Query 027149
Match_columns 227
No_of_seqs 167 out of 208
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 05:41:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027149.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027149hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14571 Di19_C: Stress-induce 100.0 3.4E-34 7.4E-39 225.9 7.7 102 120-222 1-105 (105)
2 PF05605 zf-Di19: Drought indu 99.8 2E-19 4.2E-24 125.5 3.2 53 49-101 2-54 (54)
3 KOG1280 Uncharacterized conser 98.9 1.9E-09 4.2E-14 100.4 4.6 64 20-89 56-120 (381)
4 COG5216 Uncharacterized conser 94.0 0.024 5.1E-07 41.4 0.9 33 48-89 21-55 (67)
5 KOG2923 Uncharacterized conser 93.9 0.032 6.9E-07 41.2 1.5 46 32-89 8-55 (67)
6 PF13894 zf-C2H2_4: C2H2-type 93.5 0.038 8.2E-07 30.7 1.0 23 50-72 1-24 (24)
7 PF09237 GAGA: GAGA factor; I 92.9 0.057 1.2E-06 38.3 1.5 28 75-102 21-50 (54)
8 PLN03086 PRLI-interacting fact 91.4 0.17 3.7E-06 50.7 3.3 48 48-100 452-500 (567)
9 PF13913 zf-C2HC_2: zinc-finge 90.9 0.13 2.9E-06 30.7 1.3 21 49-69 2-22 (25)
10 TIGR01206 lysW lysine biosynth 89.5 0.12 2.6E-06 36.7 0.3 31 49-88 2-32 (54)
11 PHA00732 hypothetical protein 89.4 0.38 8.2E-06 36.3 3.0 43 50-97 2-45 (79)
12 PF00096 zf-C2H2: Zinc finger, 89.4 0.12 2.5E-06 29.3 0.1 21 50-70 1-22 (23)
13 PF14354 Lar_restr_allev: Rest 88.8 0.14 3.1E-06 35.7 0.3 31 49-86 3-37 (61)
14 PF12756 zf-C2H2_2: C2H2 type 88.5 0.21 4.6E-06 36.5 1.1 48 51-98 1-72 (100)
15 COG5236 Uncharacterized conser 88.4 0.45 9.8E-06 45.7 3.4 32 49-86 220-252 (493)
16 KOG2462 C2H2-type Zn-finger pr 88.4 0.32 6.9E-06 44.9 2.3 35 48-86 160-195 (279)
17 PF13909 zf-H2C2_5: C2H2-type 88.4 0.17 3.6E-06 29.2 0.3 24 50-73 1-24 (24)
18 PRK09710 lar restriction allev 87.8 0.2 4.3E-06 36.9 0.5 31 48-87 5-36 (64)
19 smart00531 TFIIE Transcription 87.6 0.45 9.7E-06 39.2 2.5 37 48-89 98-134 (147)
20 PF08271 TF_Zn_Ribbon: TFIIB z 86.7 0.19 4E-06 33.3 -0.2 34 50-93 1-34 (43)
21 PHA00733 hypothetical protein 86.3 0.88 1.9E-05 37.0 3.6 50 48-101 72-124 (128)
22 smart00834 CxxC_CXXC_SSSS Puta 86.1 0.33 7.1E-06 31.0 0.8 33 48-88 4-36 (41)
23 PLN03086 PRLI-interacting fact 85.2 0.69 1.5E-05 46.5 2.9 38 48-88 477-514 (567)
24 PF09986 DUF2225: Uncharacteri 84.5 0.37 8E-06 42.3 0.6 19 48-66 4-22 (214)
25 TIGR02098 MJ0042_CXXC MJ0042 f 84.1 0.96 2.1E-05 28.8 2.3 32 50-87 3-34 (38)
26 PHA02768 hypothetical protein; 82.6 0.88 1.9E-05 32.5 1.8 34 49-86 5-39 (55)
27 COG1655 Uncharacterized protei 81.3 0.63 1.4E-05 42.3 0.8 13 48-60 18-30 (267)
28 PF08274 PhnA_Zn_Ribbon: PhnA 81.1 0.57 1.2E-05 29.5 0.3 24 51-86 4-27 (30)
29 TIGR02605 CxxC_CxxC_SSSS putat 80.4 1.2 2.6E-05 30.1 1.8 31 48-86 4-34 (52)
30 PLN03208 E3 ubiquitin-protein 80.4 0.63 1.4E-05 40.9 0.4 43 48-90 17-80 (193)
31 PRK14892 putative transcriptio 78.6 0.95 2E-05 35.8 0.9 34 48-89 20-53 (99)
32 PF14255 Cys_rich_CPXG: Cystei 78.4 0.72 1.6E-05 32.5 0.2 34 50-88 1-34 (52)
33 cd00350 rubredoxin_like Rubred 77.9 1.2 2.6E-05 28.1 1.0 24 50-86 2-25 (33)
34 PRK00398 rpoP DNA-directed RNA 77.6 0.95 2.1E-05 30.2 0.6 30 48-88 2-31 (46)
35 PF14206 Cys_rich_CPCC: Cystei 76.5 1.6 3.5E-05 33.2 1.6 24 50-84 2-26 (78)
36 smart00734 ZnF_Rad18 Rad18-lik 76.4 1.7 3.6E-05 26.3 1.3 19 51-69 3-21 (26)
37 KOG1842 FYVE finger-containing 76.3 0.98 2.1E-05 44.4 0.5 34 43-78 11-45 (505)
38 KOG2462 C2H2-type Zn-finger pr 76.3 2.8 6.1E-05 38.8 3.4 80 49-135 187-270 (279)
39 PF12760 Zn_Tnp_IS1595: Transp 75.9 1.3 2.8E-05 29.7 0.9 14 44-57 13-26 (46)
40 COG4888 Uncharacterized Zn rib 75.5 0.81 1.7E-05 36.6 -0.3 34 48-86 21-54 (104)
41 PF12756 zf-C2H2_2: C2H2 type 75.0 1.5 3.3E-05 31.9 1.1 25 49-73 50-75 (100)
42 PF04564 U-box: U-box domain; 74.5 2.3 5E-05 31.0 1.9 36 48-89 3-50 (73)
43 PF07754 DUF1610: Domain of un 74.3 1.8 3.9E-05 26.1 1.1 10 48-57 15-24 (24)
44 cd00729 rubredoxin_SM Rubredox 73.4 1.9 4.2E-05 27.5 1.2 26 49-87 2-27 (34)
45 smart00504 Ubox Modified RING 72.8 2.9 6.4E-05 28.6 2.1 25 58-89 22-46 (63)
46 PF04780 DUF629: Protein of un 72.4 1.9 4.1E-05 42.5 1.4 42 48-89 56-101 (466)
47 PRK14890 putative Zn-ribbon RN 70.6 2.7 5.8E-05 30.5 1.5 31 48-85 24-55 (59)
48 TIGR03655 anti_R_Lar restricti 68.6 2.1 4.6E-05 29.5 0.6 33 50-87 2-35 (53)
49 COG1592 Rubrerythrin [Energy p 67.3 4.2 9E-05 35.0 2.2 25 48-86 133-157 (166)
50 KOG2932 E3 ubiquitin ligase in 67.2 2.4 5.1E-05 40.3 0.8 58 49-106 90-177 (389)
51 PF03470 zf-XS: XS zinc finger 66.8 3.6 7.8E-05 28.1 1.4 22 81-102 1-22 (43)
52 PF09723 Zn-ribbon_8: Zinc rib 66.6 3.6 7.9E-05 27.2 1.4 31 48-86 4-34 (42)
53 PF05129 Elf1: Transcription e 66.5 2.2 4.8E-05 32.3 0.4 34 48-86 21-54 (81)
54 PF13912 zf-C2H2_6: C2H2-type 66.5 3.6 7.8E-05 23.9 1.2 23 50-72 2-25 (27)
55 PTZ00255 60S ribosomal protein 65.9 2.8 6.1E-05 32.8 0.9 14 48-61 35-49 (90)
56 PF02176 zf-TRAF: TRAF-type zi 65.1 2.9 6.3E-05 28.6 0.7 46 48-95 8-60 (60)
57 KOG3623 Homeobox transcription 64.9 1.8 3.9E-05 45.2 -0.5 49 48-96 209-260 (1007)
58 COG5175 MOT2 Transcriptional r 64.9 1.9 4.1E-05 41.5 -0.3 36 50-87 16-62 (480)
59 PF13465 zf-H2C2_2: Zinc-finge 64.9 1.8 3.9E-05 25.7 -0.3 11 49-59 14-24 (26)
60 PF03145 Sina: Seven in absent 63.6 4.3 9.3E-05 34.6 1.6 54 48-104 13-75 (198)
61 PRK06266 transcription initiat 63.5 5.7 0.00012 34.1 2.4 32 48-89 116-147 (178)
62 PRK12495 hypothetical protein; 63.2 4.3 9.3E-05 36.6 1.6 29 48-89 41-69 (226)
63 PHA00616 hypothetical protein 63.1 2.9 6.4E-05 28.6 0.4 25 50-74 2-27 (44)
64 smart00355 ZnF_C2H2 zinc finge 62.7 5 0.00011 21.8 1.3 20 50-69 1-21 (26)
65 smart00659 RPOLCX RNA polymera 61.8 5.3 0.00012 27.0 1.5 28 49-88 2-29 (44)
66 TIGR00373 conserved hypothetic 61.4 6.3 0.00014 33.1 2.2 32 48-89 108-139 (158)
67 PRK03976 rpl37ae 50S ribosomal 60.7 3.8 8.3E-05 32.0 0.7 13 48-60 35-48 (90)
68 PF12773 DZR: Double zinc ribb 60.3 6.2 0.00014 26.3 1.7 27 51-89 14-40 (50)
69 TIGR00280 L37a ribosomal prote 60.2 4 8.6E-05 32.0 0.7 13 48-60 34-47 (91)
70 KOG0320 Predicted E3 ubiquitin 59.7 3.6 7.7E-05 36.1 0.5 43 47-89 129-178 (187)
71 COG2888 Predicted Zn-ribbon RN 58.7 8.6 0.00019 28.1 2.2 31 48-85 26-57 (61)
72 PF15616 TerY-C: TerY-C metal 58.4 3.7 8E-05 34.1 0.3 38 50-89 78-116 (131)
73 PF07191 zinc-ribbons_6: zinc- 58.1 1.3 2.9E-05 33.1 -2.1 53 51-107 3-62 (70)
74 PF05605 zf-Di19: Drought indu 57.8 6.6 0.00014 26.9 1.5 25 79-103 3-28 (54)
75 PF05207 zf-CSL: CSL zinc fing 57.7 4.1 8.9E-05 28.6 0.4 46 32-89 4-51 (55)
76 PF06957 COPI_C: Coatomer (COP 57.3 4.5 9.7E-05 39.5 0.7 37 45-94 376-413 (422)
77 COG4311 SoxD Sarcosine oxidase 57.1 4.9 0.00011 31.8 0.8 9 49-57 3-11 (97)
78 PRK00464 nrdR transcriptional 56.8 7.4 0.00016 32.9 1.9 33 50-88 1-38 (154)
79 PF07282 OrfB_Zn_ribbon: Putat 56.4 8.6 0.00019 27.2 1.9 38 48-96 27-64 (69)
80 PF13719 zinc_ribbon_5: zinc-r 56.4 11 0.00025 24.2 2.3 29 50-86 3-33 (37)
81 PRK00420 hypothetical protein; 56.2 7.6 0.00016 31.4 1.8 28 49-88 23-50 (112)
82 PF11672 DUF3268: Protein of u 55.8 6.5 0.00014 31.3 1.3 38 50-90 3-43 (102)
83 PF10571 UPF0547: Uncharacteri 55.1 7.3 0.00016 23.6 1.2 8 52-59 3-10 (26)
84 PF01780 Ribosomal_L37ae: Ribo 55.1 4.4 9.6E-05 31.7 0.3 13 48-60 34-47 (90)
85 PF13395 HNH_4: HNH endonuclea 53.6 7.4 0.00016 26.8 1.2 14 52-65 1-14 (54)
86 PRK12496 hypothetical protein; 53.0 10 0.00022 32.1 2.2 27 49-88 127-153 (164)
87 PF08209 Sgf11: Sgf11 (transcr 50.5 8.3 0.00018 24.8 0.9 21 49-69 4-24 (33)
88 PF08996 zf-DNA_Pol: DNA Polym 50.3 4 8.7E-05 35.0 -0.7 40 48-89 17-56 (188)
89 PF10058 DUF2296: Predicted in 50.1 9 0.0002 27.0 1.2 10 48-57 43-52 (54)
90 PF13240 zinc_ribbon_2: zinc-r 49.9 6.9 0.00015 23.0 0.4 6 52-57 2-7 (23)
91 PF13248 zf-ribbon_3: zinc-rib 49.7 11 0.00023 22.5 1.3 10 50-59 3-12 (26)
92 PF09538 FYDLN_acid: Protein o 49.3 11 0.00024 30.1 1.7 28 48-88 8-36 (108)
93 TIGR00100 hypA hydrogenase nic 47.6 8.2 0.00018 30.8 0.7 26 48-86 69-94 (115)
94 smart00507 HNHc HNH nucleases. 47.5 5.8 0.00013 25.1 -0.1 21 50-70 11-31 (52)
95 TIGR00686 phnA alkylphosphonat 46.1 9.5 0.00021 30.9 0.9 24 51-86 4-27 (109)
96 COG1645 Uncharacterized Zn-fin 45.5 10 0.00022 31.6 0.9 25 49-86 28-52 (131)
97 PRK03922 hypothetical protein; 45.0 10 0.00023 30.8 0.9 15 49-63 49-63 (113)
98 KOG0402 60S ribosomal protein 44.9 6.6 0.00014 30.6 -0.2 12 48-59 35-47 (92)
99 COG0675 Transposase and inacti 44.9 14 0.0003 32.3 1.8 34 48-97 308-341 (364)
100 KOG2817 Predicted E3 ubiquitin 44.9 13 0.00029 36.0 1.8 15 48-62 373-387 (394)
101 TIGR00570 cdk7 CDK-activating 44.7 9.3 0.0002 35.9 0.7 40 49-89 3-54 (309)
102 COG4049 Uncharacterized protei 44.5 7.9 0.00017 28.2 0.2 26 80-105 19-46 (65)
103 PF14616 DUF4451: Domain of un 44.5 14 0.0003 30.0 1.6 27 78-104 25-56 (124)
104 PRK11088 rrmA 23S rRNA methylt 44.4 8.6 0.00019 34.0 0.4 32 49-80 2-34 (272)
105 CHL00174 accD acetyl-CoA carbo 44.2 14 0.00031 34.5 1.8 28 50-87 39-66 (296)
106 PF14446 Prok-RING_1: Prokaryo 44.1 14 0.00031 26.3 1.4 25 50-87 6-30 (54)
107 PF04475 DUF555: Protein of un 43.2 12 0.00025 30.0 0.9 15 49-63 47-61 (102)
108 PRK03824 hypA hydrogenase nick 42.8 13 0.00028 30.4 1.2 15 48-62 69-83 (135)
109 KOG2879 Predicted E3 ubiquitin 42.8 8.7 0.00019 35.8 0.2 41 48-88 238-286 (298)
110 PF09862 DUF2089: Protein of u 42.4 7.1 0.00015 31.6 -0.4 13 52-64 1-13 (113)
111 COG1499 NMD3 NMD protein affec 42.4 13 0.00028 35.5 1.2 38 48-85 5-50 (355)
112 TIGR00515 accD acetyl-CoA carb 42.4 18 0.00039 33.4 2.2 30 44-87 25-54 (285)
113 PF04981 NMD3: NMD3 family ; 42.0 17 0.00036 32.2 1.9 23 197-219 145-168 (236)
114 PF12660 zf-TFIIIC: Putative z 41.9 6.8 0.00015 30.6 -0.6 38 51-88 16-65 (99)
115 PF02146 SIR2: Sir2 family; I 41.7 14 0.00031 30.8 1.3 41 48-93 104-144 (178)
116 PRK05477 gatB aspartyl/glutamy 41.3 14 0.0003 36.6 1.4 23 67-89 26-48 (474)
117 PF14634 zf-RING_5: zinc-RING 41.3 16 0.00034 23.9 1.2 10 76-85 34-43 (44)
118 PF13717 zinc_ribbon_4: zinc-r 41.1 29 0.00062 22.3 2.4 31 50-86 3-33 (36)
119 PRK05654 acetyl-CoA carboxylas 40.7 17 0.00038 33.6 1.8 30 44-87 26-55 (292)
120 COG5189 SFP1 Putative transcri 40.6 14 0.00031 35.3 1.3 40 49-88 349-408 (423)
121 PRK12380 hydrogenase nickel in 40.1 13 0.00028 29.5 0.8 26 48-86 69-94 (113)
122 PF09706 Cas_CXXC_CXXC: CRISPR 39.8 12 0.00025 27.5 0.4 10 48-57 4-13 (69)
123 COG5109 Uncharacterized conser 39.3 15 0.00032 35.1 1.2 11 48-58 375-385 (396)
124 PRK11595 DNA utilization prote 38.8 15 0.00033 32.0 1.1 34 51-86 7-42 (227)
125 COG1198 PriA Primosomal protei 38.8 15 0.00032 38.3 1.2 38 48-87 443-484 (730)
126 PF01155 HypA: Hydrogenase exp 38.8 10 0.00022 30.1 -0.1 27 48-87 69-95 (113)
127 smart00451 ZnF_U1 U1-like zinc 37.9 25 0.00055 21.2 1.7 21 49-69 3-24 (35)
128 COG1405 SUA7 Transcription ini 37.8 20 0.00044 33.1 1.8 62 50-126 2-63 (285)
129 TIGR02300 FYDLN_acid conserved 37.8 20 0.00043 29.8 1.5 28 48-88 8-36 (129)
130 KOG2231 Predicted E3 ubiquitin 37.4 20 0.00044 37.0 1.9 26 49-74 182-208 (669)
131 PF12171 zf-C2H2_jaz: Zinc-fin 36.9 25 0.00054 20.6 1.5 20 50-69 2-22 (27)
132 PF05876 Terminase_GpA: Phage 36.5 20 0.00043 35.8 1.6 40 48-89 199-240 (557)
133 PLN02751 glutamyl-tRNA(Gln) am 35.8 19 0.00041 36.3 1.3 22 68-89 83-104 (544)
134 PF04423 Rad50_zn_hook: Rad50 35.6 13 0.00028 25.5 0.1 13 51-63 22-34 (54)
135 PRK04023 DNA polymerase II lar 35.1 22 0.00047 38.6 1.7 35 185-219 778-812 (1121)
136 smart00661 RPOL9 RNA polymeras 34.8 20 0.00044 23.7 1.0 27 51-86 2-28 (52)
137 KOG3608 Zn finger proteins [Ge 34.6 32 0.00069 33.5 2.6 49 48-97 262-313 (467)
138 TIGR03278 methan_mark_10 putat 34.5 19 0.00041 34.8 1.1 34 48-87 9-45 (404)
139 KOG3214 Uncharacterized Zn rib 34.3 18 0.00039 29.1 0.7 33 48-86 22-55 (109)
140 PF14353 CpXC: CpXC protein 33.9 20 0.00044 28.3 1.0 28 49-80 38-65 (128)
141 TIGR00133 gatB glutamyl-tRNA(G 33.9 21 0.00046 35.3 1.3 15 75-89 34-48 (478)
142 PF04267 SoxD: Sarcosine oxida 33.3 12 0.00027 28.8 -0.3 8 50-57 2-9 (84)
143 PF14311 DUF4379: Domain of un 32.6 31 0.00067 23.6 1.6 29 48-84 27-55 (55)
144 PF02934 GatB_N: GatB/GatE cat 32.6 24 0.00052 32.9 1.4 26 64-89 18-43 (289)
145 PF13824 zf-Mss51: Zinc-finger 32.5 20 0.00044 25.6 0.7 10 48-57 13-22 (55)
146 TIGR03830 CxxCG_CxxCG_HTH puta 32.3 17 0.00037 28.1 0.3 37 52-88 1-41 (127)
147 PF12230 PRP21_like_P: Pre-mRN 32.1 15 0.00033 32.1 0.0 22 77-98 167-189 (229)
148 PF09334 tRNA-synt_1g: tRNA sy 31.9 17 0.00036 34.6 0.3 40 50-89 137-177 (391)
149 TIGR01374 soxD sarcosine oxida 31.8 21 0.00045 27.6 0.7 8 50-57 2-9 (84)
150 PF00097 zf-C3HC4: Zinc finger 31.3 5 0.00011 25.3 -2.4 7 78-84 35-41 (41)
151 PRK10220 hypothetical protein; 30.8 29 0.00063 28.2 1.4 24 51-86 5-28 (111)
152 PF01844 HNH: HNH endonuclease 30.4 11 0.00025 24.1 -0.8 11 52-62 1-11 (47)
153 PF14570 zf-RING_4: RING/Ubox 30.3 13 0.00029 25.8 -0.5 32 48-86 14-45 (48)
154 KOG2177 Predicted E3 ubiquitin 30.2 15 0.00033 30.4 -0.3 38 48-85 12-54 (386)
155 PF04780 DUF629: Protein of un 29.8 22 0.00047 35.3 0.6 48 58-105 20-86 (466)
156 PF10276 zf-CHCC: Zinc-finger 29.7 21 0.00046 23.8 0.4 9 49-57 29-37 (40)
157 KOG2593 Transcription initiati 29.1 21 0.00046 35.1 0.4 32 48-86 127-161 (436)
158 COG1675 TFA1 Transcription ini 29.0 43 0.00093 29.1 2.2 31 48-88 112-142 (176)
159 TIGR01405 polC_Gram_pos DNA po 28.6 40 0.00087 37.1 2.4 47 30-88 671-718 (1213)
160 PF12230 PRP21_like_P: Pre-mRN 28.5 19 0.00041 31.5 0.0 21 49-69 168-188 (229)
161 KOG4696 Uncharacterized conser 28.0 28 0.0006 33.2 1.0 24 49-73 2-25 (393)
162 PRK14714 DNA polymerase II lar 27.9 35 0.00075 37.9 1.8 35 185-219 825-859 (1337)
163 PF02892 zf-BED: BED zinc fing 27.4 34 0.00074 22.0 1.1 9 49-57 16-24 (45)
164 PF14279 HNH_5: HNH endonuclea 26.9 26 0.00057 25.9 0.5 43 52-95 1-47 (71)
165 COG0777 AccD Acetyl-CoA carbox 26.6 38 0.00083 31.7 1.6 30 44-87 27-56 (294)
166 PRK00564 hypA hydrogenase nick 25.9 31 0.00067 27.5 0.8 27 48-86 70-96 (117)
167 PF11290 DUF3090: Protein of u 25.9 33 0.00072 29.8 1.0 14 50-63 155-168 (171)
168 cd00730 rubredoxin Rubredoxin; 25.8 34 0.00074 23.7 0.9 10 48-57 33-42 (50)
169 PHA02565 49 recombination endo 25.5 34 0.00073 29.4 1.0 42 48-89 19-66 (157)
170 COG2051 RPS27A Ribosomal prote 25.4 35 0.00077 25.4 0.9 29 50-88 20-48 (67)
171 PRK00448 polC DNA polymerase I 25.4 50 0.0011 37.1 2.4 47 30-88 896-943 (1437)
172 KOG3608 Zn finger proteins [Ge 25.1 44 0.00096 32.6 1.8 55 49-103 319-379 (467)
173 PF03966 Trm112p: Trm112p-like 25.1 38 0.00082 24.2 1.0 19 48-66 6-24 (68)
174 PF03604 DNA_RNApol_7kD: DNA d 24.7 38 0.00082 21.5 0.9 11 78-88 17-27 (32)
175 COG4391 Uncharacterized protei 24.5 35 0.00075 25.1 0.7 13 75-87 45-57 (62)
176 PF13453 zf-TFIIB: Transcripti 24.3 25 0.00054 22.8 -0.0 25 52-85 2-26 (41)
177 PF14369 zf-RING_3: zinc-finge 24.1 36 0.00079 21.8 0.7 10 50-59 22-31 (35)
178 PRK09678 DNA-binding transcrip 24.1 35 0.00076 25.5 0.7 8 50-57 2-9 (72)
179 KOG4628 Predicted E3 ubiquitin 23.9 24 0.00051 33.8 -0.3 41 48-88 228-277 (348)
180 cd03019 DsbA_DsbA DsbA family, 23.3 29 0.00062 27.7 0.1 19 48-66 23-42 (178)
181 PRK14714 DNA polymerase II lar 23.2 53 0.0012 36.5 2.1 37 49-90 667-704 (1337)
182 cd03021 DsbA_GSTK DsbA family, 23.2 18 0.00039 30.7 -1.1 12 48-59 7-18 (209)
183 PRK00423 tfb transcription ini 22.6 40 0.00087 31.0 1.0 38 48-95 10-47 (310)
184 KOG3623 Homeobox transcription 22.6 74 0.0016 33.8 2.9 48 49-98 281-331 (1007)
185 COG3058 FdhE Uncharacterized p 22.5 31 0.00066 32.4 0.2 18 77-94 184-201 (308)
186 PF00301 Rubredoxin: Rubredoxi 22.4 43 0.00092 23.0 0.8 10 48-57 33-42 (47)
187 COG1885 Uncharacterized protei 22.4 42 0.00092 27.2 0.9 16 49-64 49-64 (115)
188 PF06676 DUF1178: Protein of u 22.3 44 0.00095 28.3 1.0 10 77-86 31-40 (148)
189 smart00782 PhnA_Zn_Ribbon PhnA 22.2 26 0.00056 24.1 -0.3 39 48-88 6-46 (47)
190 PF12013 DUF3505: Protein of u 22.2 48 0.001 25.6 1.2 40 71-110 4-44 (109)
191 smart00614 ZnF_BED BED zinc fi 22.1 42 0.00091 22.5 0.8 25 49-73 18-48 (50)
192 PHA00733 hypothetical protein 22.1 57 0.0012 26.4 1.7 25 49-73 99-124 (128)
193 PF15135 UPF0515: Uncharacteri 22.0 43 0.00093 31.0 1.0 17 44-60 150-166 (278)
194 PF08273 Prim_Zn_Ribbon: Zinc- 21.9 38 0.00083 22.5 0.5 8 50-57 4-11 (40)
195 KOG4080 Mitochondrial ribosoma 21.7 39 0.00084 29.4 0.6 25 49-89 93-117 (176)
196 PRK01546 hypothetical protein; 21.5 87 0.0019 24.0 2.4 29 197-225 20-57 (79)
197 PF09889 DUF2116: Uncharacteri 21.4 51 0.0011 23.8 1.1 12 50-61 4-15 (59)
198 PF13639 zf-RING_2: Ring finge 21.3 8.4 0.00018 24.9 -2.8 27 50-84 17-43 (44)
199 PF12874 zf-met: Zinc-finger o 21.2 51 0.0011 18.4 0.9 16 81-96 3-20 (25)
200 cd03024 DsbA_FrnE DsbA family, 21.2 25 0.00054 28.9 -0.6 21 48-68 5-26 (201)
201 PRK05978 hypothetical protein; 21.2 39 0.00085 28.5 0.5 28 49-87 33-61 (148)
202 PF05979 DUF896: Bacterial pro 21.1 47 0.001 24.5 0.9 29 197-225 17-54 (65)
203 COG0178 UvrA Excinuclease ATPa 21.1 41 0.0009 35.9 0.8 34 48-86 244-277 (935)
204 PHA02929 N1R/p28-like protein; 21.1 21 0.00046 32.2 -1.1 41 48-88 173-226 (238)
205 PRK00907 hypothetical protein; 21.0 37 0.00081 26.4 0.4 21 49-69 13-35 (92)
206 COG1996 RPC10 DNA-directed RNA 21.0 57 0.0012 22.8 1.2 30 48-88 5-34 (49)
207 COG5574 PEX10 RING-finger-cont 21.0 21 0.00046 33.0 -1.2 42 49-90 215-263 (271)
208 TIGR00599 rad18 DNA repair pro 20.9 24 0.00053 34.2 -0.8 42 48-89 25-71 (397)
209 PRK14559 putative protein seri 20.5 63 0.0014 33.3 1.9 37 51-91 3-40 (645)
210 PRK00762 hypA hydrogenase nick 20.4 37 0.0008 27.4 0.2 7 50-56 93-99 (124)
211 PRK02539 hypothetical protein; 20.4 93 0.002 24.2 2.4 29 197-225 19-56 (85)
212 KOG2324 Prolyl-tRNA synthetase 20.3 58 0.0013 31.9 1.5 44 48-104 226-272 (457)
213 TIGR00244 transcriptional regu 20.2 43 0.00094 28.4 0.6 32 51-89 2-39 (147)
214 COG1997 RPL43A Ribosomal prote 20.1 34 0.00073 26.8 -0.1 13 44-58 32-44 (89)
215 cd02972 DsbA_family DsbA famil 20.1 26 0.00057 24.3 -0.6 18 48-65 5-23 (98)
No 1
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=100.00 E-value=3.4e-34 Score=225.94 Aligned_cols=102 Identities=51% Similarity=0.661 Sum_probs=83.4
Q ss_pred chhhhhHHHHhhhhhhhccCC-CCCCCCCCCCCCCccc-cccCCCCCCCcCCcCCCCCCCCC-CCCCCCccccccccccC
Q 027149 120 TISSLRKELQNAHFQSLLARS-SSSVSSSKKTSDPWLS-FIYNMPTADESESIQPALSTGEG-AEDKSSCEKTFETNAQQ 196 (227)
Q Consensus 120 ~~s~l~k~lre~~lq~llgg~-s~~~~~sn~~pDPLLS-Fi~n~~~~d~~~~~~p~~s~e~~-~~~~~s~~~~~e~~~~~ 196 (227)
|+|+|+|||||||||+||||+ +++.+++|++|||||| ||||+|.++.++.+++....++. ..++....+.+++.+ +
T Consensus 1 tlsll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~s~-~ 79 (105)
T PF14571_consen 1 TLSLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFPAPEAEEPSKSSSSSEEKKSSKKSSSEQNVKSSA-D 79 (105)
T ss_pred CcchhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCCCccccccCCccccccccccccccchhccccccc-C
Confidence 689999999999999999998 6667789999999999 99999999988888877554422 222233333444433 3
Q ss_pred CCCCHHHHHHHHhHhhHHHHHHHhhh
Q 027149 197 SSLSNEDHLEKANRSNFAQGLLFSTI 222 (227)
Q Consensus 197 ~~ls~ed~eEk~~R~eFVQgLllSTi 222 (227)
++||+||+|||+||++||||||||||
T Consensus 80 ~~lS~ee~eEk~~RseFVQ~LllSTI 105 (105)
T PF14571_consen 80 SSLSDEEQEEKAQRSEFVQGLLLSTI 105 (105)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhC
Confidence 89999999999999999999999998
No 2
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=99.77 E-value=2e-19 Score=125.52 Aligned_cols=53 Identities=38% Similarity=0.898 Sum_probs=51.6
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccchhhHhhhhcccc
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHITTQHG 101 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~~d~i~Hl~~qH~ 101 (227)
+|+||||+++||+.+|+.|+.++|+.+.+++|||||+.+++.||++||+.+|+
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 69999999999999999999999999999999999999999999999999996
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=98.86 E-value=1.9e-09 Score=100.40 Aligned_cols=64 Identities=23% Similarity=0.517 Sum_probs=58.0
Q ss_pred hhhhhhccccccccccCCcchhhhccCcceeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 20 TLKSQFAADFCIDFEDIEEDDYEEVKGEYEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 20 ~~~s~~d~d~~~g~e~~~~ddd~e~r~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
++.++.|+|+|+|+|-+--+++ ..|+||||+. +|....+.+|+...|+.....+|||||+..+.
T Consensus 56 cil~~~dfeL~f~Ge~i~~y~~------qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~ 120 (381)
T KOG1280|consen 56 CILSRVDFELYFGGEPISHYDP------QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPE 120 (381)
T ss_pred EEeeccceeeEecCcccccccc------ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcc
Confidence 4445678899999999998888 7899999999 99999999999999999999999999999765
No 4
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=93.97 E-value=0.024 Score=41.43 Aligned_cols=33 Identities=33% Similarity=0.837 Sum_probs=23.2
Q ss_pred ceeeCCCCCC--CccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 48 YEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e--~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
-+|||| ||. ++.+..|. ..-..++||-|+-.+-
T Consensus 21 ftyPCP-CGDRFeIsLeDl~--------~GE~VArCPSCSLiv~ 55 (67)
T COG5216 21 FTYPCP-CGDRFEISLEDLR--------NGEVVARCPSCSLIVC 55 (67)
T ss_pred EEecCC-CCCEeEEEHHHhh--------CCceEEEcCCceEEEE
Confidence 589999 988 44444443 3455789999988663
No 5
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.92 E-value=0.032 Score=41.16 Aligned_cols=46 Identities=35% Similarity=0.752 Sum_probs=28.8
Q ss_pred ccccCCcchhhhccCcceeeCCCCCCCc--cHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 32 DFEDIEEDDYEEVKGEYEYPCPFCSEDF--DLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 32 g~e~~~~ddd~e~r~~~~F~CPfC~e~~--d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
.++|++=|+|. -. -+|||| ||..| ....|. ..-..+.||-|+-.+.
T Consensus 8 eiedfe~~~e~-~~--y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 8 EIEDFEFDEEN-QT--YYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLIIR 55 (67)
T ss_pred EeecceeccCC-Ce--EEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEEE
Confidence 35666544331 12 589999 99844 444442 2345689999998664
No 6
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=93.47 E-value=0.038 Score=30.74 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=16.0
Q ss_pred eeCCCCCC-CccHHHhhhhhcccC
Q 027149 50 YPCPFCSE-DFDLVGLCCHIDEEH 72 (227)
Q Consensus 50 F~CPfC~e-~~d~~~L~~H~~~eH 72 (227)
|.||+|+. --+...|..|+...|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 68888888 667778888877655
No 7
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=92.93 E-value=0.057 Score=38.33 Aligned_cols=28 Identities=18% Similarity=0.557 Sum_probs=18.8
Q ss_pred CCCcccCCccccccc--hhhHhhhhccccc
Q 027149 75 EAKSGVCPVCVTRVT--MDMVDHITTQHGN 102 (227)
Q Consensus 75 e~~~vvCPVC~~~~~--~d~i~Hl~~qH~~ 102 (227)
......||+|.+.+. +|+-+||-..|+.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 344679999999765 7999999998864
No 8
>PLN03086 PRLI-interacting factor K; Provisional
Probab=91.40 E-value=0.17 Score=50.74 Aligned_cols=48 Identities=23% Similarity=0.428 Sum_probs=37.5
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc-chhhHhhhhccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV-TMDMVDHITTQH 100 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~-~~d~i~Hl~~qH 100 (227)
.-+.||+|++.|....|-.|....| +.+.|| |.... ..++..|++...
T Consensus 452 ~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~thC 500 (567)
T PLN03086 452 NHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQASTC 500 (567)
T ss_pred cCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhhccC
Confidence 4578999999888999999998765 678999 96543 368888876533
No 9
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=90.89 E-value=0.13 Score=30.72 Aligned_cols=21 Identities=33% Similarity=0.661 Sum_probs=18.6
Q ss_pred eeeCCCCCCCccHHHhhhhhc
Q 027149 49 EYPCPFCSEDFDLVGLCCHID 69 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~ 69 (227)
..+||+|+..|....|-.|..
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 468999999999999999964
No 10
>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=89.55 E-value=0.12 Score=36.68 Aligned_cols=31 Identities=19% Similarity=0.583 Sum_probs=22.1
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
.|.||-|+..+++..... .-.+.||.|.+.+
T Consensus 2 ~~~CP~CG~~iev~~~~~---------GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIELENPEL---------GELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEecCCCcc---------CCEEeCCCCCCEE
Confidence 489999999886654421 2368999997743
No 11
>PHA00732 hypothetical protein
Probab=89.41 E-value=0.38 Score=36.30 Aligned_cols=43 Identities=28% Similarity=0.634 Sum_probs=32.3
Q ss_pred eeCCCCCCCc-cHHHhhhhhcccCCCCCCcccCCccccccchhhHhhhh
Q 027149 50 YPCPFCSEDF-DLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHIT 97 (227)
Q Consensus 50 F~CPfC~e~~-d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~~d~i~Hl~ 97 (227)
|.|+.|+..| ....|..|....|.. ..|++|...-. ++..|+.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~----~~C~~CgKsF~-~l~~H~~ 45 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL----TKCPVCNKSYR-RLNQHFY 45 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC----CccCCCCCEeC-Chhhhhc
Confidence 8899999944 788899998865653 26999977553 5677763
No 12
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=89.37 E-value=0.12 Score=29.27 Aligned_cols=21 Identities=29% Similarity=0.611 Sum_probs=13.8
Q ss_pred eeCCCCCC-CccHHHhhhhhcc
Q 027149 50 YPCPFCSE-DFDLVGLCCHIDE 70 (227)
Q Consensus 50 F~CPfC~e-~~d~~~L~~H~~~ 70 (227)
|.||.|+. =-+...|..|+..
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 67888877 4455666667654
No 13
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=88.79 E-value=0.14 Score=35.68 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=19.5
Q ss_pred eeeCCCCCC-CccHHHhhhhhcccCCCCC---CcccCCcccc
Q 027149 49 EYPCPFCSE-DFDLVGLCCHIDEEHPVEA---KSGVCPVCVT 86 (227)
Q Consensus 49 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e~---~~vvCPVC~~ 86 (227)
..+|||||. .+.+.. ...... ..|.|.-|.+
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 468999987 554433 222222 5678999976
No 14
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=88.49 E-value=0.21 Score=36.51 Aligned_cols=48 Identities=25% Similarity=0.554 Sum_probs=14.0
Q ss_pred eCCCCCCC-ccHHHhhhhhcccCCCCCC---------------------cccCCcccccc--chhhHhhhhc
Q 027149 51 PCPFCSED-FDLVGLCCHIDEEHPVEAK---------------------SGVCPVCVTRV--TMDMVDHITT 98 (227)
Q Consensus 51 ~CPfC~e~-~d~~~L~~H~~~eH~~e~~---------------------~vvCPVC~~~~--~~d~i~Hl~~ 98 (227)
.|+||+.. -++..|..|+...|.+... .-.|++|.... ...+..||..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcC
Confidence 39999994 5688999999999987432 12499998865 3688889874
No 15
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=88.41 E-value=0.45 Score=45.67 Aligned_cols=32 Identities=28% Similarity=0.480 Sum_probs=26.2
Q ss_pred eeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 49 EYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 49 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
-=.|-||.. =+|-.+|..||...| -.|-||..
T Consensus 220 HP~C~FC~~~FYdDDEL~~HcR~~H------E~ChICD~ 252 (493)
T COG5236 220 HPLCIFCKIYFYDDDELRRHCRLRH------EACHICDM 252 (493)
T ss_pred CchhhhccceecChHHHHHHHHhhh------hhhhhhhc
Confidence 346999999 889999999999888 35777754
No 16
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=88.39 E-value=0.32 Score=44.89 Aligned_cols=35 Identities=23% Similarity=0.605 Sum_probs=20.0
Q ss_pred ceeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
..|.||+|++ .+.+..|--|+. .|. -.-+|+||..
T Consensus 160 ka~~C~~C~K~YvSmpALkMHir-TH~---l~c~C~iCGK 195 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIR-THT---LPCECGICGK 195 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhh-ccC---CCcccccccc
Confidence 4566666666 666666666666 332 1234555544
No 17
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=88.36 E-value=0.17 Score=29.17 Aligned_cols=24 Identities=38% Similarity=0.778 Sum_probs=16.1
Q ss_pred eeCCCCCCCccHHHhhhhhcccCC
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHP 73 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~ 73 (227)
|.||+|+..-....|..|+...|+
T Consensus 1 y~C~~C~y~t~~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTSKSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EESHHHHHHHHHHHHS
T ss_pred CCCCCCCCcCCHHHHHHHHHhhCc
Confidence 689999883337788888887664
No 18
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=87.84 E-value=0.2 Score=36.86 Aligned_cols=31 Identities=26% Similarity=0.539 Sum_probs=21.8
Q ss_pred ceeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 48 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
..-|||||+. .+.+. |......++|.-|.+.
T Consensus 5 ~lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 5 NVKPCPFCGCPSVTVK---------AISGYYRAKCNGCESR 36 (64)
T ss_pred cccCCCCCCCceeEEE---------ecCceEEEEcCCCCcC
Confidence 4569999999 65554 2333445999999774
No 19
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.55 E-value=0.45 Score=39.24 Aligned_cols=37 Identities=22% Similarity=0.530 Sum_probs=25.8
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
..|.||.|+.-|+...-..... . ....+||.|...+-
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEELE 134 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEEE
Confidence 6899999999776655433322 2 34589999988653
No 20
>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=86.69 E-value=0.19 Score=33.32 Aligned_cols=34 Identities=24% Similarity=0.556 Sum_probs=21.4
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccchhhH
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMV 93 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~~d~i 93 (227)
|.||.|+... + +.+ ......||+.|-..+..+.+
T Consensus 1 m~Cp~Cg~~~-~------~~D---~~~g~~vC~~CG~Vl~e~~i 34 (43)
T PF08271_consen 1 MKCPNCGSKE-I------VFD---PERGELVCPNCGLVLEENII 34 (43)
T ss_dssp ESBTTTSSSE-E------EEE---TTTTEEEETTT-BBEE-TTB
T ss_pred CCCcCCcCCc-e------EEc---CCCCeEECCCCCCEeecccc
Confidence 6899999843 2 111 34566899999777665544
No 21
>PHA00733 hypothetical protein
Probab=86.35 E-value=0.88 Score=37.03 Aligned_cols=50 Identities=38% Similarity=0.700 Sum_probs=35.7
Q ss_pred ceeeCCCCCCCc-cHHHhhhhhcccCCCCCCcccCCcccccc--chhhHhhhhcccc
Q 027149 48 YEYPCPFCSEDF-DLVGLCCHIDEEHPVEAKSGVCPVCVTRV--TMDMVDHITTQHG 101 (227)
Q Consensus 48 ~~F~CPfC~e~~-d~~~L~~H~~~eH~~e~~~vvCPVC~~~~--~~d~i~Hl~~qH~ 101 (227)
..|.|+.|+..| ....|..|... | .....|++|.... ..++..|+.--|+
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~-h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRY-T---EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhc-C---CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 359999999954 45667888773 2 2346999997743 3688888877775
No 22
>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=86.12 E-value=0.33 Score=31.05 Aligned_cols=33 Identities=30% Similarity=0.735 Sum_probs=23.1
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
.+|.||-||..|++..-. .+...++||.|.+.+
T Consensus 4 Y~y~C~~Cg~~fe~~~~~--------~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKI--------SDDPLATCPECGGDV 36 (41)
T ss_pred EEEEcCCCCCEEEEEEec--------CCCCCCCCCCCCCcc
Confidence 479999999977754321 125668899998743
No 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=85.18 E-value=0.69 Score=46.53 Aligned_cols=38 Identities=18% Similarity=0.314 Sum_probs=26.5
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
..|.|| |+..+....|..|+. .|+-. +...|+.|...+
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~-thCp~-Kpi~C~fC~~~v 514 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQA-STCPL-RLITCRFCGDMV 514 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhh-ccCCC-CceeCCCCCCcc
Confidence 347788 887777788888865 45543 667788887655
No 24
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.46 E-value=0.37 Score=42.27 Aligned_cols=19 Identities=21% Similarity=0.642 Sum_probs=14.8
Q ss_pred ceeeCCCCCCCccHHHhhh
Q 027149 48 YEYPCPFCSEDFDLVGLCC 66 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~ 66 (227)
-+++||+|+..|....+..
T Consensus 4 k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CceECCCCCCeeeeeEEEc
Confidence 4689999999998775543
No 25
>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=84.14 E-value=0.96 Score=28.80 Aligned_cols=32 Identities=22% Similarity=0.422 Sum_probs=20.5
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
+.||.|+.-|.+..-. .......+.||.|-..
T Consensus 3 ~~CP~C~~~~~v~~~~------~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ------LGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHH------cCCCCCEEECCCCCCE
Confidence 7899999955554321 1222346899999654
No 26
>PHA02768 hypothetical protein; Provisional
Probab=82.60 E-value=0.88 Score=32.49 Aligned_cols=34 Identities=24% Similarity=0.535 Sum_probs=25.2
Q ss_pred eeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 49 EYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 49 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
.|.||.||+ =...+.|..|... |. ++-.|..|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~-H~---k~~kc~~C~k 39 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK-HN---TNLKLSNCKR 39 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh-cC---CcccCCcccc
Confidence 489999999 5566789999997 44 4556777744
No 27
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.32 E-value=0.63 Score=42.33 Aligned_cols=13 Identities=31% Similarity=0.925 Sum_probs=10.2
Q ss_pred ceeeCCCCCCCcc
Q 027149 48 YEYPCPFCSEDFD 60 (227)
Q Consensus 48 ~~F~CPfC~e~~d 60 (227)
.++.||+|+.-|-
T Consensus 18 k~ieCPvC~tkFk 30 (267)
T COG1655 18 KTIECPVCNTKFK 30 (267)
T ss_pred ceeccCcccchhh
Confidence 5799999976554
No 28
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=81.06 E-value=0.57 Score=29.54 Aligned_cols=24 Identities=29% Similarity=0.901 Sum_probs=12.7
Q ss_pred eCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 51 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 51 ~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
+||.|+.++.. .+....|||-|..
T Consensus 4 ~Cp~C~se~~y------------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY------------EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E------------E-SSSEEETTTTE
T ss_pred CCCCCCCccee------------ccCCEEeCCcccc
Confidence 69999886655 4667789999964
No 29
>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=80.44 E-value=1.2 Score=30.09 Aligned_cols=31 Identities=29% Similarity=0.845 Sum_probs=22.1
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
.+|.|+-|+..|++. .... +...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~---~~~~-----~~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVL---QKMS-----DDPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEE---EecC-----CCCCCCCCCCCC
Confidence 479999999988853 1222 145578999976
No 30
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=80.40 E-value=0.63 Score=40.91 Aligned_cols=43 Identities=26% Similarity=0.654 Sum_probs=27.3
Q ss_pred ceeeCCCCCCCcc--HHHhhhhh-----cccCC--------------CCCCcccCCccccccch
Q 027149 48 YEYPCPFCSEDFD--LVGLCCHI-----DEEHP--------------VEAKSGVCPVCVTRVTM 90 (227)
Q Consensus 48 ~~F~CPfC~e~~d--~~~L~~H~-----~~eH~--------------~e~~~vvCPVC~~~~~~ 90 (227)
..|.||.|.+.+. +...|.|. ..... ...+...||+|...+..
T Consensus 17 ~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 17 GDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 5799999988333 44557772 32211 12345689999998864
No 31
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=78.58 E-value=0.95 Score=35.79 Aligned_cols=34 Identities=15% Similarity=0.401 Sum_probs=20.5
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
..|.||+|++ ..+ .+.-.+ ..--++||+|-..-+
T Consensus 20 t~f~CP~Cge-~~v-----~v~~~k--~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 20 KIFECPRCGK-VSI-----SVKIKK--NIAIITCGNCGLYTE 53 (99)
T ss_pred cEeECCCCCC-eEe-----eeecCC--CcceEECCCCCCccC
Confidence 5799999995 211 111111 233489999976544
No 32
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=78.40 E-value=0.72 Score=32.47 Aligned_cols=34 Identities=24% Similarity=0.586 Sum_probs=19.7
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
+.|||||+.+++ +...-.. .....-=|+||-..+
T Consensus 1 i~CPyCge~~~~--~iD~s~~---~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 1 IQCPYCGEPIEI--LIDPSAG---DQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCCeeEE--EEecCCC---CeeEEeehhhcCCcc
Confidence 479999997665 2222221 222334599996644
No 33
>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=77.86 E-value=1.2 Score=28.06 Aligned_cols=24 Identities=42% Similarity=0.888 Sum_probs=16.0
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
|.|+.||.-++... ..-+||+|.+
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCC
Confidence 67888886444332 4568999965
No 34
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=77.57 E-value=0.95 Score=30.25 Aligned_cols=30 Identities=30% Similarity=0.674 Sum_probs=20.5
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
-+|.||-||..|+..... ....||.|..++
T Consensus 2 ~~y~C~~CG~~~~~~~~~-----------~~~~Cp~CG~~~ 31 (46)
T PRK00398 2 AEYKCARCGREVELDEYG-----------TGVRCPYCGYRI 31 (46)
T ss_pred CEEECCCCCCEEEECCCC-----------CceECCCCCCeE
Confidence 368999999877653211 167899997644
No 35
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=76.52 E-value=1.6 Score=33.17 Aligned_cols=24 Identities=46% Similarity=1.233 Sum_probs=16.7
Q ss_pred eeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCcc
Q 027149 50 YPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVC 84 (227)
Q Consensus 50 F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC 84 (227)
|+||-||. -|+..+ +...-|||||
T Consensus 2 ~~CPCCg~~Tl~~~~-----------~~~ydIC~VC 26 (78)
T PF14206_consen 2 YPCPCCGYYTLEERG-----------EGTYDICPVC 26 (78)
T ss_pred ccCCCCCcEEeccCC-----------CcCceECCCC
Confidence 89999987 554322 2225699999
No 36
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=76.39 E-value=1.7 Score=26.28 Aligned_cols=19 Identities=26% Similarity=0.621 Sum_probs=10.5
Q ss_pred eCCCCCCCccHHHhhhhhc
Q 027149 51 PCPFCSEDFDLVGLCCHID 69 (227)
Q Consensus 51 ~CPfC~e~~d~~~L~~H~~ 69 (227)
.||.|+..+....+-.|++
T Consensus 3 ~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREVPENLINSHLD 21 (26)
T ss_pred cCCCCcCcccHHHHHHHHH
Confidence 4555555555555555554
No 37
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=76.32 E-value=0.98 Score=44.41 Aligned_cols=34 Identities=35% Similarity=0.609 Sum_probs=28.9
Q ss_pred hccCcceeeCCCCCCCc-cHHHhhhhhcccCCCCCCc
Q 027149 43 EVKGEYEYPCPFCSEDF-DLVGLCCHIDEEHPVEAKS 78 (227)
Q Consensus 43 e~r~~~~F~CPfC~e~~-d~~~L~~H~~~eH~~e~~~ 78 (227)
|++ .-|.||+|.++| .+..|-+|++.+|..+-+.
T Consensus 11 ~i~--egflCPiC~~dl~~~~~L~~H~d~eH~~ed~~ 45 (505)
T KOG1842|consen 11 EIL--EGFLCPICLLDLPNLSALNDHLDVEHFEEDEK 45 (505)
T ss_pred hhh--hcccCchHhhhhhhHHHHHHHHhhhccccchh
Confidence 466 789999999977 4788999999999998753
No 38
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=76.32 E-value=2.8 Score=38.79 Aligned_cols=80 Identities=28% Similarity=0.436 Sum_probs=50.2
Q ss_pred eeeCCCCCCCccHHHhh-hhhcccCCCCCCcccCCccccccc--hhhHhhhhccccccccccccccccc-CCCCcchhhh
Q 027149 49 EYPCPFCSEDFDLVGLC-CHIDEEHPVEAKSGVCPVCVTRVT--MDMVDHITTQHGNISNSWHKLKLHK-GNSNSTISSL 124 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~-~H~~~eH~~e~~~vvCPVC~~~~~--~d~i~Hl~~qH~~~~K~~r~rk~rk-~~s~s~~s~l 124 (227)
-+.|++||+-|+..=|. -|+. .|..| |.-.||.|..--. .|+-.||+. |+.. | +-+..+ +-+-+-.|+|
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiR-THTGE-KPF~C~hC~kAFADRSNLRAHmQT-HS~~-K---~~qC~~C~KsFsl~SyL 259 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIR-THTGE-KPFSCPHCGKAFADRSNLRAHMQT-HSDV-K---KHQCPRCGKSFALKSYL 259 (279)
T ss_pred CcccccccccccchHHhhcccc-cccCC-CCccCCcccchhcchHHHHHHHHh-hcCC-c---cccCcchhhHHHHHHHH
Confidence 48999999999987654 5766 66654 5679999977543 699999975 4333 1 111112 1123445677
Q ss_pred hHHHHhhhhhh
Q 027149 125 RKELQNAHFQS 135 (227)
Q Consensus 125 ~k~lre~~lq~ 135 (227)
-|-+..|=+-.
T Consensus 260 nKH~ES~C~~~ 270 (279)
T KOG2462|consen 260 NKHSESACLKY 270 (279)
T ss_pred HHhhhhccccc
Confidence 77555543333
No 39
>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=75.94 E-value=1.3 Score=29.69 Aligned_cols=14 Identities=21% Similarity=0.764 Sum_probs=12.0
Q ss_pred ccCcceeeCCCCCC
Q 027149 44 VKGEYEYPCPFCSE 57 (227)
Q Consensus 44 ~r~~~~F~CPfC~e 57 (227)
+||...|.||+||-
T Consensus 13 ~RW~~g~~CP~Cg~ 26 (46)
T PF12760_consen 13 IRWPDGFVCPHCGS 26 (46)
T ss_pred hcCCCCCCCCCCCC
Confidence 67878899999986
No 40
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=75.52 E-value=0.81 Score=36.59 Aligned_cols=34 Identities=21% Similarity=0.448 Sum_probs=21.0
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
-+|.||+|+..--++-++ .-.....+++|-+|-.
T Consensus 21 k~FtCp~Cghe~vs~ctv-----kk~~~~g~~~Cg~CGl 54 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTV-----KKTVNIGTAVCGNCGL 54 (104)
T ss_pred ceEecCccCCeeeeEEEE-----EecCceeEEEcccCcc
Confidence 589999999743332221 1123345688999955
No 41
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=74.96 E-value=1.5 Score=31.91 Aligned_cols=25 Identities=28% Similarity=0.789 Sum_probs=20.5
Q ss_pred eeeCCCCCCCc-cHHHhhhhhcccCC
Q 027149 49 EYPCPFCSEDF-DLVGLCCHIDEEHP 73 (227)
Q Consensus 49 ~F~CPfC~e~~-d~~~L~~H~~~eH~ 73 (227)
.|.|++|++.| +...|..|+...|.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccC
Confidence 59999999966 89999999997643
No 42
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=74.48 E-value=2.3 Score=30.97 Aligned_cols=36 Identities=17% Similarity=0.450 Sum_probs=22.4
Q ss_pred ceeeCCCCCC------------CccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 48 YEYPCPFCSE------------DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e------------~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
..|.||.|++ -||...+-.++.. +..+||+|...+.
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~ 50 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLS 50 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-S
T ss_pred cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCC
Confidence 3588888754 4666677666664 5689999977665
No 43
>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=74.25 E-value=1.8 Score=26.05 Aligned_cols=10 Identities=40% Similarity=1.168 Sum_probs=8.9
Q ss_pred ceeeCCCCCC
Q 027149 48 YEYPCPFCSE 57 (227)
Q Consensus 48 ~~F~CPfC~e 57 (227)
..|+||-||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 6899999996
No 44
>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=73.36 E-value=1.9 Score=27.47 Aligned_cols=26 Identities=23% Similarity=0.617 Sum_probs=17.1
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
.|.|+.||.-++... ..-+||||-+.
T Consensus 2 ~~~C~~CG~i~~g~~-------------~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEE-------------APEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCc-------------CCCcCcCCCCc
Confidence 478999997433221 23499999763
No 45
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=72.81 E-value=2.9 Score=28.56 Aligned_cols=25 Identities=16% Similarity=0.177 Sum_probs=16.2
Q ss_pred CccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 58 DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 58 ~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
-|+...+..++.. ...||+|...+.
T Consensus 22 v~~~~~i~~~~~~-------~~~cP~~~~~~~ 46 (63)
T smart00504 22 TYERRAIEKWLLS-------HGTDPVTGQPLT 46 (63)
T ss_pred EEeHHHHHHHHHH-------CCCCCCCcCCCC
Confidence 4555666666543 468999977664
No 46
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=72.36 E-value=1.9 Score=42.50 Aligned_cols=42 Identities=29% Similarity=0.420 Sum_probs=33.8
Q ss_pred ceeeCCCCCC-CccHHHhhhhhcccCCCCCCc---ccCCccccccc
Q 027149 48 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKS---GVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~---vvCPVC~~~~~ 89 (227)
.--.||+|.+ -.|..++..|+..+|...-.+ -+.|-+....|
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~~w 101 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDDDW 101 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCHHH
Confidence 4678999999 999999999999999986543 46676666544
No 47
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=70.57 E-value=2.7 Score=30.54 Aligned_cols=31 Identities=26% Similarity=0.667 Sum_probs=21.8
Q ss_pred ceeeCCCCCCC-ccHHHhhhhhcccCCCCCCcccCCccc
Q 027149 48 YEYPCPFCSED-FDLVGLCCHIDEEHPVEAKSGVCPVCV 85 (227)
Q Consensus 48 ~~F~CPfC~e~-~d~~~L~~H~~~eH~~e~~~vvCPVC~ 85 (227)
..|.||-||+. +-. |..|.. .++.-+||-|-
T Consensus 24 ~~F~CPnCG~~~I~R---C~~CRk----~~~~Y~CP~CG 55 (59)
T PRK14890 24 VKFLCPNCGEVIIYR---CEKCRK----QSNPYTCPKCG 55 (59)
T ss_pred CEeeCCCCCCeeEee---chhHHh----cCCceECCCCC
Confidence 67999999994 544 444442 35677899984
No 48
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=68.62 E-value=2.1 Score=29.50 Aligned_cols=33 Identities=27% Similarity=0.448 Sum_probs=16.8
Q ss_pred eeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 50 YPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 50 F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
-+|||||- +.-+.. .+-. ........|+-|-+.
T Consensus 2 kPCPfCGg~~~~~~~--~~~~---~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRR--GFDP---LDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEe--ccCC---CCCEEEEECCCCCCC
Confidence 38999998 442210 0100 112223479999664
No 49
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=67.28 E-value=4.2 Score=34.99 Aligned_cols=25 Identities=28% Similarity=0.751 Sum_probs=17.3
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
..+.||.||- +. -. -.+.+||||-+
T Consensus 133 ~~~vC~vCGy----------~~---~g-e~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGY----------TH---EG-EAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCC----------cc---cC-CCCCcCCCCCC
Confidence 3689999974 21 22 34689999975
No 50
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=67.22 E-value=2.4 Score=40.27 Aligned_cols=58 Identities=26% Similarity=0.528 Sum_probs=37.5
Q ss_pred eeeCCCCCCCccHHH---hhhhhcccCCCCCC-cccCCccccccc--------------------------hhhHhhhhc
Q 027149 49 EYPCPFCSEDFDLVG---LCCHIDEEHPVEAK-SGVCPVCVTRVT--------------------------MDMVDHITT 98 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~---L~~H~~~eH~~e~~-~vvCPVC~~~~~--------------------------~d~i~Hl~~ 98 (227)
.-.|--|++-+-+-+ =|+|+-=.-|.-+. -.+||.|..+|- +||-.||++
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~VqrIeq~~~g~iFmC~~~~GC~RTyLsqrDlqAHInh 169 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQRIEQIMMGGIFMCAAPHGCLRTYLSQRDLQAHINH 169 (389)
T ss_pred eEeecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHHHHHHhcccceEEeecchhHHHHHhhHHHHHHHhhh
Confidence 456777776554433 35554322222111 368999998642 799999999
Q ss_pred cccccccc
Q 027149 99 QHGNISNS 106 (227)
Q Consensus 99 qH~~~~K~ 106 (227)
+|+.++|-
T Consensus 170 rH~~~~~p 177 (389)
T KOG2932|consen 170 RHGSLLQP 177 (389)
T ss_pred hhccccCC
Confidence 99988764
No 51
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=66.84 E-value=3.6 Score=28.10 Aligned_cols=22 Identities=27% Similarity=0.505 Sum_probs=11.9
Q ss_pred CCccccccchhhHhhhhccccc
Q 027149 81 CPVCVTRVTMDMVDHITTQHGN 102 (227)
Q Consensus 81 CPVC~~~~~~d~i~Hl~~qH~~ 102 (227)
||.|..+.+.|+.=+-.+||..
T Consensus 1 CP~C~~kkk~~Y~~~~LlqHA~ 22 (43)
T PF03470_consen 1 CPFCPGKKKQDYKYRELLQHAS 22 (43)
T ss_pred CCCCCCCCCcceehhHHHHHHH
Confidence 6777666554444333455544
No 52
>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=66.55 E-value=3.6 Score=27.16 Aligned_cols=31 Identities=35% Similarity=0.855 Sum_probs=22.4
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
.+|.|+-||..|++..- + .+...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~~---~-----~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQS---I-----SEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEE---c-----CCCCCCcCCCCCC
Confidence 47999999987775432 1 1256789999976
No 53
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=66.53 E-value=2.2 Score=32.32 Aligned_cols=34 Identities=21% Similarity=0.537 Sum_probs=13.5
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
..|.||||+-.-.+ .+.-+.......+.|-+|-.
T Consensus 21 ~~F~CPfC~~~~sV-----~v~idkk~~~~~~~C~~Cg~ 54 (81)
T PF05129_consen 21 KVFDCPFCNHEKSV-----SVKIDKKEGIGILSCRVCGE 54 (81)
T ss_dssp S----TTT--SS-E-----EEEEETTTTEEEEEESSS--
T ss_pred ceEcCCcCCCCCeE-----EEEEEccCCEEEEEecCCCC
Confidence 57999999932111 12212223445578999955
No 54
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=66.46 E-value=3.6 Score=23.85 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=16.5
Q ss_pred eeCCCCCC-CccHHHhhhhhcccC
Q 027149 50 YPCPFCSE-DFDLVGLCCHIDEEH 72 (227)
Q Consensus 50 F~CPfC~e-~~d~~~L~~H~~~eH 72 (227)
|.|..|+. =-+...|..|....|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 77888888 456777888876444
No 55
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=65.94 E-value=2.8 Score=32.76 Aligned_cols=14 Identities=36% Similarity=0.959 Sum_probs=11.1
Q ss_pred ceeeCCCCCC-CccH
Q 027149 48 YEYPCPFCSE-DFDL 61 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~ 61 (227)
+.|.||||+. .+..
T Consensus 35 a~y~CpfCgk~~vkR 49 (90)
T PTZ00255 35 AKYFCPFCGKHAVKR 49 (90)
T ss_pred CCccCCCCCCCceee
Confidence 7899999987 5543
No 56
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=65.06 E-value=2.9 Score=28.56 Aligned_cols=46 Identities=35% Similarity=0.685 Sum_probs=29.6
Q ss_pred ceeeCCC--CCCCccHHHhhhhhcccCCCCCCcccCCc----cccccc-hhhHhh
Q 027149 48 YEYPCPF--CSEDFDLVGLCCHIDEEHPVEAKSGVCPV----CVTRVT-MDMVDH 95 (227)
Q Consensus 48 ~~F~CPf--C~e~~d~~~L~~H~~~eH~~e~~~vvCPV----C~~~~~-~d~i~H 95 (227)
....||+ |.+.+-...|-.|+..+=+ -+.+.||. |..++. .++..|
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~--~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECP--KRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTST--TSEEE-SS----S--EEEHHHHHHC
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCC--CCcEECCCCCCCCCCccchhHHhCC
Confidence 3588999 6667999999999985422 35789999 988765 455554
No 57
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=64.93 E-value=1.8 Score=45.15 Aligned_cols=49 Identities=22% Similarity=0.442 Sum_probs=38.4
Q ss_pred ceeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCccccccc--hhhHhhh
Q 027149 48 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT--MDMVDHI 96 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~--~d~i~Hl 96 (227)
+..+||||+. .-.+..|..|+.-.|--..-+.-|+.|..... ..+-+|+
T Consensus 209 qlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm 260 (1007)
T KOG3623|consen 209 QLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHM 260 (1007)
T ss_pred hhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHH
Confidence 4689999999 55678999999999998888889999987432 3444444
No 58
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=64.88 E-value=1.9 Score=41.46 Aligned_cols=36 Identities=31% Similarity=0.852 Sum_probs=23.3
Q ss_pred eeCCCCCCCccHHH-----------hhhhhcccCCCCCCcccCCccccc
Q 027149 50 YPCPFCSEDFDLVG-----------LCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 50 F~CPfC~e~~d~~~-----------L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
| ||.|-|.+|+.. +|..|- .|.-+.-++.||.|..+
T Consensus 16 ~-cplcie~mditdknf~pc~cgy~ic~fc~-~~irq~lngrcpacrr~ 62 (480)
T COG5175 16 Y-CPLCIEPMDITDKNFFPCPCGYQICQFCY-NNIRQNLNGRCPACRRK 62 (480)
T ss_pred c-CcccccccccccCCcccCCcccHHHHHHH-HHHHhhccCCChHhhhh
Confidence 5 888877777653 343333 33445578999999764
No 59
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=64.87 E-value=1.8 Score=25.71 Aligned_cols=11 Identities=45% Similarity=1.558 Sum_probs=9.0
Q ss_pred eeeCCCCCCCc
Q 027149 49 EYPCPFCSEDF 59 (227)
Q Consensus 49 ~F~CPfC~e~~ 59 (227)
-|.||+|+..|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 49999998754
No 60
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=63.55 E-value=4.3 Score=34.60 Aligned_cols=54 Identities=22% Similarity=0.496 Sum_probs=32.5
Q ss_pred ceeeCCC----CCCCccHHHhhhhhcccCCCCCCcccCCc----cccc-cchhhHhhhhccccccc
Q 027149 48 YEYPCPF----CSEDFDLVGLCCHIDEEHPVEAKSGVCPV----CVTR-VTMDMVDHITTQHGNIS 104 (227)
Q Consensus 48 ~~F~CPf----C~e~~d~~~L~~H~~~eH~~e~~~vvCPV----C~~~-~~~d~i~Hl~~qH~~~~ 104 (227)
-.|||+| |.+.+-......|.+ .-.-+...||+ |.-. ...++..|+...|+...
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE~---~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHEE---ECPFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHHH---T-TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhHhc---cCCCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 4699999 999888888888865 23445678999 7332 23699999999998743
No 61
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=63.54 E-value=5.7 Score=34.08 Aligned_cols=32 Identities=22% Similarity=0.402 Sum_probs=23.6
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
..|.||-|+.-|+..+-.. ..-.||+|-..+-
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME----------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCCe
Confidence 6899999999666555432 2579999988654
No 62
>PRK12495 hypothetical protein; Provisional
Probab=63.15 E-value=4.3 Score=36.57 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=22.0
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
..|.||.||..+- .+ ...++||+|-..+.
T Consensus 41 sa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 41 TNAHCDECGDPIF------------RH-DGQEFCPTCQQPVT 69 (226)
T ss_pred chhhcccccCccc------------CC-CCeeECCCCCCccc
Confidence 4699999999554 22 55688999988765
No 63
>PHA00616 hypothetical protein
Probab=63.07 E-value=2.9 Score=28.56 Aligned_cols=25 Identities=20% Similarity=0.236 Sum_probs=17.0
Q ss_pred eeCCCCCC-CccHHHhhhhhcccCCC
Q 027149 50 YPCPFCSE-DFDLVGLCCHIDEEHPV 74 (227)
Q Consensus 50 F~CPfC~e-~~d~~~L~~H~~~eH~~ 74 (227)
|.||-||. =.....|..|+...|.-
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 67888877 55566777777665544
No 64
>smart00355 ZnF_C2H2 zinc finger.
Probab=62.74 E-value=5 Score=21.83 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=12.5
Q ss_pred eeCCCCCC-CccHHHhhhhhc
Q 027149 50 YPCPFCSE-DFDLVGLCCHID 69 (227)
Q Consensus 50 F~CPfC~e-~~d~~~L~~H~~ 69 (227)
|.|+.|+. =-....|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 46777777 344556666665
No 65
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=61.84 E-value=5.3 Score=27.00 Aligned_cols=28 Identities=21% Similarity=0.489 Sum_probs=21.3
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
.|.|.-||.++++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 58999999987754 34568999996654
No 66
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=61.35 E-value=6.3 Score=33.05 Aligned_cols=32 Identities=19% Similarity=0.336 Sum_probs=24.5
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
..|.||-|+.-|+..+-..+ .-.||+|-..+-
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~~----------~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAMEL----------NFTCPRCGAMLD 139 (158)
T ss_pred CeEECCCCCcEeeHHHHHHc----------CCcCCCCCCEee
Confidence 67999999996666666542 579999988653
No 67
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=60.74 E-value=3.8 Score=32.01 Aligned_cols=13 Identities=23% Similarity=0.708 Sum_probs=10.5
Q ss_pred ceeeCCCCCC-Ccc
Q 027149 48 YEYPCPFCSE-DFD 60 (227)
Q Consensus 48 ~~F~CPfC~e-~~d 60 (227)
+.|+||||+. .+.
T Consensus 35 a~y~CpfCgk~~vk 48 (90)
T PRK03976 35 AKHVCPVCGRPKVK 48 (90)
T ss_pred cCccCCCCCCCceE
Confidence 7899999987 444
No 68
>PF12773 DZR: Double zinc ribbon
Probab=60.32 E-value=6.2 Score=26.25 Aligned_cols=27 Identities=26% Similarity=0.767 Sum_probs=17.8
Q ss_pred eCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 51 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 51 ~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
.||.||..+. ..+...++||.|.+.+.
T Consensus 14 fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 14 FCPHCGTPLP------------PPDQSKKICPNCGAENP 40 (50)
T ss_pred CChhhcCChh------------hccCCCCCCcCCcCCCc
Confidence 4777776555 34556688999977654
No 69
>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=60.16 E-value=4 Score=32.00 Aligned_cols=13 Identities=38% Similarity=1.147 Sum_probs=10.6
Q ss_pred ceeeCCCCCC-Ccc
Q 027149 48 YEYPCPFCSE-DFD 60 (227)
Q Consensus 48 ~~F~CPfC~e-~~d 60 (227)
+.|.||||+. .+.
T Consensus 34 a~y~CpfCgk~~vk 47 (91)
T TIGR00280 34 AKYVCPFCGKKTVK 47 (91)
T ss_pred cCccCCCCCCCceE
Confidence 7899999987 443
No 70
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.68 E-value=3.6 Score=36.07 Aligned_cols=43 Identities=26% Similarity=0.600 Sum_probs=26.9
Q ss_pred cceeeCCCCCCCccHHH----hhhhhcccCCC---CCCcccCCccccccc
Q 027149 47 EYEYPCPFCSEDFDLVG----LCCHIDEEHPV---EAKSGVCPVCVTRVT 89 (227)
Q Consensus 47 ~~~F~CPfC~e~~d~~~----L~~H~~~eH~~---e~~~vvCPVC~~~~~ 89 (227)
.+.|.||.|=..+.... =|-|+-=.-+. -.+.++||+|..++.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 36899999977555443 34444322221 234578999988776
No 71
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=58.69 E-value=8.6 Score=28.11 Aligned_cols=31 Identities=29% Similarity=0.750 Sum_probs=20.5
Q ss_pred ceeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCccc
Q 027149 48 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCV 85 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~ 85 (227)
..|+||-||+ .+-.-.-|.- ..+.-+||-|-
T Consensus 26 v~F~CPnCGe~~I~Rc~~CRk-------~g~~Y~Cp~CG 57 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKCRK-------LGNPYRCPKCG 57 (61)
T ss_pred eEeeCCCCCceeeehhhhHHH-------cCCceECCCcC
Confidence 6899999997 5554433332 24456888883
No 72
>PF15616 TerY-C: TerY-C metal binding domain
Probab=58.37 E-value=3.7 Score=34.07 Aligned_cols=38 Identities=18% Similarity=0.508 Sum_probs=26.9
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCC-CCCcccCCccccccc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPV-EAKSGVCPVCVTRVT 89 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~-e~~~vvCPVC~~~~~ 89 (227)
=.||+||..+-++- | -|-.-|+. ....++||-|-....
T Consensus 78 PgCP~CGn~~~fa~-C-~CGkl~Ci~g~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 78 PGCPHCGNQYAFAV-C-GCGKLFCIDGEGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCcChhcEEE-e-cCCCEEEeCCCCCEECCCCCCeee
Confidence 57999998544432 2 47777784 556899999977654
No 73
>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=58.13 E-value=1.3 Score=33.05 Aligned_cols=53 Identities=23% Similarity=0.388 Sum_probs=23.0
Q ss_pred eCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccc-------hhhHhhhhcccccccccc
Q 027149 51 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT-------MDMVDHITTQHGNISNSW 107 (227)
Q Consensus 51 ~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~-------~d~i~Hl~~qH~~~~K~~ 107 (227)
.||-|...++..+-.-||..=+..=.+.+.||-|...+- .|+.- +|++-+|++
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC----~~c~gLiSK 62 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFC----NHCHGLISK 62 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-----TTTT-EE-T
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceee----ccCCceeec
Confidence 466666666555532233221122234578999987553 35543 477777754
No 74
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=57.85 E-value=6.6 Score=26.89 Aligned_cols=25 Identities=24% Similarity=0.526 Sum_probs=20.5
Q ss_pred ccCCccccccc-hhhHhhhhcccccc
Q 027149 79 GVCPVCVTRVT-MDMVDHITTQHGNI 103 (227)
Q Consensus 79 vvCPVC~~~~~-~d~i~Hl~~qH~~~ 103 (227)
..||.|..... ..|+.|+..+|..-
T Consensus 3 f~CP~C~~~~~~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCEDEHRSE 28 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHhHCcCC
Confidence 47999988544 68999999999764
No 75
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=57.72 E-value=4.1 Score=28.62 Aligned_cols=46 Identities=28% Similarity=0.554 Sum_probs=29.8
Q ss_pred ccccCCcchhhhccCcceeeCCCCCC--CccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 32 DFEDIEEDDYEEVKGEYEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 32 g~e~~~~ddd~e~r~~~~F~CPfC~e--~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
.+||++.+++++. -+|+|+ ||- .+....|-.+ .-.+-|+-|+-.+.
T Consensus 4 ~l~d~~~~~~~~~---~~y~CR-CG~~f~i~e~~l~~~--------~~iv~C~sCSL~I~ 51 (55)
T PF05207_consen 4 SLDDMEFDEEEGV---YSYPCR-CGGEFEISEEDLEEG--------EVIVQCDSCSLWIR 51 (55)
T ss_dssp ETTTSEEETTTTE---EEEEET-TSSEEEEEHHHHHCT----------EEEETTTTEEEE
T ss_pred EhhhceecCCCCE---EEEcCC-CCCEEEEcchhccCc--------CEEEECCCCccEEE
Confidence 3566665554333 489995 998 6666666655 44578999987664
No 76
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=57.35 E-value=4.5 Score=39.46 Aligned_cols=37 Identities=30% Similarity=0.834 Sum_probs=17.7
Q ss_pred cCcceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcc-ccccchhhHh
Q 027149 45 KGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVC-VTRVTMDMVD 94 (227)
Q Consensus 45 r~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC-~~~~~~d~i~ 94 (227)
+|.+...||||+.-|.. +-+--+|||| ...||.+.+|
T Consensus 376 ~G~~~v~CP~cgA~y~~-------------~~kG~lC~vC~l~~IG~~a~G 413 (422)
T PF06957_consen 376 RGSPSVKCPYCGAKYHP-------------EYKGQLCPVCELSEIGADASG 413 (422)
T ss_dssp TTS-EEE-TTT--EEEG-------------GGTTSB-TTTTTBBTT---S-
T ss_pred CCCCCeeCCCCCCccCh-------------hhCCCCCCCCcceeeCCccee
Confidence 44467889999874421 2345699999 4477766554
No 77
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=57.14 E-value=4.9 Score=31.83 Aligned_cols=9 Identities=56% Similarity=1.619 Sum_probs=7.9
Q ss_pred eeeCCCCCC
Q 027149 49 EYPCPFCSE 57 (227)
Q Consensus 49 ~F~CPfC~e 57 (227)
-++|||||+
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 478999998
No 78
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=56.83 E-value=7.4 Score=32.94 Aligned_cols=33 Identities=27% Similarity=0.665 Sum_probs=18.5
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCc-----ccCCcccccc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKS-----GVCPVCVTRV 88 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~-----vvCPVC~~~~ 88 (227)
..|||||.... |+.+.-.....+ --||-|.-.-
T Consensus 1 m~cp~c~~~~~------~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDT------RVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCC------EeEeccccCCCCceeeeeeccccCCcc
Confidence 36999997432 233333333332 3499997643
No 79
>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=56.41 E-value=8.6 Score=27.19 Aligned_cols=38 Identities=18% Similarity=0.335 Sum_probs=27.5
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccchhhHhhh
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHI 96 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~~d~i~Hl 96 (227)
..=.||.||.-... ....+..+||.|-.....|+.+=+
T Consensus 27 TSq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~~rD~naA~ 64 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEMDRDVNAAR 64 (69)
T ss_pred CccCccCccccccc-----------ccccceEEcCCCCCEECcHHHHHH
Confidence 67789999982222 455667899999888777776533
No 80
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=56.36 E-value=11 Score=24.19 Aligned_cols=29 Identities=31% Similarity=0.764 Sum_probs=19.2
Q ss_pred eeCCCCCCCccHH--HhhhhhcccCCCCCCcccCCcccc
Q 027149 50 YPCPFCSEDFDLV--GLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 50 F~CPfC~e~~d~~--~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
..||-|+..|.+. .| +...+.|.||-|..
T Consensus 3 i~CP~C~~~f~v~~~~l--------~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKL--------PAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEcCHHHc--------ccCCcEEECCCCCc
Confidence 6799998855443 33 23456788998854
No 81
>PRK00420 hypothetical protein; Validated
Probab=56.20 E-value=7.6 Score=31.40 Aligned_cols=28 Identities=25% Similarity=0.455 Sum_probs=18.6
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
.-.||.||..+- . .....++||+|...+
T Consensus 23 ~~~CP~Cg~pLf--~----------lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLF--E----------LKDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCcce--e----------cCCCceECCCCCCee
Confidence 368999996431 1 123468999998744
No 82
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=55.81 E-value=6.5 Score=31.28 Aligned_cols=38 Identities=26% Similarity=0.513 Sum_probs=22.1
Q ss_pred eeCCCCCCCccHHH---hhhhhcccCCCCCCcccCCccccccch
Q 027149 50 YPCPFCSEDFDLVG---LCCHIDEEHPVEAKSGVCPVCVTRVTM 90 (227)
Q Consensus 50 F~CPfC~e~~d~~~---L~~H~~~eH~~e~~~vvCPVC~~~~~~ 90 (227)
-.|||||....+.. +.-|-.+++ +-.-+|+-|-+.||.
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~---~~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDG---PYLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCC---ceeEECCCCCceeee
Confidence 46999998433322 222222111 223689999999984
No 83
>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=55.11 E-value=7.3 Score=23.61 Aligned_cols=8 Identities=38% Similarity=1.244 Sum_probs=4.0
Q ss_pred CCCCCCCc
Q 027149 52 CPFCSEDF 59 (227)
Q Consensus 52 CPfC~e~~ 59 (227)
||-|+..+
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 55555544
No 84
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=55.08 E-value=4.4 Score=31.66 Aligned_cols=13 Identities=38% Similarity=1.209 Sum_probs=9.8
Q ss_pred ceeeCCCCCC-Ccc
Q 027149 48 YEYPCPFCSE-DFD 60 (227)
Q Consensus 48 ~~F~CPfC~e-~~d 60 (227)
..|.||||+. .+.
T Consensus 34 ~ky~Cp~Cgk~~vk 47 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK 47 (90)
T ss_dssp S-BEESSSSSSEEE
T ss_pred CCCcCCCCCCceeE
Confidence 7899999998 443
No 85
>PF13395 HNH_4: HNH endonuclease
Probab=53.57 E-value=7.4 Score=26.82 Aligned_cols=14 Identities=29% Similarity=1.013 Sum_probs=12.0
Q ss_pred CCCCCCCccHHHhh
Q 027149 52 CPFCSEDFDLVGLC 65 (227)
Q Consensus 52 CPfC~e~~d~~~L~ 65 (227)
|||||+.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 99999999888763
No 86
>PRK12496 hypothetical protein; Provisional
Probab=52.96 E-value=10 Score=32.06 Aligned_cols=27 Identities=22% Similarity=0.516 Sum_probs=19.0
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
.|.||-|+..|+.. ...-+||||-..+
T Consensus 127 ~~~C~gC~~~~~~~-------------~~~~~C~~CG~~~ 153 (164)
T PRK12496 127 RKVCKGCKKKYPED-------------YPDDVCEICGSPV 153 (164)
T ss_pred eEECCCCCccccCC-------------CCCCcCCCCCChh
Confidence 58999999877531 1225899996554
No 87
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=50.48 E-value=8.3 Score=24.79 Aligned_cols=21 Identities=19% Similarity=0.490 Sum_probs=10.4
Q ss_pred eeeCCCCCCCccHHHhhhhhc
Q 027149 49 EYPCPFCSEDFDLVGLCCHID 69 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~ 69 (227)
+|.||-|+..+-..-.-.|++
T Consensus 4 ~~~C~nC~R~v~a~RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVAASRFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEEGGGHHHHHH
T ss_pred eEECCCCcCCcchhhhHHHHH
Confidence 455555555555555555543
No 88
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=50.31 E-value=4 Score=34.99 Aligned_cols=40 Identities=25% Similarity=0.681 Sum_probs=20.3
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
-.|+||.|+..+...++.. .+.-........||-|.....
T Consensus 17 l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~~ 56 (188)
T PF08996_consen 17 LKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPLS 56 (188)
T ss_dssp EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B--
T ss_pred eEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcCC
Confidence 3699999999888877655 111112344678999988554
No 89
>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=50.14 E-value=9 Score=26.97 Aligned_cols=10 Identities=40% Similarity=1.464 Sum_probs=8.3
Q ss_pred ceeeCCCCCC
Q 027149 48 YEYPCPFCSE 57 (227)
Q Consensus 48 ~~F~CPfC~e 57 (227)
-.|.||+|+.
T Consensus 43 i~y~C~~Cg~ 52 (54)
T PF10058_consen 43 IQYRCPYCGA 52 (54)
T ss_pred eEEEcCCCCC
Confidence 3599999986
No 90
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.90 E-value=6.9 Score=22.97 Aligned_cols=6 Identities=50% Similarity=1.547 Sum_probs=3.2
Q ss_pred CCCCCC
Q 027149 52 CPFCSE 57 (227)
Q Consensus 52 CPfC~e 57 (227)
||.||.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 555554
No 91
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.72 E-value=11 Score=22.47 Aligned_cols=10 Identities=30% Similarity=0.919 Sum_probs=6.4
Q ss_pred eeCCCCCCCc
Q 027149 50 YPCPFCSEDF 59 (227)
Q Consensus 50 F~CPfC~e~~ 59 (227)
-.||.||..+
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 3577777643
No 92
>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=49.29 E-value=11 Score=30.14 Aligned_cols=28 Identities=36% Similarity=0.762 Sum_probs=21.2
Q ss_pred ceeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 48 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
....||-||. =||+ ...++|||-|.+..
T Consensus 8 tKR~Cp~CG~kFYDL-------------nk~PivCP~CG~~~ 36 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL-------------NKDPIVCPKCGTEF 36 (108)
T ss_pred CcccCCCCcchhccC-------------CCCCccCCCCCCcc
Confidence 7789999999 5553 23578999997754
No 93
>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=47.57 E-value=8.2 Score=30.76 Aligned_cols=26 Identities=31% Similarity=0.432 Sum_probs=20.1
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
..+.|+-|+..+..... ...||-|..
T Consensus 69 ~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECEDCSEEVSPEID-------------LYRCPKCHG 94 (115)
T ss_pred cEEEcccCCCEEecCCc-------------CccCcCCcC
Confidence 57999999987766533 367999975
No 94
>smart00507 HNHc HNH nucleases.
Probab=47.52 E-value=5.8 Score=25.13 Aligned_cols=21 Identities=19% Similarity=0.175 Sum_probs=13.8
Q ss_pred eeCCCCCCCccHHHhhhhhcc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDE 70 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~ 70 (227)
+.|+||+..++..--+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 799999996654333455553
No 95
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=46.13 E-value=9.5 Score=30.86 Aligned_cols=24 Identities=29% Similarity=1.020 Sum_probs=15.2
Q ss_pred eCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 51 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 51 ~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
+||-|+.++.-. +....|||-|+.
T Consensus 4 ~CP~C~seytY~------------dg~~~iCpeC~~ 27 (109)
T TIGR00686 4 PCPKCNSEYTYH------------DGTQLICPSCLY 27 (109)
T ss_pred cCCcCCCcceEe------------cCCeeECccccc
Confidence 588776644321 344578999965
No 96
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=45.47 E-value=10 Score=31.60 Aligned_cols=25 Identities=28% Similarity=0.636 Sum_probs=17.6
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
...||-||--+ ..| ...|+||||-.
T Consensus 28 ~~hCp~Cg~PL-----F~K--------dG~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPL-----FRK--------DGEVFCPVCGY 52 (131)
T ss_pred HhhCcccCCcc-----eee--------CCeEECCCCCc
Confidence 58999999732 112 45699999974
No 97
>PRK03922 hypothetical protein; Provisional
Probab=45.03 E-value=10 Score=30.75 Aligned_cols=15 Identities=40% Similarity=0.618 Sum_probs=11.9
Q ss_pred eeeCCCCCCCccHHH
Q 027149 49 EYPCPFCSEDFDLVG 63 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~ 63 (227)
.-.||+||++|+-.-
T Consensus 49 ~~~cP~cge~~~~af 63 (113)
T PRK03922 49 LTICPKCGEPFDSAF 63 (113)
T ss_pred cccCCCCCCcCCcEE
Confidence 568999999987543
No 98
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=44.95 E-value=6.6 Score=30.62 Aligned_cols=12 Identities=33% Similarity=1.082 Sum_probs=10.2
Q ss_pred ceeeCCCCCC-Cc
Q 027149 48 YEYPCPFCSE-DF 59 (227)
Q Consensus 48 ~~F~CPfC~e-~~ 59 (227)
+.|.|+|||. .+
T Consensus 35 aky~CsfCGK~~v 47 (92)
T KOG0402|consen 35 AKYTCSFCGKKTV 47 (92)
T ss_pred hhhhhhhcchhhh
Confidence 7899999998 44
No 99
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.91 E-value=14 Score=32.29 Aligned_cols=34 Identities=21% Similarity=0.460 Sum_probs=26.0
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccchhhHhhhh
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHIT 97 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~~d~i~Hl~ 97 (227)
+.=.||.||. ...+...||.|....-+|..+=++
T Consensus 308 tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~N 341 (364)
T COG0675 308 TSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALN 341 (364)
T ss_pred CcccccccCC----------------ccceeEECCCCCCeehhhHHHHHH
Confidence 4578999998 336678999998877777776444
No 100
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.86 E-value=13 Score=36.01 Aligned_cols=15 Identities=20% Similarity=0.691 Sum_probs=10.5
Q ss_pred ceeeCCCCCCCccHH
Q 027149 48 YEYPCPFCSEDFDLV 62 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~ 62 (227)
.+|+||||..+-+..
T Consensus 373 ~sfKCPYCP~e~~~~ 387 (394)
T KOG2817|consen 373 QSFKCPYCPVEQLAS 387 (394)
T ss_pred eeeeCCCCCcccCHH
Confidence 468999997765443
No 101
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=44.65 E-value=9.3 Score=35.93 Aligned_cols=40 Identities=30% Similarity=0.522 Sum_probs=23.8
Q ss_pred eeeCCCCCC----CccHH--------HhhhhhcccCCCCCCcccCCccccccc
Q 027149 49 EYPCPFCSE----DFDLV--------GLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 49 ~F~CPfC~e----~~d~~--------~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
.+.||.|.. +-+.. .+|..|.+..- ......||+|...+.
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~-~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLF-VRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHh-cCCCCCCCCCCCccc
Confidence 478999976 22211 23445555542 334578999977554
No 102
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=44.52 E-value=7.9 Score=28.22 Aligned_cols=26 Identities=27% Similarity=0.556 Sum_probs=18.5
Q ss_pred cCCccccc--cchhhHhhhhcccccccc
Q 027149 80 VCPVCVTR--VTMDMVDHITTQHGNISN 105 (227)
Q Consensus 80 vCPVC~~~--~~~d~i~Hl~~qH~~~~K 105 (227)
.||-|.+. -..|.++|.+-.|+.+|-
T Consensus 19 rCPRC~~~FR~~K~Y~RHVNKaH~~~~~ 46 (65)
T COG4049 19 RCPRCGMVFRRRKDYIRHVNKAHGWLFG 46 (65)
T ss_pred eCCchhHHHHHhHHHHHHhhHHhhhhhc
Confidence 45555442 336899999999999874
No 103
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=44.49 E-value=14 Score=30.03 Aligned_cols=27 Identities=30% Similarity=0.478 Sum_probs=21.2
Q ss_pred cccCCccccccc-----hhhHhhhhccccccc
Q 027149 78 SGVCPVCVTRVT-----MDMVDHITTQHGNIS 104 (227)
Q Consensus 78 ~vvCPVC~~~~~-----~d~i~Hl~~qH~~~~ 104 (227)
.+.||+|....| ..+.-||+.-||-+-
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~s 56 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGISS 56 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhcccccc
Confidence 789999986555 458889988888764
No 104
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=44.41 E-value=8.6 Score=34.05 Aligned_cols=32 Identities=28% Similarity=0.616 Sum_probs=20.3
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCCCC-CCccc
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHPVE-AKSGV 80 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~~e-~~~vv 80 (227)
.|.||.|+..+.+..=-=+|...|.++ ++.+.
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~fd~a~~Gy 34 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQFDCAKEGY 34 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCCccccCce
Confidence 389999999664322223567788884 44443
No 105
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=44.23 E-value=14 Score=34.47 Aligned_cols=28 Identities=18% Similarity=0.203 Sum_probs=22.0
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
.+||-|+.-+-...|-.. ..|||-|...
T Consensus 39 ~kc~~C~~~~~~~~l~~~----------~~vcp~c~~h 66 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSK----------MNICEQCGYH 66 (296)
T ss_pred eECCCccchhhHHHHHHc----------CCCCCCCCCC
Confidence 899999997777776443 4699999773
No 106
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=44.06 E-value=14 Score=26.28 Aligned_cols=25 Identities=32% Similarity=0.773 Sum_probs=17.4
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
-.||.|++.|.. +.-.||||.|.+.
T Consensus 6 ~~C~~Cg~~~~~-------------~dDiVvCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFKD-------------GDDIVVCPECGAP 30 (54)
T ss_pred ccChhhCCcccC-------------CCCEEECCCCCCc
Confidence 579999886631 2235899999774
No 107
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=43.20 E-value=12 Score=30.00 Aligned_cols=15 Identities=33% Similarity=0.705 Sum_probs=11.9
Q ss_pred eeeCCCCCCCccHHH
Q 027149 49 EYPCPFCSEDFDLVG 63 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~ 63 (227)
.-.||+|+++|+-.-
T Consensus 47 ~~~cP~Cge~~~~a~ 61 (102)
T PF04475_consen 47 DTICPKCGEELDSAF 61 (102)
T ss_pred cccCCCCCCccCceE
Confidence 578999999887543
No 108
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.82 E-value=13 Score=30.43 Aligned_cols=15 Identities=20% Similarity=0.550 Sum_probs=11.9
Q ss_pred ceeeCCCCCCCccHH
Q 027149 48 YEYPCPFCSEDFDLV 62 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~ 62 (227)
..+.|+-||..+...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 579999999866554
No 109
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.81 E-value=8.7 Score=35.82 Aligned_cols=41 Identities=29% Similarity=0.511 Sum_probs=25.2
Q ss_pred ceeeCCCCCC--CccHHHh-hhhhcccCCCCCCc-----ccCCcccccc
Q 027149 48 YEYPCPFCSE--DFDLVGL-CCHIDEEHPVEAKS-----GVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e--~~d~~~L-~~H~~~eH~~e~~~-----vvCPVC~~~~ 88 (227)
..-.||+||+ -+--... |.|+-=.-+..++. ..||-|.+.+
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred CCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 4578999999 3444444 77754333333332 3799987654
No 110
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=42.44 E-value=7.1 Score=31.64 Aligned_cols=13 Identities=31% Similarity=0.945 Sum_probs=10.8
Q ss_pred CCCCCCCccHHHh
Q 027149 52 CPFCSEDFDLVGL 64 (227)
Q Consensus 52 CPfC~e~~d~~~L 64 (227)
||.||..+-+..|
T Consensus 1 CPvCg~~l~vt~l 13 (113)
T PF09862_consen 1 CPVCGGELVVTRL 13 (113)
T ss_pred CCCCCCceEEEEE
Confidence 9999998877766
No 111
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=42.40 E-value=13 Score=35.54 Aligned_cols=38 Identities=32% Similarity=0.608 Sum_probs=27.6
Q ss_pred ceeeCCCCCCCcc--HHHhhhhhccc-CCC-----CCCcccCCccc
Q 027149 48 YEYPCPFCSEDFD--LVGLCCHIDEE-HPV-----EAKSGVCPVCV 85 (227)
Q Consensus 48 ~~F~CPfC~e~~d--~~~L~~H~~~e-H~~-----e~~~vvCPVC~ 85 (227)
.+-.||.||...| +.+||.=|--+ |+. +.+..+|+-|-
T Consensus 5 ~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cg 50 (355)
T COG1499 5 STILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCG 50 (355)
T ss_pred cccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCC
Confidence 5789999999887 78888766555 444 33447788885
No 112
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=42.40 E-value=18 Score=33.42 Aligned_cols=30 Identities=30% Similarity=0.513 Sum_probs=23.1
Q ss_pred ccCcceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 44 VKGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 44 ~r~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
+| ..||-|++-+-...|-.. ..|||-|...
T Consensus 25 ~~----~~c~~c~~~~~~~~l~~~----------~~vc~~c~~h 54 (285)
T TIGR00515 25 VW----TKCPKCGQVLYTKELERN----------LEVCPKCDHH 54 (285)
T ss_pred Ce----eECCCCcchhhHHHHHhh----------CCCCCCCCCc
Confidence 77 899999997777666443 3699999774
No 113
>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=42.04 E-value=17 Score=32.15 Aligned_cols=23 Identities=13% Similarity=0.070 Sum_probs=14.5
Q ss_pred CCCCHHHHHHHHhHhhHH-HHHHH
Q 027149 197 SSLSNEDHLEKANRSNFA-QGLLF 219 (227)
Q Consensus 197 ~~ls~ed~eEk~~R~eFV-QgLll 219 (227)
-.++++|.++-.+++.++ -+|+.
T Consensus 145 r~~~~~e~~~~~~~~~~~le~l~~ 168 (236)
T PF04981_consen 145 RKLTEEEKEVIHKIVFEILEQLIL 168 (236)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHh
Confidence 458888887766666654 34443
No 114
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=41.91 E-value=6.8 Score=30.56 Aligned_cols=38 Identities=29% Similarity=0.630 Sum_probs=11.7
Q ss_pred eCCCCCCCccHHHhh-hhhcccCCC-----------CCCcccCCcccccc
Q 027149 51 PCPFCSEDFDLVGLC-CHIDEEHPV-----------EAKSGVCPVCVTRV 88 (227)
Q Consensus 51 ~CPfC~e~~d~~~L~-~H~~~eH~~-----------e~~~vvCPVC~~~~ 88 (227)
.||+|++.+....+. .=|..-|.+ +.+.-+|++|..+.
T Consensus 16 ~C~~C~~~i~~~~~~~~~C~~GH~w~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 16 KCPICGAPIPFDDLDEAQCENGHVWPRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp -------------SSEEE-TTS-EEEB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred cccccccccccCCcCEeECCCCCEEeeeeeeeeeeccCCeeEcCCCCCEE
Confidence 699999977765543 346667765 55667899996643
No 115
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=41.66 E-value=14 Score=30.76 Aligned_cols=41 Identities=29% Similarity=0.639 Sum_probs=29.1
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccchhhH
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMV 93 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~~d~i 93 (227)
..+.|..|+..++...+........ ...||.|...+..|.+
T Consensus 104 ~~~~C~~C~~~~~~~~~~~~~~~~~-----~~~C~~C~~~lrp~vv 144 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVDSIDEEE-----PPRCPKCGGLLRPDVV 144 (178)
T ss_dssp EEEEETTTSBEEEGHHHHHHHHTTS-----SCBCTTTSCBEEEEE-
T ss_pred ceeeecCCCccccchhhcccccccc-----cccccccCccCCCCee
Confidence 3689999999888877766655432 2399999886655544
No 116
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=41.34 E-value=14 Score=36.57 Aligned_cols=23 Identities=26% Similarity=0.560 Sum_probs=17.4
Q ss_pred hhcccCCCCCCcccCCccccccc
Q 027149 67 HIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 67 H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
.|..+.-.+++.-|||||...||
T Consensus 26 ~c~~~~~~~PNt~vcpv~lg~PG 48 (474)
T PRK05477 26 GCSTDFGAEPNTNVCPVCLGLPG 48 (474)
T ss_pred CCCcccCCCCCCCcCccccCCCC
Confidence 34444445678899999999987
No 117
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=41.25 E-value=16 Score=23.89 Aligned_cols=10 Identities=50% Similarity=1.085 Sum_probs=7.6
Q ss_pred CCcccCCccc
Q 027149 76 AKSGVCPVCV 85 (227)
Q Consensus 76 ~~~vvCPVC~ 85 (227)
.+.++||+|.
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 5568899884
No 118
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=41.07 E-value=29 Score=22.28 Aligned_cols=31 Identities=19% Similarity=0.546 Sum_probs=19.1
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
+.||-|+.-|++.+-. =+.....|-||.|..
T Consensus 3 i~Cp~C~~~y~i~d~~------ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK------IPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHHH------CCCCCcEEECCCCCC
Confidence 6788888855444321 133456788888854
No 119
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=40.68 E-value=17 Score=33.58 Aligned_cols=30 Identities=27% Similarity=0.530 Sum_probs=23.0
Q ss_pred ccCcceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 44 VKGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 44 ~r~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
+| -.||-|+.-+-...|-.. ..|||-|...
T Consensus 26 ~~----~~c~~c~~~~~~~~l~~~----------~~vc~~c~~h 55 (292)
T PRK05654 26 LW----TKCPSCGQVLYRKELEAN----------LNVCPKCGHH 55 (292)
T ss_pred Ce----eECCCccchhhHHHHHhc----------CCCCCCCCCC
Confidence 67 899999997777766443 3599999773
No 120
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=40.63 E-value=14 Score=35.34 Aligned_cols=40 Identities=33% Similarity=0.600 Sum_probs=30.5
Q ss_pred eeeCCC--CCC-CccHHHhhhhhcccCCC-----------------CCCcccCCcccccc
Q 027149 49 EYPCPF--CSE-DFDLVGLCCHIDEEHPV-----------------EAKSGVCPVCVTRV 88 (227)
Q Consensus 49 ~F~CPf--C~e-~~d~~~L~~H~~~eH~~-----------------e~~~vvCPVC~~~~ 88 (227)
-|+||. |.+ .-.+-+|.-|...-|+. +.|.-+|+||..+-
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRY 408 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY 408 (423)
T ss_pred eecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhh
Confidence 499986 877 67788898888887732 33667899998765
No 121
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=40.08 E-value=13 Score=29.53 Aligned_cols=26 Identities=23% Similarity=0.450 Sum_probs=18.8
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
..+.|+-|+..|.+.. ....||-|-.
T Consensus 69 ~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ-------------HDAQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCC-------------cCccCcCCCC
Confidence 5699999997665543 3346999975
No 122
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=39.82 E-value=12 Score=27.46 Aligned_cols=10 Identities=50% Similarity=1.245 Sum_probs=8.1
Q ss_pred ceeeCCCCCC
Q 027149 48 YEYPCPFCSE 57 (227)
Q Consensus 48 ~~F~CPfC~e 57 (227)
..+.|-+||+
T Consensus 4 ~~~~C~~Cg~ 13 (69)
T PF09706_consen 4 KKYNCIFCGE 13 (69)
T ss_pred CCCcCcCCCC
Confidence 5689999994
No 123
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=39.30 E-value=15 Score=35.14 Aligned_cols=11 Identities=36% Similarity=1.253 Sum_probs=9.2
Q ss_pred ceeeCCCCCCC
Q 027149 48 YEYPCPFCSED 58 (227)
Q Consensus 48 ~~F~CPfC~e~ 58 (227)
.+|.||||.++
T Consensus 375 ~~FKCPYCP~~ 385 (396)
T COG5109 375 LSFKCPYCPEM 385 (396)
T ss_pred EEeeCCCCCcc
Confidence 57999999873
No 124
>PRK11595 DNA utilization protein GntX; Provisional
Probab=38.81 E-value=15 Score=32.04 Aligned_cols=34 Identities=24% Similarity=0.536 Sum_probs=21.6
Q ss_pred eCCCCCCCccH--HHhhhhhcccCCCCCCcccCCcccc
Q 027149 51 PCPFCSEDFDL--VGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 51 ~CPfC~e~~d~--~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
.|+.|+..+.. ..||.+|...=+.- ...||.|..
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~--~~~C~~Cg~ 42 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTL--KTCCPQCGL 42 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcc--cCcCccCCC
Confidence 49999885533 35888887653331 246777764
No 125
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.80 E-value=15 Score=38.29 Aligned_cols=38 Identities=29% Similarity=0.587 Sum_probs=27.0
Q ss_pred ceeeCCCCCCCcc----HHHhhhhhcccCCCCCCcccCCccccc
Q 027149 48 YEYPCPFCSEDFD----LVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 48 ~~F~CPfC~e~~d----~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
..+.||.|+..+. ...|.||-...| +...-.||=|-..
T Consensus 443 ~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 443 YIAECPNCDSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred CcccCCCCCcceEEecCCCeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 4689999987443 356666655444 6777899999875
No 126
>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=38.78 E-value=10 Score=30.07 Aligned_cols=27 Identities=22% Similarity=0.475 Sum_probs=18.2
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
..+.|+-|+..|++.... ..||-|...
T Consensus 69 ~~~~C~~Cg~~~~~~~~~-------------~~CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFD-------------FSCPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHHCC-------------HH-SSSSSS
T ss_pred CcEECCCCCCEEecCCCC-------------CCCcCCcCC
Confidence 579999999988776653 239999664
No 127
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=37.86 E-value=25 Score=21.22 Aligned_cols=21 Identities=19% Similarity=0.649 Sum_probs=14.9
Q ss_pred eeeCCCCCCCcc-HHHhhhhhc
Q 027149 49 EYPCPFCSEDFD-LVGLCCHID 69 (227)
Q Consensus 49 ~F~CPfC~e~~d-~~~L~~H~~ 69 (227)
.|.|.+|+..|. ...+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 477888888555 666777765
No 128
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=37.83 E-value=20 Score=33.10 Aligned_cols=62 Identities=19% Similarity=0.229 Sum_probs=36.2
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccchhhHhhhhcccccccccccccccccCCCCcchhhhhH
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHITTQHGNISNSWHKLKLHKGNSNSTISSLRK 126 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~~d~i~Hl~~qH~~~~K~~r~rk~rk~~s~s~~s~l~k 126 (227)
..||.|+.. + +..+ ++....||--|-.-+..+.+.+---.+.+ .++..| |.|...+.++..+
T Consensus 2 ~~CpeCg~~-~-------~~~d--~~~ge~VC~~CG~Vi~~~~id~gpewr~f---~e~~~~--r~g~P~t~~~~d~ 63 (285)
T COG1405 2 MSCPECGST-N-------IITD--YERGEIVCADCGLVLEDSLIDPGPEWRAF---DERHER--RVGAPLTPSIHDK 63 (285)
T ss_pred CCCCCCCCc-c-------ceee--ccCCeEEeccCCEEeccccccCCCCcccc---cccccc--cccCCCccccCcc
Confidence 469999985 1 1111 23556899999988877777654333322 122223 5565555555544
No 129
>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=37.83 E-value=20 Score=29.83 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=20.9
Q ss_pred ceeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 48 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
....||-||. =||+ ....+|||-|-...
T Consensus 8 tKr~Cp~cg~kFYDL-------------nk~p~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGSKFYDL-------------NRRPAVSPYTGEQF 36 (129)
T ss_pred ccccCCCcCcccccc-------------CCCCccCCCcCCcc
Confidence 7889999998 4442 24579999997643
No 130
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.41 E-value=20 Score=36.97 Aligned_cols=26 Identities=31% Similarity=0.469 Sum_probs=23.7
Q ss_pred eeeCCCCCC-CccHHHhhhhhcccCCC
Q 027149 49 EYPCPFCSE-DFDLVGLCCHIDEEHPV 74 (227)
Q Consensus 49 ~F~CPfC~e-~~d~~~L~~H~~~eH~~ 74 (227)
---|+||.+ -||...|..|+..+|.+
T Consensus 182 hp~C~~C~~~fld~~el~rH~~~~h~~ 208 (669)
T KOG2231|consen 182 HPLCKFCHERFLDDDELYRHLRFDHEF 208 (669)
T ss_pred CccchhhhhhhccHHHHHHhhccceeh
Confidence 468999999 99999999999999876
No 131
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=36.94 E-value=25 Score=20.56 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=13.1
Q ss_pred eeCCCCCC-CccHHHhhhhhc
Q 027149 50 YPCPFCSE-DFDLVGLCCHID 69 (227)
Q Consensus 50 F~CPfC~e-~~d~~~L~~H~~ 69 (227)
|.|+.|+. =-+...+..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 66777777 445666666654
No 132
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=36.53 E-value=20 Score=35.80 Aligned_cols=40 Identities=35% Similarity=0.677 Sum_probs=25.2
Q ss_pred ceeeCCCCCCCccHH--HhhhhhcccCCCCCCcccCCccccccc
Q 027149 48 YEYPCPFCSEDFDLV--GLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~--~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
-..+||-|++.+.+. .|.- ..+...+.-..+||-|-..+.
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w--~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKW--DKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EEccCCCCCCCccccccceee--cCCCCccceEEECCCCcCCCC
Confidence 368999999955443 3322 221234445578999988775
No 133
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=35.82 E-value=19 Score=36.35 Aligned_cols=22 Identities=27% Similarity=0.465 Sum_probs=17.6
Q ss_pred hcccCCCCCCcccCCccccccc
Q 027149 68 IDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 68 ~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
|..++..+++.-|||||...||
T Consensus 83 c~~~~g~~PNt~vcpvclg~PG 104 (544)
T PLN02751 83 CPYNYGAEPNTTVCPVCMGLPG 104 (544)
T ss_pred CCcccCCCCccCcCccccCCCC
Confidence 3445556889999999999988
No 134
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=35.64 E-value=13 Score=25.47 Aligned_cols=13 Identities=31% Similarity=0.774 Sum_probs=6.7
Q ss_pred eCCCCCCCccHHH
Q 027149 51 PCPFCSEDFDLVG 63 (227)
Q Consensus 51 ~CPfC~e~~d~~~ 63 (227)
.||.|+.+||...
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999988777654
No 135
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.14 E-value=22 Score=38.56 Aligned_cols=35 Identities=20% Similarity=0.159 Sum_probs=20.4
Q ss_pred CccccccccccCCCCCHHHHHHHHhHhhHHHHHHH
Q 027149 185 SCEKTFETNAQQSSLSNEDHLEKANRSNFAQGLLF 219 (227)
Q Consensus 185 s~~~~~e~~~~~~~ls~ed~eEk~~R~eFVQgLll 219 (227)
+++|.+|-.+|.--|+..=-+=-.+=+.||-.||-
T Consensus 778 ~~dQivELk~QDiil~~~aa~yll~va~fiDdLL~ 812 (1121)
T PRK04023 778 SEDQIVELKVQDVIISRDAAEYLLRVAKFIDDLLE 812 (1121)
T ss_pred CccceEEeecccEEcchHHHHHHHHHHHHHHHHHH
Confidence 44566666665323554433334667888888873
No 136
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=34.77 E-value=20 Score=23.74 Aligned_cols=27 Identities=26% Similarity=0.385 Sum_probs=14.8
Q ss_pred eCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 51 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 51 ~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
.||-||.-+-...+ + .....+||.|..
T Consensus 2 FCp~Cg~~l~~~~~------~---~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKEG------K---EKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccccC------C---CCCEEECCcCCC
Confidence 48888873322211 1 113578999954
No 137
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=34.59 E-value=32 Score=33.51 Aligned_cols=49 Identities=31% Similarity=0.535 Sum_probs=34.8
Q ss_pred ceeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCccccccc--hhhHhhhh
Q 027149 48 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT--MDMVDHIT 97 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~--~d~i~Hl~ 97 (227)
..|+||.|+- ==-.++|..|+...|.- .+.-.|--|...-- .|+..|+.
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~rHs~-dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRYRHSK-DKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred hcccccccccCCCChHHHHHHHHhhhcc-CCCccccchhhhhccHHHHHHHHH
Confidence 3588888887 33467788888888876 67778888877432 46667765
No 138
>TIGR03278 methan_mark_10 putative methanogenesis marker protein 10. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The presence of motifs with seven invariant Cys residues in the N-terminal 50 residues, including three instances of CXXC, would be consistent with function as an oxidoreductase with FeS clusters. The exact function is unknown, but likely is linked to methanogenesis. In most genomes, the member of this family is encoded by a gene next to, and divergently transcribed from, the methyl coenzyme M reductase operon.
Probab=34.45 E-value=19 Score=34.75 Aligned_cols=34 Identities=18% Similarity=0.316 Sum_probs=22.5
Q ss_pred ceeeCCCCCC--CccHHHh-hhhhcccCCCCCCcccCCccccc
Q 027149 48 YEYPCPFCSE--DFDLVGL-CCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 48 ~~F~CPfC~e--~~d~~~L-~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
.-..||||+. .-+...| |.||. ..+..||.|...
T Consensus 9 C~~~C~wC~~p~~~~~~~~~c~~C~------~~~~~C~yC~~~ 45 (404)
T TIGR03278 9 CRGFCRYCYFKKVDDEQPFGCKNCP------PGTKGCDYCTRS 45 (404)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCcCC------CCCCCCCCCCch
Confidence 4578999998 3344445 66654 335789999654
No 139
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=34.32 E-value=18 Score=29.13 Aligned_cols=33 Identities=21% Similarity=0.675 Sum_probs=18.5
Q ss_pred ceeeCCCCCCCccHHHhhhh-hcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCH-IDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H-~~~eH~~e~~~vvCPVC~~ 86 (227)
..|.||||.-+- -|.| ++..| -....-|-||..
T Consensus 22 t~FnClfcnHek----~v~~~~Dk~~--~iG~~sC~iC~e 55 (109)
T KOG3214|consen 22 TQFNCLFCNHEK----SVSCTLDKKH--NIGKASCRICEE 55 (109)
T ss_pred eeeccCcccccc----ceeeeehhhc--Ccceeeeeehhh
Confidence 459999997622 1222 22222 234567999965
No 140
>PF14353 CpXC: CpXC protein
Probab=33.95 E-value=20 Score=28.33 Aligned_cols=28 Identities=29% Similarity=0.413 Sum_probs=17.2
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCCCCCCccc
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGV 80 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vv 80 (227)
.|+||.||..+-+ .+--..|-.+.+.++
T Consensus 38 ~~~CP~Cg~~~~~----~~p~lY~D~~~~~~i 65 (128)
T PF14353_consen 38 SFTCPSCGHKFRL----EYPLLYHDPEKKFMI 65 (128)
T ss_pred EEECCCCCCceec----CCCEEEEcCCCCEEE
Confidence 7999999996644 233344544555433
No 141
>TIGR00133 gatB glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit. The heterotrimer GatABC is responsible for transferring the NH2 group that converts Glu to Gln, or Asp to Asn after the Glu or Asp has been ligated to the tRNA for Gln or Asn, respectively. In Lactobacillus, GatABC is responsible only for tRNA(Gln). In the Archaea, GatABC is responsible only for tRNA(Asn), while GatDE is responsible for tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyzes both.
Probab=33.91 E-value=21 Score=35.31 Aligned_cols=15 Identities=33% Similarity=0.789 Sum_probs=13.9
Q ss_pred CCCcccCCccccccc
Q 027149 75 EAKSGVCPVCVTRVT 89 (227)
Q Consensus 75 e~~~vvCPVC~~~~~ 89 (227)
+++..|||||...||
T Consensus 34 ~PNt~v~pvclg~PG 48 (478)
T TIGR00133 34 PPNTNVCPVCLGLPG 48 (478)
T ss_pred CCCcccCccccCCCC
Confidence 688999999999988
No 142
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=33.35 E-value=12 Score=28.81 Aligned_cols=8 Identities=50% Similarity=1.551 Sum_probs=6.4
Q ss_pred eeCCCCCC
Q 027149 50 YPCPFCSE 57 (227)
Q Consensus 50 F~CPfC~e 57 (227)
.+|||||+
T Consensus 2 I~CP~CG~ 9 (84)
T PF04267_consen 2 IPCPHCGP 9 (84)
T ss_dssp EEETTTEE
T ss_pred ccCCCCCc
Confidence 57888887
No 143
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=32.64 E-value=31 Score=23.62 Aligned_cols=29 Identities=21% Similarity=0.552 Sum_probs=18.0
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVC 84 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC 84 (227)
.-+.||.|+-.+...-=- +. .+...||.|
T Consensus 27 v~W~C~~Cgh~w~~~v~~-------R~-~~~~~CP~C 55 (55)
T PF14311_consen 27 VWWKCPKCGHEWKASVND-------RT-RRGKGCPYC 55 (55)
T ss_pred EEEECCCCCCeeEccHhh-------hc-cCCCCCCCC
Confidence 458999997755432111 11 456789988
No 144
>PF02934 GatB_N: GatB/GatE catalytic domain; InterPro: IPR006075 Glutamyl-tRNA(Gln) amidotransferase subunit B (6.3.5 from EC) [] is a microbial enzyme that furnishes a means for formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The enzyme is composed of three subunits: A (an amidase), B and C. It also exists in eukaryotes as a protein targeted to the mitochondria. ; GO: 0016874 ligase activity; PDB: 3H0M_H 3H0R_K 3H0L_K 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B 2G5H_B 2DQN_B ....
Probab=32.57 E-value=24 Score=32.90 Aligned_cols=26 Identities=35% Similarity=0.708 Sum_probs=18.1
Q ss_pred hhhhhcccCCCCCCcccCCccccccc
Q 027149 64 LCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 64 L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
|.|.|...+..+++.-|||||...||
T Consensus 18 lFc~c~~~~~~~pNt~v~~~~lg~PG 43 (289)
T PF02934_consen 18 LFCSCPNEFGAEPNTNVCPVCLGLPG 43 (289)
T ss_dssp SSSSSBSSTTSCTTSSB-TTTTT-TT
T ss_pred CCCCCCCCCCCCCccccCceeccCCC
Confidence 44455656566788999999999988
No 145
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=32.55 E-value=20 Score=25.62 Aligned_cols=10 Identities=30% Similarity=0.939 Sum_probs=8.9
Q ss_pred ceeeCCCCCC
Q 027149 48 YEYPCPFCSE 57 (227)
Q Consensus 48 ~~F~CPfC~e 57 (227)
..|.||.||.
T Consensus 13 v~~~Cp~cGi 22 (55)
T PF13824_consen 13 VNFECPDCGI 22 (55)
T ss_pred cCCcCCCCCC
Confidence 6799999986
No 146
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=32.30 E-value=17 Score=28.11 Aligned_cols=37 Identities=16% Similarity=0.358 Sum_probs=18.9
Q ss_pred CCCCCCCccHHHhhhhhcccC----CCCCCcccCCcccccc
Q 027149 52 CPFCSEDFDLVGLCCHIDEEH----PVEAKSGVCPVCVTRV 88 (227)
Q Consensus 52 CPfC~e~~d~~~L~~H~~~eH----~~e~~~vvCPVC~~~~ 88 (227)
||+|+.+.-+.....|..+.. ..+....+||.|-...
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
Confidence 999986333333333221111 0133445799997754
No 147
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=32.12 E-value=15 Score=32.10 Aligned_cols=22 Identities=23% Similarity=0.481 Sum_probs=0.0
Q ss_pred CcccCCccccccc-hhhHhhhhc
Q 027149 77 KSGVCPVCVTRVT-MDMVDHITT 98 (227)
Q Consensus 77 ~~vvCPVC~~~~~-~d~i~Hl~~ 98 (227)
..++||||-.+|- ..|-.||+.
T Consensus 167 ~~~~cPitGe~IP~~e~~eHmRi 189 (229)
T PF12230_consen 167 KMIICPITGEMIPADEMDEHMRI 189 (229)
T ss_dssp -----------------------
T ss_pred ccccccccccccccccccccccc
Confidence 3479999999876 689999974
No 148
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=31.87 E-value=17 Score=34.62 Aligned_cols=40 Identities=25% Similarity=0.524 Sum_probs=26.0
Q ss_pred eeCCCCCCCccHHHhhhhhcccC-CCCCCcccCCccccccc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEH-PVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH-~~e~~~vvCPVC~~~~~ 89 (227)
-.||+|+.+---...|++|-... +.+..+.+|.+|...+.
T Consensus 137 g~CP~C~~~~a~g~~Ce~cG~~~~~~~l~~p~~~~~g~~~~ 177 (391)
T PF09334_consen 137 GTCPYCGSDKARGDQCENCGRPLEPEELINPVCKICGSPPE 177 (391)
T ss_dssp CEETTT--SSCTTTEETTTSSBEECCCSECEEETTTS-B-E
T ss_pred ccccCcCccccCCCcccCCCCCcccccccCCccccccccCc
Confidence 57999996555567777776433 35778899999988654
No 149
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=31.80 E-value=21 Score=27.58 Aligned_cols=8 Identities=50% Similarity=1.767 Sum_probs=6.4
Q ss_pred eeCCCCCC
Q 027149 50 YPCPFCSE 57 (227)
Q Consensus 50 F~CPfC~e 57 (227)
.+||+||.
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 57999985
No 150
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=31.34 E-value=5 Score=25.34 Aligned_cols=7 Identities=57% Similarity=1.407 Sum_probs=3.3
Q ss_pred cccCCcc
Q 027149 78 SGVCPVC 84 (227)
Q Consensus 78 ~vvCPVC 84 (227)
.+.||+|
T Consensus 35 ~~~CP~C 41 (41)
T PF00097_consen 35 SVKCPLC 41 (41)
T ss_dssp SSBTTTT
T ss_pred CccCCcC
Confidence 3445554
No 151
>PRK10220 hypothetical protein; Provisional
Probab=30.76 E-value=29 Score=28.17 Aligned_cols=24 Identities=25% Similarity=0.843 Sum_probs=14.5
Q ss_pred eCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 51 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 51 ~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
+||-|+.++.- -+....|||-|+.
T Consensus 5 ~CP~C~seytY------------~d~~~~vCpeC~h 28 (111)
T PRK10220 5 HCPKCNSEYTY------------EDNGMYICPECAH 28 (111)
T ss_pred cCCCCCCcceE------------cCCCeEECCcccC
Confidence 67777654421 1234578888865
No 152
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=30.39 E-value=11 Score=24.12 Aligned_cols=11 Identities=18% Similarity=0.543 Sum_probs=4.4
Q ss_pred CCCCCCCccHH
Q 027149 52 CPFCSEDFDLV 62 (227)
Q Consensus 52 CPfC~e~~d~~ 62 (227)
|++|+..+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 88998866554
No 153
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=30.27 E-value=13 Score=25.81 Aligned_cols=32 Identities=31% Similarity=0.585 Sum_probs=11.7
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
.-+||| |+..+=+- -..++. +..+++||-|..
T Consensus 14 ~~~PC~-Cgf~IC~~-C~~~i~-----~~~~g~CPgCr~ 45 (48)
T PF14570_consen 14 DFYPCE-CGFQICRF-CYHDIL-----ENEGGRCPGCRE 45 (48)
T ss_dssp T--SST-TS----HH-HHHHHT-----TSS-SB-TTT--
T ss_pred ccccCc-CCCcHHHH-HHHHHH-----hccCCCCCCCCC
Confidence 467886 76533211 112222 245789999954
No 154
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.24 E-value=15 Score=30.40 Aligned_cols=38 Identities=34% Similarity=0.542 Sum_probs=22.2
Q ss_pred ceeeCCCCCCCccHH-Hh-hhhhcccCCCCC---CcccCCccc
Q 027149 48 YEYPCPFCSEDFDLV-GL-CCHIDEEHPVEA---KSGVCPVCV 85 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~-~L-~~H~~~eH~~e~---~~vvCPVC~ 85 (227)
..+.||.|.+.|... -| |-|---..+... ....||+|.
T Consensus 12 ~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred ccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccC
Confidence 468999998866655 22 233222111111 338999998
No 155
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=29.79 E-value=22 Score=35.30 Aligned_cols=48 Identities=17% Similarity=0.258 Sum_probs=34.2
Q ss_pred CccHHHhhhhhcccCCCCCC-----------------cccCCccccccc--hhhHhhhhcccccccc
Q 027149 58 DFDLVGLCCHIDEEHPVEAK-----------------SGVCPVCVTRVT--MDMVDHITTQHGNISN 105 (227)
Q Consensus 58 ~~d~~~L~~H~~~eH~~e~~-----------------~vvCPVC~~~~~--~d~i~Hl~~qH~~~~K 105 (227)
.+.+..|..|+...|..++. .-+||+|..+-. .++..|+...|-.-++
T Consensus 20 kVsi~eL~sy~~~~~~~~a~~~Lseal~fak~n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~ 86 (466)
T PF04780_consen 20 KVSIDELKSYYESVYDREAADALSEALSFAKENKSWRFWICPRCSKKFSDAESCLSHMEQEHPAGLK 86 (466)
T ss_pred eeEHHHHHHHHHhccchHHHHHHHHHHHHHHhcCceeEeeCCcccceeCCHHHHHHHHHHhhhhhcC
Confidence 56777777777777653322 346999997643 6899999988876553
No 156
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=29.69 E-value=21 Score=23.81 Aligned_cols=9 Identities=33% Similarity=1.206 Sum_probs=7.3
Q ss_pred eeeCCCCCC
Q 027149 49 EYPCPFCSE 57 (227)
Q Consensus 49 ~F~CPfC~e 57 (227)
.-.||||+.
T Consensus 29 ~~~CpYCg~ 37 (40)
T PF10276_consen 29 PVVCPYCGT 37 (40)
T ss_dssp EEEETTTTE
T ss_pred eEECCCCCC
Confidence 378999985
No 157
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.06 E-value=21 Score=35.07 Aligned_cols=32 Identities=25% Similarity=0.513 Sum_probs=21.6
Q ss_pred ceeeCCCCCC---CccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSE---DFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e---~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
+.|.||+|.. .+|+..|..- +...-.|-.|-.
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~~-------~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLDN-------ETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHhhcc-------cCceEEEecCCC
Confidence 6899999988 4555555442 234457777765
No 158
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=28.98 E-value=43 Score=29.07 Aligned_cols=31 Identities=23% Similarity=0.452 Sum_probs=22.3
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
..|.||-|..-+...+-+.+- -.||.|-+.+
T Consensus 112 ~~y~C~~~~~r~sfdeA~~~~----------F~Cp~Cg~~L 142 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAMELG----------FTCPKCGEDL 142 (176)
T ss_pred CceeCCCCCCcccHHHHHHhC----------CCCCCCCchh
Confidence 579999998855555444442 6999998765
No 159
>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=28.61 E-value=40 Score=37.11 Aligned_cols=47 Identities=19% Similarity=0.428 Sum_probs=31.2
Q ss_pred ccccccCCcchhhhccCcceeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 30 CIDFEDIEEDDYEEVKGEYEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 30 ~~g~e~~~~ddd~e~r~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
.+|+-|++ + ++ +-|.||-|.- +|...+-. .--++--...||.|-...
T Consensus 671 ~lgITeVd---P--L~--phy~c~~c~~~ef~~~~~~-----~sg~dlp~k~cp~c~~~~ 718 (1213)
T TIGR01405 671 MTGITEVN---P--LP--PHYLCPNCKYSEFITDGSV-----GSGFDLPDKDCPKCGAPL 718 (1213)
T ss_pred HhcCCCcC---C--Cc--ccccCcccccccccccccc-----cccccCccccCccccccc
Confidence 55777766 4 77 8999999976 77544310 112355567899998853
No 160
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=28.47 E-value=19 Score=31.48 Aligned_cols=21 Identities=19% Similarity=0.248 Sum_probs=0.0
Q ss_pred eeeCCCCCCCccHHHhhhhhc
Q 027149 49 EYPCPFCSEDFDLVGLCCHID 69 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~ 69 (227)
...||+||+-+-+..+-.|+.
T Consensus 168 ~~~cPitGe~IP~~e~~eHmR 188 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMR 188 (229)
T ss_dssp ---------------------
T ss_pred ccccccccccccccccccccc
Confidence 479999999999999999987
No 161
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.04 E-value=28 Score=33.20 Aligned_cols=24 Identities=38% Similarity=0.870 Sum_probs=20.2
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCC
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHP 73 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~ 73 (227)
+.-||||.-.+.....|.|++ .|-
T Consensus 2 e~iCP~CkLsv~~~~m~~Hie-aHF 25 (393)
T KOG4696|consen 2 EIICPFCKLSVNYDEMCFHIE-AHF 25 (393)
T ss_pred cccccceecccCHHHHHHHHH-hhc
Confidence 357999999999999999998 443
No 162
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.89 E-value=35 Score=37.88 Aligned_cols=35 Identities=20% Similarity=0.152 Sum_probs=21.1
Q ss_pred CccccccccccCCCCCHHHHHHHHhHhhHHHHHHH
Q 027149 185 SCEKTFETNAQQSSLSNEDHLEKANRSNFAQGLLF 219 (227)
Q Consensus 185 s~~~~~e~~~~~~~ls~ed~eEk~~R~eFVQgLll 219 (227)
+++|.+|-.+|.--|+.+=-+=-.+=+.||-.||-
T Consensus 825 ~~dQivELk~QDiil~~~aa~yl~~va~fiDdLL~ 859 (1337)
T PRK14714 825 HEDQVVELKVQDIVLSDGAAEYLLKVAKFVDDLLE 859 (1337)
T ss_pred CccceEEeecccEEcchHHHHHHHHHHHHHHHHHH
Confidence 45556666665334555444444667889888873
No 163
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=27.42 E-value=34 Score=22.04 Aligned_cols=9 Identities=22% Similarity=1.017 Sum_probs=4.2
Q ss_pred eeeCCCCCC
Q 027149 49 EYPCPFCSE 57 (227)
Q Consensus 49 ~F~CPfC~e 57 (227)
...|-||+.
T Consensus 16 ~a~C~~C~~ 24 (45)
T PF02892_consen 16 KAKCKYCGK 24 (45)
T ss_dssp -EEETTTTE
T ss_pred eEEeCCCCe
Confidence 345555554
No 164
>PF14279 HNH_5: HNH endonuclease
Probab=26.86 E-value=26 Score=25.85 Aligned_cols=43 Identities=19% Similarity=0.370 Sum_probs=24.3
Q ss_pred CCCCCCCccHHHh-hhhhcccCCC---CCCcccCCccccccchhhHhh
Q 027149 52 CPFCSEDFDLVGL-CCHIDEEHPV---EAKSGVCPVCVTRVTMDMVDH 95 (227)
Q Consensus 52 CPfC~e~~d~~~L-~~H~~~eH~~---e~~~vvCPVC~~~~~~d~i~H 95 (227)
|.||.++.+.... .+|+.-+=-. ..+. ||--|-...|...-.+
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~vD~~ 47 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN-VCDKCNNKFGSKVDAE 47 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc-hhHHHhHHHhHHHHHH
Confidence 9999997765442 3344322111 2334 8888888877433333
No 165
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=26.60 E-value=38 Score=31.70 Aligned_cols=30 Identities=30% Similarity=0.535 Sum_probs=22.4
Q ss_pred ccCcceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 44 VKGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 44 ~r~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
+| -+||-|++-+=..+|- .+..|||-|...
T Consensus 27 lw----~KCp~c~~~~y~~eL~----------~n~~vcp~c~~h 56 (294)
T COG0777 27 LW----TKCPSCGEMLYRKELE----------SNLKVCPKCGHH 56 (294)
T ss_pred ce----eECCCccceeeHHHHH----------hhhhcccccCcc
Confidence 77 8999999855555554 345699999773
No 166
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.87 E-value=31 Score=27.55 Aligned_cols=27 Identities=37% Similarity=0.691 Sum_probs=18.9
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
..+.|+-|+..|..... ....||-|..
T Consensus 70 ~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs 96 (117)
T PRK00564 70 VELECKDCSHVFKPNAL------------DYGVCEKCHS 96 (117)
T ss_pred CEEEhhhCCCccccCCc------------cCCcCcCCCC
Confidence 57999999976655422 2245999975
No 167
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=25.85 E-value=33 Score=29.75 Aligned_cols=14 Identities=50% Similarity=1.177 Sum_probs=10.9
Q ss_pred eeCCCCCCCccHHH
Q 027149 50 YPCPFCSEDFDLVG 63 (227)
Q Consensus 50 F~CPfC~e~~d~~~ 63 (227)
=+||+|+.-+|-.+
T Consensus 155 P~CPlCg~PlDP~G 168 (171)
T PF11290_consen 155 PPCPLCGEPLDPEG 168 (171)
T ss_pred CCCCCCCCCCCCCC
Confidence 47999999877543
No 168
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=25.81 E-value=34 Score=23.73 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=8.9
Q ss_pred ceeeCCCCCC
Q 027149 48 YEYPCPFCSE 57 (227)
Q Consensus 48 ~~F~CPfC~e 57 (227)
..|.||.|+.
T Consensus 33 ~~w~CP~C~a 42 (50)
T cd00730 33 DDWVCPVCGA 42 (50)
T ss_pred CCCCCCCCCC
Confidence 6799999987
No 169
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=25.50 E-value=34 Score=29.36 Aligned_cols=42 Identities=21% Similarity=0.444 Sum_probs=26.4
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccC-----CCCC-CcccCCccccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEH-----PVEA-KSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH-----~~e~-~~vvCPVC~~~~~ 89 (227)
+.-.||.|+..++...-..|++-.| .... +-+.|+-|-...|
T Consensus 19 Q~G~CaiC~~~l~~~~~~~~vDHDH~l~g~~TG~VRGLLC~~CN~~lG 66 (157)
T PHA02565 19 QNGICPLCKRELDGDVSKNHLDHDHELNGPNAGRVRGLLCNLCNALEG 66 (157)
T ss_pred hCCcCCCCCCccCCCccccccCCCCCCCCcccccccccCchhhhhhhh
Confidence 4578999999776432223777777 3222 4467999955433
No 170
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=25.40 E-value=35 Score=25.38 Aligned_cols=29 Identities=21% Similarity=0.460 Sum_probs=19.5
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
..||-|+- .+.--...+.+|.|++|...+
T Consensus 20 VkCpdC~N----------~q~vFshast~V~C~~CG~~l 48 (67)
T COG2051 20 VKCPDCGN----------EQVVFSHASTVVTCLICGTTL 48 (67)
T ss_pred EECCCCCC----------EEEEeccCceEEEecccccEE
Confidence 57999974 233333356779999998744
No 171
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=25.36 E-value=50 Score=37.10 Aligned_cols=47 Identities=23% Similarity=0.484 Sum_probs=30.6
Q ss_pred ccccccCCcchhhhccCcceeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 30 CIDFEDIEEDDYEEVKGEYEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 30 ~~g~e~~~~ddd~e~r~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
.+|+-+++ + +. +-|.||-|.- +|...+- -.=-++--...||.|-...
T Consensus 896 ~lgITeVd---P--L~--phy~C~~C~~~ef~~~~~-----~~sG~Dlpdk~Cp~Cg~~~ 943 (1437)
T PRK00448 896 MIGITEVN---P--LP--PHYVCPNCKYSEFFTDGS-----VGSGFDLPDKDCPKCGTKL 943 (1437)
T ss_pred HhcCCCcC---C--CC--ccccCccccccccccccc-----ccccccCccccCccccccc
Confidence 55777766 4 77 8999999976 6654331 0112344456899998853
No 172
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=25.08 E-value=44 Score=32.58 Aligned_cols=55 Identities=20% Similarity=0.307 Sum_probs=32.1
Q ss_pred eeeCCC--CCC-CccHHHhhhhhcccC-CCCCCcccCCcccc--ccchhhHhhhhcccccc
Q 027149 49 EYPCPF--CSE-DFDLVGLCCHIDEEH-PVEAKSGVCPVCVT--RVTMDMVDHITTQHGNI 103 (227)
Q Consensus 49 ~F~CPf--C~e-~~d~~~L~~H~~~eH-~~e~~~vvCPVC~~--~~~~d~i~Hl~~qH~~~ 103 (227)
.|.|-+ |-+ -=....+..|..+.| .+.+-.-.|-+|.. .-|.++.+||+-+|++-
T Consensus 319 ~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~ 379 (467)
T KOG3608|consen 319 VYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFR 379 (467)
T ss_pred ceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhccc
Confidence 344544 444 222344455555555 23333445777765 35679999999999874
No 173
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=25.07 E-value=38 Score=24.24 Aligned_cols=19 Identities=26% Similarity=0.546 Sum_probs=12.8
Q ss_pred ceeeCCCCCCCccHHHhhh
Q 027149 48 YEYPCPFCSEDFDLVGLCC 66 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~ 66 (227)
..-.||+|.-.+|-..|+.
T Consensus 6 niL~Cp~ck~pL~~~~l~~ 24 (68)
T PF03966_consen 6 NILACPVCKGPLDWEALVE 24 (68)
T ss_dssp GTBB-TTTSSBEHHHHHHH
T ss_pred hhhcCCCCCCcchHHHHHH
Confidence 4568999988776666655
No 174
>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=24.68 E-value=38 Score=21.50 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=6.1
Q ss_pred cccCCcccccc
Q 027149 78 SGVCPVCVTRV 88 (227)
Q Consensus 78 ~vvCPVC~~~~ 88 (227)
.+.||-|..++
T Consensus 17 ~irC~~CG~RI 27 (32)
T PF03604_consen 17 PIRCPECGHRI 27 (32)
T ss_dssp TSSBSSSS-SE
T ss_pred cEECCcCCCeE
Confidence 36677775443
No 175
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.54 E-value=35 Score=25.08 Aligned_cols=13 Identities=46% Similarity=0.963 Sum_probs=9.3
Q ss_pred CCCcccCCccccc
Q 027149 75 EAKSGVCPVCVTR 87 (227)
Q Consensus 75 e~~~vvCPVC~~~ 87 (227)
+.+.|+||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 5667888888664
No 176
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=24.32 E-value=25 Score=22.82 Aligned_cols=25 Identities=36% Similarity=0.905 Sum_probs=13.8
Q ss_pred CCCCCCCccHHHhhhhhcccCCCCCCcccCCccc
Q 027149 52 CPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCV 85 (227)
Q Consensus 52 CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~ 85 (227)
||-|+..+....+ .+...-+||-|.
T Consensus 2 CP~C~~~l~~~~~---------~~~~id~C~~C~ 26 (41)
T PF13453_consen 2 CPRCGTELEPVRL---------GDVEIDVCPSCG 26 (41)
T ss_pred cCCCCcccceEEE---------CCEEEEECCCCC
Confidence 7777766554444 122334577773
No 177
>PF14369 zf-RING_3: zinc-finger
Probab=24.13 E-value=36 Score=21.82 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=8.0
Q ss_pred eeCCCCCCCc
Q 027149 50 YPCPFCSEDF 59 (227)
Q Consensus 50 F~CPfC~e~~ 59 (227)
..||.|+-+|
T Consensus 22 ~~CP~C~~gF 31 (35)
T PF14369_consen 22 VACPRCHGGF 31 (35)
T ss_pred cCCcCCCCcE
Confidence 3699998766
No 178
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=24.08 E-value=35 Score=25.51 Aligned_cols=8 Identities=38% Similarity=1.547 Sum_probs=5.2
Q ss_pred eeCCCCCC
Q 027149 50 YPCPFCSE 57 (227)
Q Consensus 50 F~CPfC~e 57 (227)
|.||+|+.
T Consensus 2 m~CP~Cg~ 9 (72)
T PRK09678 2 FHCPLCQH 9 (72)
T ss_pred ccCCCCCC
Confidence 45777765
No 179
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.89 E-value=24 Score=33.79 Aligned_cols=41 Identities=22% Similarity=0.481 Sum_probs=31.2
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCC---------CcccCCcccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEA---------KSGVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~---------~~vvCPVC~~~~ 88 (227)
.++.|-.|-|+|...+.+.++-=.|.|-. +.-.||||-..+
T Consensus 228 ~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 228 ATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred CCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcC
Confidence 34899999999999888888877777732 235799995543
No 180
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=23.29 E-value=29 Score=27.74 Aligned_cols=19 Identities=26% Similarity=0.618 Sum_probs=13.0
Q ss_pred ceeeCCCCCC-CccHHHhhh
Q 027149 48 YEYPCPFCSE-DFDLVGLCC 66 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~~ 66 (227)
..|.||+|.. .-.+..+..
T Consensus 23 ~D~~Cp~C~~~~~~~~~~~~ 42 (178)
T cd03019 23 FSYGCPHCYNFEPILEAWVK 42 (178)
T ss_pred ECCCCcchhhhhHHHHHHHH
Confidence 4699999988 544554443
No 181
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.21 E-value=53 Score=36.51 Aligned_cols=37 Identities=30% Similarity=0.670 Sum_probs=22.7
Q ss_pred eeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCccccccch
Q 027149 49 EYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTM 90 (227)
Q Consensus 49 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~~ 90 (227)
.+.||-||. .+. ..|..|-. |. ++ ...||.|-+.+..
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CGs-~t-e~-vy~CPsCGaev~~ 704 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCGT-HT-EP-VYVCPDCGAEVPP 704 (1337)
T ss_pred EEECCCCCCcccc--ccCcccCC-cC-CC-ceeCccCCCccCC
Confidence 599999998 433 36666653 22 11 3478888776543
No 182
>cd03021 DsbA_GSTK DsbA family, Glutathione (GSH) S-transferase Kappa (GSTK) subfamily; GSTK is a member of the GST family of enzymes which catalyzes the transfer of the thiol of GSH to electrophilic substrates. It is specifically located in the mitochondria and peroxisomes, unlike other members of the canonical GST family, which are mainly cytosolic. The biological substrates of GSTK are not yet known. It is presumed to have a protective role during respiration when large amounts of reactive oxygen species are generated. GSTK has the same general fold as DsbA, consisting of a thioredoxin domain interrupted by an alpha-helical domain and its biological unit is a homodimer. GSTK is closely related to the bacterial enzyme, 2-hydroxychromene-2-carboxylate (HCCA) isomerase. It shows little sequence similarity to the other members of the GST family.
Probab=23.15 E-value=18 Score=30.71 Aligned_cols=12 Identities=25% Similarity=0.625 Sum_probs=9.9
Q ss_pred ceeeCCCCCCCc
Q 027149 48 YEYPCPFCSEDF 59 (227)
Q Consensus 48 ~~F~CPfC~e~~ 59 (227)
..|.||||+.+.
T Consensus 7 ~D~vcPwcylg~ 18 (209)
T cd03021 7 YDVVSPYSYLAF 18 (209)
T ss_pred EeCCChHHHHHH
Confidence 679999999843
No 183
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=22.63 E-value=40 Score=31.01 Aligned_cols=38 Identities=26% Similarity=0.524 Sum_probs=26.5
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccchhhHhh
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDH 95 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~~d~i~H 95 (227)
....||.|+.. + -+.+ ++....||.-|-.-+..++|.+
T Consensus 10 ~~~~Cp~Cg~~-~------iv~d---~~~Ge~vC~~CG~Vl~e~~iD~ 47 (310)
T PRK00423 10 EKLVCPECGSD-K------LIYD---YERGEIVCADCGLVIEENIIDQ 47 (310)
T ss_pred cCCcCcCCCCC-C------eeEE---CCCCeEeecccCCccccccccc
Confidence 35689999961 1 1222 3577899999999888777763
No 184
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=22.59 E-value=74 Score=33.81 Aligned_cols=48 Identities=25% Similarity=0.536 Sum_probs=33.9
Q ss_pred eeeCCCCCCCccHH-HhhhhhcccCCCCCCcccCCccccccc--hhhHhhhhc
Q 027149 49 EYPCPFCSEDFDLV-GLCCHIDEEHPVEAKSGVCPVCVTRVT--MDMVDHITT 98 (227)
Q Consensus 49 ~F~CPfC~e~~d~~-~L~~H~~~eH~~e~~~vvCPVC~~~~~--~d~i~Hl~~ 98 (227)
.|+|+-||+-|-.. -|-+|+. -|.. -|.--||-|-.+-. ..+-.||..
T Consensus 281 KFKCtECgKAFKfKHHLKEHlR-IHSG-EKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 281 KFKCTECGKAFKFKHHLKEHLR-IHSG-EKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred cccccccchhhhhHHHHHhhhe-eecC-CCCcCCcccccccccCCcccccccc
Confidence 79999999977653 3555555 4444 35568999998764 567777753
No 185
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=22.48 E-value=31 Score=32.42 Aligned_cols=18 Identities=33% Similarity=0.647 Sum_probs=14.3
Q ss_pred CcccCCccccccchhhHh
Q 027149 77 KSGVCPVCVTRVTMDMVD 94 (227)
Q Consensus 77 ~~vvCPVC~~~~~~d~i~ 94 (227)
+..+||||..+|-..||.
T Consensus 184 ~~~~CPvCGS~PvaSmV~ 201 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQ 201 (308)
T ss_pred ccccCCCcCCCCcceeee
Confidence 457999999998776663
No 186
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=22.37 E-value=43 Score=22.99 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=6.9
Q ss_pred ceeeCCCCCC
Q 027149 48 YEYPCPFCSE 57 (227)
Q Consensus 48 ~~F~CPfC~e 57 (227)
..|.||-|+.
T Consensus 33 ~~w~CP~C~a 42 (47)
T PF00301_consen 33 DDWVCPVCGA 42 (47)
T ss_dssp TT-B-TTTSS
T ss_pred CCCcCcCCCC
Confidence 6799999986
No 187
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.36 E-value=42 Score=27.22 Aligned_cols=16 Identities=31% Similarity=0.700 Sum_probs=12.6
Q ss_pred eeeCCCCCCCccHHHh
Q 027149 49 EYPCPFCSEDFDLVGL 64 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L 64 (227)
...||-||+.|+-.-+
T Consensus 49 ~t~CP~Cg~~~e~~fv 64 (115)
T COG1885 49 STSCPKCGEPFESAFV 64 (115)
T ss_pred cccCCCCCCccceeEE
Confidence 5789999998876543
No 188
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=22.26 E-value=44 Score=28.27 Aligned_cols=10 Identities=40% Similarity=0.823 Sum_probs=7.9
Q ss_pred CcccCCcccc
Q 027149 77 KSGVCPVCVT 86 (227)
Q Consensus 77 ~~vvCPVC~~ 86 (227)
+.+.||+|-.
T Consensus 31 glv~CP~Cgs 40 (148)
T PF06676_consen 31 GLVSCPVCGS 40 (148)
T ss_pred CCccCCCCCC
Confidence 5578999965
No 189
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=22.24 E-value=26 Score=24.13 Aligned_cols=39 Identities=13% Similarity=0.411 Sum_probs=22.4
Q ss_pred ceeeCCCCCC--CccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 48 YEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e--~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
+.=.|.+|+. ++.+-.+--+ .+=..+....+|..|..++
T Consensus 6 s~~kCELC~a~~~L~vy~Vpp~--~~~~~d~~iliC~tC~~Qi 46 (47)
T smart00782 6 CESKCELCGSDSPLVVYAVPPS--SDVTADNSVMLCDTCHSQI 46 (47)
T ss_pred cCCcccCcCCCCCceEEecCCC--CCCCccceeeechHHHHhh
Confidence 4457999997 3332222111 1123456678999997654
No 190
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=22.17 E-value=48 Score=25.56 Aligned_cols=40 Identities=15% Similarity=0.255 Sum_probs=0.0
Q ss_pred cCCCCCCcccCCccccccc-hhhHhhhhccccccccccccc
Q 027149 71 EHPVEAKSGVCPVCVTRVT-MDMVDHITTQHGNISNSWHKL 110 (227)
Q Consensus 71 eH~~e~~~vvCPVC~~~~~-~d~i~Hl~~qH~~~~K~~r~r 110 (227)
.+..+.+.+||-.|-.-|+ ..+.+||..+|..+....++.
T Consensus 4 ~y~~~~~vlIC~~C~~av~~~~v~~HL~~~H~~~~~~~~~~ 44 (109)
T PF12013_consen 4 HYNPEYRVLICRQCQYAVQPSEVESHLRKRHHILKSQERQR 44 (109)
T ss_pred eEcCcCCEEEeCCCCcccCchHHHHHHHHhcccccHHHHHH
No 191
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=22.13 E-value=42 Score=22.53 Aligned_cols=25 Identities=24% Similarity=0.670 Sum_probs=14.1
Q ss_pred eeeCCCCCCCccHH------HhhhhhcccCC
Q 027149 49 EYPCPFCSEDFDLV------GLCCHIDEEHP 73 (227)
Q Consensus 49 ~F~CPfC~e~~d~~------~L~~H~~~eH~ 73 (227)
.-.|-+|+..+... .|..|+...|+
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 46677777755433 45555554443
No 192
>PHA00733 hypothetical protein
Probab=22.11 E-value=57 Score=26.44 Aligned_cols=25 Identities=20% Similarity=0.453 Sum_probs=21.1
Q ss_pred eeeCCCCCCC-ccHHHhhhhhcccCC
Q 027149 49 EYPCPFCSED-FDLVGLCCHIDEEHP 73 (227)
Q Consensus 49 ~F~CPfC~e~-~d~~~L~~H~~~eH~ 73 (227)
.|.|+.|+.. -....|..|+...|.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 5899999995 566889999998885
No 193
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=21.95 E-value=43 Score=30.99 Aligned_cols=17 Identities=35% Similarity=0.858 Sum_probs=15.2
Q ss_pred ccCcceeeCCCCCCCcc
Q 027149 44 VKGEYEYPCPFCSEDFD 60 (227)
Q Consensus 44 ~r~~~~F~CPfC~e~~d 60 (227)
+||..+|.||-|+..|.
T Consensus 150 mwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 150 MWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccceeeeecccccccch
Confidence 78889999999998776
No 194
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=21.93 E-value=38 Score=22.55 Aligned_cols=8 Identities=50% Similarity=1.447 Sum_probs=3.7
Q ss_pred eeCCCCCC
Q 027149 50 YPCPFCSE 57 (227)
Q Consensus 50 F~CPfC~e 57 (227)
-|||.|+-
T Consensus 4 ~pCP~CGG 11 (40)
T PF08273_consen 4 GPCPICGG 11 (40)
T ss_dssp E--TTTT-
T ss_pred CCCCCCcC
Confidence 47888865
No 195
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=21.68 E-value=39 Score=29.42 Aligned_cols=25 Identities=32% Similarity=0.816 Sum_probs=17.0
Q ss_pred eeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCccccccc
Q 027149 49 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 89 (227)
Q Consensus 49 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~ 89 (227)
.-.||-|| |+.. ..+.|+-|..+|-
T Consensus 93 l~~CP~CG----------h~k~------a~~LC~~Cy~kV~ 117 (176)
T KOG4080|consen 93 LNTCPACG----------HIKP------AHTLCDYCYAKVH 117 (176)
T ss_pred cccCcccC----------cccc------ccccHHHHHHHHH
Confidence 45899998 4332 2378888877764
No 196
>PRK01546 hypothetical protein; Provisional
Probab=21.48 E-value=87 Score=23.96 Aligned_cols=29 Identities=21% Similarity=0.379 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHHh---------HhhHHHHHHHhhhccC
Q 027149 197 SSLSNEDHLEKAN---------RSNFAQGLLFSTIMDD 225 (227)
Q Consensus 197 ~~ls~ed~eEk~~---------R~eFVQgLllSTifdd 225 (227)
.-|+++|++|+.+ |..|-++|-.-.|+|+
T Consensus 20 ~gLT~eEk~Eq~~LR~eYl~~fR~~~~~~L~~i~vvD~ 57 (79)
T PRK01546 20 EGLTEEEQRERQSLREQYLKGFRQNMLNELKGIKVVNE 57 (79)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHhccceEECC
Confidence 5699999999854 6666666666666653
No 197
>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=21.38 E-value=51 Score=23.79 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=8.2
Q ss_pred eeCCCCCCCccH
Q 027149 50 YPCPFCSEDFDL 61 (227)
Q Consensus 50 F~CPfC~e~~d~ 61 (227)
=-||+||+.+..
T Consensus 4 kHC~~CG~~Ip~ 15 (59)
T PF09889_consen 4 KHCPVCGKPIPP 15 (59)
T ss_pred CcCCcCCCcCCc
Confidence 358888886553
No 198
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=21.31 E-value=8.4 Score=24.91 Aligned_cols=27 Identities=26% Similarity=0.620 Sum_probs=12.2
Q ss_pred eeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcc
Q 027149 50 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVC 84 (227)
Q Consensus 50 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC 84 (227)
+..| |+--|=..=|...+.. +..||+|
T Consensus 17 ~~l~-C~H~fh~~Ci~~~~~~-------~~~CP~C 43 (44)
T PF13639_consen 17 VKLP-CGHVFHRSCIKEWLKR-------NNSCPVC 43 (44)
T ss_dssp EEET-TSEEEEHHHHHHHHHH-------SSB-TTT
T ss_pred EEcc-CCCeeCHHHHHHHHHh-------CCcCCcc
Confidence 3444 5444444444444432 1277777
No 199
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=21.22 E-value=51 Score=18.44 Aligned_cols=16 Identities=19% Similarity=0.698 Sum_probs=6.8
Q ss_pred CCccccccc--hhhHhhh
Q 027149 81 CPVCVTRVT--MDMVDHI 96 (227)
Q Consensus 81 CPVC~~~~~--~d~i~Hl 96 (227)
|.||-.... ..|..|+
T Consensus 3 C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQHL 20 (25)
T ss_dssp ETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCcCCHHHHHHHH
Confidence 555543322 3444444
No 200
>cd03024 DsbA_FrnE DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=21.22 E-value=25 Score=28.93 Aligned_cols=21 Identities=19% Similarity=0.422 Sum_probs=15.4
Q ss_pred ceeeCCCCCC-CccHHHhhhhh
Q 027149 48 YEYPCPFCSE-DFDLVGLCCHI 68 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~~H~ 68 (227)
..|.||||+. .-.+..+....
T Consensus 5 ~D~~cP~cyl~~~~l~~~~~~~ 26 (201)
T cd03024 5 SDVVCPWCYIGKRRLEKALAEL 26 (201)
T ss_pred ecCcCccHHHHHHHHHHHHHhC
Confidence 5799999998 55666666554
No 201
>PRK05978 hypothetical protein; Provisional
Probab=21.15 E-value=39 Score=28.53 Aligned_cols=28 Identities=21% Similarity=0.441 Sum_probs=16.7
Q ss_pred eeeCCCCCC-CccHHHhhhhhcccCCCCCCcccCCccccc
Q 027149 49 EYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 87 (227)
Q Consensus 49 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~ 87 (227)
.-+||-|++ .+=. .+-.-+-.||+|-..
T Consensus 33 ~grCP~CG~G~LF~-----------g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 33 RGRCPACGEGKLFR-----------AFLKPVDHCAACGED 61 (148)
T ss_pred cCcCCCCCCCcccc-----------cccccCCCccccCCc
Confidence 468999999 4411 222334567777653
No 202
>PF05979 DUF896: Bacterial protein of unknown function (DUF896); InterPro: IPR009242 This family consists of several short, hypothetical bacterial proteins of unknown function. They may be involved in the bacterial SOS response [].; PDB: 2HEP_A 3BHP_C 2JVD_A.
Probab=21.14 E-value=47 Score=24.47 Aligned_cols=29 Identities=34% Similarity=0.479 Sum_probs=14.9
Q ss_pred CCCCHHHHHHHHh---------HhhHHHHHHHhhhccC
Q 027149 197 SSLSNEDHLEKAN---------RSNFAQGLLFSTIMDD 225 (227)
Q Consensus 197 ~~ls~ed~eEk~~---------R~eFVQgLllSTifdd 225 (227)
..|+++|.+|++. |..|-++|-.-.|.|+
T Consensus 17 ~gLT~eE~~Eq~~LR~eYl~~fR~~~~~~L~~i~ivD~ 54 (65)
T PF05979_consen 17 EGLTEEEKAEQAELRQEYLQNFRGNFRSQLENIKIVDP 54 (65)
T ss_dssp T---HHHHHHHHHHHHHHHHTTHHHHHHCSSTT-----
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcceeEECC
Confidence 5699999999854 5666666655555543
No 203
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=21.13 E-value=41 Score=35.93 Aligned_cols=34 Identities=21% Similarity=0.579 Sum_probs=23.3
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 86 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~ 86 (227)
+.|.||.|+..+..-+ ..-..|.+-.+.||-|.-
T Consensus 244 ~~~acp~~g~~~~ele-----prlFSFNsP~GaCp~C~G 277 (935)
T COG0178 244 ENFACPVCGFSIPELE-----PRLFSFNSPFGACPTCDG 277 (935)
T ss_pred cccCCCccCcccCCCC-----cccccCCCCCCCCCcCCC
Confidence 5799999987544321 112356677899999976
No 204
>PHA02929 N1R/p28-like protein; Provisional
Probab=21.10 E-value=21 Score=32.23 Aligned_cols=41 Identities=24% Similarity=0.482 Sum_probs=23.5
Q ss_pred ceeeCCCCCCCccHH----------HhhhhhcccCCC---CCCcccCCcccccc
Q 027149 48 YEYPCPFCSEDFDLV----------GLCCHIDEEHPV---EAKSGVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~----------~L~~H~~~eH~~---e~~~vvCPVC~~~~ 88 (227)
....||.|.+.+... .=|.|.--..+. -.....||+|...+
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~ 226 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF 226 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence 357899999965422 125553322221 12456899997654
No 205
>PRK00907 hypothetical protein; Provisional
Probab=21.01 E-value=37 Score=26.37 Aligned_cols=21 Identities=19% Similarity=0.271 Sum_probs=15.5
Q ss_pred eeeCCCCCC--CccHHHhhhhhc
Q 027149 49 EYPCPFCSE--DFDLVGLCCHID 69 (227)
Q Consensus 49 ~F~CPfC~e--~~d~~~L~~H~~ 69 (227)
+|||.|..+ +....+|...+.
T Consensus 13 EFPc~fpiKVmG~a~~~l~~~V~ 35 (92)
T PRK00907 13 QFPGTFELSAMGTAERGLETELP 35 (92)
T ss_pred ecCCCCeEEEEEcCchhHHHHHH
Confidence 799999977 777777665543
No 206
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=20.96 E-value=57 Score=22.81 Aligned_cols=30 Identities=33% Similarity=0.810 Sum_probs=20.7
Q ss_pred ceeeCCCCCCCccHHHhhhhhcccCCCCCCcccCCcccccc
Q 027149 48 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 88 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~ 88 (227)
..|.|--|+..|+.. .....+.||-|..++
T Consensus 5 ~~Y~C~~Cg~~~~~~-----------~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVELD-----------QETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeehh-----------hccCceeCCCCCcEE
Confidence 578999999877321 134457899997655
No 207
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.95 E-value=21 Score=33.01 Aligned_cols=42 Identities=26% Similarity=0.555 Sum_probs=29.3
Q ss_pred eeeCCCCCC--CccHHHhhhhhcccCCC-----CCCcccCCccccccch
Q 027149 49 EYPCPFCSE--DFDLVGLCCHIDEEHPV-----EAKSGVCPVCVTRVTM 90 (227)
Q Consensus 49 ~F~CPfC~e--~~d~~~L~~H~~~eH~~-----e~~~vvCPVC~~~~~~ 90 (227)
.|.|+.|-+ +-=.-..|-|+---|+. -.+...||+|.+++..
T Consensus 215 d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~p 263 (271)
T COG5574 215 DYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYP 263 (271)
T ss_pred ccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhccc
Confidence 789999988 33344567777666654 2355669999997753
No 208
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.89 E-value=24 Score=34.17 Aligned_cols=42 Identities=21% Similarity=0.455 Sum_probs=23.9
Q ss_pred ceeeCCCCCCCccHHH--hhhhhcccCCC---CCCcccCCccccccc
Q 027149 48 YEYPCPFCSEDFDLVG--LCCHIDEEHPV---EAKSGVCPVCVTRVT 89 (227)
Q Consensus 48 ~~F~CPfC~e~~d~~~--L~~H~~~eH~~---e~~~vvCPVC~~~~~ 89 (227)
..|.||.|.+.|.... =|.|.-=..|. -.....||+|...++
T Consensus 25 ~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 25 TSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred cccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 5699999988654432 34442211111 112347999988654
No 209
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.54 E-value=63 Score=33.25 Aligned_cols=37 Identities=27% Similarity=0.538 Sum_probs=0.0
Q ss_pred eCCCCCC-CccHHHhhhhhcccCCCCCCcccCCccccccchh
Q 027149 51 PCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMD 91 (227)
Q Consensus 51 ~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVC~~~~~~d 91 (227)
.||-|+. +-+-...|.+| -..-...+||-|-+.+..+
T Consensus 3 ~Cp~Cg~~n~~~akFC~~C----G~~l~~~~Cp~CG~~~~~~ 40 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKC----GTSLTHKPCPQCGTEVPVD 40 (645)
T ss_pred cCCCCCCcCCCCCcccccc----CCCCCCCcCCCCCCCCCcc
No 210
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.38 E-value=37 Score=27.40 Aligned_cols=7 Identities=43% Similarity=1.421 Sum_probs=3.6
Q ss_pred eeCCCCC
Q 027149 50 YPCPFCS 56 (227)
Q Consensus 50 F~CPfC~ 56 (227)
|.||.||
T Consensus 93 ~~CP~Cg 99 (124)
T PRK00762 93 IECPVCG 99 (124)
T ss_pred CcCcCCC
Confidence 4455555
No 211
>PRK02539 hypothetical protein; Provisional
Probab=20.36 E-value=93 Score=24.16 Aligned_cols=29 Identities=24% Similarity=0.395 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHHh---------HhhHHHHHHHhhhccC
Q 027149 197 SSLSNEDHLEKAN---------RSNFAQGLLFSTIMDD 225 (227)
Q Consensus 197 ~~ls~ed~eEk~~---------R~eFVQgLllSTifdd 225 (227)
..|+++|++|+.+ |..|-++|---.|.|+
T Consensus 19 ~gLT~eEk~Eq~~LR~eYl~~fR~~~~~~L~~i~ivD~ 56 (85)
T PRK02539 19 EGLTGEEKVEQAKLREEYIEGYRRSVRHHIEGIKIVDE 56 (85)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHhccceEECC
Confidence 5699999999854 6666666655555543
No 212
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=20.31 E-value=58 Score=31.90 Aligned_cols=44 Identities=27% Similarity=0.508 Sum_probs=26.1
Q ss_pred ceeeCCCCCC--CccHHHhhhhhcccCCCCCCcccCCcccc-ccchhhHhhhhccccccc
Q 027149 48 YEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVT-RVTMDMVDHITTQHGNIS 104 (227)
Q Consensus 48 ~~F~CPfC~e--~~d~~~L~~H~~~eH~~e~~~vvCPVC~~-~~~~d~i~Hl~~qH~~~~ 104 (227)
..+.||-|+. |.+...| ++.+.||-|.. .+.. +.-|-+.|.+++
T Consensus 226 ~l~~C~~C~~s~n~e~~~~-----------sk~~~Cp~C~~~~L~~--~~~IEVgHtF~L 272 (457)
T KOG2324|consen 226 TLMSCPSCGYSKNSEDLDL-----------SKIASCPKCNEGRLTK--TKSIEVGHTFLL 272 (457)
T ss_pred ceeecCcCCccCchhhhcC-----------CccccCCcccCCCccc--ccceEEEEEEEe
Confidence 4689999975 3332222 44589999988 3332 223345566654
No 213
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=20.18 E-value=43 Score=28.39 Aligned_cols=32 Identities=31% Similarity=0.668 Sum_probs=18.6
Q ss_pred eCCCCCC-CccHHHhhhhhcccCCCCCCcc-----cCCccccccc
Q 027149 51 PCPFCSE-DFDLVGLCCHIDEEHPVEAKSG-----VCPVCVTRVT 89 (227)
Q Consensus 51 ~CPfC~e-~~d~~~L~~H~~~eH~~e~~~v-----vCPVC~~~~~ 89 (227)
.||||+. +--| .+.-..+..+. -|+.|..+-+
T Consensus 2 ~CP~C~~~dtkV-------iDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRV-------LDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEe-------eeccccCCCCeeeecccCCccCCccc
Confidence 5999987 4322 22333333333 4999987643
No 214
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=20.09 E-value=34 Score=26.81 Aligned_cols=13 Identities=31% Similarity=0.887 Sum_probs=10.7
Q ss_pred ccCcceeeCCCCCCC
Q 027149 44 VKGEYEYPCPFCSED 58 (227)
Q Consensus 44 ~r~~~~F~CPfC~e~ 58 (227)
.+ +.+.||+|+..
T Consensus 32 ~~--~~~~Cp~C~~~ 44 (89)
T COG1997 32 QR--AKHVCPFCGRT 44 (89)
T ss_pred Hh--cCCcCCCCCCc
Confidence 55 78999999873
No 215
>cd02972 DsbA_family DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins.
Probab=20.07 E-value=26 Score=24.25 Aligned_cols=18 Identities=28% Similarity=0.713 Sum_probs=11.8
Q ss_pred ceeeCCCCCC-CccHHHhh
Q 027149 48 YEYPCPFCSE-DFDLVGLC 65 (227)
Q Consensus 48 ~~F~CPfC~e-~~d~~~L~ 65 (227)
..|.||+|.. .-.+..+.
T Consensus 5 ~d~~Cp~C~~~~~~l~~~~ 23 (98)
T cd02972 5 FDPLCPYCYLFEPELEKLL 23 (98)
T ss_pred ECCCCHhHHhhhHHHHHHH
Confidence 3588999988 44444443
Done!