Query 026824
Match_columns 232
No_of_seqs 164 out of 220
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 13:14:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026824hhsearch_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 2E-33 4.2E-38 221.8 7.3 105 119-229 1-105 (105)
2 PF05605 zf-Di19: Drought indu 99.8 1.4E-19 3.1E-24 126.4 3.6 54 45-98 1-54 (54)
3 KOG1280 Uncharacterized conser 99.6 6.3E-16 1.4E-20 142.9 7.6 199 28-231 62-330 (381)
4 COG5216 Uncharacterized conser 94.6 0.014 3E-07 42.4 0.8 34 43-85 19-54 (67)
5 KOG2923 Uncharacterized conser 94.5 0.023 4.9E-07 41.7 1.7 45 32-85 7-54 (67)
6 PF09237 GAGA: GAGA factor; I 93.8 0.038 8.2E-07 39.0 1.7 27 73-99 22-50 (54)
7 PF13894 zf-C2H2_4: C2H2-type 93.7 0.03 6.6E-07 31.1 0.9 23 47-69 1-24 (24)
8 PLN03086 PRLI-interacting fact 91.8 0.16 3.5E-06 50.9 3.7 50 43-97 450-500 (567)
9 PF13913 zf-C2HC_2: zinc-finge 91.6 0.13 2.8E-06 30.7 1.7 21 46-66 2-22 (25)
10 PF00096 zf-C2H2: Zinc finger, 90.8 0.08 1.7E-06 29.9 0.2 21 47-67 1-22 (23)
11 PHA00732 hypothetical protein 90.6 0.27 5.9E-06 37.1 3.0 42 47-93 2-44 (79)
12 PF08271 TF_Zn_Ribbon: TFIIB z 90.5 0.099 2.1E-06 34.6 0.5 35 47-91 1-35 (43)
13 PRK09710 lar restriction allev 89.6 0.15 3.3E-06 37.4 0.9 30 46-84 6-36 (64)
14 PF14354 Lar_restr_allev: Rest 89.0 0.18 4E-06 35.2 0.9 31 46-83 3-37 (61)
15 TIGR01206 lysW lysine biosynth 88.8 0.19 4.2E-06 35.5 0.9 30 46-84 2-31 (54)
16 PF13909 zf-H2C2_5: C2H2-type 88.7 0.17 3.6E-06 29.1 0.5 24 47-70 1-24 (24)
17 smart00531 TFIIE Transcription 88.2 0.4 8.8E-06 39.6 2.6 37 44-85 97-133 (147)
18 PF12756 zf-C2H2_2: C2H2 type 88.1 0.24 5.1E-06 36.4 1.1 48 48-95 1-72 (100)
19 TIGR02098 MJ0042_CXXC MJ0042 f 87.3 0.3 6.6E-06 31.1 1.1 32 47-84 3-34 (38)
20 PHA00733 hypothetical protein 86.9 0.78 1.7E-05 37.4 3.5 49 46-98 73-124 (128)
21 PRK14892 putative transcriptio 85.1 0.39 8.5E-06 37.9 0.9 36 44-87 19-54 (99)
22 PF08274 PhnA_Zn_Ribbon: PhnA 85.0 0.35 7.6E-06 30.4 0.5 25 47-83 3-27 (30)
23 PLN03086 PRLI-interacting fact 84.9 0.7 1.5E-05 46.5 2.8 38 45-85 477-514 (567)
24 smart00834 CxxC_CXXC_SSSS Puta 84.8 0.3 6.6E-06 31.2 0.1 33 45-85 4-36 (41)
25 PF09986 DUF2225: Uncharacteri 84.2 0.38 8.3E-06 42.3 0.5 18 46-63 5-22 (214)
26 PLN03208 E3 ubiquitin-protein 84.0 0.49 1.1E-05 41.5 1.1 46 44-89 16-82 (193)
27 PHA02768 hypothetical protein; 83.5 0.83 1.8E-05 32.5 1.9 34 46-83 5-39 (55)
28 PF14206 Cys_rich_CPCC: Cystei 82.9 0.61 1.3E-05 35.4 1.1 26 47-83 2-28 (78)
29 KOG2462 C2H2-type Zn-finger pr 82.9 1.1 2.3E-05 41.4 2.9 22 44-65 159-181 (279)
30 COG4888 Uncharacterized Zn rib 80.9 0.46 9.9E-06 37.8 -0.2 37 43-84 19-55 (104)
31 PF14255 Cys_rich_CPXG: Cystei 80.4 0.61 1.3E-05 32.8 0.3 34 47-85 1-34 (52)
32 smart00734 ZnF_Rad18 Rad18-lik 78.9 1.4 3.1E-05 26.5 1.6 19 48-66 3-21 (26)
33 COG1655 Uncharacterized protei 78.8 0.91 2E-05 41.2 1.0 12 46-57 19-30 (267)
34 TIGR02605 CxxC_CxxC_SSSS putat 78.6 1.1 2.5E-05 30.2 1.2 31 45-83 4-34 (52)
35 cd00350 rubredoxin_like Rubred 76.6 1.1 2.4E-05 28.1 0.7 24 47-83 2-25 (33)
36 PF04564 U-box: U-box domain; 76.5 2.2 4.8E-05 31.1 2.3 37 44-86 2-50 (73)
37 smart00504 Ubox Modified RING 76.5 2.3 5E-05 29.2 2.3 26 54-86 21-46 (63)
38 PF12756 zf-C2H2_2: C2H2 type 75.5 1.3 2.8E-05 32.4 0.8 25 45-69 49-74 (100)
39 PRK00398 rpoP DNA-directed RNA 74.4 1.1 2.3E-05 30.0 0.1 29 46-85 3-31 (46)
40 KOG1842 FYVE finger-containing 73.7 1.3 2.8E-05 43.6 0.5 33 42-74 11-44 (505)
41 KOG2462 C2H2-type Zn-finger pr 73.0 3 6.6E-05 38.5 2.8 51 46-99 187-240 (279)
42 PF05129 Elf1: Transcription e 72.2 1.6 3.4E-05 33.1 0.6 34 44-84 20-55 (81)
43 KOG3623 Homeobox transcription 72.1 1.1 2.5E-05 46.5 -0.2 42 44-85 208-250 (1007)
44 PF03470 zf-XS: XS zinc finger 71.0 2.7 5.9E-05 28.6 1.5 10 78-87 1-10 (43)
45 PRK12495 hypothetical protein; 70.9 2.6 5.6E-05 37.9 1.8 31 44-87 40-70 (226)
46 smart00355 ZnF_C2H2 zinc finge 70.6 3.4 7.4E-05 22.6 1.7 22 47-69 1-23 (26)
47 KOG2593 Transcription initiati 69.3 3.2 7E-05 40.5 2.2 62 34-102 116-191 (436)
48 PF09723 Zn-ribbon_8: Zinc rib 69.1 2 4.4E-05 28.3 0.6 31 45-83 4-34 (42)
49 cd00729 rubredoxin_SM Rubredox 68.6 2.2 4.8E-05 27.1 0.6 26 46-84 2-27 (34)
50 PHA00616 hypothetical protein 68.4 2.3 5E-05 29.0 0.7 25 47-71 2-27 (44)
51 PF07754 DUF1610: Domain of un 68.1 2.4 5.2E-05 25.4 0.6 11 44-54 14-24 (24)
52 TIGR03655 anti_R_Lar restricti 67.4 2.4 5.2E-05 29.2 0.7 31 47-84 2-35 (53)
53 COG2888 Predicted Zn-ribbon RN 67.4 4.8 0.00011 29.2 2.2 33 43-82 24-57 (61)
54 PF13912 zf-C2H2_6: C2H2-type 66.4 3.5 7.5E-05 23.9 1.1 24 46-69 1-25 (27)
55 COG5236 Uncharacterized conser 66.2 6.5 0.00014 37.9 3.5 35 43-83 217-252 (493)
56 PRK14890 putative Zn-ribbon RN 66.1 3.4 7.4E-05 29.9 1.3 32 44-82 23-55 (59)
57 PF03145 Sina: Seven in absent 66.0 3 6.6E-05 35.6 1.2 54 45-101 13-75 (198)
58 PF13465 zf-H2C2_2: Zinc-finge 65.9 1.5 3.2E-05 26.0 -0.6 11 46-56 14-24 (26)
59 PF02176 zf-TRAF: TRAF-type zi 65.7 3 6.5E-05 28.6 0.9 45 46-92 9-60 (60)
60 PRK00420 hypothetical protein; 65.5 4.6 0.0001 32.6 2.0 27 47-85 24-50 (112)
61 PF04780 DUF629: Protein of un 64.3 4 8.7E-05 40.3 1.8 40 44-83 55-98 (466)
62 PTZ00255 60S ribosomal protein 64.2 2.1 4.6E-05 33.4 -0.1 18 41-58 31-49 (90)
63 COG1592 Rubrerythrin [Energy p 62.8 4.5 9.8E-05 34.7 1.6 25 46-84 134-158 (166)
64 PRK06266 transcription initiat 62.7 5.5 0.00012 34.2 2.1 32 44-85 115-146 (178)
65 KOG0320 Predicted E3 ubiquitin 62.6 3.1 6.7E-05 36.4 0.6 43 45-87 130-179 (187)
66 PF07191 zinc-ribbons_6: zinc- 61.7 0.96 2.1E-05 33.7 -2.3 53 47-103 2-61 (70)
67 TIGR00373 conserved hypothetic 60.9 6.2 0.00013 33.1 2.1 32 44-85 107-138 (158)
68 COG5175 MOT2 Transcriptional r 60.8 2.7 6E-05 40.3 -0.0 13 72-84 50-62 (480)
69 KOG2932 E3 ubiquitin ligase in 60.3 4.6 0.0001 38.3 1.3 58 46-103 90-177 (389)
70 COG1645 Uncharacterized Zn-fin 60.0 4.8 0.0001 33.4 1.3 25 46-84 28-53 (131)
71 PF15616 TerY-C: TerY-C metal 59.9 3.7 8E-05 34.0 0.6 44 44-89 75-119 (131)
72 PF10571 UPF0547: Uncharacteri 59.8 5.5 0.00012 24.1 1.2 8 49-56 3-10 (26)
73 COG4311 SoxD Sarcosine oxidase 59.6 4.1 8.9E-05 32.1 0.7 9 46-54 3-11 (97)
74 PF12773 DZR: Double zinc ribb 58.3 6.2 0.00014 26.3 1.4 28 47-86 13-40 (50)
75 TIGR00686 phnA alkylphosphonat 58.3 5.2 0.00011 32.2 1.1 26 47-84 3-28 (109)
76 PF14353 CpXC: CpXC protein 57.9 4 8.6E-05 32.5 0.4 37 47-85 2-48 (128)
77 PF11789 zf-Nse: Zinc-finger o 57.9 9.5 0.00021 26.9 2.3 32 44-80 9-53 (57)
78 PF05605 zf-Di19: Drought indu 57.9 6.6 0.00014 26.9 1.5 24 46-70 31-54 (54)
79 COG0675 Transposase and inacti 57.7 7.8 0.00017 34.1 2.3 46 33-94 296-341 (364)
80 PF13395 HNH_4: HNH endonuclea 57.7 5.7 0.00012 27.4 1.1 14 49-62 1-14 (54)
81 smart00659 RPOLCX RNA polymera 57.6 5.9 0.00013 26.7 1.2 28 46-85 2-29 (44)
82 TIGR00280 L37a ribosomal prote 57.4 3 6.5E-05 32.6 -0.4 17 41-57 30-47 (91)
83 TIGR00100 hypA hydrogenase nic 56.6 3.6 7.9E-05 32.8 0.0 30 42-84 66-95 (115)
84 PF14446 Prok-RING_1: Prokaryo 56.5 8.1 0.00018 27.4 1.8 26 46-84 5-30 (54)
85 PF07282 OrfB_Zn_ribbon: Putat 55.1 14 0.0003 26.2 2.8 47 32-91 15-62 (69)
86 PF11672 DUF3268: Protein of u 54.9 6.8 0.00015 31.1 1.3 38 47-87 3-43 (102)
87 PRK03976 rpl37ae 50S ribosomal 54.8 3.6 7.8E-05 32.1 -0.3 16 42-57 32-48 (90)
88 PF06957 COPI_C: Coatomer (COP 54.1 4.5 9.7E-05 39.5 0.2 34 45-91 379-413 (422)
89 PF13719 zinc_ribbon_5: zinc-r 53.6 9.8 0.00021 24.4 1.7 31 47-83 3-33 (37)
90 cd00730 rubredoxin Rubredoxin; 53.6 6.9 0.00015 27.1 1.0 13 42-54 30-42 (50)
91 PRK12496 hypothetical protein; 52.8 9.5 0.00021 32.3 1.9 28 46-86 127-154 (164)
92 PF08209 Sgf11: Sgf11 (transcr 52.1 6.2 0.00013 25.3 0.5 18 76-93 5-23 (33)
93 PRK03824 hypA hydrogenase nick 51.7 6 0.00013 32.5 0.5 43 42-84 66-116 (135)
94 smart00507 HNHc HNH nucleases. 51.1 4.5 9.9E-05 25.7 -0.2 21 47-67 11-31 (52)
95 KOG0823 Predicted E3 ubiquitin 50.4 7.9 0.00017 35.0 1.1 45 44-89 45-98 (230)
96 PF08996 zf-DNA_Pol: DNA Polym 49.7 3.8 8.1E-05 35.2 -1.0 40 44-85 16-55 (188)
97 PF13240 zinc_ribbon_2: zinc-r 49.5 6.5 0.00014 23.0 0.3 6 49-54 2-7 (23)
98 PF00301 Rubredoxin: Rubredoxi 49.3 8.7 0.00019 26.3 0.9 14 41-54 29-42 (47)
99 KOG2879 Predicted E3 ubiquitin 49.1 6.3 0.00014 36.7 0.3 41 45-85 238-286 (298)
100 PF13248 zf-ribbon_3: zinc-rib 47.9 11 0.00024 22.3 1.2 9 47-55 3-11 (26)
101 PRK12380 hydrogenase nickel in 47.8 6.5 0.00014 31.3 0.2 30 42-84 66-95 (113)
102 PF01780 Ribosomal_L37ae: Ribo 46.5 7.9 0.00017 30.2 0.4 15 43-57 32-47 (90)
103 PRK03922 hypothetical protein; 45.9 10 0.00022 30.8 0.9 14 46-59 49-62 (113)
104 PF12171 zf-C2H2_jaz: Zinc-fin 45.6 16 0.00035 21.3 1.6 20 47-66 2-22 (27)
105 PF10058 DUF2296: Predicted in 45.6 9.2 0.0002 26.9 0.6 10 45-54 43-52 (54)
106 TIGR00570 cdk7 CDK-activating 45.3 11 0.00023 35.6 1.1 40 46-86 3-54 (309)
107 PF13824 zf-Mss51: Zinc-finger 44.6 12 0.00025 26.8 1.0 11 44-54 12-22 (55)
108 PRK10220 hypothetical protein; 44.4 15 0.00032 29.7 1.7 26 47-84 4-29 (111)
109 PF04981 NMD3: NMD3 family ; 44.4 16 0.00034 32.4 2.0 36 49-84 1-44 (236)
110 PF04475 DUF555: Protein of un 44.2 11 0.00024 30.0 0.9 14 46-59 47-60 (102)
111 PF14634 zf-RING_5: zinc-RING 44.1 14 0.0003 24.1 1.3 10 73-82 34-43 (44)
112 COG4049 Uncharacterized protei 43.6 9.1 0.0002 27.7 0.3 26 76-101 18-45 (65)
113 PF02146 SIR2: Sir2 family; I 43.5 10 0.00022 31.7 0.7 40 46-90 105-144 (178)
114 TIGR01374 soxD sarcosine oxida 43.4 11 0.00023 29.1 0.8 8 47-54 2-9 (84)
115 PRK11088 rrmA 23S rRNA methylt 43.2 9 0.00019 34.1 0.3 32 46-77 2-34 (272)
116 PF09538 FYDLN_acid: Protein o 42.6 20 0.00044 28.6 2.2 33 42-87 5-38 (108)
117 PF01155 HypA: Hydrogenase exp 42.6 7 0.00015 31.0 -0.4 30 42-84 66-95 (113)
118 smart00451 ZnF_U1 U1-like zinc 42.1 18 0.00038 21.9 1.5 21 46-66 3-24 (35)
119 PF04267 SoxD: Sarcosine oxida 41.9 6.4 0.00014 30.3 -0.7 8 47-54 2-9 (84)
120 KOG4628 Predicted E3 ubiquitin 41.8 8.3 0.00018 36.8 -0.1 39 47-85 230-277 (348)
121 PF09706 Cas_CXXC_CXXC: CRISPR 41.4 12 0.00025 27.5 0.6 13 72-84 48-60 (69)
122 smart00661 RPOL9 RNA polymeras 40.7 16 0.00034 24.3 1.2 9 75-83 20-28 (52)
123 PF12760 Zn_Tnp_IS1595: Transp 40.7 16 0.00034 24.3 1.2 11 44-54 16-26 (46)
124 PF12660 zf-TFIIIC: Putative z 40.6 7.6 0.00017 30.3 -0.4 38 48-85 16-65 (99)
125 KOG2817 Predicted E3 ubiquitin 40.5 14 0.00031 35.8 1.3 16 44-59 372-387 (394)
126 KOG3608 Zn finger proteins [Ge 40.5 24 0.00053 34.2 2.8 48 46-94 263-313 (467)
127 COG5189 SFP1 Putative transcri 40.5 15 0.00033 35.1 1.4 40 46-85 349-408 (423)
128 PRK00423 tfb transcription ini 39.7 17 0.00037 33.5 1.6 39 45-93 10-48 (310)
129 PF13717 zinc_ribbon_4: zinc-r 39.6 22 0.00047 22.8 1.6 31 47-83 3-33 (36)
130 COG1198 PriA Primosomal protei 39.4 15 0.00033 38.3 1.3 41 42-84 440-484 (730)
131 PRK11595 DNA utilization prote 39.1 15 0.00032 32.2 1.1 35 48-84 7-43 (227)
132 PF09334 tRNA-synt_1g: tRNA sy 37.6 13 0.00027 35.6 0.4 40 46-85 136-176 (391)
133 PF03966 Trm112p: Trm112p-like 37.4 22 0.00047 25.5 1.5 38 45-83 6-61 (68)
134 TIGR03830 CxxCG_CxxCG_HTH puta 37.1 13 0.00029 28.8 0.4 37 49-85 1-41 (127)
135 PRK05477 gatB aspartyl/glutamy 36.2 17 0.00037 36.0 1.0 22 65-86 27-48 (474)
136 PF00097 zf-C3HC4: Zinc finger 35.7 17 0.00037 22.8 0.7 9 73-81 33-41 (41)
137 PF14616 DUF4451: Domain of un 35.5 23 0.00051 28.7 1.6 27 75-101 25-56 (124)
138 PF02892 zf-BED: BED zinc fing 35.1 26 0.00057 22.6 1.6 25 73-97 14-44 (45)
139 COG1499 NMD3 NMD protein affec 35.0 22 0.00047 34.0 1.6 40 44-83 4-51 (355)
140 PF05876 Terminase_GpA: Phage 34.9 23 0.0005 35.5 1.8 42 44-87 198-241 (557)
141 COG5109 Uncharacterized conser 34.5 16 0.00036 34.8 0.6 11 44-54 374-384 (396)
142 KOG3214 Uncharacterized Zn rib 34.4 18 0.00038 29.0 0.7 36 44-84 21-56 (109)
143 PF01844 HNH: HNH endonuclease 34.4 8 0.00017 24.9 -1.1 20 49-68 1-22 (47)
144 PRK04023 DNA polymerase II lar 34.2 22 0.00047 38.5 1.5 9 218-226 804-812 (1121)
145 COG4391 Uncharacterized protei 34.1 21 0.00046 26.1 1.0 13 72-84 45-57 (62)
146 KOG0402 60S ribosomal protein 34.1 13 0.00029 28.8 -0.0 15 43-57 33-48 (92)
147 PF04423 Rad50_zn_hook: Rad50 33.6 13 0.00029 25.4 -0.1 13 48-60 22-34 (54)
148 PRK00564 hypA hydrogenase nick 33.6 15 0.00033 29.4 0.2 31 42-84 67-97 (117)
149 TIGR02300 FYDLN_acid conserved 33.6 27 0.00059 28.9 1.7 31 42-85 5-36 (129)
150 PF10276 zf-CHCC: Zinc-finger 32.6 16 0.00035 24.3 0.2 9 46-54 29-37 (40)
151 PF12230 PRP21_like_P: Pre-mRN 32.3 15 0.00033 32.2 0.0 22 74-95 167-189 (229)
152 COG4049 Uncharacterized protei 32.2 17 0.00037 26.3 0.3 26 46-71 17-43 (65)
153 COG1405 SUA7 Transcription ini 31.7 36 0.00078 31.5 2.4 43 47-99 2-44 (285)
154 PF12230 PRP21_like_P: Pre-mRN 31.7 16 0.00034 32.1 0.0 21 46-66 168-188 (229)
155 PLN02751 glutamyl-tRNA(Gln) am 31.5 22 0.00047 35.9 1.0 22 65-86 83-104 (544)
156 smart00614 ZnF_BED BED zinc fi 30.9 22 0.00047 23.9 0.6 26 45-70 17-48 (50)
157 KOG3608 Zn finger proteins [Ge 30.8 32 0.00069 33.5 1.9 56 46-102 292-381 (467)
158 COG1997 RPL43A Ribosomal prote 30.8 11 0.00023 29.4 -1.0 16 40-55 29-44 (89)
159 PRK00464 nrdR transcriptional 30.6 22 0.00047 30.1 0.7 32 47-84 1-37 (154)
160 COG1675 TFA1 Transcription ini 30.6 27 0.00058 30.3 1.3 32 44-85 111-142 (176)
161 PF14311 DUF4379: Domain of un 30.6 29 0.00064 23.7 1.3 31 43-81 25-55 (55)
162 PF14369 zf-RING_3: zinc-finge 30.5 25 0.00053 22.5 0.8 9 48-56 23-31 (35)
163 KOG1002 Nucleotide excision re 30.5 28 0.00062 35.4 1.6 53 41-93 531-593 (791)
164 PHA02929 N1R/p28-like protein; 30.4 13 0.00028 33.6 -0.7 43 44-86 172-227 (238)
165 cd03019 DsbA_DsbA DsbA family, 29.7 21 0.00045 28.7 0.4 19 45-63 23-42 (178)
166 TIGR00133 gatB glutamyl-tRNA(G 29.5 25 0.00054 34.9 1.0 15 72-86 34-48 (478)
167 PF04780 DUF629: Protein of un 29.2 21 0.00046 35.3 0.5 47 55-101 20-85 (466)
168 KOG2177 Predicted E3 ubiquitin 28.9 18 0.00038 30.3 -0.1 38 45-82 12-54 (386)
169 PF05207 zf-CSL: CSL zinc fing 28.8 21 0.00047 24.9 0.3 44 34-86 5-51 (55)
170 TIGR00515 accD acetyl-CoA carb 28.4 35 0.00076 31.6 1.7 29 46-84 26-54 (285)
171 PRK05654 acetyl-CoA carboxylas 28.4 33 0.00073 31.8 1.6 29 46-84 27-55 (292)
172 PF14570 zf-RING_4: RING/Ubox 28.3 17 0.00036 25.2 -0.3 33 44-83 13-45 (48)
173 CHL00174 accD acetyl-CoA carbo 28.2 34 0.00074 32.0 1.6 29 46-84 38-66 (296)
174 PF02934 GatB_N: GatB/GatE cat 27.9 29 0.00062 32.4 1.0 26 61-86 18-43 (289)
175 PRK14714 DNA polymerase II lar 27.8 34 0.00075 37.9 1.7 35 46-85 667-702 (1337)
176 PRK09678 DNA-binding transcrip 26.8 29 0.00062 25.9 0.7 8 47-54 2-9 (72)
177 PRK03681 hypA hydrogenase nick 26.7 24 0.00052 28.1 0.3 13 44-56 68-80 (114)
178 KOG2231 Predicted E3 ubiquitin 26.6 42 0.00091 34.8 2.1 28 44-71 180-208 (669)
179 PF12874 zf-met: Zinc-finger o 26.5 32 0.0007 19.3 0.7 18 48-65 2-20 (25)
180 TIGR01405 polC_Gram_pos DNA po 26.5 47 0.001 36.7 2.5 46 32-85 672-718 (1213)
181 PHA00733 hypothetical protein 26.4 46 0.001 27.0 1.9 25 46-70 99-124 (128)
182 PHA02565 49 recombination endo 26.3 32 0.00069 29.5 1.0 41 46-86 20-66 (157)
183 PF13462 Thioredoxin_4: Thiore 26.1 7.6 0.00016 30.7 -2.7 21 45-65 20-41 (162)
184 PF13453 zf-TFIIB: Transcripti 25.8 25 0.00055 22.8 0.2 26 49-83 2-27 (41)
185 KOG0804 Cytoplasmic Zn-finger 25.8 18 0.00039 35.9 -0.7 37 45-83 174-219 (493)
186 PF11290 DUF3090: Protein of u 25.5 35 0.00076 29.6 1.1 13 47-59 155-167 (171)
187 PF14279 HNH_5: HNH endonuclea 25.3 29 0.00063 25.6 0.5 42 49-91 1-46 (71)
188 TIGR00630 uvra excinuclease AB 25.1 41 0.00089 36.0 1.7 35 45-84 249-283 (924)
189 KOG4080 Mitochondrial ribosoma 24.9 32 0.00069 29.9 0.7 26 46-87 93-118 (176)
190 PF03604 DNA_RNApol_7kD: DNA d 24.9 44 0.00095 21.1 1.2 11 44-54 15-25 (32)
191 COG1885 Uncharacterized protei 24.8 38 0.00082 27.4 1.1 15 46-60 49-63 (115)
192 PRK14873 primosome assembly pr 24.7 31 0.00067 35.5 0.7 39 42-84 388-431 (665)
193 PRK14714 DNA polymerase II lar 24.6 41 0.00089 37.3 1.6 40 46-85 679-719 (1337)
194 PF14968 CCDC84: Coiled coil p 24.2 38 0.00083 32.2 1.2 25 42-66 54-85 (336)
195 KOG4696 Uncharacterized conser 24.1 40 0.00088 32.0 1.3 23 46-69 2-24 (393)
196 PRK05452 anaerobic nitric oxid 24.0 43 0.00093 32.9 1.5 42 43-84 422-467 (479)
197 TIGR03278 methan_mark_10 putat 23.9 35 0.00076 33.0 0.9 34 45-84 9-45 (404)
198 TIGR00595 priA primosomal prot 23.8 38 0.00082 33.4 1.1 37 45-84 221-262 (505)
199 PRK00762 hypA hydrogenase nick 23.8 31 0.00068 27.8 0.5 12 43-55 67-78 (124)
200 cd02972 DsbA_family DsbA famil 23.7 23 0.00049 24.7 -0.4 17 46-62 6-23 (98)
201 PRK00448 polC DNA polymerase I 23.4 57 0.0012 36.7 2.5 46 32-85 897-943 (1437)
202 PF11793 FANCL_C: FANCL C-term 23.3 48 0.001 24.0 1.3 45 43-87 17-67 (70)
203 COG0178 UvrA Excinuclease ATPa 23.0 42 0.00092 35.8 1.3 36 44-84 243-278 (935)
204 KOG1734 Predicted RING-contain 22.8 25 0.00054 32.9 -0.3 18 47-64 271-288 (328)
205 COG1656 Uncharacterized conser 22.7 60 0.0013 28.0 2.0 38 47-84 98-139 (165)
206 PF09889 DUF2116: Uncharacteri 22.7 46 0.001 23.9 1.1 10 48-57 5-14 (59)
207 PF08273 Prim_Zn_Ribbon: Zinc- 22.4 37 0.0008 22.5 0.5 7 48-54 5-11 (40)
208 PRK05978 hypothetical protein; 22.1 35 0.00077 28.8 0.4 27 47-84 34-61 (148)
209 TIGR00244 transcriptional regu 21.9 39 0.00084 28.6 0.7 31 48-85 2-38 (147)
210 COG5574 PEX10 RING-finger-cont 21.7 21 0.00045 33.0 -1.1 42 45-86 214-262 (271)
211 TIGR00599 rad18 DNA repair pro 21.5 25 0.00055 34.1 -0.6 44 42-85 22-70 (397)
212 PF13397 DUF4109: Domain of un 21.4 59 0.0013 26.1 1.6 17 38-54 42-58 (105)
213 PRK14559 putative protein seri 21.3 54 0.0012 33.8 1.7 39 46-87 15-53 (645)
214 PF05741 zf-nanos: Nanos RNA b 21.2 37 0.00079 24.2 0.3 10 45-54 32-41 (55)
215 PRK00241 nudC NADH pyrophospha 21.1 54 0.0012 29.6 1.4 27 47-84 100-126 (256)
216 KOG4727 U1-like Zn-finger prot 20.9 41 0.00088 29.5 0.6 19 77-95 77-97 (193)
217 PF12861 zf-Apc11: Anaphase-pr 20.9 37 0.00079 26.2 0.3 36 48-83 34-79 (85)
218 PRK05580 primosome assembly pr 20.8 48 0.001 34.0 1.2 39 44-84 388-430 (679)
219 PF06676 DUF1178: Protein of u 20.4 49 0.0011 28.0 0.9 11 74-84 31-41 (148)
220 PF14447 Prok-RING_4: Prokaryo 20.4 42 0.00092 23.9 0.5 41 45-85 6-49 (55)
221 COG1773 Rubredoxin [Energy pro 20.3 57 0.0012 23.3 1.1 14 41-54 31-44 (55)
222 cd01407 SIR2-fam SIR2 family o 20.1 61 0.0013 28.0 1.6 41 45-90 108-148 (218)
223 KOG3993 Transcription factor ( 20.1 31 0.00068 34.1 -0.3 33 45-77 457-490 (500)
No 1
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=100.00 E-value=2e-33 Score=221.84 Aligned_cols=105 Identities=55% Similarity=0.728 Sum_probs=90.1
Q ss_pred hhhccchhhhhhhhhhhcCCCCCCCCCCCCCCCCCCccccccccCCCCCchhhcccccccccccccccccCCccccccCC
Q 026824 119 ALSLLGRDLREAHLQVLLGGSGYRSSNANISNAATDPFLSSLILNFPSSEAEEISKSVVTSTEDTSAKSAAPTHMWKTSF 198 (232)
Q Consensus 119 ~~s~l~k~~r~~~lq~~~gg~s~~~~~~~ssn~~~DPlLS~fi~n~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~ 198 (232)
|||+|+|||||||||++|||+ ++++.+++|++||||||+||||+|.++.++..+....+.++++.++...++.|+++.
T Consensus 1 tlsll~kelre~~LQsllGgs--~~~~~~ssn~apDPLLSSFI~n~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~s~ 78 (105)
T PF14571_consen 1 TLSLLRKELREGYLQSLLGGS--RSSSSSSSNSAPDPLLSSFICNFPAPEAEEPSKSSSSSEEKKSSKKSSSEQNVKSSA 78 (105)
T ss_pred CcchhhhhhhhhhhhhhcCCC--cCCCCCCCCCCCcHHHHHHhcCCCCccccccCCccccccccccccccchhccccccc
Confidence 578999999999999999998 334567899999999999999999999887655544445566667777788899888
Q ss_pred CCCCCHHHHHHHHHhccchhhHHHHHHhhhc
Q 026824 199 DPSLSHEEREKRIRQGAGRASFVQDLLLSTL 229 (232)
Q Consensus 199 ~~~Ls~ee~eek~~e~~~Rs~FVQ~LllSTi 229 (232)
+++||+||||||++ |++||||||||||
T Consensus 79 ~~~lS~ee~eEk~~----RseFVQ~LllSTI 105 (105)
T PF14571_consen 79 DSSLSDEEQEEKAQ----RSEFVQGLLLSTI 105 (105)
T ss_pred CCCCCHHHHHHHHH----HHHHHHHHHHhhC
Confidence 89999999998885 9999999999998
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=1.4e-19 Score=126.37 Aligned_cols=54 Identities=48% Similarity=0.938 Sum_probs=52.1
Q ss_pred CcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhhhhhhhhhcccc
Q 026824 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHG 98 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~d~i~Hl~~qH~ 98 (232)
++|+||||+++||+.+|+.|+.++|..+.++||||||+.+++.||++||+.+|+
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 379999999999999999999999999999999999999999999999999996
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=99.62 E-value=6.3e-16 Score=142.93 Aligned_cols=199 Identities=21% Similarity=0.295 Sum_probs=128.2
Q ss_pred cccc-cCCCCCCCCCCCCCcccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccch---------hhhhhhhhhcc
Q 026824 28 QIDR-LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV---------ARDMLSHITLQ 96 (232)
Q Consensus 28 ~~~~-~~~e~~~~ddd~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v---------~~d~i~Hl~~q 96 (232)
|+++ ||+|-+..++ +..|+||||+. +|++..+.+||...|+.....+|||||++.+ +.+...|++..
T Consensus 62 dfeL~f~Ge~i~~y~--~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~~qp~~~~~~~~~~~~~~~~ 139 (381)
T KOG1280|consen 62 DFELYFGGEPISHYD--PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPEMQPIHSKETENLSVHWTEI 139 (381)
T ss_pred ceeeEecCccccccc--cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcccCchhhhhhhhhhhhhhhh
Confidence 5555 6777777665 44999999999 9999999999999999999999999999975 34555666555
Q ss_pred cccc-hhhhcccccccccCCCchhhhccchhhhhhhhhh--hcCCC-CCCCCCCCCCCC-CCCcc---ccccc-------
Q 026824 97 HGHL-FKLQRRRRLRRVAIPSSQALSLLGRDLREAHLQV--LLGGS-GYRSSNANISNA-ATDPF---LSSLI------- 161 (232)
Q Consensus 97 H~~~-~k~~r~r~~rr~~~~~~~~~s~l~k~~r~~~lq~--~~gg~-s~~~~~~~ssn~-~~DPl---LS~fi------- 161 (232)
|--- ....+.|++.++..++ +++ .+...|..++++ +++|. |......+++|. +.||+ +++..
T Consensus 140 a~~r~~~e~~~r~~~~~r~~g-~~l--v~~r~rr~~mh~~~s~~g~~Ss~~ls~spgdr~~~dpi~e~~~q~qgVr~~~~ 216 (381)
T KOG1280|consen 140 ALGRPLQDEIGREMALLRNMG-PDL--VEDRRRRTEMHTVPSLPGIRSSQRLSTSPGDRPTVDPISEVTHQDQGVRQRPL 216 (381)
T ss_pred cccccchhhhhhhhhhhcccc-ccc--cchhhhhhhhheecccCCccccccccCCCCCCccccHHHHHHhhccccccccc
Confidence 4321 1113556666777776 776 577777777765 45554 222233455665 79999 44442
Q ss_pred cCCCCCchhhc-------------------------cccccccccccccc-----------cc-CC------ccc-cccC
Q 026824 162 LNFPSSEAEEI-------------------------SKSVVTSTEDTSAK-----------SA-AP------THM-WKTS 197 (232)
Q Consensus 162 ~n~~~~~~~~~-------------------------~~~~~~~~~~~~~~-----------~~-s~------~~~-~~~~ 197 (232)
.|++.+.++.. +..+-+++++...+ +. ++ .++ ..+.
T Consensus 217 ~~~s~~~~s~~~s~~~~~Q~~~q~aq~sq~~~~t~~naa~~~~T~~~~~~~~ef~~t~~i~~tess~~~l~~t~~~~~~~ 296 (381)
T KOG1280|consen 217 ATISIYPPTSDESGDMQAQLERQSAQASQVQLETPRNAAPRTNTSDVTTTITEFTATTNIANTESSQQTLQNTQFLLTRL 296 (381)
T ss_pred cccCCCCCCchhhcccchhhhHHHHHHHHhhccCccccCCCcccCcchhhhhhhhhhcccccChHHHHHHHHHHhhhhcC
Confidence 23333333321 00001111111111 11 11 122 2344
Q ss_pred CCCCCCHHHHHHHHHhccchhhHHHHHHhhhccC
Q 026824 198 FDPSLSHEEREKRIRQGAGRASFVQDLLLSTLLI 231 (232)
Q Consensus 198 ~~~~Ls~ee~eek~~e~~~Rs~FVQ~LllSTi~~ 231 (232)
.++.+++.+|+-...+|+.|+-|||.|++||+..
T Consensus 297 ~~~~~~~~~r~sm~~~~~~~s~t~~s~~~~tl~~ 330 (381)
T KOG1280|consen 297 NDPKMSETERQSMESERADRSLTVQSLLLSTLVR 330 (381)
T ss_pred CCccccccccchhhhhccchhhhhhhhhcccccc
Confidence 5789999999888889999999999999999854
No 4
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.57 E-value=0.014 Score=42.36 Aligned_cols=34 Identities=32% Similarity=0.761 Sum_probs=24.0
Q ss_pred CCCcccCCCCCC--CccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 43 VRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 43 ~~~~F~CPfC~e--~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
..-+|+|| ||. .+.+..|. ..-..++||-|+-+|
T Consensus 19 ~~ftyPCP-CGDRFeIsLeDl~--------~GE~VArCPSCSLiv 54 (67)
T COG5216 19 KTFTYPCP-CGDRFEISLEDLR--------NGEVVARCPSCSLIV 54 (67)
T ss_pred ceEEecCC-CCCEeEEEHHHhh--------CCceEEEcCCceEEE
Confidence 35689999 988 55544443 334578999999876
No 5
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.46 E-value=0.023 Score=41.70 Aligned_cols=45 Identities=33% Similarity=0.762 Sum_probs=29.9
Q ss_pred cCCCCCC-CCCCCCCcccCCCCCCC--ccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 32 LSIDDFE-VEDDVRPDFPCPYCYED--FDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 32 ~~~e~~~-~ddd~~~~F~CPfC~e~--~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
..++|++ .++...-+|||| ||.. +....|. ..-..+.||-|+-.+
T Consensus 7 Veiedfe~~~e~~~y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I 54 (67)
T KOG2923|consen 7 VEIEDFEFDEENQTYYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLII 54 (67)
T ss_pred EEeecceeccCCCeEEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEE
Confidence 4566666 334456789999 9984 4444443 234568899999875
No 6
>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=93.82 E-value=0.038 Score=39.05 Aligned_cols=27 Identities=26% Similarity=0.738 Sum_probs=18.9
Q ss_pred CCceecCCcccch--hhhhhhhhhccccc
Q 026824 73 SKVTVCPICSVKV--ARDMLSHITLQHGH 99 (232)
Q Consensus 73 ~~~vvCPVCa~~v--~~d~i~Hl~~qH~~ 99 (232)
.....||+|.+.+ .+|+-+||-+.|+.
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 3457999999986 78999999999974
No 7
>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=93.65 E-value=0.03 Score=31.14 Aligned_cols=23 Identities=30% Similarity=0.631 Sum_probs=16.3
Q ss_pred ccCCCCCC-CccHHHHhhhhcccc
Q 026824 47 FPCPYCYE-DFDIASLCSHLEDEH 69 (232)
Q Consensus 47 F~CPfC~e-~~d~~~L~~H~~~eH 69 (232)
|.||+|+. --+...|..|+...|
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 67899988 667788888887655
No 8
>PLN03086 PRLI-interacting factor K; Provisional
Probab=91.84 E-value=0.16 Score=50.95 Aligned_cols=50 Identities=22% Similarity=0.497 Sum_probs=38.6
Q ss_pred CCCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch-hhhhhhhhhccc
Q 026824 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV-ARDMLSHITLQH 97 (232)
Q Consensus 43 ~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v-~~d~i~Hl~~qH 97 (232)
+..-+.||+|++.|....|-.|....| +.+.|| |...+ ..++..|++...
T Consensus 450 l~~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~thC 500 (567)
T PLN03086 450 AKNHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQASTC 500 (567)
T ss_pred cccCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhhccC
Confidence 344679999999888999999998765 678999 96543 567888876433
No 9
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.58 E-value=0.13 Score=30.66 Aligned_cols=21 Identities=33% Similarity=0.668 Sum_probs=18.7
Q ss_pred cccCCCCCCCccHHHHhhhhc
Q 026824 46 DFPCPYCYEDFDIASLCSHLE 66 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~ 66 (232)
..+||+||..|....|-.|..
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 578999999999999999963
No 10
>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=90.78 E-value=0.08 Score=29.93 Aligned_cols=21 Identities=24% Similarity=0.550 Sum_probs=14.9
Q ss_pred ccCCCCCC-CccHHHHhhhhcc
Q 026824 47 FPCPYCYE-DFDIASLCSHLED 67 (232)
Q Consensus 47 F~CPfC~e-~~d~~~L~~H~~~ 67 (232)
|.||.|++ =-+...|..|+..
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 67888888 5556677777654
No 11
>PHA00732 hypothetical protein
Probab=90.63 E-value=0.27 Score=37.06 Aligned_cols=42 Identities=29% Similarity=0.652 Sum_probs=32.2
Q ss_pred ccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccchhhhhhhhh
Q 026824 47 FPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHI 93 (232)
Q Consensus 47 F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~d~i~Hl 93 (232)
|.|+.|+. --....|..|....|.. ..|++|...-. ++..|+
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~----~~C~~CgKsF~-~l~~H~ 44 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL----TKCPVCNKSYR-RLNQHF 44 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC----CccCCCCCEeC-Chhhhh
Confidence 78999999 45788899998765652 26999988655 466666
No 12
>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=90.49 E-value=0.099 Score=34.62 Aligned_cols=35 Identities=29% Similarity=0.643 Sum_probs=22.6
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhhhhhh
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLS 91 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~d~i~ 91 (232)
|.||.|+... + +.+ ......||+.|-..+..+.+.
T Consensus 1 m~Cp~Cg~~~-~------~~D---~~~g~~vC~~CG~Vl~e~~i~ 35 (43)
T PF08271_consen 1 MKCPNCGSKE-I------VFD---PERGELVCPNCGLVLEENIID 35 (43)
T ss_dssp ESBTTTSSSE-E------EEE---TTTTEEEETTT-BBEE-TTBS
T ss_pred CCCcCCcCCc-e------EEc---CCCCeEECCCCCCEeeccccc
Confidence 6899999843 2 112 445678999998877666553
No 13
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=89.60 E-value=0.15 Score=37.35 Aligned_cols=30 Identities=20% Similarity=0.473 Sum_probs=21.6
Q ss_pred cccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 46 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
.-+|||||. .+.+. |......++|.-|-+.
T Consensus 6 lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPSVTVK---------AISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCceeEEE---------ecCceEEEEcCCCCcC
Confidence 568999999 66554 2333446999999885
No 14
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=88.96 E-value=0.18 Score=35.19 Aligned_cols=31 Identities=26% Similarity=0.590 Sum_probs=19.9
Q ss_pred cccCCCCCC-CccHHHHhhhhccccCCCC---CceecCCccc
Q 026824 46 DFPCPYCYE-DFDIASLCSHLEDEHSCES---KVTVCPICSV 83 (232)
Q Consensus 46 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e~---~~vvCPVCa~ 83 (232)
..+|||||. .+.+.. ...... ..|.|..|-+
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 568999997 554433 122111 5688999977
No 15
>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=88.77 E-value=0.19 Score=35.52 Aligned_cols=30 Identities=20% Similarity=0.678 Sum_probs=22.1
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
.|.||-||..+++.... ..-.+.||.|-+.
T Consensus 2 ~~~CP~CG~~iev~~~~---------~GeiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPE---------LGELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCc---------cCCEEeCCCCCCE
Confidence 58999999987664432 1336899999875
No 16
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=88.69 E-value=0.17 Score=29.10 Aligned_cols=24 Identities=29% Similarity=0.635 Sum_probs=16.4
Q ss_pred ccCCCCCCCccHHHHhhhhccccC
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHS 70 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~ 70 (232)
|.||+|+..-....|..|+...|+
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 689999883237889999887764
No 17
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.22 E-value=0.4 Score=39.58 Aligned_cols=37 Identities=19% Similarity=0.569 Sum_probs=26.2
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
...|.||.|+.-|+..+-..... . ....+||.|-..+
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEE
Confidence 66999999999766555433322 1 3458999998876
No 18
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=88.15 E-value=0.24 Score=36.44 Aligned_cols=48 Identities=21% Similarity=0.517 Sum_probs=14.2
Q ss_pred cCCCCCC-CccHHHHhhhhccccCCCCC---------------------ceecCCcccch--hhhhhhhhhc
Q 026824 48 PCPYCYE-DFDIASLCSHLEDEHSCESK---------------------VTVCPICSVKV--ARDMLSHITL 95 (232)
Q Consensus 48 ~CPfC~e-~~d~~~L~~H~~~eH~~e~~---------------------~vvCPVCa~~v--~~d~i~Hl~~ 95 (232)
.|+||+. =-++..|..|+...|.+... .-.|++|.... ...+..||..
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 3999999 45688999999999986322 13499998875 4578888874
No 19
>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=87.29 E-value=0.3 Score=31.14 Aligned_cols=32 Identities=19% Similarity=0.477 Sum_probs=20.5
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
+.||.|+.-|.+..-. .......+.||.|-..
T Consensus 3 ~~CP~C~~~~~v~~~~------~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ------LGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHH------cCCCCCEEECCCCCCE
Confidence 6899999955554322 1223347899999764
No 20
>PHA00733 hypothetical protein
Probab=86.89 E-value=0.78 Score=37.35 Aligned_cols=49 Identities=27% Similarity=0.628 Sum_probs=36.0
Q ss_pred cccCCCCCCC-ccHHHHhhhhccccCCCCCceecCCcccch--hhhhhhhhhcccc
Q 026824 46 DFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQHG 98 (232)
Q Consensus 46 ~F~CPfC~e~-~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v--~~d~i~Hl~~qH~ 98 (232)
.|.|+.|+.. -....|..|... | .....|++|.... ...+..|+.--|+
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r~-h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIRY-T---EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHhc-C---CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 5999999994 556778888763 2 1246999997764 5678888877665
No 21
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=85.10 E-value=0.39 Score=37.89 Aligned_cols=36 Identities=19% Similarity=0.469 Sum_probs=21.8
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhh
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~ 87 (232)
+..|.||+|++ ..+. +.-.+ ..-.++||+|-..-+.
T Consensus 19 pt~f~CP~Cge-~~v~-----v~~~k--~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGK-VSIS-----VKIKK--NIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCC-eEee-----eecCC--CcceEECCCCCCccCE
Confidence 46899999995 2111 11111 2445899999876443
No 22
>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=85.03 E-value=0.35 Score=30.37 Aligned_cols=25 Identities=28% Similarity=0.813 Sum_probs=13.0
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCccc
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
-+||.|+.++.. .+....|||-|..
T Consensus 3 p~Cp~C~se~~y------------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTY------------EDGELLVCPECGH 27 (30)
T ss_dssp ---TTT-----E------------E-SSSEEETTTTE
T ss_pred CCCCCCCCccee------------ccCCEEeCCcccc
Confidence 379999886655 5567889999974
No 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=84.88 E-value=0.7 Score=46.51 Aligned_cols=38 Identities=18% Similarity=0.474 Sum_probs=28.0
Q ss_pred CcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
..|.|| |+..+....|..|+. .|+- .+...|+.|...+
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~-thCp-~Kpi~C~fC~~~v 514 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQA-STCP-LRLITCRFCGDMV 514 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhh-ccCC-CCceeCCCCCCcc
Confidence 457888 888778888888873 4554 3667888887765
No 24
>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=84.77 E-value=0.3 Score=31.22 Aligned_cols=33 Identities=21% Similarity=0.632 Sum_probs=22.7
Q ss_pred CcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
.+|.||-||..|++..-. .+...++||.|.+.+
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 469999999977643221 125678899998743
No 25
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.17 E-value=0.38 Score=42.26 Aligned_cols=18 Identities=28% Similarity=0.730 Sum_probs=14.4
Q ss_pred cccCCCCCCCccHHHHhh
Q 026824 46 DFPCPYCYEDFDIASLCS 63 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~ 63 (232)
.++||+|+..|....+..
T Consensus 5 ~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRS 22 (214)
T ss_pred ceECCCCCCeeeeeEEEc
Confidence 689999999888775543
No 26
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=83.98 E-value=0.49 Score=41.55 Aligned_cols=46 Identities=26% Similarity=0.712 Sum_probs=28.5
Q ss_pred CCcccCCCCCCCcc--HHHHhhhh-----ccccC--------------CCCCceecCCcccchhhhh
Q 026824 44 RPDFPCPYCYEDFD--IASLCSHL-----EDEHS--------------CESKVTVCPICSVKVARDM 89 (232)
Q Consensus 44 ~~~F~CPfC~e~~d--~~~L~~H~-----~~eH~--------------~e~~~vvCPVCa~~v~~d~ 89 (232)
...|.||+|.+.+. +...|.|+ ..... ...+...||+|...++.+-
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 45799999988333 44557772 22211 0223468999999886543
No 27
>PHA02768 hypothetical protein; Provisional
Probab=83.52 E-value=0.83 Score=32.51 Aligned_cols=34 Identities=26% Similarity=0.529 Sum_probs=25.0
Q ss_pred cccCCCCCC-CccHHHHhhhhccccCCCCCceecCCccc
Q 026824 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 46 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
-|.||.||+ =.....|..|... |. +.-.|..|..
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 488999999 5567789999877 44 3556777754
No 28
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=82.93 E-value=0.61 Score=35.36 Aligned_cols=26 Identities=31% Similarity=0.926 Sum_probs=18.0
Q ss_pred ccCCCCCC-CccHHHHhhhhccccCCCCCceecCCccc
Q 026824 47 FPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 47 F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
|+||-||. -|+..+ +...-|||||-=
T Consensus 2 ~~CPCCg~~Tl~~~~-----------~~~ydIC~VC~W 28 (78)
T PF14206_consen 2 YPCPCCGYYTLEERG-----------EGTYDICPVCFW 28 (78)
T ss_pred ccCCCCCcEEeccCC-----------CcCceECCCCCc
Confidence 79999998 655422 223679999953
No 29
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=82.91 E-value=1.1 Score=41.45 Aligned_cols=22 Identities=27% Similarity=0.711 Sum_probs=11.2
Q ss_pred CCcccCCCCCC-CccHHHHhhhh
Q 026824 44 RPDFPCPYCYE-DFDIASLCSHL 65 (232)
Q Consensus 44 ~~~F~CPfC~e-~~d~~~L~~H~ 65 (232)
+..|.||+|++ .+.+..|.-|+
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHi 181 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHI 181 (279)
T ss_pred cccccCCCCCceeeehHHHhhHh
Confidence 34455555555 55555555554
No 30
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=80.86 E-value=0.46 Score=37.85 Aligned_cols=37 Identities=19% Similarity=0.472 Sum_probs=23.0
Q ss_pred CCCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 43 ~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
++-+|+||+|+..--+.-+++ -.....+++|-+|-..
T Consensus 19 L~k~FtCp~Cghe~vs~ctvk-----k~~~~g~~~Cg~CGls 55 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVK-----KTVNIGTAVCGNCGLS 55 (104)
T ss_pred CCceEecCccCCeeeeEEEEE-----ecCceeEEEcccCcce
Confidence 345899999998433322221 1233457899999764
No 31
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=80.45 E-value=0.61 Score=32.76 Aligned_cols=34 Identities=26% Similarity=0.732 Sum_probs=20.1
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
+.|||||+.+++ +++.-...+ ...-=|+||-..+
T Consensus 1 i~CPyCge~~~~--~iD~s~~~Q---~yiEDC~vCC~PI 34 (52)
T PF14255_consen 1 IQCPYCGEPIEI--LIDPSAGDQ---EYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCCeeEE--EEecCCCCe---eEEeehhhcCCcc
Confidence 479999997665 333322221 2234599997654
No 32
>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=78.90 E-value=1.4 Score=26.45 Aligned_cols=19 Identities=32% Similarity=0.836 Sum_probs=10.5
Q ss_pred cCCCCCCCccHHHHhhhhc
Q 026824 48 PCPYCYEDFDIASLCSHLE 66 (232)
Q Consensus 48 ~CPfC~e~~d~~~L~~H~~ 66 (232)
.||.|++.+....+-.|++
T Consensus 3 ~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREVPENLINSHLD 21 (26)
T ss_pred cCCCCcCcccHHHHHHHHH
Confidence 4555555555555555554
No 33
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=78.79 E-value=0.91 Score=41.25 Aligned_cols=12 Identities=33% Similarity=1.013 Sum_probs=9.5
Q ss_pred cccCCCCCCCcc
Q 026824 46 DFPCPYCYEDFD 57 (232)
Q Consensus 46 ~F~CPfC~e~~d 57 (232)
++.||+|+.-|-
T Consensus 19 ~ieCPvC~tkFk 30 (267)
T COG1655 19 TIECPVCNTKFK 30 (267)
T ss_pred eeccCcccchhh
Confidence 799999976554
No 34
>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=78.62 E-value=1.1 Score=30.22 Aligned_cols=31 Identities=19% Similarity=0.712 Sum_probs=21.9
Q ss_pred CcccCCCCCCCccHHHHhhhhccccCCCCCceecCCccc
Q 026824 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
.+|.|+-|+..|++. .... +...+.||.|..
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 1221 145678999987
No 35
>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=76.62 E-value=1.1 Score=28.11 Aligned_cols=24 Identities=33% Similarity=0.829 Sum_probs=14.4
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCccc
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
|.|+.||.-++... ..-+||+|.+
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCC
Confidence 56777776333322 4457888865
No 36
>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=76.51 E-value=2.2 Score=31.07 Aligned_cols=37 Identities=19% Similarity=0.363 Sum_probs=22.9
Q ss_pred CCcccCCCCCC------------CccHHHHhhhhccccCCCCCceecCCcccchh
Q 026824 44 RPDFPCPYCYE------------DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (232)
Q Consensus 44 ~~~F~CPfC~e------------~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~ 86 (232)
+..|.||.|++ -|+...+..++.. ...+||+|...++
T Consensus 2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~ 50 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLS 50 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-S
T ss_pred CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCC
Confidence 45789998855 4566666666654 5679999977654
No 37
>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=76.48 E-value=2.3 Score=29.16 Aligned_cols=26 Identities=8% Similarity=0.169 Sum_probs=16.9
Q ss_pred CCccHHHHhhhhccccCCCCCceecCCcccchh
Q 026824 54 EDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (232)
Q Consensus 54 e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~ 86 (232)
.-|+...+..++.. ...||+|-..++
T Consensus 21 ~v~~~~~i~~~~~~-------~~~cP~~~~~~~ 46 (63)
T smart00504 21 QTYERRAIEKWLLS-------HGTDPVTGQPLT 46 (63)
T ss_pred CEEeHHHHHHHHHH-------CCCCCCCcCCCC
Confidence 34666666666643 458999987663
No 38
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=75.52 E-value=1.3 Score=32.44 Aligned_cols=25 Identities=36% Similarity=0.922 Sum_probs=20.5
Q ss_pred CcccCCCCCCCc-cHHHHhhhhcccc
Q 026824 45 PDFPCPYCYEDF-DIASLCSHLEDEH 69 (232)
Q Consensus 45 ~~F~CPfC~e~~-d~~~L~~H~~~eH 69 (232)
..|.|++|++.| +...|..|+...+
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 369999999955 8999999998764
No 39
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=74.35 E-value=1.1 Score=30.00 Aligned_cols=29 Identities=17% Similarity=0.730 Sum_probs=17.9
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
+|.||-||..|+.... .....||.|...+
T Consensus 3 ~y~C~~CG~~~~~~~~-----------~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY-----------GTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC-----------CCceECCCCCCeE
Confidence 5788888876654211 1157788886643
No 40
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=73.75 E-value=1.3 Score=43.59 Aligned_cols=33 Identities=33% Similarity=0.712 Sum_probs=28.3
Q ss_pred CCCCcccCCCCCCCc-cHHHHhhhhccccCCCCC
Q 026824 42 DVRPDFPCPYCYEDF-DIASLCSHLEDEHSCESK 74 (232)
Q Consensus 42 d~~~~F~CPfC~e~~-d~~~L~~H~~~eH~~e~~ 74 (232)
+.+.-|.||+|.++| +...|.+|++.+|..+..
T Consensus 11 ~i~egflCPiC~~dl~~~~~L~~H~d~eH~~ed~ 44 (505)
T KOG1842|consen 11 EILEGFLCPICLLDLPNLSALNDHLDVEHFEEDE 44 (505)
T ss_pred hhhhcccCchHhhhhhhHHHHHHHHhhhccccch
Confidence 457789999999966 578899999999998764
No 41
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=73.03 E-value=3 Score=38.54 Aligned_cols=51 Identities=24% Similarity=0.503 Sum_probs=38.9
Q ss_pred cccCCCCCCCccHHHHh-hhhccccCCCCCceecCCcccch--hhhhhhhhhccccc
Q 026824 46 DFPCPYCYEDFDIASLC-SHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQHGH 99 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~-~H~~~eH~~e~~~vvCPVCa~~v--~~d~i~Hl~~qH~~ 99 (232)
-+.|++||+-|+..=|. -|+ -.|.. -|.-.||.|..-- ..|+-.||.. |+.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHi-RTHTG-EKPF~C~hC~kAFADRSNLRAHmQT-HS~ 240 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHI-RTHTG-EKPFSCPHCGKAFADRSNLRAHMQT-HSD 240 (279)
T ss_pred CcccccccccccchHHhhccc-ccccC-CCCccCCcccchhcchHHHHHHHHh-hcC
Confidence 58999999999988654 566 56755 4567999998876 4599999974 544
No 42
>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=72.25 E-value=1.6 Score=33.11 Aligned_cols=34 Identities=21% Similarity=0.600 Sum_probs=14.8
Q ss_pred CCcccCCCCC-C-CccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 44 RPDFPCPYCY-E-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 44 ~~~F~CPfC~-e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
+..|.||||+ + -+.+. -........+.|-+|-..
T Consensus 20 ~~~F~CPfC~~~~sV~v~-------idkk~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVK-------IDKKEGIGILSCRVCGES 55 (81)
T ss_dssp SS----TTT--SS-EEEE-------EETTTTEEEEEESSS--E
T ss_pred CceEcCCcCCCCCeEEEE-------EEccCCEEEEEecCCCCe
Confidence 4589999999 4 33221 122244456889999654
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=72.11 E-value=1.1 Score=46.48 Aligned_cols=42 Identities=26% Similarity=0.517 Sum_probs=35.7
Q ss_pred CCcccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 44 ~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
.+..+||||+. .-....|.+|+.-.|--..-+.-|+.|....
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytF 250 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTF 250 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhh
Confidence 45689999999 4567899999999998888888999998863
No 44
>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=70.97 E-value=2.7 Score=28.56 Aligned_cols=10 Identities=40% Similarity=1.042 Sum_probs=4.9
Q ss_pred cCCcccchhh
Q 026824 78 CPICSVKVAR 87 (232)
Q Consensus 78 CPVCa~~v~~ 87 (232)
||.|..+.+.
T Consensus 1 CP~C~~kkk~ 10 (43)
T PF03470_consen 1 CPFCPGKKKQ 10 (43)
T ss_pred CCCCCCCCCc
Confidence 5555554443
No 45
>PRK12495 hypothetical protein; Provisional
Probab=70.86 E-value=2.6 Score=37.88 Aligned_cols=31 Identities=19% Similarity=0.433 Sum_probs=23.3
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhh
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~ 87 (232)
...|.||.||..|- .+ ...++||+|-..+..
T Consensus 40 msa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 40 MTNAHCDECGDPIF------------RH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred cchhhcccccCccc------------CC-CCeeECCCCCCcccc
Confidence 34799999999554 22 567899999988743
No 46
>smart00355 ZnF_C2H2 zinc finger.
Probab=70.59 E-value=3.4 Score=22.56 Aligned_cols=22 Identities=27% Similarity=0.585 Sum_probs=15.2
Q ss_pred ccCCCCCC-CccHHHHhhhhcccc
Q 026824 47 FPCPYCYE-DFDIASLCSHLEDEH 69 (232)
Q Consensus 47 F~CPfC~e-~~d~~~L~~H~~~eH 69 (232)
|.|+.|+. =-....|..|+. .|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-TH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hh
Confidence 56888888 455667777775 44
No 47
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=69.31 E-value=3.2 Score=40.53 Aligned_cols=62 Identities=19% Similarity=0.395 Sum_probs=37.3
Q ss_pred CCCCCCCCCCCCcccCCCCCC---CccHHHHhhhhccccCCCCCceecCCcccch-----------hhhhhhhhhccccc
Q 026824 34 IDDFEVEDDVRPDFPCPYCYE---DFDIASLCSHLEDEHSCESKVTVCPICSVKV-----------ARDMLSHITLQHGH 99 (232)
Q Consensus 34 ~e~~~~ddd~~~~F~CPfC~e---~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v-----------~~d~i~Hl~~qH~~ 99 (232)
+++...++..++.|.||+|.. .+|+..|.. .+...-.|-.|-.-+ .+..+++++-|=-.
T Consensus 116 led~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~-------~~~~~F~C~~C~gelveDe~~~~~~e~~~~l~~~~~Q~~p 188 (436)
T KOG2593|consen 116 LEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLD-------NETGEFHCENCGGELVEDENKLPSKESRTALNRLMEQLEP 188 (436)
T ss_pred HHHHhhhccccccccCCccccchhhhHHHHhhc-------ccCceEEEecCCCchhcccccCchHHHHHHHHHHHHHHHH
Confidence 444334445588999999988 455555544 334566788886643 23455566554444
Q ss_pred chh
Q 026824 100 LFK 102 (232)
Q Consensus 100 ~~k 102 (232)
+++
T Consensus 189 i~d 191 (436)
T KOG2593|consen 189 IID 191 (436)
T ss_pred HHH
Confidence 444
No 48
>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=69.12 E-value=2 Score=28.33 Aligned_cols=31 Identities=23% Similarity=0.684 Sum_probs=21.9
Q ss_pred CcccCCCCCCCccHHHHhhhhccccCCCCCceecCCccc
Q 026824 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
.+|.|+-||..|++-.- + .+...+.||.|..
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 46999999987765321 1 2256789999987
No 49
>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=68.56 E-value=2.2 Score=27.12 Aligned_cols=26 Identities=27% Similarity=0.599 Sum_probs=16.2
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
.|.|+.||.-++... ..-+||||-+.
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 477888887433211 23489999774
No 50
>PHA00616 hypothetical protein
Probab=68.41 E-value=2.3 Score=28.96 Aligned_cols=25 Identities=20% Similarity=0.267 Sum_probs=18.8
Q ss_pred ccCCCCCC-CccHHHHhhhhccccCC
Q 026824 47 FPCPYCYE-DFDIASLCSHLEDEHSC 71 (232)
Q Consensus 47 F~CPfC~e-~~d~~~L~~H~~~eH~~ 71 (232)
|.||-||. =....+|..|+...|..
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 67888888 56677888888776654
No 51
>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=68.06 E-value=2.4 Score=25.40 Aligned_cols=11 Identities=45% Similarity=0.993 Sum_probs=9.4
Q ss_pred CCcccCCCCCC
Q 026824 44 RPDFPCPYCYE 54 (232)
Q Consensus 44 ~~~F~CPfC~e 54 (232)
...|+||-||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 46899999996
No 52
>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=67.43 E-value=2.4 Score=29.22 Aligned_cols=31 Identities=26% Similarity=0.578 Sum_probs=17.2
Q ss_pred ccCCCCCC-CccHHHHhhhhccccC--CCCCceecCCcccc
Q 026824 47 FPCPYCYE-DFDIASLCSHLEDEHS--CESKVTVCPICSVK 84 (232)
Q Consensus 47 F~CPfC~e-~~d~~~L~~H~~~eH~--~e~~~vvCPVCa~~ 84 (232)
-+|||||- +..+. ..+. .......|+-|-+.
T Consensus 2 kPCPfCGg~~~~~~-------~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLR-------RGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeE-------eccCCCCCEEEEECCCCCCC
Confidence 38999998 44221 1111 11223479999775
No 53
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=67.41 E-value=4.8 Score=29.25 Aligned_cols=33 Identities=33% Similarity=0.806 Sum_probs=22.1
Q ss_pred CCCcccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcc
Q 026824 43 VRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICS 82 (232)
Q Consensus 43 ~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa 82 (232)
-...|+||-||+ .+-.-.-|.-+ .+.-+||-|-
T Consensus 24 ~~v~F~CPnCGe~~I~Rc~~CRk~-------g~~Y~Cp~CG 57 (61)
T COG2888 24 TAVKFPCPNCGEVEIYRCAKCRKL-------GNPYRCPKCG 57 (61)
T ss_pred ceeEeeCCCCCceeeehhhhHHHc-------CCceECCCcC
Confidence 456899999997 66554444332 4556888883
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=66.40 E-value=3.5 Score=23.91 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=16.8
Q ss_pred cccCCCCCC-CccHHHHhhhhcccc
Q 026824 46 DFPCPYCYE-DFDIASLCSHLEDEH 69 (232)
Q Consensus 46 ~F~CPfC~e-~~d~~~L~~H~~~eH 69 (232)
.|.|..|++ =-+...|..|....|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 367888888 556777888875444
No 55
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=66.18 E-value=6.5 Score=37.94 Aligned_cols=35 Identities=26% Similarity=0.523 Sum_probs=28.6
Q ss_pred CCCcccCCCCCC-CccHHHHhhhhccccCCCCCceecCCccc
Q 026824 43 VRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 43 ~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
+.---.|-||.. =+|-.+|..||...|- .|-||..
T Consensus 217 FKGHP~C~FC~~~FYdDDEL~~HcR~~HE------~ChICD~ 252 (493)
T COG5236 217 FKGHPLCIFCKIYFYDDDELRRHCRLRHE------ACHICDM 252 (493)
T ss_pred cCCCchhhhccceecChHHHHHHHHhhhh------hhhhhhc
Confidence 445678999999 8999999999999984 5667655
No 56
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=66.13 E-value=3.4 Score=29.88 Aligned_cols=32 Identities=31% Similarity=0.648 Sum_probs=22.3
Q ss_pred CCcccCCCCCCC-ccHHHHhhhhccccCCCCCceecCCcc
Q 026824 44 RPDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICS 82 (232)
Q Consensus 44 ~~~F~CPfC~e~-~d~~~L~~H~~~eH~~e~~~vvCPVCa 82 (232)
...|.||-||+. +-. |..| +-.+..-+||-|-
T Consensus 23 ~~~F~CPnCG~~~I~R---C~~C----Rk~~~~Y~CP~CG 55 (59)
T PRK14890 23 AVKFLCPNCGEVIIYR---CEKC----RKQSNPYTCPKCG 55 (59)
T ss_pred cCEeeCCCCCCeeEee---chhH----HhcCCceECCCCC
Confidence 568999999994 555 4444 2235677899884
No 57
>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=65.95 E-value=3 Score=35.62 Aligned_cols=54 Identities=28% Similarity=0.577 Sum_probs=32.4
Q ss_pred CcccCCC----CCCCccHHHHhhhhccccCCCCCceecCC----cccc-hhhhhhhhhhcccccch
Q 026824 45 PDFPCPY----CYEDFDIASLCSHLEDEHSCESKVTVCPI----CSVK-VARDMLSHITLQHGHLF 101 (232)
Q Consensus 45 ~~F~CPf----C~e~~d~~~L~~H~~~eH~~e~~~vvCPV----Ca~~-v~~d~i~Hl~~qH~~~~ 101 (232)
-.|+|+| |.+.+-......|.. +-. -+...||+ |.-. ...++..|++..|+...
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE~-~C~--~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHEE-ECP--FRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHHH-T-T--TSEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhHhc-cCC--CcCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 4799999 999888889999962 222 45678999 6432 45689999999998743
No 58
>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=65.91 E-value=1.5 Score=26.02 Aligned_cols=11 Identities=45% Similarity=1.419 Sum_probs=9.1
Q ss_pred cccCCCCCCCc
Q 026824 46 DFPCPYCYEDF 56 (232)
Q Consensus 46 ~F~CPfC~e~~ 56 (232)
-|.||+|+..|
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 49999999755
No 59
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=65.73 E-value=3 Score=28.56 Aligned_cols=45 Identities=36% Similarity=0.725 Sum_probs=29.2
Q ss_pred cccCCC--CCCCccHHHHhhhhccccCCCCCceecCC----cccchh-hhhhhh
Q 026824 46 DFPCPY--CYEDFDIASLCSHLEDEHSCESKVTVCPI----CSVKVA-RDMLSH 92 (232)
Q Consensus 46 ~F~CPf--C~e~~d~~~L~~H~~~eH~~e~~~vvCPV----Ca~~v~-~d~i~H 92 (232)
...||+ |.+.+-...|-.|+..+=+ -+.+.||. |...+. .++..|
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~--~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECP--KRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTST--TSEEE-SS----S--EEEHHHHHHC
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCC--CCcEECCCCCCCCCCccchhHHhCC
Confidence 578999 6668999999999974333 35789999 988764 456554
No 60
>PRK00420 hypothetical protein; Validated
Probab=65.49 E-value=4.6 Score=32.60 Aligned_cols=27 Identities=22% Similarity=0.405 Sum_probs=18.9
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
-.||.||..+- ......++||+|...+
T Consensus 24 ~~CP~Cg~pLf------------~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLF------------ELKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCcce------------ecCCCceECCCCCCee
Confidence 58999997432 1124578999998854
No 61
>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=64.28 E-value=4 Score=40.29 Aligned_cols=40 Identities=33% Similarity=0.373 Sum_probs=32.1
Q ss_pred CCcccCCCCCC-CccHHHHhhhhccccCCCCCc---eecCCccc
Q 026824 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKV---TVCPICSV 83 (232)
Q Consensus 44 ~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~---vvCPVCa~ 83 (232)
+.--.||+|.+ -.+..++..|+..+|...-.. -+.|-+..
T Consensus 55 WrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId 98 (466)
T PF04780_consen 55 WRFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRID 98 (466)
T ss_pred eeEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccC
Confidence 55678999999 999999999999999986533 45666544
No 62
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=64.24 E-value=2.1 Score=33.36 Aligned_cols=18 Identities=17% Similarity=0.532 Sum_probs=13.4
Q ss_pred CCCCCcccCCCCCC-CccH
Q 026824 41 DDVRPDFPCPYCYE-DFDI 58 (232)
Q Consensus 41 dd~~~~F~CPfC~e-~~d~ 58 (232)
......|+||||+. .+..
T Consensus 31 ~~q~a~y~CpfCgk~~vkR 49 (90)
T PTZ00255 31 ISQHAKYFCPFCGKHAVKR 49 (90)
T ss_pred HHHhCCccCCCCCCCceee
Confidence 34578999999997 5543
No 63
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=62.76 E-value=4.5 Score=34.74 Aligned_cols=25 Identities=36% Similarity=0.805 Sum_probs=17.7
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
.+.||.||- + |.. -...+||||-+.
T Consensus 134 ~~vC~vCGy----------~---~~g-e~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGY----------T---HEG-EAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCC----------c---ccC-CCCCcCCCCCCh
Confidence 899999974 1 112 346799999763
No 64
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=62.70 E-value=5.5 Score=34.22 Aligned_cols=32 Identities=25% Similarity=0.465 Sum_probs=23.6
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
...|.||-|+.-|+..+-.. ..-.||+|-..+
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L 146 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEML 146 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCC
Confidence 56899999999555554332 257999999875
No 65
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.64 E-value=3.1 Score=36.38 Aligned_cols=43 Identities=21% Similarity=0.589 Sum_probs=27.5
Q ss_pred CcccCCCCCCCccHHH----HhhhhccccCC---CCCceecCCcccchhh
Q 026824 45 PDFPCPYCYEDFDIAS----LCSHLEDEHSC---ESKVTVCPICSVKVAR 87 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~----L~~H~~~eH~~---e~~~vvCPVCa~~v~~ 87 (232)
..|.||.|-+.+.... =|-|+-=.-+. -.+.++||+|-.+++.
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 4699999977665444 34554322222 1346789999998764
No 66
>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=61.74 E-value=0.96 Score=33.72 Aligned_cols=53 Identities=25% Similarity=0.404 Sum_probs=24.7
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch-------hhhhhhhhhcccccchhh
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV-------ARDMLSHITLQHGHLFKL 103 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v-------~~d~i~Hl~~qH~~~~k~ 103 (232)
..||-|...++..+-.-||..=+..=...+.||-|-..+ ..|+.- +|++.++.
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC----~~c~gLiS 61 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFC----NHCHGLIS 61 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-----TTTT-EE-
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceee----ccCCceee
Confidence 468888777777763333322221123468899998875 235544 46666653
No 67
>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=60.92 E-value=6.2 Score=33.14 Aligned_cols=32 Identities=22% Similarity=0.423 Sum_probs=24.5
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
...|.||-|+.-|+..+-.. ..-.||+|-..+
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME----------LNFTCPRCGAML 138 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEe
Confidence 56899999999666655554 257999998875
No 68
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=60.82 E-value=2.7 Score=40.28 Aligned_cols=13 Identities=31% Similarity=0.667 Sum_probs=10.3
Q ss_pred CCCceecCCcccc
Q 026824 72 ESKVTVCPICSVK 84 (232)
Q Consensus 72 e~~~vvCPVCa~~ 84 (232)
+.-++.||.|.-+
T Consensus 50 q~lngrcpacrr~ 62 (480)
T COG5175 50 QNLNGRCPACRRK 62 (480)
T ss_pred hhccCCChHhhhh
Confidence 4468999999875
No 69
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=60.30 E-value=4.6 Score=38.29 Aligned_cols=58 Identities=29% Similarity=0.559 Sum_probs=39.0
Q ss_pred cccCCCCCCCccHHH---HhhhhccccCCCCC-ceecCCcccch--------------------------hhhhhhhhhc
Q 026824 46 DFPCPYCYEDFDIAS---LCSHLEDEHSCESK-VTVCPICSVKV--------------------------ARDMLSHITL 95 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~---L~~H~~~eH~~e~~-~vvCPVCa~~v--------------------------~~d~i~Hl~~ 95 (232)
.-.|--|++-+-+=+ =|+|+-=.-|.-+. -.+||.|..+| -+||.+||++
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 667888877554433 36665443333222 36899999974 3699999999
Q ss_pred ccccchhh
Q 026824 96 QHGHLFKL 103 (232)
Q Consensus 96 qH~~~~k~ 103 (232)
+|+...+-
T Consensus 170 rH~~~~~p 177 (389)
T KOG2932|consen 170 RHGSLLQP 177 (389)
T ss_pred hhccccCC
Confidence 99976543
No 70
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=59.99 E-value=4.8 Score=33.39 Aligned_cols=25 Identities=28% Similarity=0.794 Sum_probs=18.2
Q ss_pred cccCCCCCCC-ccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 46 DFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 46 ~F~CPfC~e~-~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
...||-||-- |. + ...|+||||-.+
T Consensus 28 ~~hCp~Cg~PLF~-----------K---dG~v~CPvC~~~ 53 (131)
T COG1645 28 AKHCPKCGTPLFR-----------K---DGEVFCPVCGYR 53 (131)
T ss_pred HhhCcccCCccee-----------e---CCeEECCCCCce
Confidence 4789999983 32 1 457999999854
No 71
>PF15616 TerY-C: TerY-C metal binding domain
Probab=59.89 E-value=3.7 Score=34.03 Aligned_cols=44 Identities=18% Similarity=0.355 Sum_probs=30.2
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCC-CCCceecCCcccchhhhh
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSC-ESKVTVCPICSVKVARDM 89 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~-e~~~vvCPVCa~~v~~d~ 89 (232)
.-.-.||+||..+-.+- | =|-.-|+. ....++||-|-....-..
T Consensus 75 ~g~PgCP~CGn~~~fa~-C-~CGkl~Ci~g~~~~~CPwCg~~g~~~~ 119 (131)
T PF15616_consen 75 IGAPGCPHCGNQYAFAV-C-GCGKLFCIDGEGEVTCPWCGNEGSFGA 119 (131)
T ss_pred cCCCCCCCCcChhcEEE-e-cCCCEEEeCCCCCEECCCCCCeeeecc
Confidence 33478999998543332 2 47778885 456899999988764433
No 72
>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=59.81 E-value=5.5 Score=24.05 Aligned_cols=8 Identities=38% Similarity=1.111 Sum_probs=3.9
Q ss_pred CCCCCCCc
Q 026824 49 CPYCYEDF 56 (232)
Q Consensus 49 CPfC~e~~ 56 (232)
||-|+..+
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 55555443
No 73
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=59.62 E-value=4.1 Score=32.15 Aligned_cols=9 Identities=67% Similarity=1.575 Sum_probs=7.5
Q ss_pred cccCCCCCC
Q 026824 46 DFPCPYCYE 54 (232)
Q Consensus 46 ~F~CPfC~e 54 (232)
-++|||||+
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 368999998
No 74
>PF12773 DZR: Double zinc ribbon
Probab=58.29 E-value=6.2 Score=26.26 Aligned_cols=28 Identities=21% Similarity=0.562 Sum_probs=18.7
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchh
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~ 86 (232)
-.||.||..+. ..+...++||.|-+.+.
T Consensus 13 ~fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 13 KFCPHCGTPLP------------PPDQSKKICPNCGAENP 40 (50)
T ss_pred cCChhhcCChh------------hccCCCCCCcCCcCCCc
Confidence 45777777555 34456778999887653
No 75
>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=58.27 E-value=5.2 Score=32.25 Aligned_cols=26 Identities=27% Similarity=0.861 Sum_probs=17.6
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
-+||-|+.+|.. .+....|||-|+.-
T Consensus 3 p~CP~C~seytY------------~dg~~~iCpeC~~E 28 (109)
T TIGR00686 3 PPCPKCNSEYTY------------HDGTQLICPSCLYE 28 (109)
T ss_pred CcCCcCCCcceE------------ecCCeeECcccccc
Confidence 468888765532 24556899999764
No 76
>PF14353 CpXC: CpXC protein
Probab=57.94 E-value=4 Score=32.51 Aligned_cols=37 Identities=27% Similarity=0.591 Sum_probs=21.0
Q ss_pred ccCCCCCCCcc--HHHHhhhhcccc--------CCCCCceecCCcccch
Q 026824 47 FPCPYCYEDFD--IASLCSHLEDEH--------SCESKVTVCPICSVKV 85 (232)
Q Consensus 47 F~CPfC~e~~d--~~~L~~H~~~eH--------~~e~~~vvCPVCa~~v 85 (232)
.+||.|+..|+ +-.++.= ++. ..+-...+||-|....
T Consensus 2 itCP~C~~~~~~~v~~~I~~--~~~p~l~e~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINA--DEDPELKEKILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcC--cCCHHHHHHHHcCCcCEEECCCCCCce
Confidence 58999988443 3222221 111 2234468899998864
No 77
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=57.89 E-value=9.5 Score=26.91 Aligned_cols=32 Identities=16% Similarity=0.486 Sum_probs=16.0
Q ss_pred CCcccCCCCCC-------------CccHHHHhhhhccccCCCCCceecCC
Q 026824 44 RPDFPCPYCYE-------------DFDIASLCSHLEDEHSCESKVTVCPI 80 (232)
Q Consensus 44 ~~~F~CPfC~e-------------~~d~~~L~~H~~~eH~~e~~~vvCPV 80 (232)
...|.||+... -|+...+..++ ...+.+.|||
T Consensus 9 ~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHC-----TTTS-EE-SC
T ss_pred EeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCC
Confidence 45677776654 34445555554 2456788998
No 78
>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=57.86 E-value=6.6 Score=26.91 Aligned_cols=24 Identities=29% Similarity=0.656 Sum_probs=19.8
Q ss_pred cccCCCCCCCccHHHHhhhhccccC
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHS 70 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~ 70 (232)
.+.||.|...+.. .|..|+...|.
T Consensus 31 ~v~CPiC~~~~~~-~l~~Hl~~~H~ 54 (54)
T PF05605_consen 31 NVVCPICSSRVTD-NLIRHLNSQHR 54 (54)
T ss_pred CccCCCchhhhhh-HHHHHHHHhcC
Confidence 6999999986653 99999988773
No 79
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=57.73 E-value=7.8 Score=34.07 Aligned_cols=46 Identities=20% Similarity=0.346 Sum_probs=31.1
Q ss_pred CCCCCCCCCCCCCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhhhhhhhhh
Q 026824 33 SIDDFEVEDDVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHIT 94 (232)
Q Consensus 33 ~~e~~~~ddd~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~d~i~Hl~ 94 (232)
|+.-+..++....+=.||.||. ...+...||.|-...-+|..+=++
T Consensus 296 ~~~~v~~~~~~~tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~N 341 (364)
T COG0675 296 GGIVVKVVPPYYTSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALN 341 (364)
T ss_pred CCeEEEECCCCCCcccccccCC----------------ccceeEECCCCCCeehhhHHHHHH
Confidence 4333444444455688999998 336778999999887666665443
No 80
>PF13395 HNH_4: HNH endonuclease
Probab=57.69 E-value=5.7 Score=27.37 Aligned_cols=14 Identities=43% Similarity=1.058 Sum_probs=11.7
Q ss_pred CCCCCCCccHHHHh
Q 026824 49 CPYCYEDFDIASLC 62 (232)
Q Consensus 49 CPfC~e~~d~~~L~ 62 (232)
|||||+.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 89999988888764
No 81
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=57.58 E-value=5.9 Score=26.71 Aligned_cols=28 Identities=21% Similarity=0.553 Sum_probs=20.9
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
.|.|.-||.++++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 58899999877754 34568899997654
No 82
>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=57.43 E-value=3 Score=32.61 Aligned_cols=17 Identities=18% Similarity=0.704 Sum_probs=12.8
Q ss_pred CCCCCcccCCCCCC-Ccc
Q 026824 41 DDVRPDFPCPYCYE-DFD 57 (232)
Q Consensus 41 dd~~~~F~CPfC~e-~~d 57 (232)
......|+||||+. .+.
T Consensus 30 ~~q~a~y~CpfCgk~~vk 47 (91)
T TIGR00280 30 IQQKAKYVCPFCGKKTVK 47 (91)
T ss_pred HHHhcCccCCCCCCCceE
Confidence 34578999999987 544
No 83
>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=56.59 E-value=3.6 Score=32.79 Aligned_cols=30 Identities=23% Similarity=0.430 Sum_probs=22.5
Q ss_pred CCCCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 42 d~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
+.+..+.|+-|+..|..... ...||-|-..
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 45778999999987766532 4679999764
No 84
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=56.55 E-value=8.1 Score=27.44 Aligned_cols=26 Identities=31% Similarity=0.829 Sum_probs=18.3
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
.-.||.|++.|. .+.--||||.|-+-
T Consensus 5 ~~~C~~Cg~~~~-------------~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 5 GCKCPVCGKKFK-------------DGDDIVVCPECGAP 30 (54)
T ss_pred CccChhhCCccc-------------CCCCEEECCCCCCc
Confidence 357899988663 13446899999875
No 85
>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=55.06 E-value=14 Score=26.15 Aligned_cols=47 Identities=26% Similarity=0.553 Sum_probs=31.6
Q ss_pred cCCCCCCCCCCCCCcccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccchhhhhhh
Q 026824 32 LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLS 91 (232)
Q Consensus 32 ~~~e~~~~ddd~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~d~i~ 91 (232)
.|+.=++++ +.-.+=+||.||. .-+ ....+..+||.|-....+|+.+
T Consensus 15 ~G~~v~~v~-~~~TSq~C~~CG~~~~~------------~~~~r~~~C~~Cg~~~~rD~na 62 (69)
T PF07282_consen 15 YGIQVVEVD-EAYTSQTCPRCGHRNKK------------RRSGRVFTCPNCGFEMDRDVNA 62 (69)
T ss_pred hCCEEEEEC-CCCCccCccCccccccc------------ccccceEEcCCCCCEECcHHHH
Confidence 344433443 3346788999998 333 4556778999998887777655
No 86
>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=54.90 E-value=6.8 Score=31.12 Aligned_cols=38 Identities=26% Similarity=0.587 Sum_probs=21.8
Q ss_pred ccCCCCCCCccHH---HHhhhhccccCCCCCceecCCcccchhh
Q 026824 47 FPCPYCYEDFDIA---SLCSHLEDEHSCESKVTVCPICSVKVAR 87 (232)
Q Consensus 47 F~CPfC~e~~d~~---~L~~H~~~eH~~e~~~vvCPVCa~~v~~ 87 (232)
-.|||||....+. .+.-|-.+++ .-.-+|+-|-+.||.
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 4699999833322 2222221111 223689999999864
No 87
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=54.77 E-value=3.6 Score=32.07 Aligned_cols=16 Identities=25% Similarity=0.681 Sum_probs=12.4
Q ss_pred CCCCcccCCCCCC-Ccc
Q 026824 42 DVRPDFPCPYCYE-DFD 57 (232)
Q Consensus 42 d~~~~F~CPfC~e-~~d 57 (232)
.....|+||||+. .+.
T Consensus 32 ~q~a~y~CpfCgk~~vk 48 (90)
T PRK03976 32 KMRAKHVCPVCGRPKVK 48 (90)
T ss_pred HHhcCccCCCCCCCceE
Confidence 4578999999987 544
No 88
>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=54.10 E-value=4.5 Score=39.47 Aligned_cols=34 Identities=32% Similarity=0.871 Sum_probs=15.6
Q ss_pred CcccCCCCCCCccHHHHhhhhccccCCCCCceecCCc-ccchhhhhhh
Q 026824 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPIC-SVKVARDMLS 91 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC-a~~v~~d~i~ 91 (232)
+...||||+.-|. + +-+--+|||| .+.||.+-++
T Consensus 379 ~~v~CP~cgA~y~------------~-~~kG~lC~vC~l~~IG~~a~G 413 (422)
T PF06957_consen 379 PSVKCPYCGAKYH------------P-EYKGQLCPVCELSEIGADASG 413 (422)
T ss_dssp -EEE-TTT--EEE------------G-GGTTSB-TTTTTBBTT---S-
T ss_pred CCeeCCCCCCccC------------h-hhCCCCCCCCcceeeCCccee
Confidence 4567999987432 2 2345699999 4567766544
No 89
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=53.64 E-value=9.8 Score=24.42 Aligned_cols=31 Identities=26% Similarity=0.671 Sum_probs=19.3
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCccc
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
..||-|+..|.+..=. + +.....|.||-|..
T Consensus 3 i~CP~C~~~f~v~~~~--l----~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK--L----PAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEcCHHH--c----ccCCcEEECCCCCc
Confidence 5799998855544311 1 23456788998865
No 90
>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=53.59 E-value=6.9 Score=27.14 Aligned_cols=13 Identities=38% Similarity=0.945 Sum_probs=11.5
Q ss_pred CCCCcccCCCCCC
Q 026824 42 DVRPDFPCPYCYE 54 (232)
Q Consensus 42 d~~~~F~CPfC~e 54 (232)
+++..|.||.|+.
T Consensus 30 ~Lp~~w~CP~C~a 42 (50)
T cd00730 30 DLPDDWVCPVCGA 42 (50)
T ss_pred HCCCCCCCCCCCC
Confidence 5788999999987
No 91
>PRK12496 hypothetical protein; Provisional
Probab=52.80 E-value=9.5 Score=32.30 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=19.7
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchh
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~ 86 (232)
.|.|+.|+..|+. +...-+||||-..+.
T Consensus 127 ~~~C~gC~~~~~~-------------~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPE-------------DYPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccC-------------CCCCCcCCCCCChhh
Confidence 4889999987652 122358999987654
No 92
>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=52.08 E-value=6.2 Score=25.27 Aligned_cols=18 Identities=33% Similarity=0.715 Sum_probs=7.7
Q ss_pred eecCCcccch-hhhhhhhh
Q 026824 76 TVCPICSVKV-ARDMLSHI 93 (232)
Q Consensus 76 vvCPVCa~~v-~~d~i~Hl 93 (232)
+.||.|.-.| ..-|..||
T Consensus 5 ~~C~nC~R~v~a~RfA~HL 23 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAPHL 23 (33)
T ss_dssp EE-TTTSSEEEGGGHHHHH
T ss_pred EECCCCcCCcchhhhHHHH
Confidence 3455554444 23344444
No 93
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=51.69 E-value=6 Score=32.47 Aligned_cols=43 Identities=16% Similarity=0.477 Sum_probs=24.1
Q ss_pred CCCCcccCCCCCCCccHHHHhhhhcc-----ccCCC---CCceecCCcccc
Q 026824 42 DVRPDFPCPYCYEDFDIASLCSHLED-----EHSCE---SKVTVCPICSVK 84 (232)
Q Consensus 42 d~~~~F~CPfC~e~~d~~~L~~H~~~-----eH~~e---~~~vvCPVCa~~ 84 (232)
..+..+.|+-||..+....-..++.. -|-.. .....||.|-..
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 44788999999986655421111111 11111 234679999764
No 94
>smart00507 HNHc HNH nucleases.
Probab=51.05 E-value=4.5 Score=25.72 Aligned_cols=21 Identities=19% Similarity=0.281 Sum_probs=13.8
Q ss_pred ccCCCCCCCccHHHHhhhhcc
Q 026824 47 FPCPYCYEDFDIASLCSHLED 67 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~ 67 (232)
+.|+||+..++..--+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 799999996654334455543
No 95
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.44 E-value=7.9 Score=34.96 Aligned_cols=45 Identities=27% Similarity=0.594 Sum_probs=32.4
Q ss_pred CCcccCCCCCC--CccHHHHhhhhc-------cccCCCCCceecCCcccchhhhh
Q 026824 44 RPDFPCPYCYE--DFDIASLCSHLE-------DEHSCESKVTVCPICSVKVARDM 89 (232)
Q Consensus 44 ~~~F~CPfC~e--~~d~~~L~~H~~-------~eH~~e~~~vvCPVCa~~v~~d~ 89 (232)
-..|.|-.|.+ .==|..||-|+- --|. ......||||-+.|+.+-
T Consensus 45 ~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~-~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQT-RPNSKECPVCKAEVSIDT 98 (230)
T ss_pred CCceeeeeeccccCCCEEeecccceehHHHHHHHhh-cCCCeeCCccccccccce
Confidence 35799999988 555788999973 1221 345678999999986543
No 96
>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=49.75 E-value=3.8 Score=35.23 Aligned_cols=40 Identities=25% Similarity=0.613 Sum_probs=20.4
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
+-.|+||.|+..+...++.. ...-.....-..||-|....
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~ 55 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPL 55 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B-
T ss_pred ceEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcC
Confidence 45799999999887777655 11111234568899998864
No 97
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.55 E-value=6.5 Score=22.96 Aligned_cols=6 Identities=50% Similarity=1.398 Sum_probs=2.9
Q ss_pred CCCCCC
Q 026824 49 CPYCYE 54 (232)
Q Consensus 49 CPfC~e 54 (232)
||.||.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 444444
No 98
>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=49.29 E-value=8.7 Score=26.34 Aligned_cols=14 Identities=36% Similarity=0.942 Sum_probs=9.0
Q ss_pred CCCCCcccCCCCCC
Q 026824 41 DDVRPDFPCPYCYE 54 (232)
Q Consensus 41 dd~~~~F~CPfC~e 54 (232)
++++..|.||.|+.
T Consensus 29 ~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 29 EDLPDDWVCPVCGA 42 (47)
T ss_dssp GGS-TT-B-TTTSS
T ss_pred HHCCCCCcCcCCCC
Confidence 36788999999986
No 99
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.14 E-value=6.3 Score=36.66 Aligned_cols=41 Identities=27% Similarity=0.536 Sum_probs=26.7
Q ss_pred CcccCCCCCC--CccHHHH-hhhhccccCCCCCc-----eecCCcccch
Q 026824 45 PDFPCPYCYE--DFDIASL-CSHLEDEHSCESKV-----TVCPICSVKV 85 (232)
Q Consensus 45 ~~F~CPfC~e--~~d~~~L-~~H~~~eH~~e~~~-----vvCPVCa~~v 85 (232)
..-.||+||+ -+--... |.|+-=+-+..+.. ..||-|.+.+
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 4678999999 4444455 78865444443332 4799997764
No 100
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=47.87 E-value=11 Score=22.30 Aligned_cols=9 Identities=33% Similarity=0.951 Sum_probs=5.7
Q ss_pred ccCCCCCCC
Q 026824 47 FPCPYCYED 55 (232)
Q Consensus 47 F~CPfC~e~ 55 (232)
-.||.||..
T Consensus 3 ~~Cp~Cg~~ 11 (26)
T PF13248_consen 3 MFCPNCGAE 11 (26)
T ss_pred CCCcccCCc
Confidence 357777763
No 101
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=47.78 E-value=6.5 Score=31.27 Aligned_cols=30 Identities=20% Similarity=0.331 Sum_probs=21.2
Q ss_pred CCCCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 42 d~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
+.+..+.|+-|+..|.+.. ....||-|-..
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 4578899999997665433 33469999753
No 102
>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=46.45 E-value=7.9 Score=30.20 Aligned_cols=15 Identities=20% Similarity=0.868 Sum_probs=10.9
Q ss_pred CCCcccCCCCCC-Ccc
Q 026824 43 VRPDFPCPYCYE-DFD 57 (232)
Q Consensus 43 ~~~~F~CPfC~e-~~d 57 (232)
....|.||||+. .+.
T Consensus 32 q~~ky~Cp~Cgk~~vk 47 (90)
T PF01780_consen 32 QHAKYTCPFCGKTSVK 47 (90)
T ss_dssp HHS-BEESSSSSSEEE
T ss_pred HhCCCcCCCCCCceeE
Confidence 467899999998 543
No 103
>PRK03922 hypothetical protein; Provisional
Probab=45.92 E-value=10 Score=30.77 Aligned_cols=14 Identities=50% Similarity=0.736 Sum_probs=11.5
Q ss_pred cccCCCCCCCccHH
Q 026824 46 DFPCPYCYEDFDIA 59 (232)
Q Consensus 46 ~F~CPfC~e~~d~~ 59 (232)
.-.||+||+.|+-.
T Consensus 49 ~~~cP~cge~~~~a 62 (113)
T PRK03922 49 LTICPKCGEPFDSA 62 (113)
T ss_pred cccCCCCCCcCCcE
Confidence 57899999988743
No 104
>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=45.64 E-value=16 Score=21.32 Aligned_cols=20 Identities=25% Similarity=0.404 Sum_probs=13.5
Q ss_pred ccCCCCCC-CccHHHHhhhhc
Q 026824 47 FPCPYCYE-DFDIASLCSHLE 66 (232)
Q Consensus 47 F~CPfC~e-~~d~~~L~~H~~ 66 (232)
|.|+.|+. =-+...|..|+.
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 66778877 456666666664
No 105
>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=45.61 E-value=9.2 Score=26.87 Aligned_cols=10 Identities=40% Similarity=1.228 Sum_probs=8.7
Q ss_pred CcccCCCCCC
Q 026824 45 PDFPCPYCYE 54 (232)
Q Consensus 45 ~~F~CPfC~e 54 (232)
-.|.||+|+.
T Consensus 43 i~y~C~~Cg~ 52 (54)
T PF10058_consen 43 IQYRCPYCGA 52 (54)
T ss_pred eEEEcCCCCC
Confidence 3899999986
No 106
>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=45.28 E-value=11 Score=35.55 Aligned_cols=40 Identities=25% Similarity=0.529 Sum_probs=24.3
Q ss_pred cccCCCCCC-CccHH-----------HHhhhhccccCCCCCceecCCcccchh
Q 026824 46 DFPCPYCYE-DFDIA-----------SLCSHLEDEHSCESKVTVCPICSVKVA 86 (232)
Q Consensus 46 ~F~CPfC~e-~~d~~-----------~L~~H~~~eH~~e~~~vvCPVCa~~v~ 86 (232)
.+.||.|.. .+--. .+|..|.+..- ......||+|-..+.
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 378999977 22222 23555555542 334568999987653
No 107
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=44.58 E-value=12 Score=26.77 Aligned_cols=11 Identities=36% Similarity=0.866 Sum_probs=9.4
Q ss_pred CCcccCCCCCC
Q 026824 44 RPDFPCPYCYE 54 (232)
Q Consensus 44 ~~~F~CPfC~e 54 (232)
+..|.||.||.
T Consensus 12 ~v~~~Cp~cGi 22 (55)
T PF13824_consen 12 HVNFECPDCGI 22 (55)
T ss_pred ccCCcCCCCCC
Confidence 56899999986
No 108
>PRK10220 hypothetical protein; Provisional
Probab=44.41 E-value=15 Score=29.72 Aligned_cols=26 Identities=23% Similarity=0.769 Sum_probs=16.9
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
-+||-|+.++.. .+....|||-|+.-
T Consensus 4 P~CP~C~seytY------------~d~~~~vCpeC~hE 29 (111)
T PRK10220 4 PHCPKCNSEYTY------------EDNGMYICPECAHE 29 (111)
T ss_pred CcCCCCCCcceE------------cCCCeEECCcccCc
Confidence 468888765431 23456899999763
No 109
>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=44.35 E-value=16 Score=32.40 Aligned_cols=36 Identities=31% Similarity=0.616 Sum_probs=20.3
Q ss_pred CCCCCCCc--cHHHHhhhhccccCC------CCCceecCCcccc
Q 026824 49 CPYCYEDF--DIASLCSHLEDEHSC------ESKVTVCPICSVK 84 (232)
Q Consensus 49 CPfC~e~~--d~~~L~~H~~~eH~~------e~~~vvCPVCa~~ 84 (232)
||.||... ...+||.=|--+... .....+||.|-+.
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~ 44 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRY 44 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCE
Confidence 77777632 334666555433321 2345789999763
No 110
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=44.16 E-value=11 Score=30.03 Aligned_cols=14 Identities=50% Similarity=0.904 Sum_probs=11.4
Q ss_pred cccCCCCCCCccHH
Q 026824 46 DFPCPYCYEDFDIA 59 (232)
Q Consensus 46 ~F~CPfC~e~~d~~ 59 (232)
.-.||+|++.|+-.
T Consensus 47 ~~~cP~Cge~~~~a 60 (102)
T PF04475_consen 47 DTICPKCGEELDSA 60 (102)
T ss_pred cccCCCCCCccCce
Confidence 57899999988744
No 111
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=44.13 E-value=14 Score=24.14 Aligned_cols=10 Identities=50% Similarity=1.175 Sum_probs=7.4
Q ss_pred CCceecCCcc
Q 026824 73 SKVTVCPICS 82 (232)
Q Consensus 73 ~~~vvCPVCa 82 (232)
.+.++||+|-
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 5568888884
No 112
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=43.56 E-value=9.1 Score=27.75 Aligned_cols=26 Identities=35% Similarity=0.828 Sum_probs=19.2
Q ss_pred eecCCcccch--hhhhhhhhhcccccch
Q 026824 76 TVCPICSVKV--ARDMLSHITLQHGHLF 101 (232)
Q Consensus 76 vvCPVCa~~v--~~d~i~Hl~~qH~~~~ 101 (232)
..||-|.+.. ..+.++|.+--|+..+
T Consensus 18 lrCPRC~~~FR~~K~Y~RHVNKaH~~~~ 45 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHVNKAHGWLF 45 (65)
T ss_pred eeCCchhHHHHHhHHHHHHhhHHhhhhh
Confidence 4577776643 5688899998888876
No 113
>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=43.48 E-value=10 Score=31.74 Aligned_cols=40 Identities=20% Similarity=0.630 Sum_probs=29.3
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhhhhh
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDML 90 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~d~i 90 (232)
.+.|..|+..++...+...+..... ..||.|...+..+++
T Consensus 105 ~~~C~~C~~~~~~~~~~~~~~~~~~-----~~C~~C~~~lrp~vv 144 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVDSIDEEEP-----PRCPKCGGLLRPDVV 144 (178)
T ss_dssp EEEETTTSBEEEGHHHHHHHHTTSS-----CBCTTTSCBEEEEE-
T ss_pred eeeecCCCccccchhhccccccccc-----ccccccCccCCCCee
Confidence 5899999998888877766544432 399999997766554
No 114
>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=43.38 E-value=11 Score=29.08 Aligned_cols=8 Identities=63% Similarity=1.767 Sum_probs=6.2
Q ss_pred ccCCCCCC
Q 026824 47 FPCPYCYE 54 (232)
Q Consensus 47 F~CPfC~e 54 (232)
.+||+||.
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 57888885
No 115
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=43.18 E-value=9 Score=34.06 Aligned_cols=32 Identities=16% Similarity=0.412 Sum_probs=20.2
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCC-CCcee
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCE-SKVTV 77 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e-~~~vv 77 (232)
.|.||.|+..+.+..=-=+|...|.++ ++.+.
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~fd~a~~Gy 34 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQFDCAKEGY 34 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCCccccCce
Confidence 489999999664332223456688884 44443
No 116
>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=42.61 E-value=20 Score=28.58 Aligned_cols=33 Identities=24% Similarity=0.666 Sum_probs=23.1
Q ss_pred CCCCcccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccchhh
Q 026824 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (232)
Q Consensus 42 d~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~ 87 (232)
++-....||-||. =||+ ....+|||-|.+-.-.
T Consensus 5 elGtKR~Cp~CG~kFYDL-------------nk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 5 ELGTKRTCPSCGAKFYDL-------------NKDPIVCPKCGTEFPP 38 (108)
T ss_pred ccCCcccCCCCcchhccC-------------CCCCccCCCCCCccCc
Confidence 3455688999998 5543 2357899999876543
No 117
>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=42.59 E-value=7 Score=30.98 Aligned_cols=30 Identities=23% Similarity=0.550 Sum_probs=19.1
Q ss_pred CCCCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 42 d~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
..+..+.|+-|+..|++..... .||-|-..
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~-------------~CP~Cgs~ 95 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDEFDF-------------SCPRCGSP 95 (113)
T ss_dssp EE--EEEETTTS-EEECHHCCH-------------H-SSSSSS
T ss_pred ecCCcEECCCCCCEEecCCCCC-------------CCcCCcCC
Confidence 3478899999999887665442 29999764
No 118
>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=42.10 E-value=18 Score=21.91 Aligned_cols=21 Identities=33% Similarity=0.634 Sum_probs=14.5
Q ss_pred cccCCCCCCCcc-HHHHhhhhc
Q 026824 46 DFPCPYCYEDFD-IASLCSHLE 66 (232)
Q Consensus 46 ~F~CPfC~e~~d-~~~L~~H~~ 66 (232)
-|.|.+|+..|. ...+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 467888888555 666777764
No 119
>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=41.86 E-value=6.4 Score=30.29 Aligned_cols=8 Identities=50% Similarity=1.352 Sum_probs=5.3
Q ss_pred ccCCCCCC
Q 026824 47 FPCPYCYE 54 (232)
Q Consensus 47 F~CPfC~e 54 (232)
.+|||||+
T Consensus 2 I~CP~CG~ 9 (84)
T PF04267_consen 2 IPCPHCGP 9 (84)
T ss_dssp EEETTTEE
T ss_pred ccCCCCCc
Confidence 35777776
No 120
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.75 E-value=8.3 Score=36.80 Aligned_cols=39 Identities=26% Similarity=0.586 Sum_probs=30.4
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCC---------CceecCCcccch
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCES---------KVTVCPICSVKV 85 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~---------~~vvCPVCa~~v 85 (232)
+.|-.|-|+|...+.+.++-=.|.|-. +.-.||||-..+
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcC
Confidence 999999999999888777777777622 245799997754
No 121
>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=41.41 E-value=12 Score=27.47 Aligned_cols=13 Identities=31% Similarity=1.025 Sum_probs=9.1
Q ss_pred CCCceecCCcccc
Q 026824 72 ESKVTVCPICSVK 84 (232)
Q Consensus 72 e~~~vvCPVCa~~ 84 (232)
....-+||+|.-.
T Consensus 48 ~~~~~iCp~C~~i 60 (69)
T PF09706_consen 48 NNDADICPICELI 60 (69)
T ss_pred cCCCccCHHHHHH
Confidence 4455789999754
No 122
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=40.72 E-value=16 Score=24.28 Aligned_cols=9 Identities=33% Similarity=0.685 Sum_probs=7.0
Q ss_pred ceecCCccc
Q 026824 75 VTVCPICSV 83 (232)
Q Consensus 75 ~vvCPVCa~ 83 (232)
..+||.|..
T Consensus 20 ~~vC~~Cg~ 28 (52)
T smart00661 20 RFVCRKCGY 28 (52)
T ss_pred EEECCcCCC
Confidence 678998875
No 123
>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=40.71 E-value=16 Score=24.32 Aligned_cols=11 Identities=36% Similarity=0.857 Sum_probs=8.6
Q ss_pred CCcccCCCCCC
Q 026824 44 RPDFPCPYCYE 54 (232)
Q Consensus 44 ~~~F~CPfC~e 54 (232)
+..|.||+||-
T Consensus 16 ~~g~~CP~Cg~ 26 (46)
T PF12760_consen 16 PDGFVCPHCGS 26 (46)
T ss_pred CCCCCCCCCCC
Confidence 34688999986
No 124
>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=40.64 E-value=7.6 Score=30.26 Aligned_cols=38 Identities=29% Similarity=0.679 Sum_probs=11.5
Q ss_pred cCCCCCCCccHHHHh-hhhccccCC-----------CCCceecCCcccch
Q 026824 48 PCPYCYEDFDIASLC-SHLEDEHSC-----------ESKVTVCPICSVKV 85 (232)
Q Consensus 48 ~CPfC~e~~d~~~L~-~H~~~eH~~-----------e~~~vvCPVCa~~v 85 (232)
.||+|++.+....+. .=|..-|.+ +.+.-+|++|..+.
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 699999977655543 336666654 55567899987654
No 125
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.50 E-value=14 Score=35.76 Aligned_cols=16 Identities=31% Similarity=0.756 Sum_probs=11.5
Q ss_pred CCcccCCCCCCCccHH
Q 026824 44 RPDFPCPYCYEDFDIA 59 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~ 59 (232)
..+|+||||..+-+..
T Consensus 372 ~~sfKCPYCP~e~~~~ 387 (394)
T KOG2817|consen 372 SQSFKCPYCPVEQLAS 387 (394)
T ss_pred CeeeeCCCCCcccCHH
Confidence 3469999998865543
No 126
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=40.48 E-value=24 Score=34.20 Aligned_cols=48 Identities=27% Similarity=0.538 Sum_probs=31.7
Q ss_pred cccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccch--hhhhhhhhh
Q 026824 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHIT 94 (232)
Q Consensus 46 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v--~~d~i~Hl~ 94 (232)
.|+||.|+- ==-.++|..|+.-.|.- .+.-.|--|...- -.|+..|+.
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~-dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSK-DKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhcc-CCCccccchhhhhccHHHHHHHHH
Confidence 577888877 33456777788777755 6667777777652 335555554
No 127
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=40.48 E-value=15 Score=35.10 Aligned_cols=40 Identities=23% Similarity=0.517 Sum_probs=29.8
Q ss_pred cccCCC--CCC-CccHHHHhhhhccccCC-----------------CCCceecCCcccch
Q 026824 46 DFPCPY--CYE-DFDIASLCSHLEDEHSC-----------------ESKVTVCPICSVKV 85 (232)
Q Consensus 46 ~F~CPf--C~e-~~d~~~L~~H~~~eH~~-----------------e~~~vvCPVCa~~v 85 (232)
-|+||. |.+ .-..-+|.-|...-|+. +.|.-+|+||..+-
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 489986 877 66778888888777732 33567899999875
No 128
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=39.72 E-value=17 Score=33.53 Aligned_cols=39 Identities=23% Similarity=0.542 Sum_probs=27.8
Q ss_pred CcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhhhhhhhh
Q 026824 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHI 93 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~d~i~Hl 93 (232)
....||.|+.. + -+.+ ++...+||.-|-.-+..+++.+-
T Consensus 10 ~~~~Cp~Cg~~-~------iv~d---~~~Ge~vC~~CG~Vl~e~~iD~g 48 (310)
T PRK00423 10 EKLVCPECGSD-K------LIYD---YERGEIVCADCGLVIEENIIDQG 48 (310)
T ss_pred cCCcCcCCCCC-C------eeEE---CCCCeEeecccCCcccccccccC
Confidence 35689999961 1 1222 35778999999999988888643
No 129
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=39.58 E-value=22 Score=22.77 Aligned_cols=31 Identities=19% Similarity=0.601 Sum_probs=18.6
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCccc
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
+.||-|+.-|++.+-. + +.....|-||.|..
T Consensus 3 i~Cp~C~~~y~i~d~~--i----p~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK--I----PPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHHH--C----CCCCcEEECCCCCC
Confidence 5688888755544321 1 34456778888854
No 130
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=39.41 E-value=15 Score=38.28 Aligned_cols=41 Identities=24% Similarity=0.433 Sum_probs=28.2
Q ss_pred CCCCcccCCCCCCCcc----HHHHhhhhccccCCCCCceecCCcccc
Q 026824 42 DVRPDFPCPYCYEDFD----IASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 42 d~~~~F~CPfC~e~~d----~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
++...+.||.|+..+. ...|.||--..+ +...-.||-|-..
T Consensus 440 ~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 440 DCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred cCCCcccCCCCCcceEEecCCCeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 4566799999988443 345666643433 4667789999876
No 131
>PRK11595 DNA utilization protein GntX; Provisional
Probab=39.09 E-value=15 Score=32.18 Aligned_cols=35 Identities=23% Similarity=0.487 Sum_probs=21.7
Q ss_pred cCCCCCCCccH--HHHhhhhccccCCCCCceecCCcccc
Q 026824 48 PCPYCYEDFDI--ASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 48 ~CPfC~e~~d~--~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
.|+.|+..+.. ..||.+|.+.=..- ...||.|...
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~--~~~C~~Cg~~ 43 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTL--KTCCPQCGLP 43 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcc--cCcCccCCCc
Confidence 48999885432 35888886653331 2468777643
No 132
>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=37.58 E-value=13 Score=35.55 Aligned_cols=40 Identities=28% Similarity=0.497 Sum_probs=27.0
Q ss_pred cccCCCCCCCccHHHHhhhhccccC-CCCCceecCCcccch
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHS-CESKVTVCPICSVKV 85 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~-~e~~~vvCPVCa~~v 85 (232)
.-.||+|+.+--....|++|-.... .+..+.+|.+|...+
T Consensus 136 ~g~CP~C~~~~a~g~~Ce~cG~~~~~~~l~~p~~~~~g~~~ 176 (391)
T PF09334_consen 136 EGTCPYCGSDKARGDQCENCGRPLEPEELINPVCKICGSPP 176 (391)
T ss_dssp TCEETTT--SSCTTTEETTTSSBEECCCSECEEETTTS-B-
T ss_pred eccccCcCccccCCCcccCCCCCcccccccCCccccccccC
Confidence 4679999976666678888765443 567889999998864
No 133
>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=37.44 E-value=22 Score=25.52 Aligned_cols=38 Identities=24% Similarity=0.557 Sum_probs=23.5
Q ss_pred CcccCCCCCCCccHHHHhh-----------------hhc-cccCCCCCceecCCccc
Q 026824 45 PDFPCPYCYEDFDIASLCS-----------------HLE-DEHSCESKVTVCPICSV 83 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~L~~-----------------H~~-~eH~~e~~~vvCPVCa~ 83 (232)
....||+|.-.+|...|+. |.- +.|.. ....+||.|..
T Consensus 6 niL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~-eg~L~Cp~c~r 61 (68)
T PF03966_consen 6 NILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIV-EGELICPECGR 61 (68)
T ss_dssp GTBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETT-TTEEEETTTTE
T ss_pred hhhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhccccc-CCEEEcCCCCC
Confidence 3578999988776666665 211 23333 46689999954
No 134
>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=37.10 E-value=13 Score=28.79 Aligned_cols=37 Identities=16% Similarity=0.311 Sum_probs=19.4
Q ss_pred CCCCCCCccHHHHhhhhccccC----CCCCceecCCcccch
Q 026824 49 CPYCYEDFDIASLCSHLEDEHS----CESKVTVCPICSVKV 85 (232)
Q Consensus 49 CPfC~e~~d~~~L~~H~~~eH~----~e~~~vvCPVCa~~v 85 (232)
||+|+.+--+.....+....-- .+....+||.|-...
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
Confidence 9999863333333333211111 133445799997753
No 135
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=36.18 E-value=17 Score=36.02 Aligned_cols=22 Identities=23% Similarity=0.543 Sum_probs=15.5
Q ss_pred hccccCCCCCceecCCcccchh
Q 026824 65 LEDEHSCESKVTVCPICSVKVA 86 (232)
Q Consensus 65 ~~~eH~~e~~~vvCPVCa~~v~ 86 (232)
|..+...+++.-|||||...||
T Consensus 27 c~~~~~~~PNt~vcpv~lg~PG 48 (474)
T PRK05477 27 CSTDFGAEPNTNVCPVCLGLPG 48 (474)
T ss_pred CCcccCCCCCCCcCccccCCCC
Confidence 3333344678899999999863
No 136
>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=35.73 E-value=17 Score=22.80 Aligned_cols=9 Identities=44% Similarity=1.176 Sum_probs=4.6
Q ss_pred CCceecCCc
Q 026824 73 SKVTVCPIC 81 (232)
Q Consensus 73 ~~~vvCPVC 81 (232)
...+.||+|
T Consensus 33 ~~~~~CP~C 41 (41)
T PF00097_consen 33 SGSVKCPLC 41 (41)
T ss_dssp TSSSBTTTT
T ss_pred cCCccCCcC
Confidence 334456655
No 137
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=35.50 E-value=23 Score=28.66 Aligned_cols=27 Identities=22% Similarity=0.443 Sum_probs=20.5
Q ss_pred ceecCCcccch-----hhhhhhhhhcccccch
Q 026824 75 VTVCPICSVKV-----ARDMLSHITLQHGHLF 101 (232)
Q Consensus 75 ~vvCPVCa~~v-----~~d~i~Hl~~qH~~~~ 101 (232)
.+-||+|.... ...+.-||+.-||-+-
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~s 56 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGISS 56 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhcccccc
Confidence 78999998532 4568888888888765
No 138
>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=35.13 E-value=26 Score=22.56 Aligned_cols=25 Identities=20% Similarity=0.530 Sum_probs=11.4
Q ss_pred CCceecCCcccch------hhhhhhhhhccc
Q 026824 73 SKVTVCPICSVKV------ARDMLSHITLQH 97 (232)
Q Consensus 73 ~~~vvCPVCa~~v------~~d~i~Hl~~qH 97 (232)
...+.|-.|...+ +.+|.+||...|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 3445555555543 235666654433
No 139
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=35.05 E-value=22 Score=34.00 Aligned_cols=40 Identities=30% Similarity=0.547 Sum_probs=28.3
Q ss_pred CCcccCCCCCCCcc--HHHHhhhhccc-cCC-----CCCceecCCccc
Q 026824 44 RPDFPCPYCYEDFD--IASLCSHLEDE-HSC-----ESKVTVCPICSV 83 (232)
Q Consensus 44 ~~~F~CPfC~e~~d--~~~L~~H~~~e-H~~-----e~~~vvCPVCa~ 83 (232)
...-.||.||...| +.+||.=|.-+ |+. +.+..+|+.|-+
T Consensus 4 ~~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 4 ASTILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGA 51 (355)
T ss_pred CcccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCC
Confidence 34678999999777 88888776555 443 334577888864
No 140
>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=34.91 E-value=23 Score=35.48 Aligned_cols=42 Identities=29% Similarity=0.585 Sum_probs=26.9
Q ss_pred CCcccCCCCCCCccHHHHhhhhccc--cCCCCCceecCCcccchhh
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDE--HSCESKVTVCPICSVKVAR 87 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~e--H~~e~~~vvCPVCa~~v~~ 87 (232)
+-..+||-||+.+.+. ..++.-+ ...+.-..+||-|-..+..
T Consensus 198 ~~~vpCPhCg~~~~l~--~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLE--WENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EEEccCCCCCCCcccc--ccceeecCCCCccceEEECCCCcCCCCH
Confidence 4568999999955443 2223222 1344556899999998865
No 141
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=34.47 E-value=16 Score=34.78 Aligned_cols=11 Identities=55% Similarity=1.256 Sum_probs=9.2
Q ss_pred CCcccCCCCCC
Q 026824 44 RPDFPCPYCYE 54 (232)
Q Consensus 44 ~~~F~CPfC~e 54 (232)
..+|+||||.+
T Consensus 374 ~~~FKCPYCP~ 384 (396)
T COG5109 374 VLSFKCPYCPE 384 (396)
T ss_pred cEEeeCCCCCc
Confidence 34799999987
No 142
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=34.41 E-value=18 Score=29.04 Aligned_cols=36 Identities=25% Similarity=0.646 Sum_probs=19.9
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
...|.||||.-.= ..-+-++..|. ....-|-||..-
T Consensus 21 dt~FnClfcnHek---~v~~~~Dk~~~--iG~~sC~iC~es 56 (109)
T KOG3214|consen 21 DTQFNCLFCNHEK---SVSCTLDKKHN--IGKASCRICEES 56 (109)
T ss_pred heeeccCcccccc---ceeeeehhhcC--cceeeeeehhhh
Confidence 3479999997622 11111222222 345679999763
No 143
>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=34.37 E-value=8 Score=24.90 Aligned_cols=20 Identities=20% Similarity=0.333 Sum_probs=7.4
Q ss_pred CCCCCCCccHH--HHhhhhccc
Q 026824 49 CPYCYEDFDIA--SLCSHLEDE 68 (232)
Q Consensus 49 CPfC~e~~d~~--~L~~H~~~e 68 (232)
|++|+..+... -=+.|+...
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~ 22 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPR 22 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-T
T ss_pred CCCCCCcCccCcceEeECcCch
Confidence 88998855544 234444433
No 144
>PRK04023 DNA polymerase II large subunit; Validated
Probab=34.21 E-value=22 Score=38.55 Aligned_cols=9 Identities=56% Similarity=0.866 Sum_probs=6.5
Q ss_pred hhHHHHHHh
Q 026824 218 ASFVQDLLL 226 (232)
Q Consensus 218 s~FVQ~Lll 226 (232)
|.||-.||-
T Consensus 804 a~fiDdLL~ 812 (1121)
T PRK04023 804 AKFIDDLLE 812 (1121)
T ss_pred HHHHHHHHH
Confidence 678887773
No 145
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.13 E-value=21 Score=26.08 Aligned_cols=13 Identities=38% Similarity=0.976 Sum_probs=9.0
Q ss_pred CCCceecCCcccc
Q 026824 72 ESKVTVCPICSVK 84 (232)
Q Consensus 72 e~~~vvCPVCa~~ 84 (232)
+.+.|+||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 5667777777664
No 146
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=34.08 E-value=13 Score=28.83 Aligned_cols=15 Identities=13% Similarity=0.698 Sum_probs=11.9
Q ss_pred CCCcccCCCCCC-Ccc
Q 026824 43 VRPDFPCPYCYE-DFD 57 (232)
Q Consensus 43 ~~~~F~CPfC~e-~~d 57 (232)
..+.|+|+|||+ .+.
T Consensus 33 Qhaky~CsfCGK~~vK 48 (92)
T KOG0402|consen 33 QHAKYTCSFCGKKTVK 48 (92)
T ss_pred Hhhhhhhhhcchhhhh
Confidence 367899999998 543
No 147
>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=33.63 E-value=13 Score=25.37 Aligned_cols=13 Identities=31% Similarity=0.692 Sum_probs=6.7
Q ss_pred cCCCCCCCccHHH
Q 026824 48 PCPYCYEDFDIAS 60 (232)
Q Consensus 48 ~CPfC~e~~d~~~ 60 (232)
.||.|+-+|+...
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 7999988777654
No 148
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.58 E-value=15 Score=29.37 Aligned_cols=31 Identities=29% Similarity=0.612 Sum_probs=21.3
Q ss_pred CCCCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 42 d~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
+.+..+.|+-|+..|..... ....||-|...
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 35778999999976655422 22459999764
No 149
>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=33.58 E-value=27 Score=28.94 Aligned_cols=31 Identities=19% Similarity=0.367 Sum_probs=22.0
Q ss_pred CCCCcccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 42 d~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
++-....||-||. =||+ ....+|||-|-...
T Consensus 5 elGtKr~Cp~cg~kFYDL-------------nk~p~vcP~cg~~~ 36 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDL-------------NRRPAVSPYTGEQF 36 (129)
T ss_pred hhCccccCCCcCcccccc-------------CCCCccCCCcCCcc
Confidence 3445688999998 4442 34579999998754
No 150
>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=32.65 E-value=16 Score=24.28 Aligned_cols=9 Identities=44% Similarity=1.180 Sum_probs=7.8
Q ss_pred cccCCCCCC
Q 026824 46 DFPCPYCYE 54 (232)
Q Consensus 46 ~F~CPfC~e 54 (232)
.-.||||+.
T Consensus 29 ~~~CpYCg~ 37 (40)
T PF10276_consen 29 PVVCPYCGT 37 (40)
T ss_dssp EEEETTTTE
T ss_pred eEECCCCCC
Confidence 689999985
No 151
>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=32.30 E-value=15 Score=32.21 Aligned_cols=22 Identities=32% Similarity=0.705 Sum_probs=0.0
Q ss_pred CceecCCcccch-hhhhhhhhhc
Q 026824 74 KVTVCPICSVKV-ARDMLSHITL 95 (232)
Q Consensus 74 ~~vvCPVCa~~v-~~d~i~Hl~~ 95 (232)
..++||||-.+| ...|-.||..
T Consensus 167 ~~~~cPitGe~IP~~e~~eHmRi 189 (229)
T PF12230_consen 167 KMIICPITGEMIPADEMDEHMRI 189 (229)
T ss_dssp -----------------------
T ss_pred ccccccccccccccccccccccc
Confidence 347999999986 6689999965
No 152
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=32.23 E-value=17 Score=26.34 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=22.2
Q ss_pred cccCCCCCC-CccHHHHhhhhccccCC
Q 026824 46 DFPCPYCYE-DFDIASLCSHLEDEHSC 71 (232)
Q Consensus 46 ~F~CPfC~e-~~d~~~L~~H~~~eH~~ 71 (232)
-|.||-||. =-+..+-..|++..|-+
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 789999999 55778889999988865
No 153
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=31.73 E-value=36 Score=31.48 Aligned_cols=43 Identities=16% Similarity=0.404 Sum_probs=29.5
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhhhhhhhhhccccc
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHGH 99 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~d~i~Hl~~qH~~ 99 (232)
..||.|+.. + +..+ ++....||--|-.-+..+++.+---.+.|
T Consensus 2 ~~CpeCg~~-~-------~~~d--~~~ge~VC~~CG~Vi~~~~id~gpewr~f 44 (285)
T COG1405 2 MSCPECGST-N-------IITD--YERGEIVCADCGLVLEDSLIDPGPEWRAF 44 (285)
T ss_pred CCCCCCCCc-c-------ceee--ccCCeEEeccCCEEeccccccCCCCcccc
Confidence 479999985 1 1122 23567899999999988888765554444
No 154
>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=31.68 E-value=16 Score=32.11 Aligned_cols=21 Identities=19% Similarity=0.292 Sum_probs=0.0
Q ss_pred cccCCCCCCCccHHHHhhhhc
Q 026824 46 DFPCPYCYEDFDIASLCSHLE 66 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~ 66 (232)
...||+||+-+-+..+-.|+.
T Consensus 168 ~~~cPitGe~IP~~e~~eHmR 188 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMR 188 (229)
T ss_dssp ---------------------
T ss_pred ccccccccccccccccccccc
Confidence 589999999999999999984
No 155
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=31.53 E-value=22 Score=35.90 Aligned_cols=22 Identities=27% Similarity=0.472 Sum_probs=16.4
Q ss_pred hccccCCCCCceecCCcccchh
Q 026824 65 LEDEHSCESKVTVCPICSVKVA 86 (232)
Q Consensus 65 ~~~eH~~e~~~vvCPVCa~~v~ 86 (232)
|..++..+++.-|||||...||
T Consensus 83 c~~~~g~~PNt~vcpvclg~PG 104 (544)
T PLN02751 83 CPYNYGAEPNTTVCPVCMGLPG 104 (544)
T ss_pred CCcccCCCCccCcCccccCCCC
Confidence 3344455788999999999863
No 156
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=30.85 E-value=22 Score=23.94 Aligned_cols=26 Identities=27% Similarity=0.589 Sum_probs=15.0
Q ss_pred CcccCCCCCCCccHH------HHhhhhccccC
Q 026824 45 PDFPCPYCYEDFDIA------SLCSHLEDEHS 70 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~------~L~~H~~~eH~ 70 (232)
+.-.|-||+..+... .|..|+...|+
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 456677777655443 56666654443
No 157
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=30.85 E-value=32 Score=33.46 Aligned_cols=56 Identities=21% Similarity=0.438 Sum_probs=34.9
Q ss_pred cccCCCCCC-CccHHHHhhhhccccCCC-------------------------------CCceecCCcccc--hhhhhhh
Q 026824 46 DFPCPYCYE-DFDIASLCSHLEDEHSCE-------------------------------SKVTVCPICSVK--VARDMLS 91 (232)
Q Consensus 46 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e-------------------------------~~~vvCPVCa~~--v~~d~i~ 91 (232)
.|+|--|+. =+...+|..|++ .|... +-.-.|-+|..- -|.++.+
T Consensus 292 pfKCd~Cd~~c~~esdL~kH~~-~HS~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~ 370 (467)
T KOG3608|consen 292 PFKCDECDTRCVRESDLAKHVQ-VHSKTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSA 370 (467)
T ss_pred CccccchhhhhccHHHHHHHHH-hccccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHH
Confidence 477777776 667777777765 55421 122235555443 2678999
Q ss_pred hhhcccccchh
Q 026824 92 HITLQHGHLFK 102 (232)
Q Consensus 92 Hl~~qH~~~~k 102 (232)
||+-+|++-..
T Consensus 371 HL~kkH~f~~P 381 (467)
T KOG3608|consen 371 HLMKKHGFRLP 381 (467)
T ss_pred HHHHhhcccCC
Confidence 99999988543
No 158
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=30.76 E-value=11 Score=29.43 Aligned_cols=16 Identities=31% Similarity=0.800 Sum_probs=12.5
Q ss_pred CCCCCCcccCCCCCCC
Q 026824 40 EDDVRPDFPCPYCYED 55 (232)
Q Consensus 40 ddd~~~~F~CPfC~e~ 55 (232)
|..+++.+.||+|+..
T Consensus 29 e~~~~~~~~Cp~C~~~ 44 (89)
T COG1997 29 EAQQRAKHVCPFCGRT 44 (89)
T ss_pred HHHHhcCCcCCCCCCc
Confidence 4446889999999983
No 159
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=30.65 E-value=22 Score=30.12 Aligned_cols=32 Identities=22% Similarity=0.560 Sum_probs=17.9
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCc-----eecCCcccc
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKV-----TVCPICSVK 84 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~-----vvCPVCa~~ 84 (232)
..|||||.... |+.+.-.....+ --||-|...
T Consensus 1 m~cp~c~~~~~------~~~~s~~~~~~~~~~~~~~c~~c~~~ 37 (154)
T PRK00464 1 MRCPFCGHPDT------RVIDSRPAEDGNAIRRRRECLACGKR 37 (154)
T ss_pred CcCCCCCCCCC------EeEeccccCCCCceeeeeeccccCCc
Confidence 37999997331 222322232222 349999875
No 160
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=30.65 E-value=27 Score=30.29 Aligned_cols=32 Identities=19% Similarity=0.531 Sum_probs=22.1
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
...|.||-|..-++..+=+.+- -.||.|-+.+
T Consensus 111 ~~~y~C~~~~~r~sfdeA~~~~----------F~Cp~Cg~~L 142 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAMELG----------FTCPKCGEDL 142 (176)
T ss_pred CCceeCCCCCCcccHHHHHHhC----------CCCCCCCchh
Confidence 4579999998844444433331 6899998875
No 161
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=30.64 E-value=29 Score=23.71 Aligned_cols=31 Identities=19% Similarity=0.587 Sum_probs=18.9
Q ss_pred CCCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCc
Q 026824 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPIC 81 (232)
Q Consensus 43 ~~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVC 81 (232)
...-+.||.|+-.+...- .. +. .....||.|
T Consensus 25 ~~v~W~C~~Cgh~w~~~v--~~-----R~-~~~~~CP~C 55 (55)
T PF14311_consen 25 KKVWWKCPKCGHEWKASV--ND-----RT-RRGKGCPYC 55 (55)
T ss_pred CEEEEECCCCCCeeEccH--hh-----hc-cCCCCCCCC
Confidence 355699999977554321 11 11 456789988
No 162
>PF14369 zf-RING_3: zinc-finger
Probab=30.51 E-value=25 Score=22.53 Aligned_cols=9 Identities=44% Similarity=1.228 Sum_probs=7.8
Q ss_pred cCCCCCCCc
Q 026824 48 PCPYCYEDF 56 (232)
Q Consensus 48 ~CPfC~e~~ 56 (232)
.||.|+-+|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 799998876
No 163
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=30.50 E-value=28 Score=35.44 Aligned_cols=53 Identities=26% Similarity=0.574 Sum_probs=32.1
Q ss_pred CCCCCcccCCCCCC-Ccc-HHHHhhh-----hcc---ccCCCCCceecCCcccchhhhhhhhh
Q 026824 41 DDVRPDFPCPYCYE-DFD-IASLCSH-----LED---EHSCESKVTVCPICSVKVARDMLSHI 93 (232)
Q Consensus 41 dd~~~~F~CPfC~e-~~d-~~~L~~H-----~~~---eH~~e~~~vvCPVCa~~v~~d~i~Hl 93 (232)
+|-....-|-+|.+ -=| +..-|.| |.. +-..+..+|.||+|.-.++.|+..|-
T Consensus 531 ~enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~a 593 (791)
T KOG1002|consen 531 DENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPA 593 (791)
T ss_pred ccccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchh
Confidence 34466788999987 222 2333333 221 22346778999999988766655443
No 164
>PHA02929 N1R/p28-like protein; Provisional
Probab=30.44 E-value=13 Score=33.60 Aligned_cols=43 Identities=23% Similarity=0.483 Sum_probs=24.7
Q ss_pred CCcccCCCCCCCccHH----------HHhhhhccccCC---CCCceecCCcccchh
Q 026824 44 RPDFPCPYCYEDFDIA----------SLCSHLEDEHSC---ESKVTVCPICSVKVA 86 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~----------~L~~H~~~eH~~---e~~~vvCPVCa~~v~ 86 (232)
.....||.|.+.+... .=|.|+--..+. -.....||+|...+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 3467999999965432 125553222221 123568999987643
No 165
>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=29.73 E-value=21 Score=28.68 Aligned_cols=19 Identities=21% Similarity=0.627 Sum_probs=13.0
Q ss_pred CcccCCCCCC-CccHHHHhh
Q 026824 45 PDFPCPYCYE-DFDIASLCS 63 (232)
Q Consensus 45 ~~F~CPfC~e-~~d~~~L~~ 63 (232)
..|.||||.. .=.+..+..
T Consensus 23 ~D~~Cp~C~~~~~~~~~~~~ 42 (178)
T cd03019 23 FSYGCPHCYNFEPILEAWVK 42 (178)
T ss_pred ECCCCcchhhhhHHHHHHHH
Confidence 3599999988 544554444
No 166
>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=29.47 E-value=25 Score=34.85 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=12.9
Q ss_pred CCCceecCCcccchh
Q 026824 72 ESKVTVCPICSVKVA 86 (232)
Q Consensus 72 e~~~vvCPVCa~~v~ 86 (232)
+++..|||||...||
T Consensus 34 ~PNt~v~pvclg~PG 48 (478)
T TIGR00133 34 PPNTNVCPVCLGLPG 48 (478)
T ss_pred CCCcccCccccCCCC
Confidence 688899999999863
No 167
>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=29.23 E-value=21 Score=35.34 Aligned_cols=47 Identities=32% Similarity=0.409 Sum_probs=32.6
Q ss_pred CccHHHHhhhhccccCCC-----------------CCceecCCcccch--hhhhhhhhhcccccch
Q 026824 55 DFDIASLCSHLEDEHSCE-----------------SKVTVCPICSVKV--ARDMLSHITLQHGHLF 101 (232)
Q Consensus 55 ~~d~~~L~~H~~~eH~~e-----------------~~~vvCPVCa~~v--~~d~i~Hl~~qH~~~~ 101 (232)
.+.+..|..|+...|..+ -+.-+||+|..+- ...+..|+...|-.-+
T Consensus 20 kVsi~eL~sy~~~~~~~~a~~~Lseal~fak~n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 20 KVSIDELKSYYESVYDREAADALSEALSFAKENKSWRFWICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred eeEHHHHHHHHHhccchHHHHHHHHHHHHHHhcCceeEeeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 455666666666655422 2346799999764 6789999999997654
No 168
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.90 E-value=18 Score=30.26 Aligned_cols=38 Identities=29% Similarity=0.660 Sum_probs=22.1
Q ss_pred CcccCCCCCCCccHH-HH-hhhhccccCCCC---CceecCCcc
Q 026824 45 PDFPCPYCYEDFDIA-SL-CSHLEDEHSCES---KVTVCPICS 82 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~-~L-~~H~~~eH~~e~---~~vvCPVCa 82 (232)
..+.||+|.+.|... .| |-|-.-..+... ....||+|.
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 478999998866655 22 233222222111 338999999
No 169
>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=28.76 E-value=21 Score=24.92 Aligned_cols=44 Identities=23% Similarity=0.554 Sum_probs=27.9
Q ss_pred CCCCCCCC-CCCCcccCCCCCC--CccHHHHhhhhccccCCCCCceecCCcccchh
Q 026824 34 IDDFEVED-DVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (232)
Q Consensus 34 ~e~~~~dd-d~~~~F~CPfC~e--~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~ 86 (232)
++|++.++ +..-.|+|+ ||. .++...|-.+ .-.|-|+-|+-.|.
T Consensus 5 l~d~~~~~~~~~~~y~CR-CG~~f~i~e~~l~~~--------~~iv~C~sCSL~I~ 51 (55)
T PF05207_consen 5 LDDMEFDEEEGVYSYPCR-CGGEFEISEEDLEEG--------EVIVQCDSCSLWIR 51 (55)
T ss_dssp TTTSEEETTTTEEEEEET-TSSEEEEEHHHHHCT----------EEEETTTTEEEE
T ss_pred hhhceecCCCCEEEEcCC-CCCEEEEcchhccCc--------CEEEECCCCccEEE
Confidence 45544332 234689995 988 6677777665 44678999987653
No 170
>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=28.43 E-value=35 Score=31.56 Aligned_cols=29 Identities=28% Similarity=0.557 Sum_probs=21.9
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
-..||-|++-+-...|... ..|||-|...
T Consensus 26 ~~~c~~c~~~~~~~~l~~~----------~~vc~~c~~h 54 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERN----------LEVCPKCDHH 54 (285)
T ss_pred eeECCCCcchhhHHHHHhh----------CCCCCCCCCc
Confidence 4689999997766666543 3699999875
No 171
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=28.42 E-value=33 Score=31.76 Aligned_cols=29 Identities=28% Similarity=0.559 Sum_probs=21.7
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
-.+||-|++-+-...|-.. ..|||-|-..
T Consensus 27 ~~~c~~c~~~~~~~~l~~~----------~~vc~~c~~h 55 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEAN----------LNVCPKCGHH 55 (292)
T ss_pred eeECCCccchhhHHHHHhc----------CCCCCCCCCC
Confidence 4789999997666665443 3599999875
No 172
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=28.33 E-value=17 Score=25.22 Aligned_cols=33 Identities=21% Similarity=0.403 Sum_probs=11.9
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCccc
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
..-++|| |+..+=+ .-..++. +..+++||-|-.
T Consensus 13 ~~~~PC~-Cgf~IC~-~C~~~i~-----~~~~g~CPgCr~ 45 (48)
T PF14570_consen 13 KDFYPCE-CGFQICR-FCYHDIL-----ENEGGRCPGCRE 45 (48)
T ss_dssp TT--SST-TS----H-HHHHHHT-----TSS-SB-TTT--
T ss_pred CccccCc-CCCcHHH-HHHHHHH-----hccCCCCCCCCC
Confidence 4567886 6653321 1112222 235789999964
No 173
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=28.19 E-value=34 Score=31.97 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=22.1
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
-.+||-|++-+-...|-.. ..|||-|...
T Consensus 38 w~kc~~C~~~~~~~~l~~~----------~~vcp~c~~h 66 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSK----------MNICEQCGYH 66 (296)
T ss_pred eeECCCccchhhHHHHHHc----------CCCCCCCCCC
Confidence 4689999997777766543 3699999875
No 174
>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=27.85 E-value=29 Score=32.37 Aligned_cols=26 Identities=27% Similarity=0.530 Sum_probs=16.3
Q ss_pred HhhhhccccCCCCCceecCCcccchh
Q 026824 61 LCSHLEDEHSCESKVTVCPICSVKVA 86 (232)
Q Consensus 61 L~~H~~~eH~~e~~~vvCPVCa~~v~ 86 (232)
|.|.|...+..+++.-|||||...||
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 33445455555788899999999863
No 175
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.81 E-value=34 Score=37.89 Aligned_cols=35 Identities=31% Similarity=0.756 Sum_probs=20.1
Q ss_pred cccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 46 ~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
.|.||-||. .+. ..|..|-.. . +. ...||.|-+.+
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CGs~-t-e~-vy~CPsCGaev 702 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCGTH-T-EP-VYVCPDCGAEV 702 (1337)
T ss_pred EEECCCCCCcccc--ccCcccCCc-C-CC-ceeCccCCCcc
Confidence 588888888 433 366656322 1 11 23677776654
No 176
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=26.83 E-value=29 Score=25.92 Aligned_cols=8 Identities=50% Similarity=1.464 Sum_probs=6.0
Q ss_pred ccCCCCCC
Q 026824 47 FPCPYCYE 54 (232)
Q Consensus 47 F~CPfC~e 54 (232)
|.||+||.
T Consensus 2 m~CP~Cg~ 9 (72)
T PRK09678 2 FHCPLCQH 9 (72)
T ss_pred ccCCCCCC
Confidence 56888876
No 177
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=26.70 E-value=24 Score=28.09 Aligned_cols=13 Identities=15% Similarity=0.398 Sum_probs=7.3
Q ss_pred CCcccCCCCCCCc
Q 026824 44 RPDFPCPYCYEDF 56 (232)
Q Consensus 44 ~~~F~CPfC~e~~ 56 (232)
+..+.|+-|+..|
T Consensus 68 p~~~~C~~Cg~~~ 80 (114)
T PRK03681 68 EAECWCETCQQYV 80 (114)
T ss_pred CcEEEcccCCCee
Confidence 4556666665533
No 178
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.64 E-value=42 Score=34.77 Aligned_cols=28 Identities=32% Similarity=0.500 Sum_probs=25.0
Q ss_pred CCcccCCCCCC-CccHHHHhhhhccccCC
Q 026824 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSC 71 (232)
Q Consensus 44 ~~~F~CPfC~e-~~d~~~L~~H~~~eH~~ 71 (232)
+.---|+||.+ -||..+|..|+..+|.+
T Consensus 180 rGhp~C~~C~~~fld~~el~rH~~~~h~~ 208 (669)
T KOG2231|consen 180 RGHPLCKFCHERFLDDDELYRHLRFDHEF 208 (669)
T ss_pred cCCccchhhhhhhccHHHHHHhhccceeh
Confidence 44678999999 99999999999999976
No 179
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=26.54 E-value=32 Score=19.26 Aligned_cols=18 Identities=33% Similarity=0.421 Sum_probs=7.3
Q ss_pred cCCCCCC-CccHHHHhhhh
Q 026824 48 PCPYCYE-DFDIASLCSHL 65 (232)
Q Consensus 48 ~CPfC~e-~~d~~~L~~H~ 65 (232)
.|..|+. =-+...|..|+
T Consensus 2 ~C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHL 20 (25)
T ss_dssp EETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCcCCHHHHHHHH
Confidence 3444444 33334444443
No 180
>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=26.45 E-value=47 Score=36.69 Aligned_cols=46 Identities=20% Similarity=0.490 Sum_probs=31.2
Q ss_pred cCCCCCCCCCCCCCcccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 32 LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 32 ~~~e~~~~ddd~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
+|+-+++. +++-|.||-|.- +|...+-. ---++--...||.|-..+
T Consensus 672 lgITeVdP---L~phy~c~~c~~~ef~~~~~~-----~sg~dlp~k~cp~c~~~~ 718 (1213)
T TIGR01405 672 TGITEVNP---LPPHYLCPNCKYSEFITDGSV-----GSGFDLPDKDCPKCGAPL 718 (1213)
T ss_pred hcCCCcCC---CcccccCcccccccccccccc-----cccccCccccCccccccc
Confidence 57776553 689999999977 77554311 112455567899998864
No 181
>PHA00733 hypothetical protein
Probab=26.35 E-value=46 Score=26.99 Aligned_cols=25 Identities=24% Similarity=0.483 Sum_probs=21.3
Q ss_pred cccCCCCCCC-ccHHHHhhhhccccC
Q 026824 46 DFPCPYCYED-FDIASLCSHLEDEHS 70 (232)
Q Consensus 46 ~F~CPfC~e~-~d~~~L~~H~~~eH~ 70 (232)
.|.|+.|++. -....|..|+...|.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 5999999994 566889999999885
No 182
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=26.32 E-value=32 Score=29.45 Aligned_cols=41 Identities=22% Similarity=0.542 Sum_probs=25.1
Q ss_pred cccCCCCCCCccHHHHhhhhcccc-----CCC-CCceecCCcccchh
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEH-----SCE-SKVTVCPICSVKVA 86 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH-----~~e-~~~vvCPVCa~~v~ 86 (232)
--.||.|+..++..--..|++=.| ... -+-+.|+-|-..+|
T Consensus 20 ~G~CaiC~~~l~~~~~~~~vDHDH~l~g~~TG~VRGLLC~~CN~~lG 66 (157)
T PHA02565 20 NGICPLCKRELDGDVSKNHLDHDHELNGPNAGRVRGLLCNLCNALEG 66 (157)
T ss_pred CCcCCCCCCccCCCccccccCCCCCCCCcccccccccCchhhhhhhh
Confidence 457999999775432223776667 222 23466888876443
No 183
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=26.13 E-value=7.6 Score=30.70 Aligned_cols=21 Identities=29% Similarity=0.641 Sum_probs=16.7
Q ss_pred CcccCCCCCC-CccHHHHhhhh
Q 026824 45 PDFPCPYCYE-DFDIASLCSHL 65 (232)
Q Consensus 45 ~~F~CPfC~e-~~d~~~L~~H~ 65 (232)
..|.||+|.. .-.+..|..+.
T Consensus 20 ~d~~Cp~C~~~~~~~~~~~~~~ 41 (162)
T PF13462_consen 20 FDFQCPHCAKFHEELEKLLKKY 41 (162)
T ss_dssp E-TTSHHHHHHHHHHHHHHHHH
T ss_pred ECCCCHhHHHHHHHHhhhhhhc
Confidence 3699999999 77777888885
No 184
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=25.82 E-value=25 Score=22.75 Aligned_cols=26 Identities=31% Similarity=0.855 Sum_probs=13.6
Q ss_pred CCCCCCCccHHHHhhhhccccCCCCCceecCCccc
Q 026824 49 CPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (232)
Q Consensus 49 CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~ 83 (232)
||-|+..+....+ .+-..-+||-|.-
T Consensus 2 CP~C~~~l~~~~~---------~~~~id~C~~C~G 27 (41)
T PF13453_consen 2 CPRCGTELEPVRL---------GDVEIDVCPSCGG 27 (41)
T ss_pred cCCCCcccceEEE---------CCEEEEECCCCCe
Confidence 7777665554433 1223345776654
No 185
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=25.82 E-value=18 Score=35.86 Aligned_cols=37 Identities=32% Similarity=0.695 Sum_probs=21.6
Q ss_pred CcccCCCCCCCccHHH------HhhhhccccCCC---CCceecCCccc
Q 026824 45 PDFPCPYCYEDFDIAS------LCSHLEDEHSCE---SKVTVCPICSV 83 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~------L~~H~~~eH~~e---~~~vvCPVCa~ 83 (232)
.--+||.|-|-+|... ||.| ..|+.- -...-||||.-
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~~c~H--sfh~~cl~~w~~~scpvcR~ 219 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTILCNH--SFHCSCLMKWWDSSCPVCRY 219 (493)
T ss_pred cCCCcchhHhhcCccccceeeeeccc--ccchHHHhhcccCcChhhhh
Confidence 3579999998555443 5555 333321 13466888753
No 186
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=25.50 E-value=35 Score=29.58 Aligned_cols=13 Identities=46% Similarity=0.958 Sum_probs=10.6
Q ss_pred ccCCCCCCCccHH
Q 026824 47 FPCPYCYEDFDIA 59 (232)
Q Consensus 47 F~CPfC~e~~d~~ 59 (232)
-+||+||.-+|-.
T Consensus 155 P~CPlCg~PlDP~ 167 (171)
T PF11290_consen 155 PPCPLCGEPLDPE 167 (171)
T ss_pred CCCCCCCCCCCCC
Confidence 6899999977754
No 187
>PF14279 HNH_5: HNH endonuclease
Probab=25.25 E-value=29 Score=25.57 Aligned_cols=42 Identities=21% Similarity=0.431 Sum_probs=23.5
Q ss_pred CCCCCCCccHHHH-hhhhccccCC---CCCceecCCcccchhhhhhh
Q 026824 49 CPYCYEDFDIASL-CSHLEDEHSC---ESKVTVCPICSVKVARDMLS 91 (232)
Q Consensus 49 CPfC~e~~d~~~L-~~H~~~eH~~---e~~~vvCPVCa~~v~~d~i~ 91 (232)
|.||.++.+.... .+|+.-+=-. ..+. ||--|-...+..+-+
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~vD~ 46 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN-VCDKCNNKFGSKVDA 46 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc-hhHHHhHHHhHHHHH
Confidence 9999997665432 3344322111 2234 888887776654333
No 188
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.11 E-value=41 Score=36.01 Aligned_cols=35 Identities=26% Similarity=0.335 Sum_probs=24.2
Q ss_pred CcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
..+.||.|+..|..-.-- ...+.+..+.||.|.-.
T Consensus 249 ~~~~c~~~g~~~~~~~~~-----~FSfNsp~G~Cp~C~G~ 283 (924)
T TIGR00630 249 KHAACPECGFSLPELEPR-----LFSFNSPYGACPECSGL 283 (924)
T ss_pred hcccCcccCcccCcCChh-----hcCCCCCcCCCCCCccc
Confidence 469999999866532211 23566778999999664
No 189
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=24.88 E-value=32 Score=29.86 Aligned_cols=26 Identities=31% Similarity=0.672 Sum_probs=17.9
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhh
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~ 87 (232)
.-+||-||- +. ...+.|+-|.++|..
T Consensus 93 l~~CP~CGh----------~k------~a~~LC~~Cy~kV~k 118 (176)
T KOG4080|consen 93 LNTCPACGH----------IK------PAHTLCDYCYAKVHK 118 (176)
T ss_pred cccCcccCc----------cc------cccccHHHHHHHHHH
Confidence 568999973 22 234788899888743
No 190
>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=24.86 E-value=44 Score=21.12 Aligned_cols=11 Identities=27% Similarity=0.667 Sum_probs=7.9
Q ss_pred CCcccCCCCCC
Q 026824 44 RPDFPCPYCYE 54 (232)
Q Consensus 44 ~~~F~CPfC~e 54 (232)
.....||+||-
T Consensus 15 ~~~irC~~CG~ 25 (32)
T PF03604_consen 15 GDPIRCPECGH 25 (32)
T ss_dssp SSTSSBSSSS-
T ss_pred CCcEECCcCCC
Confidence 44679999985
No 191
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.81 E-value=38 Score=27.38 Aligned_cols=15 Identities=40% Similarity=0.747 Sum_probs=12.1
Q ss_pred cccCCCCCCCccHHH
Q 026824 46 DFPCPYCYEDFDIAS 60 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~ 60 (232)
...||-||+.|+-.-
T Consensus 49 ~t~CP~Cg~~~e~~f 63 (115)
T COG1885 49 STSCPKCGEPFESAF 63 (115)
T ss_pred cccCCCCCCccceeE
Confidence 678999999887543
No 192
>PRK14873 primosome assembly protein PriA; Provisional
Probab=24.69 E-value=31 Score=35.52 Aligned_cols=39 Identities=18% Similarity=0.420 Sum_probs=25.4
Q ss_pred CCCCcccCCCCCCCccH----HHH-hhhhccccCCCCCceecCCcccc
Q 026824 42 DVRPDFPCPYCYEDFDI----ASL-CSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 42 d~~~~F~CPfC~e~~d~----~~L-~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
++...+.||.|+-.+.. ..| |.||.- + ...-.||-|-..
T Consensus 388 ~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~-~---~~p~~Cp~Cgs~ 431 (665)
T PRK14873 388 RCRTPARCRHCTGPLGLPSAGGTPRCRWCGR-A---APDWRCPRCGSD 431 (665)
T ss_pred hCcCeeECCCCCCceeEecCCCeeECCCCcC-C---CcCccCCCCcCC
Confidence 45567999999985554 246 555542 2 235699999774
No 193
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.63 E-value=41 Score=37.34 Aligned_cols=40 Identities=28% Similarity=0.544 Sum_probs=29.1
Q ss_pred cccCCCCCCCccHHHHhhhhccccCC-CCCceecCCcccch
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSC-ESKVTVCPICSVKV 85 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~-e~~~vvCPVCa~~v 85 (232)
.+.||.||........|-.|..+=.. +.....||-|-..+
T Consensus 679 ~~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtpl 719 (1337)
T PRK14714 679 ENRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVEL 719 (1337)
T ss_pred cccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcc
Confidence 46999999977666788888765332 23367899998764
No 194
>PF14968 CCDC84: Coiled coil protein 84
Probab=24.17 E-value=38 Score=32.20 Aligned_cols=25 Identities=24% Similarity=0.454 Sum_probs=18.9
Q ss_pred CCCCcccCCCCCCCccHH-------HHhhhhc
Q 026824 42 DVRPDFPCPYCYEDFDIA-------SLCSHLE 66 (232)
Q Consensus 42 d~~~~F~CPfC~e~~d~~-------~L~~H~~ 66 (232)
+-+..|=|+||+.++... +++.|+-
T Consensus 54 ~~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLa 85 (336)
T PF14968_consen 54 EHRNRFWCVFCDCEVREHDSSFACGGAIEHLA 85 (336)
T ss_pred cccceeEeeCccchhhhccchhhhccHHhhcC
Confidence 446789999999987755 6776664
No 195
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.09 E-value=40 Score=32.04 Aligned_cols=23 Identities=30% Similarity=0.924 Sum_probs=19.9
Q ss_pred cccCCCCCCCccHHHHhhhhcccc
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEH 69 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH 69 (232)
+.-||||.-.+.....|.|++ -|
T Consensus 2 e~iCP~CkLsv~~~~m~~Hie-aH 24 (393)
T KOG4696|consen 2 EIICPFCKLSVNYDEMCFHIE-AH 24 (393)
T ss_pred cccccceecccCHHHHHHHHH-hh
Confidence 457999998999999999997 55
No 196
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=23.96 E-value=43 Score=32.86 Aligned_cols=42 Identities=19% Similarity=0.407 Sum_probs=22.9
Q ss_pred CCCcccCCCCCC--CccHHHHhhhhccccCCC--CCceecCCcccc
Q 026824 43 VRPDFPCPYCYE--DFDIASLCSHLEDEHSCE--SKVTVCPICSVK 84 (232)
Q Consensus 43 ~~~~F~CPfC~e--~~d~~~L~~H~~~eH~~e--~~~vvCPVCa~~ 84 (232)
....|.|+.||- +=.+..--.-+..--+++ +..-+||+|.+.
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 356799999976 433332222222222222 234689999765
No 197
>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=23.86 E-value=35 Score=33.00 Aligned_cols=34 Identities=24% Similarity=0.455 Sum_probs=21.4
Q ss_pred CcccCCCCCC--CccHHHH-hhhhccccCCCCCceecCCcccc
Q 026824 45 PDFPCPYCYE--DFDIASL-CSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 45 ~~F~CPfC~e--~~d~~~L-~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
.-..||||+. .-+...| |.||. ..+..||.|...
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 3578999998 3334444 44442 235689999665
No 198
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.84 E-value=38 Score=33.44 Aligned_cols=37 Identities=24% Similarity=0.477 Sum_probs=21.6
Q ss_pred CcccCCCCCCCccH----HHHhhh-hccccCCCCCceecCCcccc
Q 026824 45 PDFPCPYCYEDFDI----ASLCSH-LEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 45 ~~F~CPfC~e~~d~----~~L~~H-~~~eH~~e~~~vvCPVCa~~ 84 (232)
....||.|+..+.. ..|.|| |.-. ..-.-.||.|...
T Consensus 221 ~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~---~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 221 YILCCPNCDVSLTYHKKEGKLRCHYCGYQ---EPIPKTCPQCGSE 262 (505)
T ss_pred CccCCCCCCCceEEecCCCeEEcCCCcCc---CCCCCCCCCCCCC
Confidence 34679999875543 345454 3211 1224689999764
No 199
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.84 E-value=31 Score=27.81 Aligned_cols=12 Identities=17% Similarity=0.553 Sum_probs=7.2
Q ss_pred CCCcccCCCCCCC
Q 026824 43 VRPDFPCPYCYED 55 (232)
Q Consensus 43 ~~~~F~CPfC~e~ 55 (232)
.+..+.| -|+..
T Consensus 67 vp~~~~C-~Cg~~ 78 (124)
T PRK00762 67 IPVEIEC-ECGYE 78 (124)
T ss_pred cCeeEEe-eCcCc
Confidence 3556666 66654
No 200
>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=23.66 E-value=23 Score=24.72 Aligned_cols=17 Identities=41% Similarity=0.960 Sum_probs=11.2
Q ss_pred cccCCCCCC-CccHHHHh
Q 026824 46 DFPCPYCYE-DFDIASLC 62 (232)
Q Consensus 46 ~F~CPfC~e-~~d~~~L~ 62 (232)
.|.||||.. .-.+..+.
T Consensus 6 d~~Cp~C~~~~~~l~~~~ 23 (98)
T cd02972 6 DPLCPYCYLFEPELEKLL 23 (98)
T ss_pred CCCCHhHHhhhHHHHHHH
Confidence 578999988 44444443
No 201
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=23.42 E-value=57 Score=36.69 Aligned_cols=46 Identities=22% Similarity=0.545 Sum_probs=30.8
Q ss_pred cCCCCCCCCCCCCCcccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccch
Q 026824 32 LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (232)
Q Consensus 32 ~~~e~~~~ddd~~~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v 85 (232)
+|+-+++. +++-|.||-|.- +|...+-. -=-++--...||.|-+.+
T Consensus 897 lgITeVdP---L~phy~C~~C~~~ef~~~~~~-----~sG~Dlpdk~Cp~Cg~~~ 943 (1437)
T PRK00448 897 IGITEVNP---LPPHYVCPNCKYSEFFTDGSV-----GSGFDLPDKDCPKCGTKL 943 (1437)
T ss_pred hcCCCcCC---CCccccCcccccccccccccc-----cccccCccccCccccccc
Confidence 67776553 689999999976 77544311 012344567899998864
No 202
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=23.28 E-value=48 Score=24.03 Aligned_cols=45 Identities=24% Similarity=0.502 Sum_probs=20.6
Q ss_pred CCCcccCC--CCCCCccHHHHhhhhccccC----CCCCceecCCcccchhh
Q 026824 43 VRPDFPCP--YCYEDFDIASLCSHLEDEHS----CESKVTVCPICSVKVAR 87 (232)
Q Consensus 43 ~~~~F~CP--fC~e~~d~~~L~~H~~~eH~----~e~~~vvCPVCa~~v~~ 87 (232)
..+...|| -|+.-|=..=|.+....... +....+.||.|...++-
T Consensus 17 ~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 17 EIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp ----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 34578887 88887777777777765433 34556779999887643
No 203
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=22.96 E-value=42 Score=35.83 Aligned_cols=36 Identities=25% Similarity=0.465 Sum_probs=24.7
Q ss_pred CCcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 44 ~~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
-.-|.||.|+..+..-+= .-..+.+-.+.||-|.-.
T Consensus 243 S~~~acp~~g~~~~elep-----rlFSFNsP~GaCp~C~Gl 278 (935)
T COG0178 243 SENFACPVCGFSIPELEP-----RLFSFNSPFGACPTCDGL 278 (935)
T ss_pred ecccCCCccCcccCCCCc-----ccccCCCCCCCCCcCCCc
Confidence 467999999875543221 223466778999999874
No 204
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.79 E-value=25 Score=32.90 Aligned_cols=18 Identities=39% Similarity=0.931 Sum_probs=15.1
Q ss_pred ccCCCCCCCccHHHHhhh
Q 026824 47 FPCPYCYEDFDIASLCSH 64 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H 64 (232)
-+||||-|.+|.+.+.+.
T Consensus 271 qtCPYCKekVdl~rmfsn 288 (328)
T KOG1734|consen 271 QTCPYCKEKVDLKRMFSN 288 (328)
T ss_pred CCCchHHHHhhHhhhccC
Confidence 589999999998887654
No 205
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=22.73 E-value=60 Score=28.00 Aligned_cols=38 Identities=16% Similarity=0.382 Sum_probs=21.5
Q ss_pred ccCCCCCC---CccHHHHhhhhccccCCC-CCceecCCcccc
Q 026824 47 FPCPYCYE---DFDIASLCSHLEDEHSCE-SKVTVCPICSVK 84 (232)
Q Consensus 47 F~CPfC~e---~~d~~~L~~H~~~eH~~e-~~~vvCPVCa~~ 84 (232)
=.||+|+. .+...+-..-+.+.|.-. ...-+||.|-..
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 36888876 444444444444444432 234568888664
No 206
>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=22.70 E-value=46 Score=23.93 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=6.9
Q ss_pred cCCCCCCCcc
Q 026824 48 PCPYCYEDFD 57 (232)
Q Consensus 48 ~CPfC~e~~d 57 (232)
-||+||+.+.
T Consensus 5 HC~~CG~~Ip 14 (59)
T PF09889_consen 5 HCPVCGKPIP 14 (59)
T ss_pred cCCcCCCcCC
Confidence 4888887554
No 207
>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=22.40 E-value=37 Score=22.53 Aligned_cols=7 Identities=57% Similarity=1.554 Sum_probs=3.3
Q ss_pred cCCCCCC
Q 026824 48 PCPYCYE 54 (232)
Q Consensus 48 ~CPfC~e 54 (232)
+||.|+=
T Consensus 5 pCP~CGG 11 (40)
T PF08273_consen 5 PCPICGG 11 (40)
T ss_dssp --TTTT-
T ss_pred CCCCCcC
Confidence 6888865
No 208
>PRK05978 hypothetical protein; Provisional
Probab=22.06 E-value=35 Score=28.77 Aligned_cols=27 Identities=26% Similarity=0.463 Sum_probs=16.9
Q ss_pred ccCCCCCC-CccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 47 FPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 47 F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
-+||-||+ .+=. .+-.-+-.||+|-..
T Consensus 34 grCP~CG~G~LF~-----------g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 34 GRCPACGEGKLFR-----------AFLKPVDHCAACGED 61 (148)
T ss_pred CcCCCCCCCcccc-----------cccccCCCccccCCc
Confidence 68999999 4421 233334567777664
No 209
>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=21.89 E-value=39 Score=28.62 Aligned_cols=31 Identities=23% Similarity=0.662 Sum_probs=18.7
Q ss_pred cCCCCCC-CccHHHHhhhhccccCCCCCcee-----cCCcccch
Q 026824 48 PCPYCYE-DFDIASLCSHLEDEHSCESKVTV-----CPICSVKV 85 (232)
Q Consensus 48 ~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vv-----CPVCa~~v 85 (232)
.||||+. +-.| .+.-..+..+.| |+.|..+-
T Consensus 2 ~CP~C~~~dtkV-------iDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 2 HCPFCQHHNTRV-------LDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCEe-------eeccccCCCCeeeecccCCccCCcc
Confidence 5999998 4333 233333333333 99999874
No 210
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.75 E-value=21 Score=33.04 Aligned_cols=42 Identities=31% Similarity=0.665 Sum_probs=29.0
Q ss_pred CcccCCCCCC--CccHHHHhhhhccccCC-----CCCceecCCcccchh
Q 026824 45 PDFPCPYCYE--DFDIASLCSHLEDEHSC-----ESKVTVCPICSVKVA 86 (232)
Q Consensus 45 ~~F~CPfC~e--~~d~~~L~~H~~~eH~~-----e~~~vvCPVCa~~v~ 86 (232)
..|.|+.|-+ +-=.-..|-|+---|+. -.+..-||+|.+++.
T Consensus 214 ~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred cccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 3799999988 33444567777666664 234556999999863
No 211
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.48 E-value=25 Score=34.07 Aligned_cols=44 Identities=25% Similarity=0.548 Sum_probs=24.9
Q ss_pred CCCCcccCCCCCCCccHHH--HhhhhccccCCC---CCceecCCcccch
Q 026824 42 DVRPDFPCPYCYEDFDIAS--LCSHLEDEHSCE---SKVTVCPICSVKV 85 (232)
Q Consensus 42 d~~~~F~CPfC~e~~d~~~--L~~H~~~eH~~e---~~~vvCPVCa~~v 85 (232)
++...|.||.|.+.|.... =|.|.-=..|.. .....||+|-..+
T Consensus 22 ~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~ 70 (397)
T TIGR00599 22 PLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAED 70 (397)
T ss_pred ccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCcc
Confidence 3456899999988554432 244422111110 1234799998854
No 212
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=21.42 E-value=59 Score=26.09 Aligned_cols=17 Identities=29% Similarity=0.667 Sum_probs=14.3
Q ss_pred CCCCCCCCcccCCCCCC
Q 026824 38 EVEDDVRPDFPCPYCYE 54 (232)
Q Consensus 38 ~~ddd~~~~F~CPfC~e 54 (232)
..|.|++.+..||.||.
T Consensus 42 a~eAevP~~WeC~~cG~ 58 (105)
T PF13397_consen 42 AAEAEVPATWECPRCGL 58 (105)
T ss_pred cccCCCCCceeCCCCCC
Confidence 35678899999999998
No 213
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.33 E-value=54 Score=33.75 Aligned_cols=39 Identities=18% Similarity=0.445 Sum_probs=22.4
Q ss_pred cccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhh
Q 026824 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (232)
Q Consensus 46 ~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~ 87 (232)
.-.||.||..+.. .-|-+|-.+-+.+ ...||-|-..++.
T Consensus 15 akFC~~CG~~l~~-~~Cp~CG~~~~~~--~~fC~~CG~~~~~ 53 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQCGTEVPVD--EAHCPNCGAETGT 53 (645)
T ss_pred CccccccCCCCCC-CcCCCCCCCCCcc--cccccccCCcccc
Confidence 3457777775543 2466665554433 3368888776543
No 214
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=21.18 E-value=37 Score=24.17 Aligned_cols=10 Identities=30% Similarity=0.959 Sum_probs=4.0
Q ss_pred CcccCCCCCC
Q 026824 45 PDFPCPYCYE 54 (232)
Q Consensus 45 ~~F~CPfC~e 54 (232)
..|+||.||.
T Consensus 32 r~y~Cp~CgA 41 (55)
T PF05741_consen 32 RKYVCPICGA 41 (55)
T ss_dssp GG---TTT--
T ss_pred hcCcCCCCcC
Confidence 4699999998
No 215
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=21.07 E-value=54 Score=29.57 Aligned_cols=27 Identities=22% Similarity=0.525 Sum_probs=17.3
Q ss_pred ccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccc
Q 026824 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 47 F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
=-||+||..+... .+....+||-|...
T Consensus 100 ~fC~~CG~~~~~~-----------~~~~~~~C~~c~~~ 126 (256)
T PRK00241 100 RFCGYCGHPMHPS-----------KTEWAMLCPHCRER 126 (256)
T ss_pred ccccccCCCCeec-----------CCceeEECCCCCCE
Confidence 4699999855432 12345678888754
No 216
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=20.94 E-value=41 Score=29.48 Aligned_cols=19 Identities=32% Similarity=0.695 Sum_probs=16.0
Q ss_pred ecCCcccch--hhhhhhhhhc
Q 026824 77 VCPICSVKV--ARDMLSHITL 95 (232)
Q Consensus 77 vCPVCa~~v--~~d~i~Hl~~ 95 (232)
.|-||...| +.||+.||+.
T Consensus 77 yCdVCdcvvKDSinflDHiNg 97 (193)
T KOG4727|consen 77 YCDVCDCVVKDSINFLDHING 97 (193)
T ss_pred eeeecceeehhhHHHHHHhcc
Confidence 399998887 7799999963
No 217
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=20.92 E-value=37 Score=26.24 Aligned_cols=36 Identities=33% Similarity=0.555 Sum_probs=23.4
Q ss_pred cCCCCCC-CccH---HHHhhhhccccCC------CCCceecCCccc
Q 026824 48 PCPYCYE-DFDI---ASLCSHLEDEHSC------ESKVTVCPICSV 83 (232)
Q Consensus 48 ~CPfC~e-~~d~---~~L~~H~~~eH~~------e~~~vvCPVCa~ 83 (232)
.||-|.. +-+- -+-|.|.--.|+. +..+..||+|..
T Consensus 34 ~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~ 79 (85)
T PF12861_consen 34 CCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQ 79 (85)
T ss_pred CCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCC
Confidence 4888877 5443 2457777666653 344689999965
No 218
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.85 E-value=48 Score=33.98 Aligned_cols=39 Identities=23% Similarity=0.369 Sum_probs=22.4
Q ss_pred CCcccCCCCCCCcc----HHHHhhhhccccCCCCCceecCCcccc
Q 026824 44 RPDFPCPYCYEDFD----IASLCSHLEDEHSCESKVTVCPICSVK 84 (232)
Q Consensus 44 ~~~F~CPfC~e~~d----~~~L~~H~~~eH~~e~~~vvCPVCa~~ 84 (232)
...+.||.|+..+. ...|.||--... ....-.||.|-..
T Consensus 388 g~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~--~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 388 GWVAECPHCDASLTLHRFQRRLRCHHCGYQ--EPIPKACPECGST 430 (679)
T ss_pred cCccCCCCCCCceeEECCCCeEECCCCcCC--CCCCCCCCCCcCC
Confidence 44678999988543 334544432211 1224579999664
No 219
>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=20.41 E-value=49 Score=27.96 Aligned_cols=11 Identities=27% Similarity=0.996 Sum_probs=8.5
Q ss_pred CceecCCcccc
Q 026824 74 KVTVCPICSVK 84 (232)
Q Consensus 74 ~~vvCPVCa~~ 84 (232)
+.+.||||-..
T Consensus 31 glv~CP~Cgs~ 41 (148)
T PF06676_consen 31 GLVSCPVCGST 41 (148)
T ss_pred CCccCCCCCCC
Confidence 56889999663
No 220
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=20.37 E-value=42 Score=23.95 Aligned_cols=41 Identities=24% Similarity=0.610 Sum_probs=29.7
Q ss_pred CcccCCCCCC--CccHHHHhhhhccccCCCC-CceecCCcccch
Q 026824 45 PDFPCPYCYE--DFDIASLCSHLEDEHSCES-KVTVCPICSVKV 85 (232)
Q Consensus 45 ~~F~CPfC~e--~~d~~~L~~H~~~eH~~e~-~~vvCPVCa~~v 85 (232)
...+|=+|++ ..-+..=|.|+.=.++++. +.--||+|-..+
T Consensus 6 ~~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~~rYngCPfC~~~~ 49 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKGTVLPCGHLICDNCFPGERYNGCPFCGTPF 49 (55)
T ss_pred cceeEEEccccccccccccccceeeccccChhhccCCCCCCCcc
Confidence 3567778877 5556666888888888864 456799997764
No 221
>COG1773 Rubredoxin [Energy production and conversion]
Probab=20.29 E-value=57 Score=23.27 Aligned_cols=14 Identities=36% Similarity=0.859 Sum_probs=11.3
Q ss_pred CCCCCcccCCCCCC
Q 026824 41 DDVRPDFPCPYCYE 54 (232)
Q Consensus 41 dd~~~~F~CPfC~e 54 (232)
+|++..+.||-|+.
T Consensus 31 edlPd~w~CP~Cg~ 44 (55)
T COG1773 31 EDLPDDWVCPECGV 44 (55)
T ss_pred hhCCCccCCCCCCC
Confidence 35677899999986
No 222
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=20.15 E-value=61 Score=28.04 Aligned_cols=41 Identities=20% Similarity=0.502 Sum_probs=26.7
Q ss_pred CcccCCCCCCCccHHHHhhhhccccCCCCCceecCCcccchhhhhh
Q 026824 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDML 90 (232)
Q Consensus 45 ~~F~CPfC~e~~d~~~L~~H~~~eH~~e~~~vvCPVCa~~v~~d~i 90 (232)
....|..|+..+....+..++. +...-.||.|...+..+++
T Consensus 108 ~~~~C~~C~~~~~~~~~~~~~~-----~~~~p~C~~Cg~~lrP~Vv 148 (218)
T cd01407 108 FRVRCTKCGKEYPRDELQADID-----REEVPRCPKCGGLLRPDVV 148 (218)
T ss_pred CcceeCCCcCCCcHHHHhHhhc-----cCCCCcCCCCCCccCCCeE
Confidence 3578999999877776653332 2234579999876544443
No 223
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=20.07 E-value=31 Score=34.07 Aligned_cols=33 Identities=24% Similarity=0.545 Sum_probs=24.7
Q ss_pred CcccCCCCCC-CccHHHHhhhhccccCCCCCcee
Q 026824 45 PDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTV 77 (232)
Q Consensus 45 ~~F~CPfC~e-~~d~~~L~~H~~~eH~~e~~~vv 77 (232)
+.|+|-||-. =|...+|-.|++.-|+.+.++|+
T Consensus 457 q~f~~ky~~atfyss~~ltrhin~~Hpse~rqv~ 490 (500)
T KOG3993|consen 457 QGFTCKYCPATFYSSPGLTRHINKCHPSELRQVA 490 (500)
T ss_pred hccccccchHhhhcCcchHhHhhhcChHHhhhhH
Confidence 4688888866 66777788888888887777664
Done!