666666666666653
No 61
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=56.08 E-value=6.1 Score=24.55 Aligned_cols=32 Identities=28% Similarity=0.628 Sum_probs=19.6
Q ss_pred CCccccccCcc--cccceeeecCCceEeecCCCcccc
Q 029119 1 MEYRCVKCGFR--IKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 1 ~~~~Ci~C~~~--v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
|.-.|.+|+.. ++. .+- ++.-+--+|++|++.
T Consensus 1 M~i~Cp~C~~~y~i~d--~~i-p~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDD--EKI-PPKGRKVRCSKCGHV 34 (36)
T ss_pred CEEECCCCCCEEeCCH--HHC-CCCCcEEECCCCCCE
Confidence 34578899876 221 111 234467789999974
No 62
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=53.85 E-value=7.8 Score=29.24 Aligned_cols=28 Identities=29% Similarity=0.618 Sum_probs=20.1
Q ss_pred CCccccccCcc-cccceeeecCCceEeecCCCcccc
Q 029119 1 MEYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 1 ~~~~Ci~C~~~-v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
+.|.|..||.+ |+. -+. -+=+|++|+..
T Consensus 34 ~~~~Cp~C~~~~VkR----~a~---GIW~C~kCg~~ 62 (89)
T COG1997 34 AKHVCPFCGRTTVKR----IAT---GIWKCRKCGAK 62 (89)
T ss_pred cCCcCCCCCCcceee----ecc---CeEEcCCCCCe
Confidence 36899999998 333 333 46789999963
No 63
>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=53.78 E-value=4.3 Score=30.02 Aligned_cols=34 Identities=26% Similarity=0.619 Sum_probs=25.8
Q ss_pred cccccCcccc--cceeeecCCceEeecCCCcccccc
Q 029119 4 RCVKCGFRIK--TLFVQYSPGNIRLMKCENCRAVAD 37 (198)
Q Consensus 4 ~Ci~C~~~v~--~l~~~y~~~~i~l~~C~~C~~~~D 37 (198)
.|-|||.|++ .-++.--.|.-|.-=|+-|..++.
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 455555555667788999998865
No 64
>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=53.27 E-value=5 Score=31.53 Aligned_cols=25 Identities=32% Similarity=0.708 Sum_probs=19.1
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
-+|.||+++.+-|= |...|..|+++
T Consensus 70 V~CP~C~K~TKmLG--------r~D~CM~C~~p 94 (114)
T PF11023_consen 70 VECPNCGKQTKMLG--------RVDACMHCKEP 94 (114)
T ss_pred eECCCCCChHhhhc--------hhhccCcCCCc
Confidence 36999999987761 33589999986
No 65
>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=53.25 E-value=4.4 Score=25.08 Aligned_cols=31 Identities=23% Similarity=0.491 Sum_probs=20.0
Q ss_pred ccccCcccccceeeecCCceEeecCCCcccccc
Q 029119 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (198)
Q Consensus 5 Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (198)
|.+|+..-..++++-.+++ .+.|..|+-.-.
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 8899999999999887664 447988875433
No 66
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=51.41 E-value=9.5 Score=34.70 Aligned_cols=29 Identities=28% Similarity=0.528 Sum_probs=25.1
Q ss_pred cccccCcccccceeeecCCceEeecCCCcccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.|.+|..+-+.+..+|+.| -|.|+.||.+
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 5999999888999999886 4799999964
No 67
>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=50.64 E-value=4.8 Score=27.30 Aligned_cols=34 Identities=21% Similarity=0.461 Sum_probs=26.3
Q ss_pred cccccCcccccceeeecCCceEeecCCCcccccccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY 39 (198)
+|.+||..-..++++..++ .-+.|..|+-.--||
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 68
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=50.55 E-value=7.3 Score=30.23 Aligned_cols=26 Identities=23% Similarity=0.636 Sum_probs=16.4
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.+|-+||+..+. +......||+||..
T Consensus 72 ~~C~~Cg~~~~~-------~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 72 LECKDCSHVFKP-------NALDYGVCEKCHSK 97 (117)
T ss_pred EEhhhCCCcccc-------CCccCCcCcCCCCC
Confidence 479999955332 11233469999975
No 69
>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=49.64 E-value=8.2 Score=31.00 Aligned_cols=28 Identities=18% Similarity=0.129 Sum_probs=20.9
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (198)
..+|.+||++---| |-.-..||+||...
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 70
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=49.02 E-value=12 Score=26.12 Aligned_cols=38 Identities=32% Similarity=0.870 Sum_probs=21.2
Q ss_pred CccccccCcccccc--eeeec-C--CceEeecCCCcccccccc
Q 029119 2 EYRCVKCGFRIKTL--FVQYS-P--GNIRLMKCENCRAVADEY 39 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l--~~~y~-~--~~i~l~~C~~C~~~~DkY 39 (198)
.+.|+-||.++... +.++. | |..-+..|.+|.+..-.|
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~~~Y 49 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQSNPY 49 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcCCce
Confidence 46799999886421 33331 1 233355566666655555
No 71
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=48.91 E-value=9.2 Score=29.55 Aligned_cols=26 Identities=23% Similarity=0.604 Sum_probs=16.9
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.+|-+||+..+.. ......||+||..
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 72
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=47.81 E-value=11 Score=33.70 Aligned_cols=37 Identities=27% Similarity=0.696 Sum_probs=26.7
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccccc-cccccch
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA-DEYIECE 43 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~-DkYiE~d 43 (198)
++.|-|||.. .+-++|..|. ..|..||-+. |++|..+
T Consensus 1 ~~~CpeCg~~--~~~~d~~~ge---~VC~~CG~Vi~~~~id~g 38 (285)
T COG1405 1 VMSCPECGST--NIITDYERGE---IVCADCGLVLEDSLIDPG 38 (285)
T ss_pred CCCCCCCCCc--cceeeccCCe---EEeccCCEEeccccccCC
Confidence 3689999998 6667777653 5799999854 4466555
No 73
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=47.21 E-value=9 Score=36.58 Aligned_cols=23 Identities=35% Similarity=0.853 Sum_probs=17.6
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
.|+|.|||..-+. =+-+||+|+.
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 3448999994
No 74
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=47.18 E-value=16 Score=31.02 Aligned_cols=35 Identities=20% Similarity=0.583 Sum_probs=26.6
Q ss_pred cccccCcccccceeeecCCceEeecCCCccc--ccccccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA--VADEYIE 41 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~--~~DkYiE 41 (198)
.|-+|+.|=..|-++ +.+-..+|..||. .+|++-+
T Consensus 100 ~C~~C~~pdT~l~k~---~~~~~l~C~aCGa~~~v~~~~~ 136 (201)
T PRK12336 100 ICSECGLPDTRLVKE---DRVLMLRCDACGAHRPVKKRKA 136 (201)
T ss_pred ECCCCCCCCcEEEEc---CCeEEEEcccCCCCcccccccc
Confidence 599999998888654 4566789999996 4565544
No 75
>PRK07591 threonine synthase; Validated
Probab=46.76 E-value=9.3 Score=35.62 Aligned_cols=30 Identities=23% Similarity=0.635 Sum_probs=21.0
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccccccch
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d 43 (198)
.+|+.||+.- .++. . -.||.|+..-| ++||
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 6899999764 3332 2 57999998877 4444
No 76
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=46.72 E-value=12 Score=24.08 Aligned_cols=28 Identities=25% Similarity=0.538 Sum_probs=16.7
Q ss_pred cccccCcccccceeeecCCceEeecCCCcccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
-|.+||..+ +.+-..++ ..-.|++|+..
T Consensus 2 FCp~Cg~~l---~~~~~~~~-~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNML---IPKEGKEK-RRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCcc---ccccCCCC-CEEECCcCCCe
Confidence 489999965 22222222 25579999953
No 77
>PRK05978 hypothetical protein; Provisional
Probab=45.78 E-value=9.8 Score=31.11 Aligned_cols=27 Identities=30% Similarity=0.675 Sum_probs=19.8
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
-+|-+||+. .+|+.|-+ --..|+.||.
T Consensus 34 grCP~CG~G--~LF~g~Lk---v~~~C~~CG~ 60 (148)
T PRK05978 34 GRCPACGEG--KLFRAFLK---PVDHCAACGE 60 (148)
T ss_pred CcCCCCCCC--cccccccc---cCCCccccCC
Confidence 479999985 57777744 3357999996
No 78
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=45.47 E-value=9.7 Score=32.78 Aligned_cols=30 Identities=27% Similarity=0.664 Sum_probs=22.6
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccc----cccccccchh
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA----VADEYIECEI 44 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~----~~DkYiE~d~ 44 (198)
++| +||.+++. | ..|.+|+. .||-|.+--.
T Consensus 1 ~~C-rCG~~l~~------p-----~~Cl~Cg~~~av~~~vy~~~~r 34 (227)
T COG4031 1 LIC-RCGAELSS------P-----AFCLNCGRRHAVGCGVYVSESR 34 (227)
T ss_pred Ccc-ccCCcccc------c-----chhcccCCcceeEeeeeccccE
Confidence 589 99999864 3 47999997 4777777553
No 79
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=44.56 E-value=11 Score=29.06 Aligned_cols=25 Identities=16% Similarity=0.484 Sum_probs=15.6
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.+|-+||+..+. +. ....||+||..
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 12249999965
No 80
>PHA02768 hypothetical protein; Provisional
Probab=43.20 E-value=5.2 Score=27.58 Aligned_cols=40 Identities=33% Similarity=0.650 Sum_probs=23.1
Q ss_pred CccccccCccc---ccceeeecCCceEeecCCCcccc---ccccccc
Q 029119 2 EYRCVKCGFRI---KTLFVQYSPGNIRLMKCENCRAV---ADEYIEC 42 (198)
Q Consensus 2 ~~~Ci~C~~~v---~~l~~~y~~~~i~l~~C~~C~~~---~DkYiE~ 42 (198)
+|.|-+||..- ++|.+--...+ +--+|.+|++. --+|||.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~f~~~s~l~~~ 50 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRISLRTGEYIEI 50 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC-CcccCCcccceecccceeEEE
Confidence 57899999873 33322111112 34577888774 3566664
No 81
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=42.01 E-value=17 Score=33.73 Aligned_cols=32 Identities=25% Similarity=0.712 Sum_probs=24.2
Q ss_pred CccccccCcccccce---------eeec----CCceEeecCCCcc
Q 029119 2 EYRCVKCGFRIKTLF---------VQYS----PGNIRLMKCENCR 33 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~---------~~y~----~~~i~l~~C~~C~ 33 (198)
.-.|..||.+++.+. ..++ |+.+.+..|.+||
T Consensus 6 ~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cg 50 (355)
T COG1499 6 TILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCG 50 (355)
T ss_pred ccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCC
Confidence 357999999996443 2332 5689999999999
No 82
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.62 E-value=13 Score=29.63 Aligned_cols=34 Identities=21% Similarity=0.553 Sum_probs=18.5
Q ss_pred CccccccCcccccce------------eeecCCc-eEeecCCCcccc
Q 029119 2 EYRCVKCGFRIKTLF------------VQYSPGN-IRLMKCENCRAV 35 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~------------~~y~~~~-i~l~~C~~C~~~ 35 (198)
..+|-+||+..+.-- ..|.|+. -....||+||..
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 368999996532210 0122221 133569999975
No 83
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.29 E-value=16 Score=30.45 Aligned_cols=35 Identities=29% Similarity=0.769 Sum_probs=25.6
Q ss_pred ccccccCcccccceee--ecCCceEeecCCCccc---cccc
Q 029119 3 YRCVKCGFRIKTLFVQ--YSPGNIRLMKCENCRA---VADE 38 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~--y~~~~i~l~~C~~C~~---~~Dk 38 (198)
|.|--||++...-+.+ |.+|. .+-+|+.|+. +||.
T Consensus 80 yTCkvCntRs~ktisk~AY~~Gv-VivqC~gC~~~HliaDn 119 (165)
T KOG3277|consen 80 YTCKVCNTRSTKTISKQAYEKGV-VIVQCPGCKNHHLIADN 119 (165)
T ss_pred EEeeccCCccccccChhhhhCce-EEEECCCCccceeehhh
Confidence 7899999997655543 66655 6778999985 5664
No 84
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=40.81 E-value=15 Score=24.66 Aligned_cols=23 Identities=30% Similarity=0.681 Sum_probs=17.8
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
..||-.|+.+.+- +-+.|.+||.
T Consensus 14 k~ICrkC~ARnp~----------~A~~CRKCg~ 36 (48)
T PRK04136 14 KKICMRCNARNPW----------RATKCRKCGY 36 (48)
T ss_pred ccchhcccCCCCc----------cccccccCCC
Confidence 4689999887643 6778999985
No 85
>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=40.64 E-value=8.2 Score=29.66 Aligned_cols=25 Identities=24% Similarity=0.769 Sum_probs=14.6
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
-+|-+||+.-+- +..+ ..||+||..
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 1212 459999986
No 86
>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=39.99 E-value=17 Score=26.28 Aligned_cols=34 Identities=18% Similarity=0.311 Sum_probs=16.6
Q ss_pred ccccccCcccccceeee-----cCCceEeecCCCccccc
Q 029119 3 YRCVKCGFRIKTLFVQY-----SPGNIRLMKCENCRAVA 36 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y-----~~~~i~l~~C~~C~~~~ 36 (198)
-.|..|.++.+.-..+| ..+..+...||.|++.-
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHH
Confidence 35777777755444334 23466777888888764
No 87
>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=39.81 E-value=9.2 Score=22.81 Aligned_cols=27 Identities=26% Similarity=0.540 Sum_probs=13.8
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.-|-.||.|.... + .-.-.+|++|+..
T Consensus 4 rfC~~CG~~t~~~-----~-~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTKPA-----P-GGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEEE------S-SSS-EEESSSS-E
T ss_pred cccCcCCccccCC-----C-CcCEeECCCCcCE
Confidence 3588899997553 2 1245579999863
No 88
>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=39.16 E-value=38 Score=25.49 Aligned_cols=50 Identities=20% Similarity=0.289 Sum_probs=32.2
Q ss_pred ccccCc--cccccee---eecCC----ceEeecCCCccccccccccchhHHHHHHHHhc
Q 029119 5 CVKCGF--RIKTLFV---QYSPG----NIRLMKCENCRAVADEYIECEIMILLIDLILH 54 (198)
Q Consensus 5 Ci~C~~--~v~~l~~---~y~~~----~i~l~~C~~C~~~~DkYiE~d~~i~~iDl~L~ 54 (198)
|.-|+. ..++.-+ +|.+| .||-..|-.|.+--..|++-+.+--+=|.+++
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 2444444 44443 45666677777777889998877776665543
No 89
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=38.75 E-value=17 Score=29.24 Aligned_cols=24 Identities=29% Similarity=0.634 Sum_probs=17.2
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
..|-.||.|. |+ +.+. ..||.|+.
T Consensus 29 ~hCp~Cg~PL---F~-KdG~----v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPL---FR-KDGE----VFCPVCGY 52 (131)
T ss_pred hhCcccCCcc---ee-eCCe----EECCCCCc
Confidence 5799999995 55 3332 37999994
No 90
>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=37.94 E-value=38 Score=20.99 Aligned_cols=27 Identities=37% Similarity=0.849 Sum_probs=16.3
Q ss_pred ccccccCcccccceeee-cCCceEeecCCC
Q 029119 3 YRCVKCGFRIKTLFVQY-SPGNIRLMKCEN 31 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y-~~~~i~l~~C~~ 31 (198)
..|..||..| |--.| .+|.|+.-.|++
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 91
>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=37.77 E-value=5.2 Score=32.52 Aligned_cols=30 Identities=23% Similarity=0.477 Sum_probs=14.2
Q ss_pred ccccccCcccccce--eeecCCceEeecCCCccc
Q 029119 3 YRCVKCGFRIKTLF--VQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~--~~y~~~~i~l~~C~~C~~ 34 (198)
.+|.+|++..+.-. .....+ ...+|+.|+.
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 35777777543221 111111 2226777776
No 92
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=37.63 E-value=24 Score=29.68 Aligned_cols=41 Identities=24% Similarity=0.452 Sum_probs=31.3
Q ss_pred ccccccCc-ccccceeee-cCCceEeecCCCccccccccccch
Q 029119 3 YRCVKCGF-RIKTLFVQY-SPGNIRLMKCENCRAVADEYIECE 43 (198)
Q Consensus 3 ~~Ci~C~~-~v~~l~~~y-~~~~i~l~~C~~C~~~~DkYiE~d 43 (198)
.+|-+|+. |+.-=|++- +.+.+++..|.+|-+.-..|.+-|
T Consensus 1 miCq~CqqnpAti~~tkI~~~~k~e~~vCe~Ca~~~s~a~~~e 43 (176)
T COG3880 1 MICQNCQQNPATIHFTKIINGEKIELYVCETCAKPHSEAYDIE 43 (176)
T ss_pred CcchhhcCCcceEEEEEeecCCeeEeehhhcCCCchhhhccch
Confidence 37999999 777777665 567889999999988755555544
No 93
>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=37.59 E-value=24 Score=24.13 Aligned_cols=30 Identities=30% Similarity=0.700 Sum_probs=18.8
Q ss_pred CccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
...|.+||..+.- =.... | .+-.|+.||.-
T Consensus 2 ~~~CP~CG~~iev-~~~~~-G--eiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIEL-ENPEL-G--ELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEec-CCCcc-C--CEEeCCCCCCE
Confidence 4689999998632 11122 2 24489999963
No 94
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.36 E-value=20 Score=37.71 Aligned_cols=40 Identities=23% Similarity=0.482 Sum_probs=18.0
Q ss_pred ccccccCcccccceeeecCC-ceEeecCCCccccccccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPG-NIRLMKCENCRAVADEYIEC 42 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~-~i~l~~C~~C~~~~DkYiE~ 42 (198)
.+|.+||.+.+..|+=..=+ ...-..||+|+.....+-..
T Consensus 639 frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~~s~~ 679 (1121)
T PRK04023 639 RRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTPYSKR 679 (1121)
T ss_pred ccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCccceE
Confidence 35666666544443211100 00113577777765554433
No 95
>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=37.06 E-value=20 Score=24.42 Aligned_cols=30 Identities=23% Similarity=0.545 Sum_probs=17.3
Q ss_pred CccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
+.+|-+|++-.-.- ..|.. ---+||+|+.+
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 56888898764321 01221 12379999864
No 96
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=36.88 E-value=26 Score=26.50 Aligned_cols=28 Identities=25% Similarity=0.599 Sum_probs=21.0
Q ss_pred CccccccCcc-cccceeeecCCceEeecCCCccccc
Q 029119 2 EYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAVA 36 (198)
Q Consensus 2 ~~~Ci~C~~~-v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (198)
.|.|..||.+ ++.. ..-+=.|.+|++..
T Consensus 36 ~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~~ 64 (90)
T PRK03976 36 KHVCPVCGRPKVKRV-------GTGIWECRKCGAKF 64 (90)
T ss_pred CccCCCCCCCceEEE-------EEEEEEcCCCCCEE
Confidence 5889999876 4443 55678999999753
No 97
>PRK02935 hypothetical protein; Provisional
Probab=36.63 E-value=18 Score=28.23 Aligned_cols=24 Identities=29% Similarity=0.533 Sum_probs=17.9
Q ss_pred cccccCcccccceeeecCCceEeecCCCcccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.|.+|+++.+-|= |...|-.|+++
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 5888888887761 45578888875
No 98
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=36.30 E-value=16 Score=28.24 Aligned_cols=26 Identities=19% Similarity=0.630 Sum_probs=16.7
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVA 36 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (198)
-+|-+||+..+.- . ....||+||..-
T Consensus 71 ~~C~~Cg~~~~~~-------~-~~~~CP~Cgs~~ 96 (115)
T TIGR00100 71 CECEDCSEEVSPE-------I-DLYRCPKCHGIM 96 (115)
T ss_pred EEcccCCCEEecC-------C-cCccCcCCcCCC
Confidence 4799999654321 1 134699999753
No 99
>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=34.99 E-value=16 Score=32.78 Aligned_cols=21 Identities=33% Similarity=0.914 Sum_probs=16.7
Q ss_pred cccccCcccccceeeecCCceEeecCCCccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
.|-+||..|..+ -+.||+|+.
T Consensus 84 ~C~~CGa~V~~~----------e~~Cp~C~S 104 (314)
T PF09567_consen 84 KCNNCGANVSRL----------EESCPNCGS 104 (314)
T ss_pred hhccccceeeeh----------hhcCCCCCc
Confidence 699999999874 236999984
No 100
>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=34.88 E-value=17 Score=30.18 Aligned_cols=32 Identities=19% Similarity=0.347 Sum_probs=16.4
Q ss_pred cccccCcccccceee-----ecCCceEeecCCCcccc
Q 029119 4 RCVKCGFRIKTLFVQ-----YSPGNIRLMKCENCRAV 35 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~-----y~~~~i~l~~C~~C~~~ 35 (198)
.|.+|++|+..=|.. +++++-.-.-|.+||+.
T Consensus 41 ~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkp 77 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKP 77 (158)
T ss_pred HCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCC
Confidence 366666666544321 22333344556666653
No 101
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=34.68 E-value=18 Score=27.57 Aligned_cols=26 Identities=35% Similarity=0.998 Sum_probs=18.8
Q ss_pred CccccccCcccccceeeecCCceE-eecCCCccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIR-LMKCENCRA 34 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~-l~~C~~C~~ 34 (198)
.++|-.||..-.. +.|+ -+.||+|+.
T Consensus 58 Pa~CkkCGfef~~-------~~ik~pSRCP~CKS 84 (97)
T COG3357 58 PARCKKCGFEFRD-------DKIKKPSRCPKCKS 84 (97)
T ss_pred ChhhcccCccccc-------cccCCcccCCcchh
Confidence 4789999976433 3444 679999985
No 102
>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=34.06 E-value=22 Score=22.16 Aligned_cols=28 Identities=29% Similarity=0.457 Sum_probs=16.7
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
.+|..||+.-.-.|.--. .-.+|++||.
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 368889876443333222 3348999986
No 103
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=33.98 E-value=22 Score=28.42 Aligned_cols=30 Identities=30% Similarity=0.834 Sum_probs=18.4
Q ss_pred cccccCcccccceeeecCCceEeecCCCcccccc-ccccch
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD-EYIECE 43 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D-kYiE~d 43 (198)
+|-+||+-- |-|. ..|++|+.-.| +.+|..
T Consensus 31 kC~~CG~v~------~PPr----~~Cp~C~~~~~~E~vels 61 (140)
T COG1545 31 KCKKCGRVY------FPPR----AYCPKCGSETELEWVELS 61 (140)
T ss_pred EcCCCCeEE------cCCc----ccCCCCCCCCceEEEEeC
Confidence 577777642 2222 36777777766 777754
No 104
>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=33.58 E-value=16 Score=33.79 Aligned_cols=27 Identities=30% Similarity=0.781 Sum_probs=13.3
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
+.|-+||.+.-++. +|.. ..|++||..
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 4533 389999964
No 105
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=33.44 E-value=21 Score=28.12 Aligned_cols=29 Identities=21% Similarity=0.678 Sum_probs=18.9
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY 39 (198)
-.|-.|+++++..-..| .||+||..-.+-
T Consensus 71 ~~C~~C~~~~~~e~~~~--------~CP~C~s~~~~i 99 (115)
T COG0375 71 CWCLDCGQEVELEELDY--------RCPKCGSINLRI 99 (115)
T ss_pred EEeccCCCeecchhhee--------ECCCCCCCceEE
Confidence 36889988875532222 299999765543
No 106
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=33.22 E-value=15 Score=30.56 Aligned_cols=32 Identities=19% Similarity=0.429 Sum_probs=20.0
Q ss_pred CccccccCcccccceeeecCCceEeecCCCccccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE 38 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk 38 (198)
.|+|.+||.+.+.+=- .+. -=.||.||..--.
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 5899999977533210 111 2379999986544
No 107
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=32.64 E-value=34 Score=24.70 Aligned_cols=29 Identities=24% Similarity=0.576 Sum_probs=17.5
Q ss_pred cccccCcccccceeeecCCceEeecCCCccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
.|. ||......=+ .+.+.+++..|++|+-
T Consensus 15 ~c~-~g~~f~~~ST-~~~~~i~vdi~s~~HP 43 (72)
T PRK00019 15 TCS-CGNVFETRST-LGKDEINVDVCSKCHP 43 (72)
T ss_pred EEC-CCCEEEEeec-CCCCcEEEEeCCCCCC
Confidence 455 6665322111 2344699999999983
No 108
>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=32.25 E-value=11 Score=35.23 Aligned_cols=39 Identities=21% Similarity=0.439 Sum_probs=35.8
Q ss_pred cCCCccccccccccchhHHHHHHHHhcCcchheeeeccc
Q 029119 28 KCENCRAVADEYIECEIMILLIDLILHKPQAYRHLLYNV 66 (198)
Q Consensus 28 ~C~~C~~~~DkYiE~d~~i~~iDl~L~k~~ayRHllfN~ 66 (198)
-|+.|.++|++-.||.++..-.+.-+-+|.-|++|..+-
T Consensus 123 GC~~C~~ia~~C~eYGPi~~~~~~~~~~~~hfk~L~itD 161 (390)
T PF06542_consen 123 GCEKCSNIAKKCEEYGPIQFSVLQRFKKPKHFKKLIITD 161 (390)
T ss_pred hHHHHHHHHhhhhhcCCccHhHHhccCCCCCCCEEEEcH
Confidence 488999999999999999999988899999999998875
No 109
>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=32.07 E-value=19 Score=25.04 Aligned_cols=12 Identities=33% Similarity=0.664 Sum_probs=9.9
Q ss_pred ccccccCccccc
Q 029119 3 YRCVKCGFRIKT 14 (198)
Q Consensus 3 ~~Ci~C~~~v~~ 14 (198)
..|+.||.|++.
T Consensus 4 kHC~~CG~~Ip~ 15 (59)
T PF09889_consen 4 KHCPVCGKPIPP 15 (59)
T ss_pred CcCCcCCCcCCc
Confidence 469999999874
No 110
>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=32.04 E-value=28 Score=28.52 Aligned_cols=31 Identities=26% Similarity=0.425 Sum_probs=17.1
Q ss_pred ccccccCcccccceeee-----cCCceEeecCCCcc
Q 029119 3 YRCVKCGFRIKTLFVQY-----SPGNIRLMKCENCR 33 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y-----~~~~i~l~~C~~C~ 33 (198)
-.|.+||++...-...| +.--|.-..|++||
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CG 37 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCG 37 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT-
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCC
Confidence 46999999864433333 22244555899999
No 111
>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=31.89 E-value=34 Score=25.90 Aligned_cols=28 Identities=29% Similarity=0.660 Sum_probs=20.7
Q ss_pred CccccccCcc-cccceeeecCCceEeecCCCccccc
Q 029119 2 EYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAVA 36 (198)
Q Consensus 2 ~~~Ci~C~~~-v~~l~~~y~~~~i~l~~C~~C~~~~ 36 (198)
.|.|..||.+ ++.. ..-+=+|.+|++..
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 4432 45678999999753
No 112
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=31.63 E-value=25 Score=33.42 Aligned_cols=29 Identities=28% Similarity=0.574 Sum_probs=22.0
Q ss_pred CccccccCcccccceeeecCCceEeecCCCcccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (198)
.|+|-.||...++.=+. =-+|++|+.-+.
T Consensus 350 ~p~Cp~Cg~~m~S~G~~-------g~rC~kCg~~~~ 378 (421)
T COG1571 350 NPVCPRCGGRMKSAGRN-------GFRCKKCGTRAR 378 (421)
T ss_pred CCCCCccCCchhhcCCC-------CcccccccccCC
Confidence 58999999999885221 348999997654
No 113
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.58 E-value=27 Score=37.58 Aligned_cols=15 Identities=20% Similarity=0.625 Sum_probs=8.8
Q ss_pred ecCCCcccccccccc
Q 029119 27 MKCENCRAVADEYIE 41 (198)
Q Consensus 27 ~~C~~C~~~~DkYiE 41 (198)
+.||+|+...-.|-.
T Consensus 710 ~~CP~CGtplv~~~~ 724 (1337)
T PRK14714 710 VECPRCDVELTPYQR 724 (1337)
T ss_pred ccCCCCCCcccccce
Confidence 367777765544443
No 114
>PRK06386 replication factor A; Reviewed
Probab=31.48 E-value=22 Score=32.96 Aligned_cols=24 Identities=25% Similarity=0.498 Sum_probs=0.0
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY 39 (198)
.+|.+|+..++. ..|+.|++ ++.|
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 115
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=31.45 E-value=36 Score=27.97 Aligned_cols=30 Identities=30% Similarity=0.489 Sum_probs=19.6
Q ss_pred cccccCcccccceeeec-----CCceEeecCCCcc
Q 029119 4 RCVKCGFRIKTLFVQYS-----PGNIRLMKCENCR 33 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~-----~~~i~l~~C~~C~ 33 (198)
.|.+||++...-...++ .=-+--..|++||
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CG 36 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCG 36 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCC
Confidence 59999988654444432 2234457899998
No 116
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.40 E-value=23 Score=27.72 Aligned_cols=30 Identities=17% Similarity=0.440 Sum_probs=15.0
Q ss_pred ccccccCcccccceeeecCCceE-eecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIR-LMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~-l~~C~~C~~~ 35 (198)
-+| +||+..+.-- ....... ...||+||..
T Consensus 71 ~~C-~Cg~~~~~~~--~~~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 71 IEC-ECGYEGVVDE--DEIDHYAAVIECPVCGNK 101 (124)
T ss_pred EEe-eCcCcccccc--cchhccccCCcCcCCCCC
Confidence 479 9996632210 0000001 1369999954
No 117
>PRK07218 replication factor A; Provisional
Probab=31.34 E-value=23 Score=33.57 Aligned_cols=20 Identities=20% Similarity=0.227 Sum_probs=13.0
Q ss_pred HHHHHHhcCcchheeeeccc
Q 029119 47 LLIDLILHKPQAYRHLLYNV 66 (198)
Q Consensus 47 ~~iDl~L~k~~ayRHllfN~ 66 (198)
+.|+.+|-.=--+.-.+||+
T Consensus 324 lrik~vLDDGtg~~~~~~~~ 343 (423)
T PRK07218 324 LRIKAILDDGTGSVTVILDR 343 (423)
T ss_pred eEEEEEEECCCCeEEEEECh
Confidence 45566666666666667776
No 118
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=31.30 E-value=13 Score=25.15 Aligned_cols=22 Identities=32% Similarity=0.587 Sum_probs=16.9
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
.||-.||.+.+ .+-|+|.+|+-
T Consensus 15 kIC~rC~Arnp----------~~A~kCRkC~~ 36 (50)
T COG1552 15 KICRRCYARNP----------PRATKCRKCGY 36 (50)
T ss_pred HHHHHhcCCCC----------cchhHHhhccC
Confidence 58899988764 36788999973
No 119
>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=31.15 E-value=18 Score=30.41 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=28.9
Q ss_pred CccccccCcccccceee--ecCCceEeecCCCc---ccccccc
Q 029119 2 EYRCVKCGFRIKTLFVQ--YSPGNIRLMKCENC---RAVADEY 39 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~--y~~~~i~l~~C~~C---~~~~DkY 39 (198)
+-+|.-||++..-.|+- |+.+++. ..||-| |+-|+||
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 34799999998887764 7888888 899999 4566664
No 120
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.55 E-value=23 Score=35.28 Aligned_cols=7 Identities=29% Similarity=1.056 Sum_probs=3.7
Q ss_pred cCCCccc
Q 029119 28 KCENCRA 34 (198)
Q Consensus 28 ~C~~C~~ 34 (198)
.|++||.
T Consensus 29 ~Cp~CG~ 35 (645)
T PRK14559 29 PCPQCGT 35 (645)
T ss_pred cCCCCCC
Confidence 4555554
No 121
>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=30.53 E-value=22 Score=22.38 Aligned_cols=18 Identities=22% Similarity=0.709 Sum_probs=11.3
Q ss_pred ecCCCccccccccccchh
Q 029119 27 MKCENCRAVADEYIECEI 44 (198)
Q Consensus 27 ~~C~~C~~~~DkYiE~d~ 44 (198)
-+|++|+...-+|.++|.
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 479999999999999884
No 122
>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=30.47 E-value=14 Score=31.71 Aligned_cols=14 Identities=21% Similarity=0.662 Sum_probs=7.2
Q ss_pred CceEeecCCCcccc
Q 029119 22 GNIRLMKCENCRAV 35 (198)
Q Consensus 22 ~~i~l~~C~~C~~~ 35 (198)
|++...+|.+|++.
T Consensus 112 G~l~~~~C~~C~~~ 125 (235)
T cd01408 112 GSFATAHCIKCKHK 125 (235)
T ss_pred cCCCccccccCCCc
Confidence 44455555555553
No 123
>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=30.43 E-value=17 Score=30.55 Aligned_cols=31 Identities=23% Similarity=0.534 Sum_probs=16.6
Q ss_pred ccccccCcccccce--eeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLF--VQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~--~~y~~~~i~l~~C~~C~~~ 35 (198)
.+|..|++..+.-. .... .-.+..|++|+..
T Consensus 110 ~~C~~C~~~~~~~~~~~~~~--~~~~p~C~~Cg~~ 142 (218)
T cd01407 110 VRCTKCGKEYPRDELQADID--REEVPRCPKCGGL 142 (218)
T ss_pred ceeCCCcCCCcHHHHhHhhc--cCCCCcCCCCCCc
Confidence 46888887643211 0111 1235678888765
No 124
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=30.38 E-value=10 Score=26.79 Aligned_cols=19 Identities=32% Similarity=0.684 Sum_probs=13.9
Q ss_pred ccccccCcccccceeeecC
Q 029119 3 YRCVKCGFRIKTLFVQYSP 21 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~ 21 (198)
-||-.||+++.++|..|..
T Consensus 5 iRCFsCGkvi~~~w~~y~~ 23 (63)
T COG1644 5 VRCFSCGKVIGHKWEEYKR 23 (63)
T ss_pred eEeecCCCCHHHHHHHHHH
Confidence 3677888888888777743
No 125
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.89 E-value=40 Score=25.48 Aligned_cols=27 Identities=26% Similarity=0.806 Sum_probs=20.1
Q ss_pred CccccccCcc-cccceeeecCCceEeecCCCcccc
Q 029119 2 EYRCVKCGFR-IKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 2 ~~~Ci~C~~~-v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.|.|..||.+ ++.. ..-+=.|.+|++.
T Consensus 36 ~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~ 63 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQ-------AVGIWRCKGCKKT 63 (90)
T ss_pred CccCCCCCCCceeee-------eeEEEEcCCCCCE
Confidence 5889999976 4432 4467899999975
No 126
>PRK04023 DNA polymerase II large subunit; Validated
Probab=29.85 E-value=31 Score=36.42 Aligned_cols=11 Identities=27% Similarity=0.779 Sum_probs=9.3
Q ss_pred CccccccCccc
Q 029119 2 EYRCVKCGFRI 12 (198)
Q Consensus 2 ~~~Ci~C~~~v 12 (198)
...|.+||+..
T Consensus 626 ~RfCpsCG~~t 636 (1121)
T PRK04023 626 RRKCPSCGKET 636 (1121)
T ss_pred CccCCCCCCcC
Confidence 46899999985
No 127
>PF10977 DUF2797: Protein of unknown function (DUF2797); InterPro: IPR021246 This family of proteins has no known function.
Probab=29.71 E-value=21 Score=31.22 Aligned_cols=29 Identities=38% Similarity=0.910 Sum_probs=20.2
Q ss_pred cccccCcccccceee-e-cCCceEeecCCCc
Q 029119 4 RCVKCGFRIKTLFVQ-Y-SPGNIRLMKCENC 32 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~-y-~~~~i~l~~C~~C 32 (198)
.|++||...+.-|.+ | -+.--++.+|+.|
T Consensus 13 ~c~~cG~~~~~s~~qg~C~~C~~~~aqC~~C 43 (235)
T PF10977_consen 13 QCLNCGRKTKKSFRQGYCYPCFQTLAQCDEC 43 (235)
T ss_pred EEecCCccccccCCCCceeCCCCcCccChhH
Confidence 699999998777766 2 1223366688877
No 128
>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=28.81 E-value=15 Score=25.82 Aligned_cols=16 Identities=38% Similarity=0.868 Sum_probs=8.9
Q ss_pred cccccCcccccceeee
Q 029119 4 RCVKCGFRIKTLFVQY 19 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y 19 (198)
||-.||.++.+.|.+|
T Consensus 6 RCFTCGkvi~~~~e~y 21 (60)
T PF01194_consen 6 RCFTCGKVIGNKWEEY 21 (60)
T ss_dssp S-STTTSBTCGHHHHH
T ss_pred ecCCCCCChhHhHHHH
Confidence 4556666666555555
No 129
>PRK06424 transcription factor; Provisional
Probab=28.56 E-value=26 Score=28.39 Aligned_cols=37 Identities=24% Similarity=0.496 Sum_probs=27.3
Q ss_pred ccccCcccccceeeecCCceEeecCCCccccccccccc
Q 029119 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIEC 42 (198)
Q Consensus 5 Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~ 42 (198)
|==||..++.+|+.-=.|. .+..|+.|.++--+=.++
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 130
>PRK06260 threonine synthase; Validated
Probab=28.34 E-value=26 Score=32.20 Aligned_cols=28 Identities=21% Similarity=0.765 Sum_probs=19.2
Q ss_pred CccccccCcccccceeeecCCceEeecCCCcccccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (198)
..+|+.||+.- +++. ....||.|+..-|
T Consensus 3 ~~~C~~cg~~~-------~~~~-~~~~Cp~cg~~l~ 30 (397)
T PRK06260 3 WLKCIECGKEY-------DPDE-IIYTCPECGGLLE 30 (397)
T ss_pred EEEECCCCCCC-------CCCC-ccccCCCCCCeEE
Confidence 46899999764 3322 2457999997655
No 131
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=28.33 E-value=13 Score=26.30 Aligned_cols=17 Identities=29% Similarity=0.769 Sum_probs=10.6
Q ss_pred cccccCcccccceeeec
Q 029119 4 RCVKCGFRIKTLFVQYS 20 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~ 20 (198)
||-.||.++.+.|.+|.
T Consensus 6 RCFTCGkvi~~~we~y~ 22 (62)
T PRK04016 6 RCFTCGKVIAEKWEEFK 22 (62)
T ss_pred EecCCCCChHHHHHHHH
Confidence 56666666666666663
No 132
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=28.19 E-value=19 Score=33.28 Aligned_cols=31 Identities=16% Similarity=0.652 Sum_probs=16.5
Q ss_pred ccccccCccccc--ceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKT--LFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~--l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.+|..|+++.+. .+.+..++ ++.+|++|+.+
T Consensus 148 ~~C~~C~~~~~~~~~~~~~~~~--~vP~C~~CgG~ 180 (349)
T PTZ00410 148 ASCIECHTPYDIEQAYLEARSG--KVPHCSTCGGI 180 (349)
T ss_pred eEeCCCCCCcchhHHHHHhhcC--CCCCCCCCCCc
Confidence 468888865431 11111111 34678888753
No 133
>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=28.16 E-value=48 Score=19.23 Aligned_cols=29 Identities=21% Similarity=0.493 Sum_probs=15.5
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
-.|--|+++++..-. +.-....|++|.++
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 358889988766422 23345689999763
No 134
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=27.72 E-value=45 Score=28.22 Aligned_cols=30 Identities=23% Similarity=0.437 Sum_probs=20.1
Q ss_pred cccccCcccccceeeec------CCceEeecCCCcc
Q 029119 4 RCVKCGFRIKTLFVQYS------PGNIRLMKCENCR 33 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~------~~~i~l~~C~~C~ 33 (198)
-|.+||.+.......+. .=-+--..|++||
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CG 37 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCG 37 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCC
Confidence 49999987655444444 2234456899999
No 135
>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=27.41 E-value=27 Score=29.77 Aligned_cols=9 Identities=11% Similarity=0.146 Sum_probs=5.2
Q ss_pred eecCCCccc
Q 029119 26 LMKCENCRA 34 (198)
Q Consensus 26 l~~C~~C~~ 34 (198)
.-.|++|+.
T Consensus 136 ~p~C~~Cgg 144 (225)
T cd01411 136 SPYHAKCGG 144 (225)
T ss_pred CCCCCCCCC
Confidence 345666664
No 136
>PF14800 DUF4481: Domain of unknown function (DUF4481)
Probab=27.30 E-value=4.2e+02 Score=24.35 Aligned_cols=24 Identities=38% Similarity=0.474 Sum_probs=20.8
Q ss_pred hhHHHHHHHHhcCcchheeeeccc
Q 029119 43 EIMILLIDLILHKPQAYRHLLYNV 66 (198)
Q Consensus 43 d~~i~~iDl~L~k~~ayRHllfN~ 66 (198)
|...-.+...+.+||++|-++||.
T Consensus 39 e~y~~~~E~al~~p~VRRy~~yNs 62 (308)
T PF14800_consen 39 EDYVHLMESALLDPQVRRYTLYNS 62 (308)
T ss_pred HHHHHHHHHhccchhheeeeeecc
Confidence 344567899999999999999998
No 137
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=27.14 E-value=45 Score=24.34 Aligned_cols=29 Identities=28% Similarity=0.598 Sum_probs=18.8
Q ss_pred cccccCcccccceeeecCCceEeecCCCcc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCR 33 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~ 33 (198)
.|..||.....- ...+.+.|++..|++|+
T Consensus 16 ~~~s~g~~f~~~-ST~~~~~i~vdV~s~~H 44 (75)
T COG0254 16 VCSSCGNEFTTR-STKGTDEINLDVCSKCH 44 (75)
T ss_pred EeCCCCCEEEEE-eccCCceEEEEeCCCCC
Confidence 466676653221 12344689999999998
No 138
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.12 E-value=39 Score=25.80 Aligned_cols=50 Identities=26% Similarity=0.597 Sum_probs=27.7
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccc----ccc-chhHHHHHHHHhcC
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADE----YIE-CEIMILLIDLILHK 55 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~Dk----YiE-~d~~i~~iDl~L~k 55 (198)
..|.+||+. .+--.-.. ++-...|++||.--.. --| .|..--|||...-.
T Consensus 22 f~CP~Cge~--~v~v~~~k-~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wiD~~~eg 76 (99)
T PRK14892 22 FECPRCGKV--SISVKIKK-NIAIITCGNCGLYTEFEVPSVYDEVDVYNKFIDLYLEG 76 (99)
T ss_pred eECCCCCCe--EeeeecCC-CcceEECCCCCCccCEECCccccchhhHHHHHHHHHhc
Confidence 468999954 22212222 4567789999954222 111 25555677766543
No 139
>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=27.05 E-value=46 Score=22.55 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=17.2
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
-||-+|....... .+-..+.+ --+|++|+.
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 12333344 557888875
No 140
>KOG2682 consensus NAD-dependent histone deacetylases and class I sirtuins (SIR2 family) [Chromatin structure and dynamics; Transcription]
Probab=27.04 E-value=13 Score=33.27 Aligned_cols=38 Identities=18% Similarity=0.401 Sum_probs=25.0
Q ss_pred cccc-ccCcccccceeeecCCceEeecCCCccccccccc
Q 029119 3 YRCV-KCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYI 40 (198)
Q Consensus 3 ~~Ci-~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYi 40 (198)
-.|| +|+++.+.=|.+-.=-.-+.-+|+.|+..+.+=|
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 7999977655443222225559999998765533
No 141
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.80 E-value=34 Score=34.16 Aligned_cols=14 Identities=29% Similarity=0.544 Sum_probs=10.0
Q ss_pred eecCCCcccccccc
Q 029119 26 LMKCENCRAVADEY 39 (198)
Q Consensus 26 l~~C~~C~~~~DkY 39 (198)
-..|++||...++-
T Consensus 41 ~~fC~~CG~~~~~~ 54 (645)
T PRK14559 41 EAHCPNCGAETGTI 54 (645)
T ss_pred cccccccCCcccch
Confidence 34799999876653
No 142
>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]
Probab=26.76 E-value=32 Score=34.86 Aligned_cols=33 Identities=36% Similarity=0.867 Sum_probs=25.4
Q ss_pred CccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.|.|..||.+. .-|-+-++.-+|.+.|++|+..
T Consensus 292 ky~C~KC~~vl-gPF~qs~n~evkp~~C~~cqSk 324 (854)
T KOG0477|consen 292 KYDCLKCGFVL-GPFVQSSNSEVKPGSCPECQSK 324 (854)
T ss_pred hhhHHhhCCcc-CceeeccCceeCCCCCccccCC
Confidence 37899999543 4456667778899999999865
No 143
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=26.68 E-value=28 Score=19.79 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=7.3
Q ss_pred eecCCCccc
Q 029119 26 LMKCENCRA 34 (198)
Q Consensus 26 l~~C~~C~~ 34 (198)
+.+|+.||+
T Consensus 2 l~~C~~CgR 10 (25)
T PF13913_consen 2 LVPCPICGR 10 (25)
T ss_pred CCcCCCCCC
Confidence 468999997
No 144
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.61 E-value=33 Score=23.62 Aligned_cols=19 Identities=21% Similarity=0.455 Sum_probs=14.2
Q ss_pred cCCCccc-----------cccccccchhHH
Q 029119 28 KCENCRA-----------VADEYIECEIMI 46 (198)
Q Consensus 28 ~C~~C~~-----------~~DkYiE~d~~i 46 (198)
.||.||. +.|||-+|-..+
T Consensus 19 ~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~ 48 (56)
T PRK13130 19 ICPVCGGKTKNPHPPRFSPEDKYGKYRRAL 48 (56)
T ss_pred cCcCCCCCCCCCCCCCCCCCCccHHHHHHH
Confidence 6889983 479999887443
No 145
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=26.55 E-value=49 Score=24.17 Aligned_cols=50 Identities=16% Similarity=0.305 Sum_probs=23.1
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccccc-----cchhHHHHHHHH
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYI-----ECEIMILLIDLI 52 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYi-----E~d~~i~~iDl~ 52 (198)
+.|..|||.-.---+.=....+-.-.|..|+....--| ..|..--|||+.
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L~epiDVY~~wiD~~ 77 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPLSEPIDVYSEWIDAC 77 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS--TTHHHHHHHHHH
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCccCcccchhHHHHHHH
Confidence 57999997743333333445667778999985422111 234444566654
No 146
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=26.48 E-value=11 Score=26.72 Aligned_cols=34 Identities=15% Similarity=0.186 Sum_probs=20.4
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccccccchhHHHHH
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECEIMILLI 49 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d~~i~~i 49 (198)
..|.+|..-++. +.||.||.- |-==+++.+++++
T Consensus 6 ~AC~~C~~i~~~------------~~Cp~Cgs~-~~S~~w~G~v~i~ 39 (64)
T PRK06393 6 RACKKCKRLTPE------------KTCPVHGDE-KTTTEWFGFLIIT 39 (64)
T ss_pred hhHhhCCcccCC------------CcCCCCCCC-cCCcCcceEEEEE
Confidence 468899877631 289999974 3233444444433
No 147
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=26.48 E-value=14 Score=33.48 Aligned_cols=25 Identities=24% Similarity=0.425 Sum_probs=14.8
Q ss_pred cccccCcccccceeeecCCc-eEeecCCCccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGN-IRLMKCENCRA 34 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~-i~l~~C~~C~~ 34 (198)
.|-+|++.+ |.++- -.+..||+|+.
T Consensus 40 kc~~C~~~~------~~~~l~~~~~vcp~c~~ 65 (296)
T CHL00174 40 QCENCYGLN------YKKFLKSKMNICEQCGY 65 (296)
T ss_pred ECCCccchh------hHHHHHHcCCCCCCCCC
Confidence 577888765 22211 12458999984
No 148
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=26.38 E-value=41 Score=30.33 Aligned_cols=27 Identities=19% Similarity=0.366 Sum_probs=19.2
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.-|-.||++... ...-.-..|++|++.
T Consensus 112 RFCg~CG~~~~~------~~~g~~~~C~~cg~~ 138 (279)
T COG2816 112 RFCGRCGTKTYP------REGGWARVCPKCGHE 138 (279)
T ss_pred cCCCCCCCcCcc------ccCceeeeCCCCCCc
Confidence 359999999743 333356689999975
No 149
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=25.77 E-value=46 Score=22.86 Aligned_cols=23 Identities=22% Similarity=0.473 Sum_probs=13.1
Q ss_pred cccccCcccccceeeecCCceEeecCCCcccccc
Q 029119 4 RCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (198)
.|-+||++.. ....|++||---+
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 4667776532 2446777774433
No 150
>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=25.69 E-value=39 Score=23.05 Aligned_cols=19 Identities=32% Similarity=0.623 Sum_probs=13.9
Q ss_pred ecCCCccc-----------cccccccchhH
Q 029119 27 MKCENCRA-----------VADEYIECEIM 45 (198)
Q Consensus 27 ~~C~~C~~-----------~~DkYiE~d~~ 45 (198)
.+|+.||. +-|||-+|-..
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 46999888643
No 151
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=25.48 E-value=33 Score=22.71 Aligned_cols=8 Identities=50% Similarity=1.414 Sum_probs=5.0
Q ss_pred cccccCcc
Q 029119 4 RCVKCGFR 11 (198)
Q Consensus 4 ~Ci~C~~~ 11 (198)
+|-+|||.
T Consensus 30 ~C~~Cgh~ 37 (55)
T PF14311_consen 30 KCPKCGHE 37 (55)
T ss_pred ECCCCCCe
Confidence 46666665
No 152
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=25.46 E-value=36 Score=27.19 Aligned_cols=28 Identities=18% Similarity=0.479 Sum_probs=18.0
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (198)
+.|..|+..+.. .+. ..-.|++|++..+
T Consensus 35 ~aC~~C~kkv~~----~~~---~~~~C~~C~~~~~ 62 (166)
T cd04476 35 PACPGCNKKVVE----EGN---GTYRCEKCNKSVP 62 (166)
T ss_pred ccccccCcccEe----CCC---CcEECCCCCCcCC
Confidence 468888887643 111 3457999987653
No 153
>PRK01397 50S ribosomal protein L31; Provisional
Probab=25.35 E-value=58 Score=23.86 Aligned_cols=14 Identities=14% Similarity=-0.026 Sum_probs=11.8
Q ss_pred CCceEeecCCCccc
Q 029119 21 PGNIRLMKCENCRA 34 (198)
Q Consensus 21 ~~~i~l~~C~~C~~ 34 (198)
++.|+++.|++|+-
T Consensus 29 ~~~i~vdi~s~~HP 42 (78)
T PRK01397 29 TGEILMDVDFRKHP 42 (78)
T ss_pred CCcEEEEeCCCCCC
Confidence 46799999999983
No 154
>PRK07218 replication factor A; Provisional
Probab=25.29 E-value=39 Score=32.02 Aligned_cols=20 Identities=20% Similarity=0.433 Sum_probs=14.0
Q ss_pred cCCceEeecCCCcccccccc
Q 029119 20 SPGNIRLMKCENCRAVADEY 39 (198)
Q Consensus 20 ~~~~i~l~~C~~C~~~~DkY 39 (198)
.++..=++.||.|+++.+++
T Consensus 291 ~~gsgli~rCP~C~r~v~~~ 310 (423)
T PRK07218 291 RDGSGLIERCPECGRVIQKG 310 (423)
T ss_pred ccCCcceecCcCccccccCC
Confidence 34445667888888888774
No 155
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=25.03 E-value=54 Score=22.02 Aligned_cols=33 Identities=24% Similarity=0.485 Sum_probs=17.1
Q ss_pred ccccccCcccccceee--ecCCceEee-cCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQ--YSPGNIRLM-KCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~--y~~~~i~l~-~C~~C~~~ 35 (198)
..|.+|+...-...+. -.++.+.+- -||.|++-
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 3699999873222111 122323332 38888864
No 156
>PHA02637 TNF-alpha-receptor-like protein; Provisional
Probab=24.84 E-value=45 Score=26.72 Aligned_cols=31 Identities=26% Similarity=0.596 Sum_probs=22.9
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEY 39 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkY 39 (198)
..|.-|.... |++..+ .+++|-.|+..+||=
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 666544 568999999999984
No 157
>PRK08402 replication factor A; Reviewed
Probab=24.81 E-value=34 Score=31.62 Aligned_cols=9 Identities=22% Similarity=0.866 Sum_probs=4.2
Q ss_pred cccccCccc
Q 029119 4 RCVKCGFRI 12 (198)
Q Consensus 4 ~Ci~C~~~v 12 (198)
+|.+|+..+
T Consensus 214 aCp~CnKkv 222 (355)
T PRK08402 214 ACPECRRKV 222 (355)
T ss_pred cCCCCCeEE
Confidence 455554443
No 158
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=24.41 E-value=33 Score=34.06 Aligned_cols=22 Identities=23% Similarity=0.652 Sum_probs=14.9
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
-+|-+||.. ..+ ...||+||+-
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 379999962 222 1689999963
No 159
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=24.35 E-value=17 Score=26.34 Aligned_cols=18 Identities=33% Similarity=0.671 Sum_probs=11.6
Q ss_pred cccccCcccccceeeecC
Q 029119 4 RCVKCGFRIKTLFVQYSP 21 (198)
Q Consensus 4 ~Ci~C~~~v~~l~~~y~~ 21 (198)
||-.||+++.+.|.+|..
T Consensus 6 RCFTCGkvig~~we~y~~ 23 (71)
T PLN00032 6 RCFTCGKVIGNKWDTYLD 23 (71)
T ss_pred eecCCCCCcHHHHHHHHH
Confidence 566677777666666643
No 160
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=23.92 E-value=42 Score=24.07 Aligned_cols=9 Identities=44% Similarity=1.021 Sum_probs=6.6
Q ss_pred cccccCccc
Q 029119 4 RCVKCGFRI 12 (198)
Q Consensus 4 ~Ci~C~~~v 12 (198)
.|+.||...
T Consensus 6 kCpKCgn~~ 14 (68)
T COG3478 6 KCPKCGNTN 14 (68)
T ss_pred cCCCcCCcc
Confidence 488898753
No 161
>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=23.56 E-value=27 Score=36.11 Aligned_cols=41 Identities=20% Similarity=0.460 Sum_probs=0.0
Q ss_pred ccccccCcccccceeeec-CCceEeecCCCccccccccccch
Q 029119 3 YRCVKCGFRIKTLFVQYS-PGNIRLMKCENCRAVADEYIECE 43 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~-~~~i~l~~C~~C~~~~DkYiE~d 43 (198)
.+|-+||.+....|.=-. .....-..|++|+..+..|-...
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 356666666554432110 11112237888888777776544
No 162
>PRK12366 replication factor A; Reviewed
Probab=23.44 E-value=37 Score=33.61 Aligned_cols=25 Identities=32% Similarity=0.671 Sum_probs=15.4
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
++|.+|+..+.. ++ ..-.|++|++.
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 578888777642 11 22368888876
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=23.36 E-value=37 Score=28.57 Aligned_cols=29 Identities=24% Similarity=0.559 Sum_probs=14.6
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
.+|..|+.....- +.......-.|++|+.
T Consensus 110 ~~C~~C~~~~~~~---~~~~~~~~p~C~~Cgg 138 (224)
T cd01412 110 VRCSSCGYVGENN---EEIPEEELPRCPKCGG 138 (224)
T ss_pred cccCCCCCCCCcc---hhhhccCCCCCCCCCC
Confidence 4677777654321 1111123456777774
No 164
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=23.26 E-value=43 Score=31.79 Aligned_cols=26 Identities=19% Similarity=0.514 Sum_probs=18.3
Q ss_pred cccccCccc--ccceeeecCCceEeecCCCcccc
Q 029119 4 RCVKCGFRI--KTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 4 ~Ci~C~~~v--~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.|-||+..+ +.| ++ -+...||+||..
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 256799999963
No 165
>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=23.22 E-value=57 Score=26.93 Aligned_cols=29 Identities=31% Similarity=0.693 Sum_probs=17.8
Q ss_pred ccccCcc-cccceeee-----cCCceEeecCCCcc
Q 029119 5 CVKCGFR-IKTLFVQY-----SPGNIRLMKCENCR 33 (198)
Q Consensus 5 Ci~C~~~-v~~l~~~y-----~~~~i~l~~C~~C~ 33 (198)
|-.||++ .......+ +.=-|--..|++||
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CG 35 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCG 35 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCC
Confidence 8889987 33322222 23345567899999
No 166
>smart00507 HNHc HNH nucleases.
Probab=23.06 E-value=35 Score=20.77 Aligned_cols=11 Identities=27% Similarity=0.507 Sum_probs=7.9
Q ss_pred ccccccCcccc
Q 029119 3 YRCVKCGFRIK 13 (198)
Q Consensus 3 ~~Ci~C~~~v~ 13 (198)
+.|..||.+.+
T Consensus 11 ~~C~~C~~~~~ 21 (52)
T smart00507 11 GVCAYCGKPAS 21 (52)
T ss_pred CCCcCCcCCCC
Confidence 57888887764
No 167
>PRK06450 threonine synthase; Validated
Probab=22.86 E-value=41 Score=30.46 Aligned_cols=32 Identities=25% Similarity=0.542 Sum_probs=21.8
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccccccccccch
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIECE 43 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE~d 43 (198)
++|..||+.-+ +. ....|+.|+..-|--.+++
T Consensus 4 ~~C~~Cg~~~~-------~~--~~~~C~~cg~~l~~~~d~~ 35 (338)
T PRK06450 4 EVCMKCGKERE-------SI--YEIRCKKCGGPFEILIDFE 35 (338)
T ss_pred eEECCcCCcCC-------Cc--ccccCCcCCCEeEEeeccc
Confidence 68999997642 21 1358999998777544444
No 168
>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=22.41 E-value=31 Score=21.81 Aligned_cols=14 Identities=21% Similarity=0.636 Sum_probs=7.8
Q ss_pred EeecCCCccccccc
Q 029119 25 RLMKCENCRAVADE 38 (198)
Q Consensus 25 ~l~~C~~C~~~~Dk 38 (198)
++..|+.|+.+.|.
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 46789999998874
No 169
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=22.26 E-value=32 Score=21.71 Aligned_cols=9 Identities=67% Similarity=1.597 Sum_probs=6.5
Q ss_pred ccccccCcc
Q 029119 3 YRCVKCGFR 11 (198)
Q Consensus 3 ~~Ci~C~~~ 11 (198)
|+|.+||+.
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 578888764
No 170
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=21.99 E-value=65 Score=22.94 Aligned_cols=13 Identities=0% Similarity=-0.054 Sum_probs=11.2
Q ss_pred CceEeecCCCccc
Q 029119 22 GNIRLMKCENCRA 34 (198)
Q Consensus 22 ~~i~l~~C~~C~~ 34 (198)
+.+++..|++|+-
T Consensus 31 ~~i~vdv~s~~HP 43 (68)
T CHL00136 31 PELNVDIWSGNHP 43 (68)
T ss_pred CCEEEEeCCCCCc
Confidence 5699999999983
No 171
>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=21.96 E-value=11 Score=28.64 Aligned_cols=33 Identities=24% Similarity=0.556 Sum_probs=19.3
Q ss_pred ccccccCcc-cccceeee-cCCceEeecCCCcccc
Q 029119 3 YRCVKCGFR-IKTLFVQY-SPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~-v~~l~~~y-~~~~i~l~~C~~C~~~ 35 (198)
-.|+.|+.. |..-|..- .+....+..|++|++.
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 356777654 55555544 3445566677777654
No 172
>PRK05638 threonine synthase; Validated
Probab=21.89 E-value=50 Score=30.88 Aligned_cols=25 Identities=24% Similarity=0.538 Sum_probs=17.1
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVAD 37 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~D 37 (198)
.+|+.||+.-+ ++. . ..| .|+..-|
T Consensus 2 l~C~~Cg~~~~-------~~~-~-~~C-~c~~~l~ 26 (442)
T PRK05638 2 MKCPKCGREYN-------SYI-P-PFC-ICGELLE 26 (442)
T ss_pred eEeCCCCCCCC-------CCC-c-eec-CCCCcEE
Confidence 68999998743 222 1 569 7987765
No 173
>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=21.73 E-value=59 Score=19.71 Aligned_cols=15 Identities=27% Similarity=0.704 Sum_probs=8.2
Q ss_pred CCceEeecCCCcccc
Q 029119 21 PGNIRLMKCENCRAV 35 (198)
Q Consensus 21 ~~~i~l~~C~~C~~~ 35 (198)
.+.+...+|++|+++
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 456778888888865
No 174
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.46 E-value=44 Score=36.03 Aligned_cols=30 Identities=27% Similarity=0.542 Sum_probs=17.3
Q ss_pred ccccccCcccccceeeecC----CceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSP----GNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~----~~i~l~~C~~C~~~ 35 (198)
.+|.+||+++... +-| ..-....|++||..
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 175
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=21.31 E-value=46 Score=28.48 Aligned_cols=9 Identities=56% Similarity=1.202 Sum_probs=6.0
Q ss_pred ccccccCcc
Q 029119 3 YRCVKCGFR 11 (198)
Q Consensus 3 ~~Ci~C~~~ 11 (198)
.+|..|+..
T Consensus 123 ~~C~~C~~~ 131 (242)
T PRK00481 123 ARCTKCGQT 131 (242)
T ss_pred eeeCCCCCC
Confidence 467777654
No 176
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.16 E-value=57 Score=24.34 Aligned_cols=37 Identities=27% Similarity=0.579 Sum_probs=25.2
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc------ccccccch
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV------ADEYIECE 43 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~------~DkYiE~d 43 (198)
..|..||.....- ...++.+..||+|..+ -||-||-.
T Consensus 2 llCP~C~v~l~~~----~rs~vEiD~CPrCrGVWLDrGELdKli~r~ 44 (88)
T COG3809 2 LLCPICGVELVMS----VRSGVEIDYCPRCRGVWLDRGELDKLIERS 44 (88)
T ss_pred cccCcCCceeeee----eecCceeeeCCccccEeecchhHHHHHHHh
Confidence 3689999874321 2347889999999975 45655554
No 177
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=20.97 E-value=48 Score=36.20 Aligned_cols=34 Identities=18% Similarity=0.409 Sum_probs=20.4
Q ss_pred CccccccCcccccceeeecCC-ceEeecCCCcccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPG-NIRLMKCENCRAV 35 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~-~i~l~~C~~C~~~ 35 (198)
.|+|.+|.+.-=..--.+++| .+.--.||+||..
T Consensus 908 hy~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~ 942 (1437)
T PRK00448 908 HYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTK 942 (1437)
T ss_pred cccCcccccccccccccccccccCccccCcccccc
Confidence 589999976421111123333 4556689999965
No 178
>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=20.72 E-value=95 Score=18.99 Aligned_cols=30 Identities=23% Similarity=0.535 Sum_probs=15.9
Q ss_pred ccccCcc-cccce----eeecCCce-----EeecCCCccc
Q 029119 5 CVKCGFR-IKTLF----VQYSPGNI-----RLMKCENCRA 34 (198)
Q Consensus 5 Ci~C~~~-v~~l~----~~y~~~~i-----~l~~C~~C~~ 34 (198)
|..||.. ++... ..|+...+ .-..|++||.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE 40 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGE 40 (46)
T ss_pred CCCCCCceecceEEEEEEEeCCEEEEEeCCCccccccCCC
Confidence 6678533 33332 34544433 3345999986
No 179
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=20.69 E-value=35 Score=23.71 Aligned_cols=35 Identities=29% Similarity=0.651 Sum_probs=22.5
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccccccccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAVADEYIE 41 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~~DkYiE 41 (198)
-||..||.-.... -+.+++. -+||+|+.+-.-|+.
T Consensus 5 iRC~~CnKlLa~a---~~~~yle-~KCPrCK~vN~~~~~ 39 (60)
T COG4416 5 IRCAKCNKLLAEA---EGQAYLE-KKCPRCKEVNEFYIK 39 (60)
T ss_pred eehHHHhHHHHhc---ccceeee-ecCCccceeeeeecc
Confidence 4788898764432 2233333 379999988776664
No 180
>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=20.69 E-value=18 Score=27.75 Aligned_cols=29 Identities=24% Similarity=0.595 Sum_probs=16.3
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRAV 35 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~ 35 (198)
.+|.+||.+-++ |-.-+.-.-.|..|..+
T Consensus 14 ~~CaDCg~~~p~----w~s~~~GiflC~~Cag~ 42 (116)
T PF01412_consen 14 KVCADCGAPNPT----WASLNYGIFLCLECAGI 42 (116)
T ss_dssp TB-TTT-SBS------EEETTTTEEE-HHHHHH
T ss_pred CcCCCCCCCCCC----EEEeecChhhhHHHHHH
Confidence 579999988774 54445556778888643
No 181
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=20.41 E-value=60 Score=20.59 Aligned_cols=17 Identities=12% Similarity=0.421 Sum_probs=11.1
Q ss_pred ecCCceEeecCCCcccc
Q 029119 19 YSPGNIRLMKCENCRAV 35 (198)
Q Consensus 19 y~~~~i~l~~C~~C~~~ 35 (198)
.+......+.|+.||-.
T Consensus 6 ~gq~~~~~~~C~~CgM~ 22 (41)
T PF13878_consen 6 LGQKSFGATTCPTCGML 22 (41)
T ss_pred CCCCccCCcCCCCCCCE
Confidence 34444456799999854
No 182
>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=20.22 E-value=57 Score=21.31 Aligned_cols=30 Identities=20% Similarity=0.501 Sum_probs=19.0
Q ss_pred ccccccCcccccceeeecCCceEeecCCCcc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCR 33 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~ 33 (198)
|.|-.||....+++-.... .-+-..|+.|=
T Consensus 1 y~C~~Cg~D~t~vryh~~~-~~~~dLC~~CF 30 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLK-AKKYDLCPSCY 30 (45)
T ss_pred CcccCCCCccCceEEEecC-CCccccChHHH
Confidence 5788999999874333322 22466777773
No 183
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=20.06 E-value=37 Score=30.57 Aligned_cols=36 Identities=19% Similarity=0.463 Sum_probs=24.8
Q ss_pred ccccccCcccccceeee----cCCceEeecCCCccc-cccc
Q 029119 3 YRCVKCGFRIKTLFVQY----SPGNIRLMKCENCRA-VADE 38 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y----~~~~i~l~~C~~C~~-~~Dk 38 (198)
-.|.-||..-.+-|.-= +....|--.|+.|++ +||+
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADR 228 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADR 228 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCcccchhcch
Confidence 46888888876544321 234557778999997 8886
No 184
>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=20.03 E-value=51 Score=22.30 Aligned_cols=34 Identities=18% Similarity=0.443 Sum_probs=14.2
Q ss_pred ccccCcccccceeeecCCceEeecCCCcccc----ccccc
Q 029119 5 CVKCGFRIKTLFVQYSPGNIRLMKCENCRAV----ADEYI 40 (198)
Q Consensus 5 Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~~----~DkYi 40 (198)
|-.|..+.+..=.+ +++...-+|++|++. +|-||
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 56677776653111 111345589999984 45554
No 185
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=20.03 E-value=48 Score=23.57 Aligned_cols=22 Identities=18% Similarity=0.400 Sum_probs=15.8
Q ss_pred ccccccCcccccceeeecCCceEeecCCCccc
Q 029119 3 YRCVKCGFRIKTLFVQYSPGNIRLMKCENCRA 34 (198)
Q Consensus 3 ~~Ci~C~~~v~~l~~~y~~~~i~l~~C~~C~~ 34 (198)
..|.+|..-++. .-+.||.||.
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 186
>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=20.03 E-value=52 Score=35.30 Aligned_cols=34 Identities=21% Similarity=0.439 Sum_probs=20.2
Q ss_pred CccccccCcccccceeeecCC-ceEeecCCCcccc
Q 029119 2 EYRCVKCGFRIKTLFVQYSPG-NIRLMKCENCRAV 35 (198)
Q Consensus 2 ~~~Ci~C~~~v~~l~~~y~~~-~i~l~~C~~C~~~ 35 (198)
.|+|.+|.+.-=..=-.+++| .+.--.||+||..
T Consensus 683 hy~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~~ 717 (1213)
T TIGR01405 683 HYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAP 717 (1213)
T ss_pred cccCcccccccccccccccccccCccccCcccccc
Confidence 589999986411100123332 4556689999965
Done!