Query 027247
Match_columns 226
No_of_seqs 165 out of 209
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 07:07:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027247.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027247hhsearch_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 4.3E-34 9.3E-39 225.1 7.7 102 119-221 1-105 (105)
2 PF05605 zf-Di19: Drought indu 99.8 2E-19 4.4E-24 125.3 2.8 53 48-100 2-54 (54)
3 KOG1280 Uncharacterized conser 98.6 2.7E-08 5.8E-13 92.7 3.0 58 24-88 62-120 (381)
4 COG5216 Uncharacterized conser 94.8 0.013 2.7E-07 42.7 1.0 33 47-88 21-55 (67)
5 KOG2923 Uncharacterized conser 93.9 0.03 6.5E-07 41.2 1.4 47 30-88 7-55 (67)
6 PF09237 GAGA: GAGA factor; I 93.1 0.056 1.2E-06 38.3 1.6 27 75-101 22-50 (54)
7 PF13894 zf-C2H2_4: C2H2-type 92.5 0.049 1.1E-06 30.2 0.6 23 49-71 1-24 (24)
8 PF14354 Lar_restr_allev: Rest 90.6 0.1 2.2E-06 36.4 0.7 31 48-85 3-37 (61)
9 PLN03086 PRLI-interacting fact 90.5 0.2 4.4E-06 50.2 2.9 46 47-97 452-498 (567)
10 PRK09710 lar restriction allev 89.7 0.14 2.9E-06 37.7 0.7 32 47-87 5-37 (64)
11 PF08271 TF_Zn_Ribbon: TFIIB z 89.5 0.1 2.3E-06 34.5 0.0 35 49-93 1-35 (43)
12 PF13913 zf-C2HC_2: zinc-finge 89.3 0.19 4.1E-06 30.0 1.0 20 48-67 2-21 (25)
13 COG5236 Uncharacterized conser 88.8 0.38 8.2E-06 46.1 3.2 32 48-85 220-252 (493)
14 TIGR01206 lysW lysine biosynth 88.6 0.18 4E-06 35.7 0.7 31 48-87 2-32 (54)
15 PHA00732 hypothetical protein 88.5 0.42 9E-06 36.0 2.6 43 49-96 2-45 (79)
16 smart00834 CxxC_CXXC_SSSS Puta 88.2 0.25 5.5E-06 31.5 1.1 33 47-87 4-36 (41)
17 smart00531 TFIIE Transcription 88.1 0.39 8.4E-06 39.6 2.5 37 47-88 98-134 (147)
18 PF12756 zf-C2H2_2: C2H2 type 87.8 0.26 5.7E-06 36.0 1.1 48 50-97 1-72 (100)
19 PF00096 zf-C2H2: Zinc finger, 87.8 0.14 3.1E-06 28.8 -0.2 20 49-68 1-21 (23)
20 KOG2462 C2H2-type Zn-finger pr 87.4 0.36 7.9E-06 44.4 2.1 21 47-67 160-181 (279)
21 PF13909 zf-H2C2_5: C2H2-type 87.3 0.18 3.9E-06 29.0 0.0 24 49-72 1-24 (24)
22 TIGR02098 MJ0042_CXXC MJ0042 f 86.5 0.63 1.4E-05 29.6 2.2 33 49-87 3-35 (38)
23 PF09986 DUF2225: Uncharacteri 86.5 0.29 6.3E-06 42.9 0.9 19 47-65 4-22 (214)
24 KOG1842 FYVE finger-containing 86.2 0.23 5.1E-06 48.5 0.2 33 42-76 11-44 (505)
25 PHA00733 hypothetical protein 85.6 0.92 2E-05 36.9 3.3 51 47-101 72-125 (128)
26 PLN03086 PRLI-interacting fact 85.4 0.61 1.3E-05 46.8 2.7 38 47-87 477-514 (567)
27 PF08274 PhnA_Zn_Ribbon: PhnA 83.5 0.4 8.7E-06 30.2 0.3 24 50-85 4-27 (30)
28 PRK14892 putative transcriptio 83.3 0.58 1.3E-05 36.9 1.2 35 47-89 20-54 (99)
29 TIGR02605 CxxC_CxxC_SSSS putat 83.2 0.65 1.4E-05 31.4 1.3 31 47-85 4-34 (52)
30 PF14255 Cys_rich_CPXG: Cystei 80.4 0.59 1.3E-05 32.8 0.3 34 49-87 1-34 (52)
31 PRK00398 rpoP DNA-directed RNA 80.2 0.83 1.8E-05 30.5 0.9 30 47-87 2-31 (46)
32 PHA02768 hypothetical protein; 78.6 1.2 2.7E-05 31.7 1.4 34 48-85 5-39 (55)
33 cd00350 rubredoxin_like Rubred 78.3 1.2 2.5E-05 28.0 1.1 24 49-85 2-25 (33)
34 smart00734 ZnF_Rad18 Rad18-lik 77.6 1.2 2.6E-05 26.8 1.0 19 50-68 3-21 (26)
35 COG1655 Uncharacterized protei 77.3 0.89 1.9E-05 41.3 0.5 13 47-59 18-30 (267)
36 PF14206 Cys_rich_CPCC: Cystei 77.1 1.1 2.4E-05 34.0 0.9 24 49-83 2-26 (78)
37 PF12760 Zn_Tnp_IS1595: Transp 75.4 1.4 2.9E-05 29.6 0.9 14 43-56 13-26 (46)
38 PF04780 DUF629: Protein of un 75.3 1.5 3.3E-05 43.1 1.5 42 47-88 56-101 (466)
39 PF07754 DUF1610: Domain of un 75.2 1.7 3.7E-05 26.1 1.1 10 47-56 15-24 (24)
40 COG4888 Uncharacterized Zn rib 74.7 1 2.2E-05 35.9 0.1 34 47-85 21-54 (104)
41 KOG2462 C2H2-type Zn-finger pr 74.4 3.5 7.5E-05 38.2 3.5 78 48-132 187-268 (279)
42 cd00729 rubredoxin_SM Rubredox 74.0 2 4.3E-05 27.4 1.3 26 48-86 2-27 (34)
43 PLN03208 E3 ubiquitin-protein 73.7 1.3 2.8E-05 38.9 0.6 43 47-89 17-80 (193)
44 PF09723 Zn-ribbon_8: Zinc rib 73.1 1.8 3.8E-05 28.6 0.9 31 47-85 4-34 (42)
45 PF12756 zf-C2H2_2: C2H2 type 73.0 1.5 3.3E-05 31.9 0.7 25 48-72 50-75 (100)
46 COG2888 Predicted Zn-ribbon RN 71.3 3.3 7.2E-05 30.2 2.1 31 47-84 26-57 (61)
47 smart00504 Ubox Modified RING 71.0 2.9 6.4E-05 28.5 1.7 12 77-88 35-46 (63)
48 PF06957 COPI_C: Coatomer (COP 70.5 1.9 4.1E-05 42.0 0.9 37 44-93 376-413 (422)
49 COG5175 MOT2 Transcriptional r 69.5 1.2 2.6E-05 42.6 -0.6 36 49-86 16-62 (480)
50 TIGR03655 anti_R_Lar restricti 69.3 2 4.4E-05 29.6 0.6 33 49-86 2-35 (53)
51 COG1592 Rubrerythrin [Energy p 68.2 3.8 8.3E-05 35.2 2.2 26 47-86 133-158 (166)
52 PRK14890 putative Zn-ribbon RN 67.6 3.9 8.4E-05 29.6 1.8 31 47-84 24-55 (59)
53 PF05129 Elf1: Transcription e 66.9 2.2 4.7E-05 32.3 0.4 32 47-85 21-54 (81)
54 PRK12495 hypothetical protein; 66.2 3.4 7.3E-05 37.2 1.5 30 47-89 41-70 (226)
55 smart00659 RPOLCX RNA polymera 65.9 4.3 9.3E-05 27.4 1.6 28 48-87 2-29 (44)
56 KOG2932 E3 ubiquitin ligase in 65.9 2.6 5.6E-05 39.9 0.8 58 48-105 90-177 (389)
57 PF13465 zf-H2C2_2: Zinc-finge 65.2 1.8 3.9E-05 25.6 -0.3 11 48-58 14-24 (26)
58 PRK06266 transcription initiat 64.8 5.4 0.00012 34.2 2.5 32 47-88 116-147 (178)
59 PTZ00255 60S ribosomal protein 64.2 3 6.6E-05 32.5 0.8 13 47-59 35-48 (90)
60 PF02176 zf-TRAF: TRAF-type zi 63.4 3.2 6.8E-05 28.4 0.6 46 47-94 8-60 (60)
61 PF14446 Prok-RING_1: Prokaryo 63.3 2.8 6E-05 29.9 0.3 26 48-86 5-30 (54)
62 PF03470 zf-XS: XS zinc finger 62.9 4.4 9.6E-05 27.6 1.3 23 80-102 1-23 (43)
63 PF14279 HNH_5: HNH endonuclea 62.5 2.8 6E-05 31.0 0.3 40 51-95 1-48 (71)
64 PRK03976 rpl37ae 50S ribosomal 61.9 3.5 7.7E-05 32.1 0.7 13 47-59 35-48 (90)
65 TIGR00373 conserved hypothetic 61.6 6.2 0.00013 33.1 2.2 32 47-88 108-139 (158)
66 PF13719 zinc_ribbon_5: zinc-r 61.3 8.3 0.00018 24.8 2.3 31 49-85 3-33 (37)
67 PF12773 DZR: Double zinc ribb 61.3 5.9 0.00013 26.3 1.7 27 50-88 14-40 (50)
68 TIGR00280 L37a ribosomal prote 61.1 3.7 8.1E-05 32.1 0.7 10 47-56 34-43 (91)
69 PF11672 DUF3268: Protein of u 60.9 4.9 0.00011 31.9 1.4 38 49-89 3-43 (102)
70 PRK12496 hypothetical protein; 60.5 4.4 9.6E-05 34.2 1.2 27 48-87 127-153 (164)
71 PF05605 zf-Di19: Drought indu 60.1 6.1 0.00013 27.0 1.6 25 78-102 3-28 (54)
72 PF03145 Sina: Seven in absent 59.8 4 8.7E-05 34.7 0.8 54 47-103 13-75 (198)
73 PF13912 zf-C2H2_6: C2H2-type 59.8 4.6 9.9E-05 23.4 0.8 22 49-70 2-24 (27)
74 PRK00420 hypothetical protein; 59.4 4.7 0.0001 32.5 1.1 28 48-87 23-50 (112)
75 PF07282 OrfB_Zn_ribbon: Putat 59.3 7.4 0.00016 27.5 2.0 38 47-95 27-64 (69)
76 PF10571 UPF0547: Uncharacteri 58.1 6.1 0.00013 23.9 1.2 9 50-58 2-10 (26)
77 PF15616 TerY-C: TerY-C metal 57.8 4.2 9.1E-05 33.7 0.6 39 48-88 77-116 (131)
78 COG4311 SoxD Sarcosine oxidase 57.0 5 0.00011 31.7 0.8 9 48-56 3-11 (97)
79 smart00355 ZnF_C2H2 zinc finge 56.9 5.7 0.00012 21.6 0.9 20 49-68 1-21 (26)
80 PHA00616 hypothetical protein 56.6 3 6.5E-05 28.5 -0.4 24 49-72 2-26 (44)
81 PF01780 Ribosomal_L37ae: Ribo 56.3 4.1 8.9E-05 31.8 0.3 10 47-56 34-43 (90)
82 KOG3623 Homeobox transcription 56.1 3.3 7E-05 43.3 -0.4 49 47-95 209-260 (1007)
83 PRK00464 nrdR transcriptional 56.1 7.6 0.00017 32.8 1.9 33 49-87 1-38 (154)
84 PF08996 zf-DNA_Pol: DNA Polym 55.4 3.7 7.9E-05 35.2 -0.2 40 47-88 17-56 (188)
85 PF04564 U-box: U-box domain; 54.6 8.9 0.00019 27.8 1.8 37 47-89 3-51 (73)
86 PF13395 HNH_4: HNH endonuclea 53.8 7.2 0.00016 26.8 1.1 14 51-64 1-14 (54)
87 COG4049 Uncharacterized protei 53.2 4.9 0.00011 29.2 0.2 26 79-104 19-46 (65)
88 KOG2879 Predicted E3 ubiquitin 52.5 5.3 0.00011 37.1 0.4 41 47-87 238-286 (298)
89 TIGR00686 phnA alkylphosphonat 52.3 6.9 0.00015 31.6 0.9 24 50-85 4-27 (109)
90 KOG0320 Predicted E3 ubiquitin 52.2 4 8.7E-05 35.7 -0.4 44 46-89 129-179 (187)
91 smart00507 HNHc HNH nucleases. 52.0 4.9 0.00011 25.5 0.1 21 49-69 11-31 (52)
92 PF13248 zf-ribbon_3: zinc-rib 51.7 9.5 0.00021 22.6 1.3 10 49-58 3-12 (26)
93 PF05207 zf-CSL: CSL zinc fing 51.7 5.5 0.00012 27.9 0.3 46 31-88 4-51 (55)
94 PF13240 zinc_ribbon_2: zinc-r 51.3 6.6 0.00014 23.0 0.5 7 51-57 2-8 (23)
95 PRK03824 hypA hydrogenase nick 50.9 9.1 0.0002 31.3 1.5 40 47-86 69-116 (135)
96 TIGR00100 hypA hydrogenase nic 50.5 7.4 0.00016 31.0 0.9 27 47-86 69-95 (115)
97 KOG2593 Transcription initiati 50.0 6.3 0.00014 38.5 0.5 33 47-86 127-162 (436)
98 PF09538 FYDLN_acid: Protein o 49.8 9.4 0.0002 30.5 1.4 28 47-87 8-36 (108)
99 PF08209 Sgf11: Sgf11 (transcr 49.6 8.2 0.00018 24.7 0.8 21 47-67 3-23 (33)
100 PF09862 DUF2089: Protein of u 49.4 5.1 0.00011 32.4 -0.2 62 51-120 1-66 (113)
101 COG0675 Transposase and inacti 48.7 12 0.00025 32.7 1.9 34 47-96 308-341 (364)
102 CHL00174 accD acetyl-CoA carbo 48.0 11 0.00025 35.0 1.8 28 49-86 39-66 (296)
103 PF13717 zinc_ribbon_4: zinc-r 47.9 19 0.00042 23.0 2.4 31 49-85 3-33 (36)
104 PRK11088 rrmA 23S rRNA methylt 47.6 8 0.00017 34.2 0.7 32 48-79 2-34 (272)
105 PRK03922 hypothetical protein; 46.9 9.2 0.0002 31.0 0.9 16 48-63 49-64 (113)
106 TIGR00515 accD acetyl-CoA carb 46.7 14 0.0003 34.1 2.1 30 43-86 25-54 (285)
107 KOG0402 60S ribosomal protein 46.4 6 0.00013 30.8 -0.2 11 46-56 34-44 (92)
108 PF07191 zinc-ribbons_6: zinc- 45.8 4.8 0.0001 30.1 -0.8 53 50-106 3-62 (70)
109 PHA02565 49 recombination endo 45.7 11 0.00023 32.3 1.1 42 47-88 19-66 (157)
110 PF02146 SIR2: Sir2 family; I 45.0 11 0.00023 31.5 1.1 41 47-92 104-144 (178)
111 PRK05654 acetyl-CoA carboxylas 44.8 14 0.0003 34.2 1.8 30 43-86 26-55 (292)
112 PF04475 DUF555: Protein of un 44.8 10 0.00022 30.2 0.9 16 48-63 47-62 (102)
113 KOG2817 Predicted E3 ubiquitin 44.3 14 0.00029 35.9 1.7 15 47-61 373-387 (394)
114 COG1645 Uncharacterized Zn-fin 44.3 11 0.00024 31.3 1.0 25 48-85 28-52 (131)
115 TIGR00244 transcriptional regu 43.4 13 0.00028 31.5 1.3 32 50-88 2-39 (147)
116 PRK12380 hydrogenase nickel in 42.9 12 0.00026 29.7 1.0 26 47-85 69-94 (113)
117 COG1198 PriA Primosomal protei 42.7 13 0.00027 38.7 1.4 38 47-86 443-484 (730)
118 PF05876 Terminase_GpA: Phage 42.7 15 0.00033 36.6 1.9 41 47-89 199-241 (557)
119 PF10058 DUF2296: Predicted in 42.7 13 0.00029 26.1 1.1 10 47-56 43-52 (54)
120 PF14616 DUF4451: Domain of un 42.2 16 0.00034 29.6 1.6 27 77-103 25-56 (124)
121 PF01155 HypA: Hydrogenase exp 42.1 10 0.00022 30.0 0.4 27 47-86 69-95 (113)
122 COG4391 Uncharacterized protei 41.9 11 0.00024 27.6 0.6 12 47-58 47-58 (62)
123 PF12660 zf-TFIIIC: Putative z 41.0 8.2 0.00018 30.0 -0.2 38 50-87 16-65 (99)
124 TIGR00570 cdk7 CDK-activating 41.0 11 0.00023 35.5 0.5 40 48-88 3-54 (309)
125 PF09706 Cas_CXXC_CXXC: CRISPR 40.9 11 0.00024 27.5 0.5 10 47-56 4-13 (69)
126 COG1327 Predicted transcriptio 40.3 15 0.00032 31.4 1.2 32 50-88 2-39 (156)
127 COG5189 SFP1 Putative transcri 40.3 14 0.0003 35.4 1.1 40 48-87 349-408 (423)
128 COG1499 NMD3 NMD protein affec 38.9 15 0.00032 35.0 1.1 38 47-84 5-50 (355)
129 PF04981 NMD3: NMD3 family ; 38.8 19 0.00041 31.8 1.7 23 196-218 145-168 (236)
130 PF14311 DUF4379: Domain of un 38.7 22 0.00048 24.3 1.7 29 47-83 27-55 (55)
131 PF09334 tRNA-synt_1g: tRNA sy 38.5 13 0.00028 35.4 0.6 40 49-88 137-177 (391)
132 COG5109 Uncharacterized conser 38.1 16 0.00035 34.8 1.2 11 47-57 375-385 (396)
133 PRK11595 DNA utilization prote 36.8 16 0.00034 31.9 0.9 34 50-85 7-42 (227)
134 PRK10220 hypothetical protein; 36.7 21 0.00046 28.9 1.5 24 50-85 5-28 (111)
135 PF12230 PRP21_like_P: Pre-mRN 36.5 12 0.00025 32.8 0.0 21 77-97 168-189 (229)
136 PF02892 zf-BED: BED zinc fing 36.5 8.9 0.00019 24.8 -0.6 25 47-71 15-44 (45)
137 PF14634 zf-RING_5: zinc-RING 36.4 18 0.00038 23.6 0.8 10 75-84 34-43 (44)
138 PF14353 CpXC: CpXC protein 36.3 19 0.0004 28.5 1.1 28 48-79 38-65 (128)
139 PRK04023 DNA polymerase II lar 36.0 22 0.00047 38.6 1.8 35 184-218 778-812 (1121)
140 TIGR02300 FYDLN_acid conserved 35.8 23 0.0005 29.4 1.6 28 47-87 8-36 (129)
141 PF09855 DUF2082: Nucleic-acid 35.3 13 0.00029 27.1 0.1 35 49-84 1-43 (64)
142 PF04423 Rad50_zn_hook: Rad50 35.0 14 0.0003 25.3 0.2 13 50-62 22-34 (54)
143 COG1405 SUA7 Transcription ini 34.6 23 0.00051 32.7 1.6 37 49-95 2-38 (285)
144 PF01844 HNH: HNH endonuclease 34.6 10 0.00023 24.3 -0.5 35 51-85 1-42 (47)
145 smart00661 RPOL9 RNA polymeras 34.6 22 0.00048 23.5 1.1 27 50-85 2-28 (52)
146 smart00451 ZnF_U1 U1-like zinc 34.5 26 0.00057 21.1 1.4 21 48-68 3-24 (35)
147 TIGR03830 CxxCG_CxxCG_HTH puta 34.4 16 0.00035 28.2 0.5 37 51-87 1-41 (127)
148 PF14570 zf-RING_4: RING/Ubox 34.3 10 0.00022 26.3 -0.5 32 47-85 14-45 (48)
149 cd00162 RING RING-finger (Real 33.8 7.9 0.00017 23.6 -1.1 11 76-86 34-44 (45)
150 PRK05477 gatB aspartyl/glutamy 33.8 23 0.00049 35.1 1.5 22 67-88 27-48 (474)
151 KOG2231 Predicted E3 ubiquitin 33.6 25 0.00053 36.4 1.7 26 48-73 182-208 (669)
152 PF12171 zf-C2H2_jaz: Zinc-fin 33.4 29 0.00063 20.2 1.4 20 49-68 2-22 (27)
153 PF04267 SoxD: Sarcosine oxida 33.1 13 0.00027 28.7 -0.3 8 49-56 2-9 (84)
154 KOG2177 Predicted E3 ubiquitin 32.1 6.5 0.00014 32.6 -2.2 38 47-84 12-54 (386)
155 smart00782 PhnA_Zn_Ribbon PhnA 31.9 16 0.00034 25.2 0.0 39 47-87 6-46 (47)
156 PF13824 zf-Mss51: Zinc-finger 31.9 21 0.00045 25.5 0.7 10 47-56 13-22 (55)
157 TIGR01374 soxD sarcosine oxida 31.4 21 0.00046 27.5 0.7 8 49-56 2-9 (84)
158 KOG3214 Uncharacterized Zn rib 31.3 19 0.00042 28.9 0.5 34 47-85 22-55 (109)
159 TIGR03278 methan_mark_10 putat 31.0 26 0.00057 33.8 1.4 34 47-86 9-45 (404)
160 PRK14714 DNA polymerase II lar 31.0 30 0.00064 38.3 1.9 35 184-218 825-859 (1337)
161 KOG3608 Zn finger proteins [Ge 30.6 36 0.00078 33.1 2.2 48 48-96 263-313 (467)
162 PRK14714 DNA polymerase II lar 30.6 34 0.00074 37.9 2.3 37 48-89 667-704 (1337)
163 PHA00626 hypothetical protein 30.5 32 0.0007 24.9 1.4 37 50-93 2-39 (59)
164 COG1675 TFA1 Transcription ini 30.0 32 0.0007 29.8 1.7 31 47-87 112-142 (176)
165 PF10276 zf-CHCC: Zinc-finger 29.7 21 0.00046 23.8 0.4 9 48-56 29-37 (40)
166 COG0777 AccD Acetyl-CoA carbox 29.7 42 0.00092 31.3 2.4 30 43-86 27-56 (294)
167 PRK03681 hypA hydrogenase nick 29.0 21 0.00046 28.4 0.3 14 47-60 69-82 (114)
168 PF13453 zf-TFIIB: Transcripti 28.6 20 0.00044 23.2 0.1 26 50-84 1-26 (41)
169 PRK00423 tfb transcription ini 28.3 28 0.00061 32.0 1.1 38 47-94 10-47 (310)
170 smart00614 ZnF_BED BED zinc fi 28.1 22 0.00047 23.9 0.2 26 47-72 17-48 (50)
171 PF12230 PRP21_like_P: Pre-mRN 27.7 20 0.00043 31.3 0.0 21 48-68 168-188 (229)
172 KOG1705 Uncharacterized conser 27.5 26 0.00057 27.8 0.6 39 48-88 27-65 (110)
173 PRK00564 hypA hydrogenase nick 27.5 31 0.00067 27.5 1.0 27 47-85 70-96 (117)
174 PF00097 zf-C3HC4: Zinc finger 27.3 6.5 0.00014 24.8 -2.4 6 78-83 36-41 (41)
175 PF03966 Trm112p: Trm112p-like 27.1 34 0.00074 24.4 1.1 19 47-65 6-24 (68)
176 PF14369 zf-RING_3: zinc-finge 27.0 30 0.00065 22.2 0.7 10 49-58 22-31 (35)
177 PF03604 DNA_RNApol_7kD: DNA d 27.0 35 0.00075 21.6 1.0 27 49-87 1-27 (32)
178 PF04780 DUF629: Protein of un 26.8 26 0.00056 34.7 0.6 48 57-104 20-86 (466)
179 PLN02751 glutamyl-tRNA(Gln) am 26.7 35 0.00075 34.4 1.4 20 69-88 85-104 (544)
180 KOG0978 E3 ubiquitin ligase in 26.4 20 0.00044 37.1 -0.2 43 47-89 642-690 (698)
181 KOG4080 Mitochondrial ribosoma 26.1 26 0.00056 30.4 0.4 25 48-88 93-117 (176)
182 KOG0804 Cytoplasmic Zn-finger 26.0 19 0.00041 35.7 -0.5 35 48-84 175-218 (493)
183 PF11290 DUF3090: Protein of u 25.9 33 0.00071 29.8 1.0 14 49-62 155-168 (171)
184 COG1885 Uncharacterized protei 25.6 33 0.00072 27.7 0.9 17 48-64 49-65 (115)
185 PRK09678 DNA-binding transcrip 25.5 32 0.00068 25.7 0.7 8 49-56 2-9 (72)
186 PF02934 GatB_N: GatB/GatE cat 25.3 41 0.00088 31.3 1.5 26 63-88 18-43 (289)
187 TIGR01405 polC_Gram_pos DNA po 25.2 44 0.00094 36.8 1.9 47 29-87 671-718 (1213)
188 TIGR00133 gatB glutamyl-tRNA(G 24.9 39 0.00086 33.4 1.5 15 74-88 34-48 (478)
189 TIGR00599 rad18 DNA repair pro 24.8 20 0.00044 34.7 -0.6 42 47-88 25-71 (397)
190 cd00730 rubredoxin Rubredoxin; 24.8 36 0.00079 23.5 0.9 10 47-56 33-42 (50)
191 KOG4696 Uncharacterized conser 23.9 32 0.00069 32.7 0.6 24 48-72 2-25 (393)
192 PHA02929 N1R/p28-like protein; 23.9 19 0.00042 32.5 -0.8 41 47-87 173-226 (238)
193 PRK14873 primosome assembly pr 23.6 41 0.00089 34.5 1.3 37 47-86 391-431 (665)
194 PRK05978 hypothetical protein; 23.6 35 0.00076 28.8 0.7 28 48-86 33-61 (148)
195 PRK00762 hypA hydrogenase nick 23.6 30 0.00065 27.9 0.3 8 49-56 93-100 (124)
196 PF15135 UPF0515: Uncharacteri 23.4 39 0.00085 31.2 1.0 18 43-60 150-167 (278)
197 PF12013 DUF3505: Protein of u 23.4 53 0.0011 25.3 1.6 29 74-102 8-37 (109)
198 COG0178 UvrA Excinuclease ATPa 23.0 36 0.00078 36.3 0.8 34 47-85 244-277 (935)
199 COG1996 RPC10 DNA-directed RNA 22.9 50 0.0011 23.1 1.2 30 47-87 5-34 (49)
200 KOG1002 Nucleotide excision re 22.8 28 0.00061 35.5 0.0 49 47-95 535-593 (791)
201 COG2331 Uncharacterized protei 22.5 33 0.00071 26.3 0.3 46 47-105 11-56 (82)
202 PRK00448 polC DNA polymerase I 22.5 52 0.0011 36.9 1.9 47 29-87 896-943 (1437)
203 cd03021 DsbA_GSTK DsbA family, 22.4 19 0.00041 30.5 -1.1 12 47-58 7-18 (209)
204 PF08273 Prim_Zn_Ribbon: Zinc- 22.4 37 0.0008 22.6 0.5 8 49-56 4-11 (40)
205 KOG1100 Predicted E3 ubiquitin 22.2 36 0.00078 29.9 0.6 37 51-87 161-199 (207)
206 KOG3608 Zn finger proteins [Ge 22.2 51 0.0011 32.1 1.6 56 48-103 319-380 (467)
207 PF00301 Rubredoxin: Rubredoxi 21.7 42 0.00091 23.0 0.7 10 47-56 33-42 (47)
208 TIGR01562 FdhE formate dehydro 21.5 46 0.001 31.1 1.2 9 48-56 184-192 (305)
209 COG1656 Uncharacterized conser 21.5 64 0.0014 27.8 1.9 39 50-88 99-141 (165)
210 PRK01546 hypothetical protein; 21.3 89 0.0019 23.9 2.4 29 196-224 20-57 (79)
211 PF03833 PolC_DP2: DNA polymer 21.2 32 0.00069 36.6 0.0 38 48-89 655-692 (900)
212 PF06676 DUF1178: Protein of u 21.2 50 0.0011 27.9 1.2 10 76-85 31-40 (148)
213 PRK14559 putative protein seri 21.2 61 0.0013 33.3 2.0 37 50-90 3-40 (645)
214 cd01407 SIR2-fam SIR2 family o 21.2 57 0.0012 28.1 1.6 40 47-91 108-147 (218)
215 COG1997 RPL43A Ribosomal prote 21.1 31 0.00066 27.0 -0.1 13 43-57 32-44 (89)
216 KOG2324 Prolyl-tRNA synthetase 21.1 64 0.0014 31.6 2.0 44 47-103 226-272 (457)
217 PF09889 DUF2116: Uncharacteri 21.0 51 0.0011 23.7 1.0 12 49-60 4-15 (59)
218 PF06221 zf-C2HC5: Putative zi 20.7 48 0.001 23.7 0.8 10 48-57 35-44 (57)
219 PF10609 ParA: ParA/MinD ATPas 20.7 39 0.00085 25.7 0.4 14 47-60 64-77 (81)
220 TIGR00618 sbcc exonuclease Sbc 20.6 32 0.00069 36.6 -0.2 34 47-87 500-534 (1042)
221 PF05979 DUF896: Bacterial pro 20.6 49 0.0011 24.3 0.9 29 196-224 17-54 (65)
222 KOG3002 Zn finger protein [Gen 20.5 38 0.00082 31.5 0.4 42 47-88 47-91 (299)
223 cd03024 DsbA_FrnE DsbA family, 20.5 26 0.00057 28.8 -0.7 21 47-67 5-26 (201)
224 cd03019 DsbA_DsbA DsbA family, 20.4 36 0.00077 27.2 0.1 18 47-64 23-41 (178)
225 COG3058 FdhE Uncharacterized p 20.4 36 0.00078 31.9 0.2 18 76-93 184-201 (308)
226 PRK02539 hypothetical protein; 20.1 95 0.0021 24.1 2.4 29 196-224 19-56 (85)
No 1
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=100.00 E-value=4.3e-34 Score=225.14 Aligned_cols=102 Identities=51% Similarity=0.661 Sum_probs=83.4
Q ss_pred chhhhhHHHHhhhhhhhccCC-CCCCCCCCCCCCCccc-cccCCCCCCCcCccCCCCCCCC-CCCCCCcccccccccccC
Q 027247 119 TISSLRKELQNAHFQSLLARS-SSSVSSSKKTSDPWLS-FIYNMPTADESESIQPALSTGE-GAEDKSSCEKTFETNAQQ 195 (226)
Q Consensus 119 ~~s~l~k~lre~~lq~llgg~-s~~~~~sn~~pDPLLS-Fi~n~~~~d~~~~~~p~~s~e~-~~~~~~s~~~~~e~~~~~ 195 (226)
|+|+|+|||||||||+||||+ +++.+++|++|||||| ||||+|.++.++.+++....++ ...++....+.+++.+ +
T Consensus 1 tlsll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~s~-~ 79 (105)
T PF14571_consen 1 TLSLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFPAPEAEEPSKSSSSSEEKKSSKKSSSEQNVKSSA-D 79 (105)
T ss_pred CcchhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCCCccccccCCccccccccccccccchhccccccc-C
Confidence 689999999999999999998 6667789999999999 9999999998888887655442 2222233334444444 3
Q ss_pred CCCCHHHHHHHHhHhhHHHHHHHhhh
Q 027247 196 SSLSNEDHLEKANRSNFAQGLLFSTI 221 (226)
Q Consensus 196 ~~ls~ed~eEk~~R~eFVQ~LllSTi 221 (226)
++|++||+|||+||++||||||||||
T Consensus 80 ~~lS~ee~eEk~~RseFVQ~LllSTI 105 (105)
T PF14571_consen 80 SSLSDEEQEEKAQRSEFVQGLLLSTI 105 (105)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhC
Confidence 89999999999999999999999998
No 2
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=99.76 E-value=2e-19 Score=125.33 Aligned_cols=53 Identities=38% Similarity=0.898 Sum_probs=51.7
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcchhhHhhhhhccc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHITTQHG 100 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~i~Hl~~qH~ 100 (226)
+|+||||+++||+.+|+.|+.++|..+.+++|||||+.+++.||++||+.+|+
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 69999999999999999999999999999999999999999999999999996
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=98.58 E-value=2.7e-08 Score=92.72 Aligned_cols=58 Identities=26% Similarity=0.558 Sum_probs=52.8
Q ss_pred ccccccCCccCCCcchhhhccCcceeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 24 QFADFCIDFEDIEEDDYEEVKGEYEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 24 ~~d~~~~~~e~~~~d~d~e~~~~~~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
.||+ |+|+|-+--+++ ..|+||||+. +|....+.+|+..+|+.....+|||||+..+.
T Consensus 62 dfeL-~f~Ge~i~~y~~------qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~ 120 (381)
T KOG1280|consen 62 DFEL-YFGGEPISHYDP------QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPE 120 (381)
T ss_pred ceee-EecCcccccccc------ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcc
Confidence 4777 888888888888 7899999999 99999999999999999999999999999764
No 4
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.75 E-value=0.013 Score=42.72 Aligned_cols=33 Identities=33% Similarity=0.837 Sum_probs=23.5
Q ss_pred ceeeCCCCCC--CccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 47 YEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 47 ~~f~CPfC~e--~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
-+|||| ||. ++.+..|. ..-..++||-|+-.+-
T Consensus 21 ftyPCP-CGDRFeIsLeDl~--------~GE~VArCPSCSLiv~ 55 (67)
T COG5216 21 FTYPCP-CGDRFEISLEDLR--------NGEVVARCPSCSLIVC 55 (67)
T ss_pred EEecCC-CCCEeEEEHHHhh--------CCceEEEcCCceEEEE
Confidence 589999 998 55555553 2345689999987653
No 5
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.92 E-value=0.03 Score=41.17 Aligned_cols=47 Identities=32% Similarity=0.716 Sum_probs=29.5
Q ss_pred CCccCCCcchhhhccCcceeeCCCCCCC--ccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 30 IDFEDIEEDDYEEVKGEYEYPCPFCSED--FDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 30 ~~~e~~~~d~d~e~~~~~~f~CPfC~e~--~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
+.++|++=|+|. -. .+|||| ||.- +....|. ..-..+.||-|+-.+.
T Consensus 7 Veiedfe~~~e~-~~--y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 7 VEIEDFEFDEEN-QT--YYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLIIR 55 (67)
T ss_pred EEeecceeccCC-Ce--EEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEEE
Confidence 445666644441 12 589999 9984 4444553 2345688999988664
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=93.06 E-value=0.056 Score=38.31 Aligned_cols=27 Identities=19% Similarity=0.575 Sum_probs=18.5
Q ss_pred CccccCCccccCcc--hhhHhhhhhcccc
Q 027247 75 AKSGVCPVCVTRVT--MDMVDHITTQHGN 101 (226)
Q Consensus 75 ~~~vvCPVC~~~v~--~d~i~Hl~~qH~~ 101 (226)
.....||+|.+.+. +|+-+|+-+.|+.
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 34579999998765 7999999988875
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=92.50 E-value=0.049 Score=30.22 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=14.2
Q ss_pred eeCCCCCC-CccHhhhhhcccccC
Q 027247 49 YPCPFCSE-DFDLVGLCCHIDEEH 71 (226)
Q Consensus 49 f~CPfC~e-~~dv~~L~~H~~~eH 71 (226)
|.||+|+. --+...|..|+...|
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 67888888 556667777765544
No 8
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=90.64 E-value=0.1 Score=36.41 Aligned_cols=31 Identities=26% Similarity=0.487 Sum_probs=19.7
Q ss_pred eeeCCCCCC-CccHhhhhhcccccCCCCC---ccccCCcccc
Q 027247 48 EYPCPFCSE-DFDLVGLCCHIDEEHPVEA---KSGVCPVCVT 85 (226)
Q Consensus 48 ~f~CPfC~e-~~dv~~L~~H~~~eH~~e~---~~vvCPVC~~ 85 (226)
..+|||||. .+.+... ..... ..|.|..|.+
T Consensus 3 LkPCPFCG~~~~~~~~~-------~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQD-------EGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeecc-------cCCCCCCEEEEEcCCCCC
Confidence 468999997 5544432 12111 5678999976
No 9
>PLN03086 PRLI-interacting factor K; Provisional
Probab=90.54 E-value=0.2 Score=50.17 Aligned_cols=46 Identities=24% Similarity=0.456 Sum_probs=35.9
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc-chhhHhhhhh
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV-TMDMVDHITT 97 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v-~~d~i~Hl~~ 97 (226)
.-+.||+|++.|....|-.|....| +.+.|| |...+ ..++..|++.
T Consensus 452 ~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~t 498 (567)
T PLN03086 452 NHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQAS 498 (567)
T ss_pred cCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhhc
Confidence 4568999999888899999987755 678999 96543 3588888754
No 10
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=89.71 E-value=0.14 Score=37.66 Aligned_cols=32 Identities=25% Similarity=0.523 Sum_probs=22.2
Q ss_pred ceeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
..-||||||. .+.+. |..-...++|.-|.+..
T Consensus 5 ~lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 5 NVKPCPFCGCPSVTVK---------AISGYYRAKCNGCESRT 37 (64)
T ss_pred cccCCCCCCCceeEEE---------ecCceEEEEcCCCCcCc
Confidence 4569999999 65554 23334459999997753
No 11
>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=89.54 E-value=0.1 Score=34.47 Aligned_cols=35 Identities=26% Similarity=0.584 Sum_probs=22.3
Q ss_pred eeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcchhhHh
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVD 93 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~i~ 93 (226)
|.||.|+... + +.+ ......||+.|...+..+.+.
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 2 111 445678999998777655543
No 12
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=89.25 E-value=0.19 Score=30.01 Aligned_cols=20 Identities=35% Similarity=0.685 Sum_probs=17.9
Q ss_pred eeeCCCCCCCccHhhhhhcc
Q 027247 48 EYPCPFCSEDFDLVGLCCHI 67 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~ 67 (226)
..+||+||.-|....|-.|.
T Consensus 2 l~~C~~CgR~F~~~~l~~H~ 21 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHE 21 (25)
T ss_pred CCcCCCCCCEECHHHHHHHH
Confidence 46899999999999999986
No 13
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=88.83 E-value=0.38 Score=46.11 Aligned_cols=32 Identities=28% Similarity=0.480 Sum_probs=26.0
Q ss_pred eeeCCCCCC-CccHhhhhhcccccCCCCCccccCCcccc
Q 027247 48 EYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 48 ~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
-=.|-||.. =+|-.+|..||...| -.|-||..
T Consensus 220 HP~C~FC~~~FYdDDEL~~HcR~~H------E~ChICD~ 252 (493)
T COG5236 220 HPLCIFCKIYFYDDDELRRHCRLRH------EACHICDM 252 (493)
T ss_pred CchhhhccceecChHHHHHHHHhhh------hhhhhhhc
Confidence 347999999 889999999999888 35777754
No 14
>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=88.63 E-value=0.18 Score=35.66 Aligned_cols=31 Identities=19% Similarity=0.569 Sum_probs=22.4
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
.|.||-||..+++.... ..-.+.||.|.+.+
T Consensus 2 ~~~CP~CG~~iev~~~~---------~GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIELENPE---------LGELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEecCCCc---------cCCEEeCCCCCCEE
Confidence 48999999988765543 13367999997753
No 15
>PHA00732 hypothetical protein
Probab=88.52 E-value=0.42 Score=36.03 Aligned_cols=43 Identities=28% Similarity=0.634 Sum_probs=32.3
Q ss_pred eeCCCCCCCc-cHhhhhhcccccCCCCCccccCCccccCcchhhHhhhh
Q 027247 49 YPCPFCSEDF-DLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHIT 96 (226)
Q Consensus 49 f~CPfC~e~~-dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~i~Hl~ 96 (226)
|.|+.|+..| ....|..|....|.. ..|++|...-. ++..|++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~----~~C~~CgKsF~-~l~~H~~ 45 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL----TKCPVCNKSYR-RLNQHFY 45 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC----CccCCCCCEeC-Chhhhhc
Confidence 7899999954 788899998755642 26999977554 5777773
No 16
>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=88.19 E-value=0.25 Score=31.55 Aligned_cols=33 Identities=30% Similarity=0.735 Sum_probs=23.5
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
..|.||-||..|++..-. .+...++||.|.+.+
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 479999999988754322 115668899998743
No 17
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.14 E-value=0.39 Score=39.57 Aligned_cols=37 Identities=22% Similarity=0.530 Sum_probs=25.6
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
..|.||.|+.-|+...-....+ + ....+||.|...+-
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEELE 134 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEEE
Confidence 6899999999666555433222 2 34489999988763
No 18
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=87.77 E-value=0.26 Score=36.01 Aligned_cols=48 Identities=25% Similarity=0.554 Sum_probs=13.9
Q ss_pred eCCCCCCC-ccHhhhhhcccccCCCCCc---------------------cccCCccccCc--chhhHhhhhh
Q 027247 50 PCPFCSED-FDLVGLCCHIDEEHPVEAK---------------------SGVCPVCVTRV--TMDMVDHITT 97 (226)
Q Consensus 50 ~CPfC~e~-~dv~~L~~H~~~eH~~e~~---------------------~vvCPVC~~~v--~~d~i~Hl~~ 97 (226)
.|+||+.. -++..|..|+...|.+... .-.|++|.... ...+..||..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcC
Confidence 39999994 5688999999999987432 12499998865 3688889864
No 19
>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=87.76 E-value=0.14 Score=28.83 Aligned_cols=20 Identities=30% Similarity=0.635 Sum_probs=11.6
Q ss_pred eeCCCCCC-CccHhhhhhccc
Q 027247 49 YPCPFCSE-DFDLVGLCCHID 68 (226)
Q Consensus 49 f~CPfC~e-~~dv~~L~~H~~ 68 (226)
|.||.|+. =-+...|..|+.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 56777777 334455555554
No 20
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=87.40 E-value=0.36 Score=44.44 Aligned_cols=21 Identities=24% Similarity=0.668 Sum_probs=12.6
Q ss_pred ceeeCCCCCC-CccHhhhhhcc
Q 027247 47 YEYPCPFCSE-DFDLVGLCCHI 67 (226)
Q Consensus 47 ~~f~CPfC~e-~~dv~~L~~H~ 67 (226)
..|.||+|++ .+.+..|.-||
T Consensus 160 ka~~C~~C~K~YvSmpALkMHi 181 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHI 181 (279)
T ss_pred ccccCCCCCceeeehHHHhhHh
Confidence 3566666666 56666666665
No 21
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=87.29 E-value=0.18 Score=28.98 Aligned_cols=24 Identities=38% Similarity=0.778 Sum_probs=15.3
Q ss_pred eeCCCCCCCccHhhhhhcccccCC
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHP 72 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~ 72 (226)
|.||+|...-....|..|+...|+
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 678888883337788888776664
No 22
>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=86.52 E-value=0.63 Score=29.63 Aligned_cols=33 Identities=21% Similarity=0.383 Sum_probs=21.5
Q ss_pred eeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
+.||.|+.-|.+..-. .......+.||.|...+
T Consensus 3 ~~CP~C~~~~~v~~~~------~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ------LGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHH------cCCCCCEEECCCCCCEE
Confidence 7899999966655422 12233468999996643
No 23
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.51 E-value=0.29 Score=42.91 Aligned_cols=19 Identities=21% Similarity=0.642 Sum_probs=15.1
Q ss_pred ceeeCCCCCCCccHhhhhh
Q 027247 47 YEYPCPFCSEDFDLVGLCC 65 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~ 65 (226)
-+++||+|+..|....+..
T Consensus 4 k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CceECCCCCCeeeeeEEEc
Confidence 4689999999998775543
No 24
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=86.21 E-value=0.23 Score=48.54 Aligned_cols=33 Identities=36% Similarity=0.627 Sum_probs=28.6
Q ss_pred hccCcceeeCCCCCCCc-cHhhhhhcccccCCCCCc
Q 027247 42 EVKGEYEYPCPFCSEDF-DLVGLCCHIDEEHPVEAK 76 (226)
Q Consensus 42 e~~~~~~f~CPfC~e~~-dv~~L~~H~~~eH~~e~~ 76 (226)
|++ .-|-||+|..+| ++..|-+|++.+|..+-.
T Consensus 11 ~i~--egflCPiC~~dl~~~~~L~~H~d~eH~~ed~ 44 (505)
T KOG1842|consen 11 EIL--EGFLCPICLLDLPNLSALNDHLDVEHFEEDE 44 (505)
T ss_pred hhh--hcccCchHhhhhhhHHHHHHHHhhhccccch
Confidence 466 789999999977 478899999999999875
No 25
>PHA00733 hypothetical protein
Probab=85.64 E-value=0.92 Score=36.87 Aligned_cols=51 Identities=37% Similarity=0.668 Sum_probs=35.7
Q ss_pred ceeeCCCCCCCc-cHhhhhhcccccCCCCCccccCCccccCc--chhhHhhhhhcccc
Q 027247 47 YEYPCPFCSEDF-DLVGLCCHIDEEHPVEAKSGVCPVCVTRV--TMDMVDHITTQHGN 101 (226)
Q Consensus 47 ~~f~CPfC~e~~-dv~~L~~H~~~eH~~e~~~vvCPVC~~~v--~~d~i~Hl~~qH~~ 101 (226)
..|.|+.|+..| ....|..|... | .....|++|.... ...+..|+.--|+-
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~-h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRY-T---EHSKVCPVCGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhc-C---CcCccCCCCCCccCCHHHHHHHHHHhcCc
Confidence 359999999954 45667788753 2 2346999997753 35788888776653
No 26
>PLN03086 PRLI-interacting factor K; Provisional
Probab=85.44 E-value=0.61 Score=46.82 Aligned_cols=38 Identities=18% Similarity=0.316 Sum_probs=26.4
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
..|.|| |+..+....|..|+ ..|+-. +...|+.|...+
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~-~thCp~-Kpi~C~fC~~~v 514 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQ-ASTCPL-RLITCRFCGDMV 514 (567)
T ss_pred CCccCC-CCCCcchhHHHhhh-hccCCC-CceeCCCCCCcc
Confidence 357788 88777778888886 345543 667788887655
No 27
>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=83.51 E-value=0.4 Score=30.17 Aligned_cols=24 Identities=29% Similarity=0.901 Sum_probs=12.7
Q ss_pred eCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 50 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
+||.|+.++.. .+....|||-|..
T Consensus 4 ~Cp~C~se~~y------------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY------------EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E------------E-SSSEEETTTTE
T ss_pred CCCCCCCccee------------ccCCEEeCCcccc
Confidence 69999986665 4666789999964
No 28
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=83.33 E-value=0.58 Score=36.92 Aligned_cols=35 Identities=14% Similarity=0.397 Sum_probs=20.8
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcch
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~ 89 (226)
..|.||+|++ ..+. +.-.+ ..--++||+|-..-+.
T Consensus 20 t~f~CP~Cge-~~v~-----v~~~k--~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGK-VSIS-----VKIKK--NIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCC-eEee-----eecCC--CcceEECCCCCCccCE
Confidence 6799999995 2221 11111 1334799999776543
No 29
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=83.16 E-value=0.65 Score=31.39 Aligned_cols=31 Identities=29% Similarity=0.845 Sum_probs=22.2
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
.+|.|+-|+..|++. ....+ ...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~---~~~~~-----~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVL---QKMSD-----DPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEE---EecCC-----CCCCCCCCCCC
Confidence 579999999988853 12211 45578999976
No 30
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=80.40 E-value=0.59 Score=32.83 Aligned_cols=34 Identities=21% Similarity=0.564 Sum_probs=20.5
Q ss_pred eeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
+.|||||+.+++. ...-.. .....-=|+||-..+
T Consensus 1 i~CPyCge~~~~~--iD~s~~---~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 1 IQCPYCGEPIEIL--IDPSAG---DQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCCeeEEE--EecCCC---CeeEEeehhhcCCcc
Confidence 4799999977662 222211 233345599997654
No 31
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=80.17 E-value=0.83 Score=30.50 Aligned_cols=30 Identities=30% Similarity=0.674 Sum_probs=21.0
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
-+|.||-||..|++.... ....||-|...+
T Consensus 2 ~~y~C~~CG~~~~~~~~~-----------~~~~Cp~CG~~~ 31 (46)
T PRK00398 2 AEYKCARCGREVELDEYG-----------TGVRCPYCGYRI 31 (46)
T ss_pred CEEECCCCCCEEEECCCC-----------CceECCCCCCeE
Confidence 369999999977663221 168899997654
No 32
>PHA02768 hypothetical protein; Provisional
Probab=78.60 E-value=1.2 Score=31.67 Aligned_cols=34 Identities=24% Similarity=0.535 Sum_probs=24.4
Q ss_pred eeeCCCCCC-CccHhhhhhcccccCCCCCccccCCcccc
Q 027247 48 EYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 48 ~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
.|.||.||+ =.....|..|... |. ++-.|..|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~-H~---k~~kc~~C~k 39 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK-HN---TNLKLSNCKR 39 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh-cC---CcccCCcccc
Confidence 489999999 4456788899866 54 4556777754
No 33
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=78.31 E-value=1.2 Score=28.04 Aligned_cols=24 Identities=42% Similarity=0.888 Sum_probs=16.1
Q ss_pred eeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
|.|+.||.-++... ..-+||+|.+
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCC
Confidence 67888886444322 4568999965
No 34
>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=77.61 E-value=1.2 Score=26.83 Aligned_cols=19 Identities=26% Similarity=0.621 Sum_probs=9.8
Q ss_pred eCCCCCCCccHhhhhhccc
Q 027247 50 PCPFCSEDFDLVGLCCHID 68 (226)
Q Consensus 50 ~CPfC~e~~dv~~L~~H~~ 68 (226)
.||.|+..+....+-.|++
T Consensus 3 ~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREVPENLINSHLD 21 (26)
T ss_pred cCCCCcCcccHHHHHHHHH
Confidence 4555555555555555543
No 35
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=77.28 E-value=0.89 Score=41.30 Aligned_cols=13 Identities=31% Similarity=0.925 Sum_probs=10.4
Q ss_pred ceeeCCCCCCCcc
Q 027247 47 YEYPCPFCSEDFD 59 (226)
Q Consensus 47 ~~f~CPfC~e~~d 59 (226)
.++.||+|+.-|-
T Consensus 18 k~ieCPvC~tkFk 30 (267)
T COG1655 18 KTIECPVCNTKFK 30 (267)
T ss_pred ceeccCcccchhh
Confidence 5799999987554
No 36
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=77.12 E-value=1.1 Score=33.97 Aligned_cols=24 Identities=46% Similarity=1.233 Sum_probs=16.8
Q ss_pred eeCCCCCC-CccHhhhhhcccccCCCCCccccCCcc
Q 027247 49 YPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVC 83 (226)
Q Consensus 49 f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC 83 (226)
|+||-||. -|+..+ +...-|||||
T Consensus 2 ~~CPCCg~~Tl~~~~-----------~~~ydIC~VC 26 (78)
T PF14206_consen 2 YPCPCCGYYTLEERG-----------EGTYDICPVC 26 (78)
T ss_pred ccCCCCCcEEeccCC-----------CcCceECCCC
Confidence 89999998 554432 2225699999
No 37
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=75.45 E-value=1.4 Score=29.57 Aligned_cols=14 Identities=21% Similarity=0.764 Sum_probs=12.2
Q ss_pred ccCcceeeCCCCCC
Q 027247 43 VKGEYEYPCPFCSE 56 (226)
Q Consensus 43 ~~~~~~f~CPfC~e 56 (226)
+||...|.||+||.
T Consensus 13 ~RW~~g~~CP~Cg~ 26 (46)
T PF12760_consen 13 IRWPDGFVCPHCGS 26 (46)
T ss_pred hcCCCCCCCCCCCC
Confidence 68878899999997
No 38
>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=75.31 E-value=1.5 Score=43.07 Aligned_cols=42 Identities=29% Similarity=0.420 Sum_probs=33.4
Q ss_pred ceeeCCCCCC-CccHhhhhhcccccCCCCCcc---ccCCccccCcc
Q 027247 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKS---GVCPVCVTRVT 88 (226)
Q Consensus 47 ~~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~---vvCPVC~~~v~ 88 (226)
.--.||+|.+ -.|..++..|+..+|...-.+ -+.|-+....|
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~~w 101 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDDDW 101 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCHHH
Confidence 4678999999 999999999999999986644 45666655444
No 39
>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=75.20 E-value=1.7 Score=26.11 Aligned_cols=10 Identities=40% Similarity=1.168 Sum_probs=8.9
Q ss_pred ceeeCCCCCC
Q 027247 47 YEYPCPFCSE 56 (226)
Q Consensus 47 ~~f~CPfC~e 56 (226)
..|+||-||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 6799999996
No 40
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=74.72 E-value=1 Score=35.93 Aligned_cols=34 Identities=21% Similarity=0.448 Sum_probs=20.9
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
-+|+||+|+..--++-+. .-.....+++|-+|-.
T Consensus 21 k~FtCp~Cghe~vs~ctv-----kk~~~~g~~~Cg~CGl 54 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTV-----KKTVNIGTAVCGNCGL 54 (104)
T ss_pred ceEecCccCCeeeeEEEE-----EecCceeEEEcccCcc
Confidence 589999999843332221 1122344688999954
No 41
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=74.38 E-value=3.5 Score=38.16 Aligned_cols=78 Identities=27% Similarity=0.439 Sum_probs=49.4
Q ss_pred eeeCCCCCCCccHhhhh-hcccccCCCCCccccCCccccCcc--hhhHhhhhhcccccccccccccccc-CCCCcchhhh
Q 027247 48 EYPCPFCSEDFDLVGLC-CHIDEEHPVEAKSGVCPVCVTRVT--MDMVDHITTQHGNISNSWHKLKLHK-GNSNSTISSL 123 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~-~H~~~eH~~e~~~vvCPVC~~~v~--~d~i~Hl~~qH~~~~K~~r~rk~rk-~~s~s~~s~l 123 (226)
-+.|++||+-|+..=|. -|+ ..|..| |.-.||.|..--. .|+-.||.. |+..=| -...+ +-+-+-.|+|
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHi-RTHTGE-KPF~C~hC~kAFADRSNLRAHmQT-HS~~K~----~qC~~C~KsFsl~SyL 259 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHI-RTHTGE-KPFSCPHCGKAFADRSNLRAHMQT-HSDVKK----HQCPRCGKSFALKSYL 259 (279)
T ss_pred CcccccccccccchHHhhccc-ccccCC-CCccCCcccchhcchHHHHHHHHh-hcCCcc----ccCcchhhHHHHHHHH
Confidence 48999999999977554 565 566665 5679999977543 599999965 444311 11222 1133445677
Q ss_pred hHHHHhhhh
Q 027247 124 RKELQNAHF 132 (226)
Q Consensus 124 ~k~lre~~l 132 (226)
-|-+..|=+
T Consensus 260 nKH~ES~C~ 268 (279)
T KOG2462|consen 260 NKHSESACL 268 (279)
T ss_pred HHhhhhccc
Confidence 775554433
No 42
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=73.99 E-value=2 Score=27.36 Aligned_cols=26 Identities=23% Similarity=0.617 Sum_probs=17.3
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccC
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
.|.|+.||.-++... ..-+||||.+.
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 478999997444321 23499999763
No 43
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=73.72 E-value=1.3 Score=38.87 Aligned_cols=43 Identities=26% Similarity=0.654 Sum_probs=27.5
Q ss_pred ceeeCCCCCCCcc--Hhhhhhcc-----cccCC--------------CCCccccCCccccCcch
Q 027247 47 YEYPCPFCSEDFD--LVGLCCHI-----DEEHP--------------VEAKSGVCPVCVTRVTM 89 (226)
Q Consensus 47 ~~f~CPfC~e~~d--v~~L~~H~-----~~eH~--------------~e~~~vvCPVC~~~v~~ 89 (226)
..|.||.|.+.+. +...|.|. -.... ...+...||+|...+..
T Consensus 17 ~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 17 GDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 5799999999433 44557773 22111 12345689999998864
No 44
>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=73.11 E-value=1.8 Score=28.65 Aligned_cols=31 Identities=32% Similarity=0.801 Sum_probs=22.9
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
.+|.|+-||..|++..-. .+...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~~~--------~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSI--------SEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEc--------CCCCCCcCCCCCC
Confidence 479999999988764322 1256789999976
No 45
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=72.95 E-value=1.5 Score=31.89 Aligned_cols=25 Identities=28% Similarity=0.789 Sum_probs=20.3
Q ss_pred eeeCCCCCCCc-cHhhhhhcccccCC
Q 027247 48 EYPCPFCSEDF-DLVGLCCHIDEEHP 72 (226)
Q Consensus 48 ~f~CPfC~e~~-dv~~L~~H~~~eH~ 72 (226)
.|.|++|++.| +...|..|+...|.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccC
Confidence 59999999966 89999999987643
No 46
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=71.31 E-value=3.3 Score=30.16 Aligned_cols=31 Identities=29% Similarity=0.750 Sum_probs=20.9
Q ss_pred ceeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccc
Q 027247 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCV 84 (226)
Q Consensus 47 ~~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~ 84 (226)
..|+||-||+ .+-.-.-|.- ..+.-+||-|-
T Consensus 26 v~F~CPnCGe~~I~Rc~~CRk-------~g~~Y~Cp~CG 57 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKCRK-------LGNPYRCPKCG 57 (61)
T ss_pred eEeeCCCCCceeeehhhhHHH-------cCCceECCCcC
Confidence 6899999997 6555444422 24556899883
No 47
>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=70.96 E-value=2.9 Score=28.52 Aligned_cols=12 Identities=33% Similarity=0.385 Sum_probs=9.1
Q ss_pred cccCCccccCcc
Q 027247 77 SGVCPVCVTRVT 88 (226)
Q Consensus 77 ~vvCPVC~~~v~ 88 (226)
...||+|...+.
T Consensus 35 ~~~cP~~~~~~~ 46 (63)
T smart00504 35 HGTDPVTGQPLT 46 (63)
T ss_pred CCCCCCCcCCCC
Confidence 468999987664
No 48
>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=70.46 E-value=1.9 Score=41.95 Aligned_cols=37 Identities=32% Similarity=0.923 Sum_probs=17.9
Q ss_pred cCcceeeCCCCCCCccHhhhhhcccccCCCCCccccCCcc-ccCcchhhHh
Q 027247 44 KGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVC-VTRVTMDMVD 93 (226)
Q Consensus 44 ~~~~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC-~~~v~~d~i~ 93 (226)
+|.+...||||+.-|. + +-+.-+|||| ...||.+.++
T Consensus 376 ~G~~~v~CP~cgA~y~------------~-~~kG~lC~vC~l~~IG~~a~G 413 (422)
T PF06957_consen 376 RGSPSVKCPYCGAKYH------------P-EYKGQLCPVCELSEIGADASG 413 (422)
T ss_dssp TTS-EEE-TTT--EEE------------G-GGTTSB-TTTTTBBTT---S-
T ss_pred CCCCCeeCCCCCCccC------------h-hhCCCCCCCCcceeeCCccee
Confidence 4446788999997432 2 2345699999 4577776665
No 49
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=69.53 E-value=1.2 Score=42.63 Aligned_cols=36 Identities=31% Similarity=0.853 Sum_probs=23.6
Q ss_pred eeCCCCCCCccHhh-----------hhhcccccCCCCCccccCCccccC
Q 027247 49 YPCPFCSEDFDLVG-----------LCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 49 f~CPfC~e~~dv~~-----------L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
| ||.|-|.+|+.. +|..| -.|.-+.-|+.||.|..+
T Consensus 16 ~-cplcie~mditdknf~pc~cgy~ic~fc-~~~irq~lngrcpacrr~ 62 (480)
T COG5175 16 Y-CPLCIEPMDITDKNFFPCPCGYQICQFC-YNNIRQNLNGRCPACRRK 62 (480)
T ss_pred c-CcccccccccccCCcccCCcccHHHHHH-HHHHHhhccCCChHhhhh
Confidence 5 888877777653 34433 334445578999999764
No 50
>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=69.29 E-value=2 Score=29.57 Aligned_cols=33 Identities=27% Similarity=0.444 Sum_probs=16.9
Q ss_pred eeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccC
Q 027247 49 YPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 49 f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
-+|||||- +.-+.. .+- -........|+-|-+.
T Consensus 2 kPCPfCGg~~~~~~~--~~~---~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRR--GFD---PLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEe--ccC---CCCCEEEEECCCCCCC
Confidence 38999998 442210 010 0011223479999664
No 51
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=68.24 E-value=3.8 Score=35.17 Aligned_cols=26 Identities=31% Similarity=0.782 Sum_probs=17.4
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccC
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
..+.||.||- + |-. --+.+||||.+.
T Consensus 133 ~~~vC~vCGy----------~---~~g-e~P~~CPiCga~ 158 (166)
T COG1592 133 KVWVCPVCGY----------T---HEG-EAPEVCPICGAP 158 (166)
T ss_pred CEEEcCCCCC----------c---ccC-CCCCcCCCCCCh
Confidence 3689999974 1 111 345799999753
No 52
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=67.57 E-value=3.9 Score=29.65 Aligned_cols=31 Identities=26% Similarity=0.629 Sum_probs=21.4
Q ss_pred ceeeCCCCCCC-ccHhhhhhcccccCCCCCccccCCccc
Q 027247 47 YEYPCPFCSED-FDLVGLCCHIDEEHPVEAKSGVCPVCV 84 (226)
Q Consensus 47 ~~f~CPfC~e~-~dv~~L~~H~~~eH~~e~~~vvCPVC~ 84 (226)
..|.||-||+. +-. |..| +-.+..-+||-|-
T Consensus 24 ~~F~CPnCG~~~I~R---C~~C----Rk~~~~Y~CP~CG 55 (59)
T PRK14890 24 VKFLCPNCGEVIIYR---CEKC----RKQSNPYTCPKCG 55 (59)
T ss_pred CEeeCCCCCCeeEee---chhH----HhcCCceECCCCC
Confidence 67999999994 544 3333 2235677899984
No 53
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=66.88 E-value=2.2 Score=32.33 Aligned_cols=32 Identities=25% Similarity=0.544 Sum_probs=13.4
Q ss_pred ceeeCCCCC-C-CccHhhhhhcccccCCCCCccccCCcccc
Q 027247 47 YEYPCPFCS-E-DFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 47 ~~f~CPfC~-e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
..|.||||+ + -+.+.- ........+.|-+|..
T Consensus 21 ~~F~CPfC~~~~sV~v~i-------dkk~~~~~~~C~~Cg~ 54 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKI-------DKKEGIGILSCRVCGE 54 (81)
T ss_dssp S----TTT--SS-EEEEE-------ETTTTEEEEEESSS--
T ss_pred ceEcCCcCCCCCeEEEEE-------EccCCEEEEEecCCCC
Confidence 579999999 3 332221 1123344577999955
No 54
>PRK12495 hypothetical protein; Provisional
Probab=66.21 E-value=3.4 Score=37.16 Aligned_cols=30 Identities=23% Similarity=0.449 Sum_probs=22.3
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcch
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~ 89 (226)
..|.||.||..|- .+ ...++||+|-..+..
T Consensus 41 sa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 41 TNAHCDECGDPIF------------RH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred chhhcccccCccc------------CC-CCeeECCCCCCcccc
Confidence 4699999999654 12 456889999887653
No 55
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=65.94 E-value=4.3 Score=27.41 Aligned_cols=28 Identities=21% Similarity=0.489 Sum_probs=21.4
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
.|.|.-||.++++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 58999999988755 34568999996654
No 56
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=65.91 E-value=2.6 Score=39.94 Aligned_cols=58 Identities=26% Similarity=0.528 Sum_probs=38.6
Q ss_pred eeeCCCCCCCccHhh---hhhcccccCCCCCc-cccCCccccCcc--------------------------hhhHhhhhh
Q 027247 48 EYPCPFCSEDFDLVG---LCCHIDEEHPVEAK-SGVCPVCVTRVT--------------------------MDMVDHITT 97 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~---L~~H~~~eH~~e~~-~vvCPVC~~~v~--------------------------~d~i~Hl~~ 97 (226)
.-.|--|++-+-|-+ =|+|+-=.-|.-+. --+||.|..+|- +||-.||+.
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 456777777655544 35555433333222 368999998641 699999999
Q ss_pred cccccccc
Q 027247 98 QHGNISNS 105 (226)
Q Consensus 98 qH~~~~K~ 105 (226)
+|+.++|-
T Consensus 170 rH~~~~~p 177 (389)
T KOG2932|consen 170 RHGSLLQP 177 (389)
T ss_pred hhccccCC
Confidence 99998764
No 57
>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=65.24 E-value=1.8 Score=25.64 Aligned_cols=11 Identities=45% Similarity=1.558 Sum_probs=9.1
Q ss_pred eeeCCCCCCCc
Q 027247 48 EYPCPFCSEDF 58 (226)
Q Consensus 48 ~f~CPfC~e~~ 58 (226)
-|+||+|+..|
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 49999999754
No 58
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=64.78 E-value=5.4 Score=34.17 Aligned_cols=32 Identities=22% Similarity=0.402 Sum_probs=23.7
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
..|.||-|+.-|+...-.. ..-.||+|...+-
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME----------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCCe
Confidence 6899999999665554432 3679999988764
No 59
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=64.24 E-value=3 Score=32.50 Aligned_cols=13 Identities=38% Similarity=1.088 Sum_probs=10.6
Q ss_pred ceeeCCCCCC-Ccc
Q 027247 47 YEYPCPFCSE-DFD 59 (226)
Q Consensus 47 ~~f~CPfC~e-~~d 59 (226)
+.|.||||+. .+.
T Consensus 35 a~y~CpfCgk~~vk 48 (90)
T PTZ00255 35 AKYFCPFCGKHAVK 48 (90)
T ss_pred CCccCCCCCCCcee
Confidence 7899999987 443
No 60
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=63.38 E-value=3.2 Score=28.37 Aligned_cols=46 Identities=35% Similarity=0.685 Sum_probs=29.3
Q ss_pred ceeeCCC--CCCCccHhhhhhcccccCCCCCccccCCc----cccCcc-hhhHhh
Q 027247 47 YEYPCPF--CSEDFDLVGLCCHIDEEHPVEAKSGVCPV----CVTRVT-MDMVDH 94 (226)
Q Consensus 47 ~~f~CPf--C~e~~dv~~L~~H~~~eH~~e~~~vvCPV----C~~~v~-~d~i~H 94 (226)
...+||+ |.+.+-...|-.|+..+=+ .+.+.||. |..++. .++..|
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~--~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECP--KRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTST--TSEEE-SS----S--EEEHHHHHHC
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCC--CCcEECCCCCCCCCCccchhHHhCC
Confidence 4689999 6667999999999864432 35789999 988765 355554
No 61
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=63.32 E-value=2.8 Score=29.85 Aligned_cols=26 Identities=31% Similarity=0.701 Sum_probs=17.7
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccC
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
.-.||.|++.|... .-.||||.|.+.
T Consensus 5 ~~~C~~Cg~~~~~~-------------dDiVvCp~Cgap 30 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG-------------DDIVVCPECGAP 30 (54)
T ss_pred CccChhhCCcccCC-------------CCEEECCCCCCc
Confidence 35799999876321 224899999764
No 62
>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=62.88 E-value=4.4 Score=27.59 Aligned_cols=23 Identities=26% Similarity=0.418 Sum_probs=13.4
Q ss_pred CCccccCcchhhHhhhhhccccc
Q 027247 80 CPVCVTRVTMDMVDHITTQHGNI 102 (226)
Q Consensus 80 CPVC~~~v~~d~i~Hl~~qH~~~ 102 (226)
||-|..+.+.|+.=+-.+||..-
T Consensus 1 CP~C~~kkk~~Y~~~~LlqHA~g 23 (43)
T PF03470_consen 1 CPFCPGKKKQDYKYRELLQHASG 23 (43)
T ss_pred CCCCCCCCCcceehhHHHHHHHh
Confidence 77777766655444444556554
No 63
>PF14279 HNH_5: HNH endonuclease
Probab=62.50 E-value=2.8 Score=31.01 Aligned_cols=40 Identities=20% Similarity=0.556 Sum_probs=26.6
Q ss_pred CCCCCCCccHhhhhhcccccCCC--------CCccccCCccccCcchhhHhhh
Q 027247 51 CPFCSEDFDLVGLCCHIDEEHPV--------EAKSGVCPVCVTRVTMDMVDHI 95 (226)
Q Consensus 51 CPfC~e~~dv~~L~~H~~~eH~~--------e~~~vvCPVC~~~v~~d~i~Hl 95 (226)
|.||.++.+....- .||-. ..+. ||--|....|...-+++
T Consensus 1 Ci~C~~~~~~~~~s----~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~vD~~l 48 (71)
T PF14279_consen 1 CIYCNKEKSESNFS----EEHIIPESLGGKLKINN-VCDKCNNKFGSKVDAEL 48 (71)
T ss_pred CccCCCCCCccCCC----ccccCchhcCCcccccc-hhHHHhHHHhHHHHHHH
Confidence 99999987665432 45544 2334 99999998885444444
No 64
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=61.91 E-value=3.5 Score=32.14 Aligned_cols=13 Identities=23% Similarity=0.708 Sum_probs=10.4
Q ss_pred ceeeCCCCCC-Ccc
Q 027247 47 YEYPCPFCSE-DFD 59 (226)
Q Consensus 47 ~~f~CPfC~e-~~d 59 (226)
+.|+||||+. .+.
T Consensus 35 a~y~CpfCgk~~vk 48 (90)
T PRK03976 35 AKHVCPVCGRPKVK 48 (90)
T ss_pred cCccCCCCCCCceE
Confidence 7899999987 443
No 65
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=61.58 E-value=6.2 Score=33.08 Aligned_cols=32 Identities=19% Similarity=0.333 Sum_probs=24.3
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
..|.||-|+.-|+...-.. ..-.||+|...+-
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME----------LNFTCPRCGAMLD 139 (158)
T ss_pred CeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEee
Confidence 6799999999666665553 2679999988653
No 66
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=61.26 E-value=8.3 Score=24.79 Aligned_cols=31 Identities=26% Similarity=0.642 Sum_probs=19.9
Q ss_pred eeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
..||-|+..|.+..=. + +...+.|.||-|..
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 6799998855554321 1 33456788998854
No 67
>PF12773 DZR: Double zinc ribbon
Probab=61.26 E-value=5.9 Score=26.33 Aligned_cols=27 Identities=26% Similarity=0.767 Sum_probs=18.1
Q ss_pred eCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 50 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
.||.||..+. ..+...++||.|.+.+.
T Consensus 14 fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 14 FCPHCGTPLP------------PPDQSKKICPNCGAENP 40 (50)
T ss_pred CChhhcCChh------------hccCCCCCCcCCcCCCc
Confidence 5777777555 34555678999977654
No 68
>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=61.08 E-value=3.7 Score=32.09 Aligned_cols=10 Identities=50% Similarity=1.471 Sum_probs=9.2
Q ss_pred ceeeCCCCCC
Q 027247 47 YEYPCPFCSE 56 (226)
Q Consensus 47 ~~f~CPfC~e 56 (226)
..|+||||+.
T Consensus 34 a~y~CpfCgk 43 (91)
T TIGR00280 34 AKYVCPFCGK 43 (91)
T ss_pred cCccCCCCCC
Confidence 7899999987
No 69
>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=60.88 E-value=4.9 Score=31.91 Aligned_cols=38 Identities=26% Similarity=0.513 Sum_probs=22.5
Q ss_pred eeCCCCCCCccHhh---hhhcccccCCCCCccccCCccccCcch
Q 027247 49 YPCPFCSEDFDLVG---LCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (226)
Q Consensus 49 f~CPfC~e~~dv~~---L~~H~~~eH~~e~~~vvCPVC~~~v~~ 89 (226)
..|||||....+.. +.-|-.+++ ...-+|+-|.+.||.
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 47999999443322 222221111 123689999999984
No 70
>PRK12496 hypothetical protein; Provisional
Probab=60.51 E-value=4.4 Score=34.23 Aligned_cols=27 Identities=22% Similarity=0.516 Sum_probs=19.1
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
.|.|+.|+..|+.. ...-+||||-..+
T Consensus 127 ~~~C~gC~~~~~~~-------------~~~~~C~~CG~~~ 153 (164)
T PRK12496 127 RKVCKGCKKKYPED-------------YPDDVCEICGSPV 153 (164)
T ss_pred eEECCCCCccccCC-------------CCCCcCCCCCChh
Confidence 59999999877532 1225899996654
No 71
>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=60.09 E-value=6.1 Score=27.04 Aligned_cols=25 Identities=24% Similarity=0.526 Sum_probs=20.7
Q ss_pred ccCCccccCcc-hhhHhhhhhccccc
Q 027247 78 GVCPVCVTRVT-MDMVDHITTQHGNI 102 (226)
Q Consensus 78 vvCPVC~~~v~-~d~i~Hl~~qH~~~ 102 (226)
..||.|..... ..++.|+..+|..-
T Consensus 3 f~CP~C~~~~~~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCEDEHRSE 28 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHhHCcCC
Confidence 47999998654 58999999999874
No 72
>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=59.77 E-value=4 Score=34.73 Aligned_cols=54 Identities=28% Similarity=0.568 Sum_probs=32.1
Q ss_pred ceeeCCC----CCCCccHhhhhhcccccCCCCCccccCCc----ccc-CcchhhHhhhhhcccccc
Q 027247 47 YEYPCPF----CSEDFDLVGLCCHIDEEHPVEAKSGVCPV----CVT-RVTMDMVDHITTQHGNIS 103 (226)
Q Consensus 47 ~~f~CPf----C~e~~dv~~L~~H~~~eH~~e~~~vvCPV----C~~-~v~~d~i~Hl~~qH~~~~ 103 (226)
-.|||+| |.+-+-......|. ++-.+ +...||+ |.- ....++..|++..|+...
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE-~~C~~--~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHE-EECPF--RPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHH-HT-TT--SEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhHh-ccCCC--cCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 4699999 99988888888885 33333 4567999 733 233699999999999854
No 73
>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=59.76 E-value=4.6 Score=23.36 Aligned_cols=22 Identities=23% Similarity=0.369 Sum_probs=14.5
Q ss_pred eeCCCCCC-CccHhhhhhccccc
Q 027247 49 YPCPFCSE-DFDLVGLCCHIDEE 70 (226)
Q Consensus 49 f~CPfC~e-~~dv~~L~~H~~~e 70 (226)
|.|..|+. =-+...|..|....
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 67777777 44566777776443
No 74
>PRK00420 hypothetical protein; Validated
Probab=59.42 E-value=4.7 Score=32.53 Aligned_cols=28 Identities=29% Similarity=0.481 Sum_probs=18.6
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
.-.||.||..+- .| ....++||+|...+
T Consensus 23 ~~~CP~Cg~pLf--~l----------k~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLF--EL----------KDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCcce--ec----------CCCceECCCCCCee
Confidence 468999996432 11 23468999998744
No 75
>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=59.32 E-value=7.4 Score=27.50 Aligned_cols=38 Identities=18% Similarity=0.335 Sum_probs=27.5
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcchhhHhhh
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHI 95 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~i~Hl 95 (226)
..=.||.||.-... ....+..+||.|-....+|+.+=+
T Consensus 27 TSq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~~rD~naA~ 64 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEMDRDVNAAR 64 (69)
T ss_pred CccCccCccccccc-----------ccccceEEcCCCCCEECcHHHHHH
Confidence 67789999983222 445667899999888877776643
No 76
>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=58.15 E-value=6.1 Score=23.92 Aligned_cols=9 Identities=33% Similarity=1.110 Sum_probs=4.8
Q ss_pred eCCCCCCCc
Q 027247 50 PCPFCSEDF 58 (226)
Q Consensus 50 ~CPfC~e~~ 58 (226)
.||-|+..+
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 356565544
No 77
>PF15616 TerY-C: TerY-C metal binding domain
Probab=57.82 E-value=4.2 Score=33.70 Aligned_cols=39 Identities=15% Similarity=0.384 Sum_probs=27.2
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCC-CCccccCCccccCcc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPV-EAKSGVCPVCVTRVT 88 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~-e~~~vvCPVC~~~v~ 88 (226)
.=.||+||..+-++-. -|-.-|++ ....++||-|-....
T Consensus 77 ~PgCP~CGn~~~fa~C--~CGkl~Ci~g~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVC--GCGKLFCIDGEGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCCcChhcEEEe--cCCCEEEeCCCCCEECCCCCCeee
Confidence 3579999995444322 46677784 456799999977654
No 78
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=57.03 E-value=5 Score=31.73 Aligned_cols=9 Identities=56% Similarity=1.619 Sum_probs=7.9
Q ss_pred eeeCCCCCC
Q 027247 48 EYPCPFCSE 56 (226)
Q Consensus 48 ~f~CPfC~e 56 (226)
-++|||||+
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 479999998
No 79
>smart00355 ZnF_C2H2 zinc finger.
Probab=56.93 E-value=5.7 Score=21.56 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=11.0
Q ss_pred eeCCCCCC-CccHhhhhhccc
Q 027247 49 YPCPFCSE-DFDLVGLCCHID 68 (226)
Q Consensus 49 f~CPfC~e-~~dv~~L~~H~~ 68 (226)
|.|+.|+. =-....|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 45666666 334445555553
No 80
>PHA00616 hypothetical protein
Probab=56.64 E-value=3 Score=28.46 Aligned_cols=24 Identities=21% Similarity=0.267 Sum_probs=13.6
Q ss_pred eeCCCCCC-CccHhhhhhcccccCC
Q 027247 49 YPCPFCSE-DFDLVGLCCHIDEEHP 72 (226)
Q Consensus 49 f~CPfC~e-~~dv~~L~~H~~~eH~ 72 (226)
|.||-||. =.....|..|+...|.
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg 26 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHK 26 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcC
Confidence 56777766 4445556666544443
No 81
>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=56.33 E-value=4.1 Score=31.78 Aligned_cols=10 Identities=50% Similarity=1.534 Sum_probs=8.5
Q ss_pred ceeeCCCCCC
Q 027247 47 YEYPCPFCSE 56 (226)
Q Consensus 47 ~~f~CPfC~e 56 (226)
..|.||||+.
T Consensus 34 ~ky~Cp~Cgk 43 (90)
T PF01780_consen 34 AKYTCPFCGK 43 (90)
T ss_dssp S-BEESSSSS
T ss_pred CCCcCCCCCC
Confidence 7899999998
No 82
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=56.12 E-value=3.3 Score=43.26 Aligned_cols=49 Identities=22% Similarity=0.442 Sum_probs=38.4
Q ss_pred ceeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCcc--hhhHhhh
Q 027247 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT--MDMVDHI 95 (226)
Q Consensus 47 ~~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~--~d~i~Hl 95 (226)
+..+||||.. .-.+..|..|+.-.|--..-+.-|+.|..... .-+-+|+
T Consensus 209 qlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm 260 (1007)
T KOG3623|consen 209 QLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHM 260 (1007)
T ss_pred hhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHH
Confidence 4689999999 55678999999999998888889999987432 3444554
No 83
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=56.12 E-value=7.6 Score=32.79 Aligned_cols=33 Identities=27% Similarity=0.665 Sum_probs=18.0
Q ss_pred eeCCCCCCCccHhhhhhcccccCCCCCcc-----ccCCccccCc
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKS-----GVCPVCVTRV 87 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~~e~~~-----vvCPVC~~~v 87 (226)
..|||||.... |+.+.-.....| --||-|...-
T Consensus 1 m~cp~c~~~~~------~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDT------RVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCC------EeEeccccCCCCceeeeeeccccCCcc
Confidence 36999998431 222222222332 3499997653
No 84
>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=55.44 E-value=3.7 Score=35.20 Aligned_cols=40 Identities=25% Similarity=0.681 Sum_probs=20.6
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
-.|+||.|+..+...++.. .+.-........||-|.....
T Consensus 17 l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~~ 56 (188)
T PF08996_consen 17 LKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPLS 56 (188)
T ss_dssp EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B--
T ss_pred eEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcCC
Confidence 3699999999888888754 111122344578999988654
No 85
>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=54.58 E-value=8.9 Score=27.78 Aligned_cols=37 Identities=16% Similarity=0.420 Sum_probs=20.6
Q ss_pred ceeeCCCCCC------------CccHhhhhhcccccCCCCCccccCCccccCcch
Q 027247 47 YEYPCPFCSE------------DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (226)
Q Consensus 47 ~~f~CPfC~e------------~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~ 89 (226)
..|.||.|++ -||...+..++.. ...+||+|...+..
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-SG
T ss_pred cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCCc
Confidence 3577888776 3455555555533 56899999776653
No 86
>PF13395 HNH_4: HNH endonuclease
Probab=53.77 E-value=7.2 Score=26.84 Aligned_cols=14 Identities=29% Similarity=1.013 Sum_probs=12.1
Q ss_pred CCCCCCCccHhhhh
Q 027247 51 CPFCSEDFDLVGLC 64 (226)
Q Consensus 51 CPfC~e~~dv~~L~ 64 (226)
|||||+.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 99999999988763
No 87
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=53.24 E-value=4.9 Score=29.22 Aligned_cols=26 Identities=27% Similarity=0.556 Sum_probs=18.3
Q ss_pred cCCccccC--cchhhHhhhhhccccccc
Q 027247 79 VCPVCVTR--VTMDMVDHITTQHGNISN 104 (226)
Q Consensus 79 vCPVC~~~--v~~d~i~Hl~~qH~~~~K 104 (226)
.||-|.+. -..|.++|.+-.|+.+|-
T Consensus 19 rCPRC~~~FR~~K~Y~RHVNKaH~~~~~ 46 (65)
T COG4049 19 RCPRCGMVFRRRKDYIRHVNKAHGWLFG 46 (65)
T ss_pred eCCchhHHHHHhHHHHHHhhHHhhhhhc
Confidence 34555432 236899999999999884
No 88
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.53 E-value=5.3 Score=37.15 Aligned_cols=41 Identities=29% Similarity=0.511 Sum_probs=26.7
Q ss_pred ceeeCCCCCC--CccHhhh-hhcccccCCCCCcc-----ccCCccccCc
Q 027247 47 YEYPCPFCSE--DFDLVGL-CCHIDEEHPVEAKS-----GVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e--~~dv~~L-~~H~~~eH~~e~~~-----vvCPVC~~~v 87 (226)
..-.||+||+ -+--... |.|+-=+-|..+.- ..||-|.+.+
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred CCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 4578999999 4444455 88865554443332 3799997754
No 89
>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=52.28 E-value=6.9 Score=31.59 Aligned_cols=24 Identities=29% Similarity=1.020 Sum_probs=15.9
Q ss_pred eCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 50 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
+||-|+.++.-. +....|||-|+.
T Consensus 4 ~CP~C~seytY~------------dg~~~iCpeC~~ 27 (109)
T TIGR00686 4 PCPKCNSEYTYH------------DGTQLICPSCLY 27 (109)
T ss_pred cCCcCCCcceEe------------cCCeeECccccc
Confidence 688887654321 344579999965
No 90
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.19 E-value=4 Score=35.68 Aligned_cols=44 Identities=25% Similarity=0.577 Sum_probs=28.0
Q ss_pred cceeeCCCCCCCccHhh----hhhcccccCCC---CCccccCCccccCcch
Q 027247 46 EYEYPCPFCSEDFDLVG----LCCHIDEEHPV---EAKSGVCPVCVTRVTM 89 (226)
Q Consensus 46 ~~~f~CPfC~e~~dv~~----L~~H~~~eH~~---e~~~vvCPVC~~~v~~ 89 (226)
...|.||.|=..+.... =|-|+-=.-+. -.+.++||+|..+|..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 36899999988665443 34454322222 1245789999988763
No 91
>smart00507 HNHc HNH nucleases.
Probab=51.98 E-value=4.9 Score=25.46 Aligned_cols=21 Identities=19% Similarity=0.175 Sum_probs=13.9
Q ss_pred eeCCCCCCCccHhhhhhcccc
Q 027247 49 YPCPFCSEDFDLVGLCCHIDE 69 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~ 69 (226)
+.|+||+..++..--+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 799999996654334455543
No 92
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.71 E-value=9.5 Score=22.65 Aligned_cols=10 Identities=30% Similarity=0.919 Sum_probs=6.6
Q ss_pred eeCCCCCCCc
Q 027247 49 YPCPFCSEDF 58 (226)
Q Consensus 49 f~CPfC~e~~ 58 (226)
..||.||..+
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 4678887643
No 93
>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=51.69 E-value=5.5 Score=27.93 Aligned_cols=46 Identities=28% Similarity=0.554 Sum_probs=29.0
Q ss_pred CccCCCcchhhhccCcceeeCCCCCC--CccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 31 DFEDIEEDDYEEVKGEYEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 31 ~~e~~~~d~d~e~~~~~~f~CPfC~e--~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
.++|++.+++++. -.|+|+ ||- .+....|-.+ .-.+-|+-|+-.+.
T Consensus 4 ~l~d~~~~~~~~~---~~y~CR-CG~~f~i~e~~l~~~--------~~iv~C~sCSL~I~ 51 (55)
T PF05207_consen 4 SLDDMEFDEEEGV---YSYPCR-CGGEFEISEEDLEEG--------EVIVQCDSCSLWIR 51 (55)
T ss_dssp ETTTSEEETTTTE---EEEEET-TSSEEEEEHHHHHCT----------EEEETTTTEEEE
T ss_pred EhhhceecCCCCE---EEEcCC-CCCEEEEcchhccCc--------CEEEECCCCccEEE
Confidence 3566665554333 489995 998 5566666544 34577999987654
No 94
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=51.29 E-value=6.6 Score=22.99 Aligned_cols=7 Identities=43% Similarity=1.455 Sum_probs=3.8
Q ss_pred CCCCCCC
Q 027247 51 CPFCSED 57 (226)
Q Consensus 51 CPfC~e~ 57 (226)
||.||..
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 5555553
No 95
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=50.93 E-value=9.1 Score=31.32 Aligned_cols=40 Identities=25% Similarity=0.456 Sum_probs=22.4
Q ss_pred ceeeCCCCCCCccHhhhhhcccc-----cCCCC---CccccCCccccC
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDE-----EHPVE---AKSGVCPVCVTR 86 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~-----eH~~e---~~~vvCPVC~~~ 86 (226)
..+.|+-||..+.+..-..++.. -|-.. .....||.|-..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 57999999986665421111111 11111 344679999653
No 96
>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=50.51 E-value=7.4 Score=30.96 Aligned_cols=27 Identities=30% Similarity=0.386 Sum_probs=20.6
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccC
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
..+.|+-|+..+.+... ...||-|...
T Consensus 69 ~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 69 VECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred cEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 57999999987776543 3679999753
No 97
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=50.03 E-value=6.3 Score=38.53 Aligned_cols=33 Identities=24% Similarity=0.467 Sum_probs=23.5
Q ss_pred ceeeCCCCCC---CccHhhhhhcccccCCCCCccccCCccccC
Q 027247 47 YEYPCPFCSE---DFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 47 ~~f~CPfC~e---~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
+.|.||+|.. .+|+..|.. .+...-.|-.|..-
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~-------~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLD-------NETGEFHCENCGGE 162 (436)
T ss_pred ccccCCccccchhhhHHHHhhc-------ccCceEEEecCCCc
Confidence 6899999999 566666653 23455678888763
No 98
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=49.77 E-value=9.4 Score=30.45 Aligned_cols=28 Identities=36% Similarity=0.762 Sum_probs=21.2
Q ss_pred ceeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
....||-||. =||+ ...++|||-|.+..
T Consensus 8 tKR~Cp~CG~kFYDL-------------nk~PivCP~CG~~~ 36 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL-------------NKDPIVCPKCGTEF 36 (108)
T ss_pred CcccCCCCcchhccC-------------CCCCccCCCCCCcc
Confidence 7889999999 4443 23568999997754
No 99
>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=49.65 E-value=8.2 Score=24.74 Aligned_cols=21 Identities=19% Similarity=0.398 Sum_probs=10.5
Q ss_pred ceeeCCCCCCCccHhhhhhcc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHI 67 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~ 67 (226)
++|.||-|+..+-..-.-.|+
T Consensus 3 ~~~~C~nC~R~v~a~RfA~HL 23 (33)
T PF08209_consen 3 PYVECPNCGRPVAASRFAPHL 23 (33)
T ss_dssp -EEE-TTTSSEEEGGGHHHHH
T ss_pred CeEECCCCcCCcchhhhHHHH
Confidence 345566665555555555554
No 100
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=49.43 E-value=5.1 Score=32.42 Aligned_cols=62 Identities=21% Similarity=0.427 Sum_probs=30.4
Q ss_pred CCCCCCCccHhhhhh-cccccCCCCCccccCCccccCcc-hhhHhhhhhcccccccccccccccc--CCCCcch
Q 027247 51 CPFCSEDFDLVGLCC-HIDEEHPVEAKSGVCPVCVTRVT-MDMVDHITTQHGNISNSWHKLKLHK--GNSNSTI 120 (226)
Q Consensus 51 CPfC~e~~dv~~L~~-H~~~eH~~e~~~vvCPVC~~~v~-~d~i~Hl~~qH~~~~K~~r~rk~rk--~~s~s~~ 120 (226)
||.||..+-|..|.| ||... .+...-.|++|.-..- .+|+.-+....|++-.+ .| +.||+|.
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~--i~G~F~l~~~~~L~~E~~~Fi~~Fi~~rGnlKe~------e~~lgiSYPTv 66 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTE--IEGEFELPWFARLSPEQLEFIKLFIKNRGNLKEM------EKELGISYPTV 66 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCE--EEeeeccchhhcCCHHHHHHHHHHHHhcCCHHHH------HHHHCCCcHHH
Confidence 999999888777631 11100 1222223333322111 36666555556665332 23 4478874
No 101
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=48.69 E-value=12 Score=32.74 Aligned_cols=34 Identities=21% Similarity=0.460 Sum_probs=26.2
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcchhhHhhhh
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHIT 96 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~i~Hl~ 96 (226)
..-.||.||. ...+...||.|....-+|..+=++
T Consensus 308 tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~N 341 (364)
T COG0675 308 TSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALN 341 (364)
T ss_pred CcccccccCC----------------ccceeEECCCCCCeehhhHHHHHH
Confidence 4578999998 335678999998887777776554
No 102
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=47.99 E-value=11 Score=35.04 Aligned_cols=28 Identities=18% Similarity=0.203 Sum_probs=22.4
Q ss_pred eeCCCCCCCccHhhhhhcccccCCCCCccccCCccccC
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
.+||-|+.-+-...|-.. ..|||-|...
T Consensus 39 ~kc~~C~~~~~~~~l~~~----------~~vcp~c~~h 66 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSK----------MNICEQCGYH 66 (296)
T ss_pred eECCCccchhhHHHHHHc----------CCCCCCCCCC
Confidence 899999998877777533 4799999774
No 103
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.95 E-value=19 Score=23.03 Aligned_cols=31 Identities=19% Similarity=0.546 Sum_probs=20.0
Q ss_pred eeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
+.||-|+.-|++..-. =+-....+-||.|..
T Consensus 3 i~Cp~C~~~y~i~d~~------ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK------IPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHHH------CCCCCcEEECCCCCC
Confidence 6788888855554321 144566788888854
No 104
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=47.56 E-value=8 Score=34.23 Aligned_cols=32 Identities=28% Similarity=0.557 Sum_probs=20.6
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCC-CCcccc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPV-EAKSGV 79 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~-e~~~vv 79 (226)
.|.||.|+..+.+..=-=+|...|.+ -++.+.
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~fd~a~~Gy 34 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQFDCAKEGY 34 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCCccccCce
Confidence 38999999976533222346778888 344443
No 105
>PRK03922 hypothetical protein; Provisional
Probab=46.95 E-value=9.2 Score=31.00 Aligned_cols=16 Identities=38% Similarity=0.617 Sum_probs=12.7
Q ss_pred eeeCCCCCCCccHhhh
Q 027247 48 EYPCPFCSEDFDLVGL 63 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L 63 (226)
.-.||+||++|+-.-+
T Consensus 49 ~~~cP~cge~~~~afv 64 (113)
T PRK03922 49 LTICPKCGEPFDSAFV 64 (113)
T ss_pred cccCCCCCCcCCcEEE
Confidence 5789999999986544
No 106
>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=46.67 E-value=14 Score=34.13 Aligned_cols=30 Identities=30% Similarity=0.509 Sum_probs=23.6
Q ss_pred ccCcceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccC
Q 027247 43 VKGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 43 ~~~~~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
+| .+||-|++-+-...|-. +..|||-|...
T Consensus 25 ~~----~~c~~c~~~~~~~~l~~----------~~~vc~~c~~h 54 (285)
T TIGR00515 25 VW----TKCPKCGQVLYTKELER----------NLEVCPKCDHH 54 (285)
T ss_pred Ce----eECCCCcchhhHHHHHh----------hCCCCCCCCCc
Confidence 77 89999999777777753 23799999774
No 107
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=46.44 E-value=6 Score=30.78 Aligned_cols=11 Identities=36% Similarity=1.189 Sum_probs=9.7
Q ss_pred cceeeCCCCCC
Q 027247 46 EYEYPCPFCSE 56 (226)
Q Consensus 46 ~~~f~CPfC~e 56 (226)
++.|.|+|||.
T Consensus 34 haky~CsfCGK 44 (92)
T KOG0402|consen 34 HAKYTCSFCGK 44 (92)
T ss_pred hhhhhhhhcch
Confidence 37899999998
No 108
>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=45.75 E-value=4.8 Score=30.08 Aligned_cols=53 Identities=23% Similarity=0.388 Sum_probs=23.5
Q ss_pred eCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcc-------hhhHhhhhhccccccccc
Q 027247 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT-------MDMVDHITTQHGNISNSW 106 (226)
Q Consensus 50 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~-------~d~i~Hl~~qH~~~~K~~ 106 (226)
.||-|...++..+-.-||..=+..=.+.+.||-|...+- .|+.- +|++-+|++
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC----~~c~gLiSK 62 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFC----NHCHGLISK 62 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-----TTTT-EE-T
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceee----ccCCceeec
Confidence 466666666655533333222222234578999987653 35543 477777653
No 109
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=45.66 E-value=11 Score=32.33 Aligned_cols=42 Identities=21% Similarity=0.466 Sum_probs=27.7
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCC-----C-CccccCCccccCcc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPV-----E-AKSGVCPVCVTRVT 88 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~-----e-~~~vvCPVC~~~v~ 88 (226)
+--.||.|+..++...-..|++-.|+. . -+-+.|+-|...+|
T Consensus 19 Q~G~CaiC~~~l~~~~~~~~vDHDH~l~g~~TG~VRGLLC~~CN~~lG 66 (157)
T PHA02565 19 QNGICPLCKRELDGDVSKNHLDHDHELNGPNAGRVRGLLCNLCNALEG 66 (157)
T ss_pred hCCcCCCCCCccCCCccccccCCCCCCCCcccccccccCchhhhhhhh
Confidence 457899999977644333478777722 2 24467999977554
No 110
>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=45.03 E-value=11 Score=31.46 Aligned_cols=41 Identities=29% Similarity=0.639 Sum_probs=28.7
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcchhhH
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMV 92 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~i 92 (226)
..+.|..|+..++...+...+.... ...||.|...+..|++
T Consensus 104 ~~~~C~~C~~~~~~~~~~~~~~~~~-----~~~C~~C~~~lrp~vv 144 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVDSIDEEE-----PPRCPKCGGLLRPDVV 144 (178)
T ss_dssp EEEEETTTSBEEEGHHHHHHHHTTS-----SCBCTTTSCBEEEEE-
T ss_pred ceeeecCCCccccchhhcccccccc-----cccccccCccCCCCee
Confidence 3689999999888777765543332 2399999887665554
No 111
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=44.84 E-value=14 Score=34.22 Aligned_cols=30 Identities=27% Similarity=0.530 Sum_probs=23.5
Q ss_pred ccCcceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccC
Q 027247 43 VKGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 43 ~~~~~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
+| .+||-|++-+-...|-.. ..|||-|...
T Consensus 26 ~~----~~c~~c~~~~~~~~l~~~----------~~vc~~c~~h 55 (292)
T PRK05654 26 LW----TKCPSCGQVLYRKELEAN----------LNVCPKCGHH 55 (292)
T ss_pred Ce----eECCCccchhhHHHHHhc----------CCCCCCCCCC
Confidence 77 899999997777777532 3699999774
No 112
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=44.84 E-value=10 Score=30.21 Aligned_cols=16 Identities=31% Similarity=0.698 Sum_probs=12.6
Q ss_pred eeeCCCCCCCccHhhh
Q 027247 48 EYPCPFCSEDFDLVGL 63 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L 63 (226)
.-.||+|+++|+-.-+
T Consensus 47 ~~~cP~Cge~~~~a~v 62 (102)
T PF04475_consen 47 DTICPKCGEELDSAFV 62 (102)
T ss_pred cccCCCCCCccCceEE
Confidence 5789999999885543
No 113
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.29 E-value=14 Score=35.89 Aligned_cols=15 Identities=20% Similarity=0.691 Sum_probs=10.9
Q ss_pred ceeeCCCCCCCccHh
Q 027247 47 YEYPCPFCSEDFDLV 61 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~ 61 (226)
.+|+||||-.+-+..
T Consensus 373 ~sfKCPYCP~e~~~~ 387 (394)
T KOG2817|consen 373 QSFKCPYCPVEQLAS 387 (394)
T ss_pred eeeeCCCCCcccCHH
Confidence 469999998765544
No 114
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=44.27 E-value=11 Score=31.28 Aligned_cols=25 Identities=28% Similarity=0.636 Sum_probs=17.5
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
...||-||--+ ..| ...|+||||-.
T Consensus 28 ~~hCp~Cg~PL-----F~K--------dG~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPL-----FRK--------DGEVFCPVCGY 52 (131)
T ss_pred HhhCcccCCcc-----eee--------CCeEECCCCCc
Confidence 58999999732 111 34589999974
No 115
>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=43.37 E-value=13 Score=31.45 Aligned_cols=32 Identities=31% Similarity=0.780 Sum_probs=19.1
Q ss_pred eCCCCCC-CccHhhhhhcccccCCCCCcccc-----CCccccCcc
Q 027247 50 PCPFCSE-DFDLVGLCCHIDEEHPVEAKSGV-----CPVCVTRVT 88 (226)
Q Consensus 50 ~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vv-----CPVC~~~v~ 88 (226)
.||||+. +--|. +.-+.+..+.| |+.|..+-+
T Consensus 2 ~CP~C~~~dtkVi-------DSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVL-------DSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEee-------eccccCCCCeeeecccCCccCCccc
Confidence 5999998 43332 22233333333 999987654
No 116
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=42.93 E-value=12 Score=29.74 Aligned_cols=26 Identities=23% Similarity=0.450 Sum_probs=19.0
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
..+.|+-|+..|.+.. ....||-|..
T Consensus 69 ~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ-------------HDAQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCC-------------cCccCcCCCC
Confidence 5699999998666543 2346999975
No 117
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=42.75 E-value=13 Score=38.72 Aligned_cols=38 Identities=29% Similarity=0.587 Sum_probs=27.3
Q ss_pred ceeeCCCCCCCcc----HhhhhhcccccCCCCCccccCCccccC
Q 027247 47 YEYPCPFCSEDFD----LVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 47 ~~f~CPfC~e~~d----v~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
..+.||.|+..+. ...|.||-...| +...-.||-|...
T Consensus 443 ~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 443 YIAECPNCDSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred CcccCCCCCcceEEecCCCeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 4689999998543 346666654544 6677899999875
No 118
>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=42.72 E-value=15 Score=36.58 Aligned_cols=41 Identities=34% Similarity=0.644 Sum_probs=25.9
Q ss_pred ceeeCCCCCCCccHh--hhhhcccccCCCCCccccCCccccCcch
Q 027247 47 YEYPCPFCSEDFDLV--GLCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~--~L~~H~~~eH~~e~~~vvCPVC~~~v~~ 89 (226)
-..+||-||+.+.+. .|.- +.+...+.--.+||-|-..+..
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w--~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKW--DKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EEccCCCCCCCccccccceee--cCCCCccceEEECCCCcCCCCH
Confidence 468999999955543 3322 2222334445789999887753
No 119
>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=42.66 E-value=13 Score=26.06 Aligned_cols=10 Identities=40% Similarity=1.464 Sum_probs=8.4
Q ss_pred ceeeCCCCCC
Q 027247 47 YEYPCPFCSE 56 (226)
Q Consensus 47 ~~f~CPfC~e 56 (226)
-.|.||+|+.
T Consensus 43 i~y~C~~Cg~ 52 (54)
T PF10058_consen 43 IQYRCPYCGA 52 (54)
T ss_pred eEEEcCCCCC
Confidence 3599999986
No 120
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=42.20 E-value=16 Score=29.62 Aligned_cols=27 Identities=30% Similarity=0.478 Sum_probs=20.5
Q ss_pred cccCCccccCcc-----hhhHhhhhhcccccc
Q 027247 77 SGVCPVCVTRVT-----MDMVDHITTQHGNIS 103 (226)
Q Consensus 77 ~vvCPVC~~~v~-----~d~i~Hl~~qH~~~~ 103 (226)
.+.||+|....| ..+.-||+.-||-+-
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~s 56 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGISS 56 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhcccccc
Confidence 789999986555 357888888888753
No 121
>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=42.10 E-value=10 Score=30.03 Aligned_cols=27 Identities=22% Similarity=0.475 Sum_probs=18.6
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccC
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
..+.|+-|+..|++.... ..||-|...
T Consensus 69 ~~~~C~~Cg~~~~~~~~~-------------~~CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFD-------------FSCPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHHCC-------------HH-SSSSSS
T ss_pred CcEECCCCCCEEecCCCC-------------CCCcCCcCC
Confidence 579999999988877654 239999764
No 122
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.95 E-value=11 Score=27.58 Aligned_cols=12 Identities=42% Similarity=1.090 Sum_probs=9.0
Q ss_pred ceeeCCCCCCCc
Q 027247 47 YEYPCPFCSEDF 58 (226)
Q Consensus 47 ~~f~CPfC~e~~ 58 (226)
-+..||||+.-|
T Consensus 47 gev~CPYC~t~y 58 (62)
T COG4391 47 GEVVCPYCSTRY 58 (62)
T ss_pred CcEecCccccEE
Confidence 468899998743
No 123
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=41.01 E-value=8.2 Score=30.05 Aligned_cols=38 Identities=29% Similarity=0.630 Sum_probs=11.4
Q ss_pred eCCCCCCCccHhhhh-hcccccCCC-----------CCccccCCccccCc
Q 027247 50 PCPFCSEDFDLVGLC-CHIDEEHPV-----------EAKSGVCPVCVTRV 87 (226)
Q Consensus 50 ~CPfC~e~~dv~~L~-~H~~~eH~~-----------e~~~vvCPVC~~~v 87 (226)
.||+|++.+....+. .=|..-|.+ +.+.-+|++|..+.
T Consensus 16 ~C~~C~~~i~~~~~~~~~C~~GH~w~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 16 KCPICGAPIPFDDLDEAQCENGHVWPRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp -------------SSEEE-TTS-EEEB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred cccccccccccCCcCEeECCCCCEEeeeeeeeeeeccCCeeEcCCCCCEE
Confidence 699999977765543 335666655 45557899996643
No 124
>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=41.00 E-value=11 Score=35.48 Aligned_cols=40 Identities=28% Similarity=0.557 Sum_probs=23.1
Q ss_pred eeeCCCCCCC-ccHhh-----------hhhcccccCCCCCccccCCccccCcc
Q 027247 48 EYPCPFCSED-FDLVG-----------LCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 48 ~f~CPfC~e~-~dv~~-----------L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
.+.||.|..+ +--.. +|..|.+.. +......||+|...+.
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l-~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLL-FVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHH-hcCCCCCCCCCCCccc
Confidence 4789999882 22222 233344433 2334578999977654
No 125
>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=40.92 E-value=11 Score=27.51 Aligned_cols=10 Identities=50% Similarity=1.245 Sum_probs=8.1
Q ss_pred ceeeCCCCCC
Q 027247 47 YEYPCPFCSE 56 (226)
Q Consensus 47 ~~f~CPfC~e 56 (226)
..+.|-+||+
T Consensus 4 ~~~~C~~Cg~ 13 (69)
T PF09706_consen 4 KKYNCIFCGE 13 (69)
T ss_pred CCCcCcCCCC
Confidence 4689999994
No 126
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=40.30 E-value=15 Score=31.38 Aligned_cols=32 Identities=34% Similarity=0.850 Sum_probs=18.9
Q ss_pred eCCCCCC-CccHhhhhhcccccCCCCCccc-----cCCccccCcc
Q 027247 50 PCPFCSE-DFDLVGLCCHIDEEHPVEAKSG-----VCPVCVTRVT 88 (226)
Q Consensus 50 ~CPfC~e-~~dv~~L~~H~~~eH~~e~~~v-----vCPVC~~~v~ 88 (226)
.||||+- +--|. +--+.+-.+. .||-|..+-+
T Consensus 2 ~CPfC~~~~tkVi-------DSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVI-------DSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeee-------ecccccccchhhhhhcccccccccc
Confidence 5999998 43332 2223333333 4999987654
No 127
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=40.30 E-value=14 Score=35.37 Aligned_cols=40 Identities=33% Similarity=0.600 Sum_probs=30.3
Q ss_pred eeeCCC--CCC-CccHhhhhhcccccCCC-----------------CCccccCCccccCc
Q 027247 48 EYPCPF--CSE-DFDLVGLCCHIDEEHPV-----------------EAKSGVCPVCVTRV 87 (226)
Q Consensus 48 ~f~CPf--C~e-~~dv~~L~~H~~~eH~~-----------------e~~~vvCPVC~~~v 87 (226)
-|+||. |.+ .-..-+|.-|...-|+. +.|.-+|+||.++-
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 499987 777 67788888888877732 33567899998865
No 128
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=38.92 E-value=15 Score=35.05 Aligned_cols=38 Identities=32% Similarity=0.608 Sum_probs=26.7
Q ss_pred ceeeCCCCCCCcc--Hhhhhhccccc-CCC-----CCccccCCccc
Q 027247 47 YEYPCPFCSEDFD--LVGLCCHIDEE-HPV-----EAKSGVCPVCV 84 (226)
Q Consensus 47 ~~f~CPfC~e~~d--v~~L~~H~~~e-H~~-----e~~~vvCPVC~ 84 (226)
..-.||.||...| +.+||.=|.-+ |+. +.+..+|+.|-
T Consensus 5 ~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cg 50 (355)
T COG1499 5 STILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCG 50 (355)
T ss_pred cccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCC
Confidence 5678999999887 77787666544 443 33446788885
No 129
>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=38.84 E-value=19 Score=31.77 Aligned_cols=23 Identities=13% Similarity=0.070 Sum_probs=14.4
Q ss_pred CCCCHHHHHHHHhHhhHH-HHHHH
Q 027247 196 SSLSNEDHLEKANRSNFA-QGLLF 218 (226)
Q Consensus 196 ~~ls~ed~eEk~~R~eFV-Q~Lll 218 (226)
-.++++|.++-.+++.++ -+|+.
T Consensus 145 r~~~~~e~~~~~~~~~~~le~l~~ 168 (236)
T PF04981_consen 145 RKLTEEEKEVIHKIVFEILEQLIL 168 (236)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHh
Confidence 358888877666666654 34433
No 130
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=38.67 E-value=22 Score=24.28 Aligned_cols=29 Identities=21% Similarity=0.537 Sum_probs=18.7
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCcc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVC 83 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC 83 (226)
.-+.||.|+-.+...-=-. + .+...||.|
T Consensus 27 v~W~C~~Cgh~w~~~v~~R-------~-~~~~~CP~C 55 (55)
T PF14311_consen 27 VWWKCPKCGHEWKASVNDR-------T-RRGKGCPYC 55 (55)
T ss_pred EEEECCCCCCeeEccHhhh-------c-cCCCCCCCC
Confidence 4589999987665432211 1 456789988
No 131
>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=38.53 E-value=13 Score=35.40 Aligned_cols=40 Identities=25% Similarity=0.524 Sum_probs=26.4
Q ss_pred eeCCCCCCCccHhhhhhcccccC-CCCCccccCCccccCcc
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEH-PVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH-~~e~~~vvCPVC~~~v~ 88 (226)
-.||+|+.+---...|.+|-... +.+..+.+|.+|...+.
T Consensus 137 g~CP~C~~~~a~g~~Ce~cG~~~~~~~l~~p~~~~~g~~~~ 177 (391)
T PF09334_consen 137 GTCPYCGSDKARGDQCENCGRPLEPEELINPVCKICGSPPE 177 (391)
T ss_dssp CEETTT--SSCTTTEETTTSSBEECCCSECEEETTTS-B-E
T ss_pred ccccCcCccccCCCcccCCCCCcccccccCCccccccccCc
Confidence 67999996656667777775443 35778899999988653
No 132
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=38.05 E-value=16 Score=34.82 Aligned_cols=11 Identities=36% Similarity=1.253 Sum_probs=9.2
Q ss_pred ceeeCCCCCCC
Q 027247 47 YEYPCPFCSED 57 (226)
Q Consensus 47 ~~f~CPfC~e~ 57 (226)
..|+||||.++
T Consensus 375 ~~FKCPYCP~~ 385 (396)
T COG5109 375 LSFKCPYCPEM 385 (396)
T ss_pred EEeeCCCCCcc
Confidence 47999999873
No 133
>PRK11595 DNA utilization protein GntX; Provisional
Probab=36.83 E-value=16 Score=31.92 Aligned_cols=34 Identities=24% Similarity=0.536 Sum_probs=21.2
Q ss_pred eCCCCCCCccH--hhhhhcccccCCCCCccccCCcccc
Q 027247 50 PCPFCSEDFDL--VGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 50 ~CPfC~e~~dv--~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
.|+.|+..+.. ..||.+|...=++- ...||.|..
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~--~~~C~~Cg~ 42 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTL--KTCCPQCGL 42 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcc--cCcCccCCC
Confidence 48899885533 35888886553331 246777764
No 134
>PRK10220 hypothetical protein; Provisional
Probab=36.75 E-value=21 Score=28.92 Aligned_cols=24 Identities=25% Similarity=0.843 Sum_probs=15.3
Q ss_pred eCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 50 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
+||-|+.++.- -+....|||-|+.
T Consensus 5 ~CP~C~seytY------------~d~~~~vCpeC~h 28 (111)
T PRK10220 5 HCPKCNSEYTY------------EDNGMYICPECAH 28 (111)
T ss_pred cCCCCCCcceE------------cCCCeEECCcccC
Confidence 68888765431 1233578999965
No 135
>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=36.51 E-value=12 Score=32.79 Aligned_cols=21 Identities=19% Similarity=0.453 Sum_probs=0.0
Q ss_pred cccCCccccCcc-hhhHhhhhh
Q 027247 77 SGVCPVCVTRVT-MDMVDHITT 97 (226)
Q Consensus 77 ~vvCPVC~~~v~-~d~i~Hl~~ 97 (226)
.++||||..+|- ..|-.||++
T Consensus 168 ~~~cPitGe~IP~~e~~eHmRi 189 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMRI 189 (229)
T ss_dssp ----------------------
T ss_pred cccccccccccccccccccccc
Confidence 379999999876 589999964
No 136
>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=36.49 E-value=8.9 Score=24.83 Aligned_cols=25 Identities=20% Similarity=0.535 Sum_probs=10.9
Q ss_pred ceeeCCCCCCCccH-----hhhhhcccccC
Q 027247 47 YEYPCPFCSEDFDL-----VGLCCHIDEEH 71 (226)
Q Consensus 47 ~~f~CPfC~e~~dv-----~~L~~H~~~eH 71 (226)
....|-||+..+.. ..|..|+...|
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 34666666664433 24555543333
No 137
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=36.37 E-value=18 Score=23.62 Aligned_cols=10 Identities=50% Similarity=1.085 Sum_probs=7.4
Q ss_pred CccccCCccc
Q 027247 75 AKSGVCPVCV 84 (226)
Q Consensus 75 ~~~vvCPVC~ 84 (226)
.+.++||+|.
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 5568888884
No 138
>PF14353 CpXC: CpXC protein
Probab=36.25 E-value=19 Score=28.54 Aligned_cols=28 Identities=29% Similarity=0.426 Sum_probs=17.8
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCcccc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGV 79 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vv 79 (226)
.|+||.||..+-+. +--.+|..+.+.++
T Consensus 38 ~~~CP~Cg~~~~~~----~p~lY~D~~~~~~i 65 (128)
T PF14353_consen 38 SFTCPSCGHKFRLE----YPLLYHDPEKKFMI 65 (128)
T ss_pred EEECCCCCCceecC----CCEEEEcCCCCEEE
Confidence 79999999966542 33345555555543
No 139
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.98 E-value=22 Score=38.56 Aligned_cols=35 Identities=20% Similarity=0.159 Sum_probs=19.9
Q ss_pred cccccccccccCCCCCHHHHHHHHhHhhHHHHHHH
Q 027247 184 SCEKTFETNAQQSSLSNEDHLEKANRSNFAQGLLF 218 (226)
Q Consensus 184 s~~~~~e~~~~~~~ls~ed~eEk~~R~eFVQ~Lll 218 (226)
+++|.+|-.+|.--|+..=-+=-.+=+.||-.||-
T Consensus 778 ~~dQivELk~QDiil~~~aa~yll~va~fiDdLL~ 812 (1121)
T PRK04023 778 SEDQIVELKVQDVIISRDAAEYLLRVAKFIDDLLE 812 (1121)
T ss_pred CccceEEeecccEEcchHHHHHHHHHHHHHHHHHH
Confidence 34555666665223444333334667888888874
No 140
>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=35.85 E-value=23 Score=29.37 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=20.9
Q ss_pred ceeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
....||-||. =||+ ....+|||-|....
T Consensus 8 tKr~Cp~cg~kFYDL-------------nk~p~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGSKFYDL-------------NRRPAVSPYTGEQF 36 (129)
T ss_pred ccccCCCcCcccccc-------------CCCCccCCCcCCcc
Confidence 7899999998 4442 24579999996643
No 141
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=35.28 E-value=13 Score=27.09 Aligned_cols=35 Identities=23% Similarity=0.603 Sum_probs=20.8
Q ss_pred eeCCCCCC-CccHhhhh------hcc-cccCCCCCccccCCccc
Q 027247 49 YPCPFCSE-DFDLVGLC------CHI-DEEHPVEAKSGVCPVCV 84 (226)
Q Consensus 49 f~CPfC~e-~~dv~~L~------~H~-~~eH~~e~~~vvCPVC~ 84 (226)
|.||-|+. ++++..+. ..+ +-+|. .-..++|+-|-
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~-~f~~v~C~~CG 43 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNK-KFTTVSCTNCG 43 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCc-EEEEEECCCCC
Confidence 67999998 77765442 222 21222 23457888884
No 142
>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=34.97 E-value=14 Score=25.31 Aligned_cols=13 Identities=31% Similarity=0.774 Sum_probs=6.5
Q ss_pred eCCCCCCCccHhh
Q 027247 50 PCPFCSEDFDLVG 62 (226)
Q Consensus 50 ~CPfC~e~~dv~~ 62 (226)
.||.|+.+||...
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 8888888777543
No 143
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=34.63 E-value=23 Score=32.66 Aligned_cols=37 Identities=22% Similarity=0.414 Sum_probs=25.5
Q ss_pred eeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcchhhHhhh
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHI 95 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~i~Hl 95 (226)
..||.|+.. ++ .. -++....||--|-.-+..+.+.+-
T Consensus 2 ~~CpeCg~~-~~-------~~--d~~~ge~VC~~CG~Vi~~~~id~g 38 (285)
T COG1405 2 MSCPECGST-NI-------IT--DYERGEIVCADCGLVLEDSLIDPG 38 (285)
T ss_pred CCCCCCCCc-cc-------ee--eccCCeEEeccCCEEeccccccCC
Confidence 479999986 11 11 123567899999988887777643
No 144
>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=34.63 E-value=10 Score=24.28 Aligned_cols=35 Identities=20% Similarity=0.374 Sum_probs=13.8
Q ss_pred CCCCCCCccHh--hhhhcccccCC---CCCc--cccCCcccc
Q 027247 51 CPFCSEDFDLV--GLCCHIDEEHP---VEAK--SGVCPVCVT 85 (226)
Q Consensus 51 CPfC~e~~dv~--~L~~H~~~eH~---~e~~--~vvCPVC~~ 85 (226)
|++|+..+... -=+.|+..... ++.. ..+|+.|..
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~~lC~~Ch~ 42 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLILLCPSCHR 42 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEEEEEHHHHH
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHHHHhHHHHH
Confidence 89999966554 23344433331 1222 255777743
No 145
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=34.55 E-value=22 Score=23.54 Aligned_cols=27 Identities=26% Similarity=0.336 Sum_probs=14.9
Q ss_pred eCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 50 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
.||.||.-+-...+- .....+||.|..
T Consensus 2 FCp~Cg~~l~~~~~~---------~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKEGK---------EKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccccCC---------CCCEEECCcCCC
Confidence 488888733222211 112578999954
No 146
>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=34.46 E-value=26 Score=21.10 Aligned_cols=21 Identities=19% Similarity=0.649 Sum_probs=13.8
Q ss_pred eeeCCCCCCCcc-Hhhhhhccc
Q 027247 48 EYPCPFCSEDFD-LVGLCCHID 68 (226)
Q Consensus 48 ~f~CPfC~e~~d-v~~L~~H~~ 68 (226)
-|.|.+|+..|. ...+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 467888887555 666666653
No 147
>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=34.37 E-value=16 Score=28.24 Aligned_cols=37 Identities=16% Similarity=0.358 Sum_probs=19.3
Q ss_pred CCCCCCCccHhhhhhcccccC----CCCCccccCCccccCc
Q 027247 51 CPFCSEDFDLVGLCCHIDEEH----PVEAKSGVCPVCVTRV 87 (226)
Q Consensus 51 CPfC~e~~dv~~L~~H~~~eH----~~e~~~vvCPVC~~~v 87 (226)
||+|+.+--+.....|.-... .++....+||.|-...
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
Confidence 999996333333333221111 1133446799997754
No 148
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=34.25 E-value=10 Score=26.28 Aligned_cols=32 Identities=31% Similarity=0.645 Sum_probs=11.6
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
.-+||| |+.-+=.- -..++ .+..+++||-|-.
T Consensus 14 ~~~PC~-Cgf~IC~~-C~~~i-----~~~~~g~CPgCr~ 45 (48)
T PF14570_consen 14 DFYPCE-CGFQICRF-CYHDI-----LENEGGRCPGCRE 45 (48)
T ss_dssp T--SST-TS----HH-HHHHH-----TTSS-SB-TTT--
T ss_pred ccccCc-CCCcHHHH-HHHHH-----HhccCCCCCCCCC
Confidence 568886 76533111 11122 2245799999954
No 149
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=33.77 E-value=7.9 Score=23.61 Aligned_cols=11 Identities=36% Similarity=0.951 Sum_probs=7.3
Q ss_pred ccccCCccccC
Q 027247 76 KSGVCPVCVTR 86 (226)
Q Consensus 76 ~~vvCPVC~~~ 86 (226)
....||+|...
T Consensus 34 ~~~~Cp~C~~~ 44 (45)
T cd00162 34 GKNTCPLCRTP 44 (45)
T ss_pred CcCCCCCCCCc
Confidence 35679988653
No 150
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=33.76 E-value=23 Score=35.05 Aligned_cols=22 Identities=27% Similarity=0.607 Sum_probs=16.2
Q ss_pred ccccCCCCCccccCCccccCcc
Q 027247 67 IDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 67 ~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
|..+...+++..|||||...||
T Consensus 27 c~~~~~~~PNt~vcpv~lg~PG 48 (474)
T PRK05477 27 CSTDFGAEPNTNVCPVCLGLPG 48 (474)
T ss_pred CCcccCCCCCCCcCccccCCCC
Confidence 3333344678899999999988
No 151
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.58 E-value=25 Score=36.36 Aligned_cols=26 Identities=31% Similarity=0.469 Sum_probs=23.6
Q ss_pred eeeCCCCCC-CccHhhhhhcccccCCC
Q 027247 48 EYPCPFCSE-DFDLVGLCCHIDEEHPV 73 (226)
Q Consensus 48 ~f~CPfC~e-~~dv~~L~~H~~~eH~~ 73 (226)
---|+||.+ -||...|..|+..+|.+
T Consensus 182 hp~C~~C~~~fld~~el~rH~~~~h~~ 208 (669)
T KOG2231|consen 182 HPLCKFCHERFLDDDELYRHLRFDHEF 208 (669)
T ss_pred CccchhhhhhhccHHHHHHhhccceeh
Confidence 568999999 99999999999988876
No 152
>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=33.44 E-value=29 Score=20.21 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=12.1
Q ss_pred eeCCCCCC-CccHhhhhhccc
Q 027247 49 YPCPFCSE-DFDLVGLCCHID 68 (226)
Q Consensus 49 f~CPfC~e-~~dv~~L~~H~~ 68 (226)
|.|+.|+. =-+...+..|+.
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 56777777 345556666653
No 153
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=33.09 E-value=13 Score=28.69 Aligned_cols=8 Identities=50% Similarity=1.551 Sum_probs=6.7
Q ss_pred eeCCCCCC
Q 027247 49 YPCPFCSE 56 (226)
Q Consensus 49 f~CPfC~e 56 (226)
.+||+||.
T Consensus 2 I~CP~CG~ 9 (84)
T PF04267_consen 2 IPCPHCGP 9 (84)
T ss_dssp EEETTTEE
T ss_pred ccCCCCCc
Confidence 57999988
No 154
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.08 E-value=6.5 Score=32.64 Aligned_cols=38 Identities=34% Similarity=0.542 Sum_probs=23.1
Q ss_pred ceeeCCCCCCCccHh-hh-hhcccccCCCCC---ccccCCccc
Q 027247 47 YEYPCPFCSEDFDLV-GL-CCHIDEEHPVEA---KSGVCPVCV 84 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~-~L-~~H~~~eH~~e~---~~vvCPVC~ 84 (226)
..+.||.|.+.|... .| |-|.--..+... ....||+|.
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 468999999976666 22 333322222222 337999998
No 155
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=31.92 E-value=16 Score=25.17 Aligned_cols=39 Identities=13% Similarity=0.411 Sum_probs=23.3
Q ss_pred ceeeCCCCCC--CccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 47 YEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e--~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
+.=+|..|+. ++.+-.+--+ .+-..+....+|..|..++
T Consensus 6 s~~kCELC~a~~~L~vy~Vpp~--~~~~~d~~iliC~tC~~Qi 46 (47)
T smart00782 6 CESKCELCGSDSPLVVYAVPPS--SDVTADNSVMLCDTCHSQI 46 (47)
T ss_pred cCCcccCcCCCCCceEEecCCC--CCCCccceeeechHHHHhh
Confidence 4557999997 4433332211 1223466678999997654
No 156
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=31.89 E-value=21 Score=25.50 Aligned_cols=10 Identities=30% Similarity=0.939 Sum_probs=8.8
Q ss_pred ceeeCCCCCC
Q 027247 47 YEYPCPFCSE 56 (226)
Q Consensus 47 ~~f~CPfC~e 56 (226)
..|.||.||.
T Consensus 13 v~~~Cp~cGi 22 (55)
T PF13824_consen 13 VNFECPDCGI 22 (55)
T ss_pred cCCcCCCCCC
Confidence 6799999986
No 157
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=31.41 E-value=21 Score=27.48 Aligned_cols=8 Identities=50% Similarity=1.767 Sum_probs=6.5
Q ss_pred eeCCCCCC
Q 027247 49 YPCPFCSE 56 (226)
Q Consensus 49 f~CPfC~e 56 (226)
.+||+||.
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 57999995
No 158
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=31.32 E-value=19 Score=28.87 Aligned_cols=34 Identities=24% Similarity=0.819 Sum_probs=18.7
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
..|.||||.-+- ..-+-++..| -....-|-||..
T Consensus 22 t~FnClfcnHek---~v~~~~Dk~~--~iG~~sC~iC~e 55 (109)
T KOG3214|consen 22 TQFNCLFCNHEK---SVSCTLDKKH--NIGKASCRICEE 55 (109)
T ss_pred eeeccCcccccc---ceeeeehhhc--Ccceeeeeehhh
Confidence 459999997632 1111122222 234567999954
No 159
>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=30.99 E-value=26 Score=33.78 Aligned_cols=34 Identities=18% Similarity=0.316 Sum_probs=22.5
Q ss_pred ceeeCCCCCC--CccHhhh-hhcccccCCCCCccccCCccccC
Q 027247 47 YEYPCPFCSE--DFDLVGL-CCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 47 ~~f~CPfC~e--~~dv~~L-~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
.-..||||+. .-+...| |.||. ..+..||-|...
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 4478999998 4444445 66662 235789999654
No 160
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=30.98 E-value=30 Score=38.33 Aligned_cols=35 Identities=20% Similarity=0.152 Sum_probs=20.7
Q ss_pred cccccccccccCCCCCHHHHHHHHhHhhHHHHHHH
Q 027247 184 SCEKTFETNAQQSSLSNEDHLEKANRSNFAQGLLF 218 (226)
Q Consensus 184 s~~~~~e~~~~~~~ls~ed~eEk~~R~eFVQ~Lll 218 (226)
+++|.+|-.+|.--|+..=-+=-.+=+.||-.||-
T Consensus 825 ~~dQivELk~QDiil~~~aa~yl~~va~fiDdLL~ 859 (1337)
T PRK14714 825 HEDQVVELKVQDIVLSDGAAEYLLKVAKFVDDLLE 859 (1337)
T ss_pred CccceEEeecccEEcchHHHHHHHHHHHHHHHHHH
Confidence 34555666665223555444444667889888874
No 161
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=30.59 E-value=36 Score=33.09 Aligned_cols=48 Identities=31% Similarity=0.578 Sum_probs=33.6
Q ss_pred eeeCCCCCCC-ccHhhhhhcccccCCCCCccccCCccccCcc--hhhHhhhh
Q 027247 48 EYPCPFCSED-FDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT--MDMVDHIT 96 (226)
Q Consensus 48 ~f~CPfC~e~-~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~--~d~i~Hl~ 96 (226)
.|+||.|+-. =-.++|..|+.-.|.- .|.-.|--|...-- .|+..|+.
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 5888888773 3456788888877776 67777888876432 36666665
No 162
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=30.56 E-value=34 Score=37.88 Aligned_cols=37 Identities=30% Similarity=0.670 Sum_probs=21.8
Q ss_pred eeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCcch
Q 027247 48 EYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (226)
Q Consensus 48 ~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~ 89 (226)
.+.||-||. .+. ..|..|- .|. +. ...||.|-+.+..
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CG-s~t-e~-vy~CPsCGaev~~ 704 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCG-THT-EP-VYVCPDCGAEVPP 704 (1337)
T ss_pred EEECCCCCCcccc--ccCcccC-CcC-CC-ceeCccCCCccCC
Confidence 589999998 333 3665553 222 11 2368877775543
No 163
>PHA00626 hypothetical protein
Probab=30.51 E-value=32 Score=24.89 Aligned_cols=37 Identities=19% Similarity=0.264 Sum_probs=25.7
Q ss_pred eCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCcchhhHh
Q 027247 50 PCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVD 93 (226)
Q Consensus 50 ~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~i~ 93 (226)
.||-||. ++-..+.|. -.+..-+||-|--+-+.|..+
T Consensus 2 ~CP~CGS~~Ivrcg~cr-------~~snrYkCkdCGY~ft~~~~~ 39 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR-------GWSDDYVCCDCGYNDSKDAFG 39 (59)
T ss_pred CCCCCCCceeeeeceec-------ccCcceEcCCCCCeechhhhh
Confidence 5999998 665444432 123446899999988888876
No 164
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=29.96 E-value=32 Score=29.77 Aligned_cols=31 Identities=23% Similarity=0.505 Sum_probs=21.3
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
..|.||-|..-+....-+.+ .-.||.|.+.+
T Consensus 112 ~~y~C~~~~~r~sfdeA~~~----------~F~Cp~Cg~~L 142 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAMEL----------GFTCPKCGEDL 142 (176)
T ss_pred CceeCCCCCCcccHHHHHHh----------CCCCCCCCchh
Confidence 57999999984444443322 16999998765
No 165
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=29.75 E-value=21 Score=23.77 Aligned_cols=9 Identities=33% Similarity=1.206 Sum_probs=7.4
Q ss_pred eeeCCCCCC
Q 027247 48 EYPCPFCSE 56 (226)
Q Consensus 48 ~f~CPfC~e 56 (226)
...||||+.
T Consensus 29 ~~~CpYCg~ 37 (40)
T PF10276_consen 29 PVVCPYCGT 37 (40)
T ss_dssp EEEETTTTE
T ss_pred eEECCCCCC
Confidence 478999985
No 166
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=29.66 E-value=42 Score=31.34 Aligned_cols=30 Identities=30% Similarity=0.535 Sum_probs=23.1
Q ss_pred ccCcceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccC
Q 027247 43 VKGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 43 ~~~~~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
+| -+||-|++-+=..+|- .+..|||-|...
T Consensus 27 lw----~KCp~c~~~~y~~eL~----------~n~~vcp~c~~h 56 (294)
T COG0777 27 LW----TKCPSCGEMLYRKELE----------SNLKVCPKCGHH 56 (294)
T ss_pred ce----eECCCccceeeHHHHH----------hhhhcccccCcc
Confidence 77 8999999866556664 445899999774
No 167
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=29.03 E-value=21 Score=28.35 Aligned_cols=14 Identities=29% Similarity=0.463 Sum_probs=8.6
Q ss_pred ceeeCCCCCCCccH
Q 027247 47 YEYPCPFCSEDFDL 60 (226)
Q Consensus 47 ~~f~CPfC~e~~dv 60 (226)
..+.|+-|+..|..
T Consensus 69 ~~~~C~~Cg~~~~~ 82 (114)
T PRK03681 69 AECWCETCQQYVTL 82 (114)
T ss_pred cEEEcccCCCeeec
Confidence 45777777765443
No 168
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=28.63 E-value=20 Score=23.22 Aligned_cols=26 Identities=35% Similarity=0.862 Sum_probs=15.2
Q ss_pred eCCCCCCCccHhhhhhcccccCCCCCccccCCccc
Q 027247 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCV 84 (226)
Q Consensus 50 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~ 84 (226)
.||-|+..+....+ .+-..-+||-|.
T Consensus 1 ~CP~C~~~l~~~~~---------~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTELEPVRL---------GDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcccceEEE---------CCEEEEECCCCC
Confidence 38888776654444 223344688774
No 169
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=28.32 E-value=28 Score=32.00 Aligned_cols=38 Identities=29% Similarity=0.575 Sum_probs=27.0
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcchhhHhh
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDH 94 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~i~H 94 (226)
....||.|+.. + + +.+ ++...+||.-|-.-+..++|.+
T Consensus 10 ~~~~Cp~Cg~~-~---i---v~d---~~~Ge~vC~~CG~Vl~e~~iD~ 47 (310)
T PRK00423 10 EKLVCPECGSD-K---L---IYD---YERGEIVCADCGLVIEENIIDQ 47 (310)
T ss_pred cCCcCcCCCCC-C---e---eEE---CCCCeEeecccCCccccccccc
Confidence 35689999962 1 1 122 3577899999999888887763
No 170
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=28.10 E-value=22 Score=23.91 Aligned_cols=26 Identities=23% Similarity=0.622 Sum_probs=15.0
Q ss_pred ceeeCCCCCCCccHh------hhhhcccccCC
Q 027247 47 YEYPCPFCSEDFDLV------GLCCHIDEEHP 72 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~------~L~~H~~~eH~ 72 (226)
+.-.|-+|+..+... .|..|+...|+
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 346777887755443 45555544443
No 171
>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=27.75 E-value=20 Score=31.32 Aligned_cols=21 Identities=19% Similarity=0.248 Sum_probs=0.0
Q ss_pred eeeCCCCCCCccHhhhhhccc
Q 027247 48 EYPCPFCSEDFDLVGLCCHID 68 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~ 68 (226)
...||+||+-+-+..+-.|+.
T Consensus 168 ~~~cPitGe~IP~~e~~eHmR 188 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMR 188 (229)
T ss_dssp ---------------------
T ss_pred ccccccccccccccccccccc
Confidence 479999999999999999984
No 172
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=27.52 E-value=26 Score=27.82 Aligned_cols=39 Identities=21% Similarity=0.354 Sum_probs=30.0
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
.=+||.|+..+.-..|..-| ++-.|.+....|-||.. ||
T Consensus 27 DgkC~ICDS~VRP~tlVRiC-~eC~~Gs~q~~ciic~~-~g 65 (110)
T KOG1705|consen 27 DGKCVICDSYVRPCTLVRIC-DECNYGSYQGRCVICGG-VG 65 (110)
T ss_pred CCcccccccccccceeeeee-hhcCCccccCceEEecC-Cc
Confidence 45799998877777777544 66688888899999976 55
No 173
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.50 E-value=31 Score=27.53 Aligned_cols=27 Identities=37% Similarity=0.691 Sum_probs=19.0
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
..+.|+-|+..+.+... ....||-|..
T Consensus 70 ~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs 96 (117)
T PRK00564 70 VELECKDCSHVFKPNAL------------DYGVCEKCHS 96 (117)
T ss_pred CEEEhhhCCCccccCCc------------cCCcCcCCCC
Confidence 57999999976665422 2245999975
No 174
>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=27.31 E-value=6.5 Score=24.77 Aligned_cols=6 Identities=50% Similarity=1.519 Sum_probs=2.8
Q ss_pred ccCCcc
Q 027247 78 GVCPVC 83 (226)
Q Consensus 78 vvCPVC 83 (226)
..||+|
T Consensus 36 ~~CP~C 41 (41)
T PF00097_consen 36 VKCPLC 41 (41)
T ss_dssp SBTTTT
T ss_pred ccCCcC
Confidence 345544
No 175
>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=27.13 E-value=34 Score=24.43 Aligned_cols=19 Identities=26% Similarity=0.546 Sum_probs=12.7
Q ss_pred ceeeCCCCCCCccHhhhhh
Q 027247 47 YEYPCPFCSEDFDLVGLCC 65 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~ 65 (226)
..-.||+|.-.+|-..|..
T Consensus 6 niL~Cp~ck~pL~~~~l~~ 24 (68)
T PF03966_consen 6 NILACPVCKGPLDWEALVE 24 (68)
T ss_dssp GTBB-TTTSSBEHHHHHHH
T ss_pred hhhcCCCCCCcchHHHHHH
Confidence 4578999988776565554
No 176
>PF14369 zf-RING_3: zinc-finger
Probab=27.04 E-value=30 Score=22.15 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=8.2
Q ss_pred eeCCCCCCCc
Q 027247 49 YPCPFCSEDF 58 (226)
Q Consensus 49 f~CPfC~e~~ 58 (226)
..||.|+.+|
T Consensus 22 ~~CP~C~~gF 31 (35)
T PF14369_consen 22 VACPRCHGGF 31 (35)
T ss_pred cCCcCCCCcE
Confidence 4799999876
No 177
>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=27.04 E-value=35 Score=21.62 Aligned_cols=27 Identities=30% Similarity=0.705 Sum_probs=13.6
Q ss_pred eeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 49 f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
|.|.-|+..+++.. ...+.||-|..++
T Consensus 1 Y~C~~Cg~~~~~~~------------~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELKP------------GDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BST------------SSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEcCC------------CCcEECCcCCCeE
Confidence 45666766655211 2236777775543
No 178
>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=26.83 E-value=26 Score=34.69 Aligned_cols=48 Identities=17% Similarity=0.258 Sum_probs=33.4
Q ss_pred CccHhhhhhcccccCCCCCc-----------------cccCCccccCcc--hhhHhhhhhccccccc
Q 027247 57 DFDLVGLCCHIDEEHPVEAK-----------------SGVCPVCVTRVT--MDMVDHITTQHGNISN 104 (226)
Q Consensus 57 ~~dv~~L~~H~~~eH~~e~~-----------------~vvCPVC~~~v~--~d~i~Hl~~qH~~~~K 104 (226)
-+.+..|..|+...|..++. .-+||+|..+-. .++..|+...|-.-++
T Consensus 20 kVsi~eL~sy~~~~~~~~a~~~Lseal~fak~n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~ 86 (466)
T PF04780_consen 20 KVSIDELKSYYESVYDREAADALSEALSFAKENKSWRFWICPRCSKKFSDAESCLSHMEQEHPAGLK 86 (466)
T ss_pred eeEHHHHHHHHHhccchHHHHHHHHHHHHHHhcCceeEeeCCcccceeCCHHHHHHHHHHhhhhhcC
Confidence 45666777777666543322 346999997643 6899999988877653
No 179
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=26.65 E-value=35 Score=34.44 Aligned_cols=20 Identities=30% Similarity=0.541 Sum_probs=16.1
Q ss_pred ccCCCCCccccCCccccCcc
Q 027247 69 EEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 69 ~eH~~e~~~vvCPVC~~~v~ 88 (226)
.+...+++.-|||||...||
T Consensus 85 ~~~g~~PNt~vcpvclg~PG 104 (544)
T PLN02751 85 YNYGAEPNTTVCPVCMGLPG 104 (544)
T ss_pred cccCCCCccCcCccccCCCC
Confidence 34455788899999999988
No 180
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=26.44 E-value=20 Score=37.12 Aligned_cols=43 Identities=26% Similarity=0.564 Sum_probs=31.5
Q ss_pred ceeeCCCCCCCc-c-HhhhhhcccccCCC----CCccccCCccccCcch
Q 027247 47 YEYPCPFCSEDF-D-LVGLCCHIDEEHPV----EAKSGVCPVCVTRVTM 89 (226)
Q Consensus 47 ~~f~CPfC~e~~-d-v~~L~~H~~~eH~~----e~~~vvCPVC~~~v~~ 89 (226)
...+||.|.... | +-..|-|+.=+-|. +++.--||.|.+.-|.
T Consensus 642 ~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred hceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 789999999833 2 34556677655554 6677789999988775
No 181
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=26.10 E-value=26 Score=30.43 Aligned_cols=25 Identities=24% Similarity=0.598 Sum_probs=16.5
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcc
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
.-+||-||-.. ...+.|+-|..+|-
T Consensus 93 l~~CP~CGh~k----------------~a~~LC~~Cy~kV~ 117 (176)
T KOG4080|consen 93 LNTCPACGHIK----------------PAHTLCDYCYAKVH 117 (176)
T ss_pred cccCcccCccc----------------cccccHHHHHHHHH
Confidence 46899998432 22367888877664
No 182
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=26.03 E-value=19 Score=35.68 Aligned_cols=35 Identities=37% Similarity=0.687 Sum_probs=19.5
Q ss_pred eeeCCCCCCCccHhh------hhhcccccCCC---CCccccCCccc
Q 027247 48 EYPCPFCSEDFDLVG------LCCHIDEEHPV---EAKSGVCPVCV 84 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~------L~~H~~~eH~~---e~~~vvCPVC~ 84 (226)
-=+||.|=|-+|... ||.| ..|+. --.+.-||||.
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~H--sfh~~cl~~w~~~scpvcR 218 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNH--SFHCSCLMKWWDSSCPVCR 218 (493)
T ss_pred CCCcchhHhhcCccccceeeeeccc--ccchHHHhhcccCcChhhh
Confidence 358999999555433 5555 23332 11345677764
No 183
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=25.86 E-value=33 Score=29.75 Aligned_cols=14 Identities=50% Similarity=1.177 Sum_probs=11.0
Q ss_pred eeCCCCCCCccHhh
Q 027247 49 YPCPFCSEDFDLVG 62 (226)
Q Consensus 49 f~CPfC~e~~dv~~ 62 (226)
=+||+||.-+|-.+
T Consensus 155 P~CPlCg~PlDP~G 168 (171)
T PF11290_consen 155 PPCPLCGEPLDPEG 168 (171)
T ss_pred CCCCCCCCCCCCCC
Confidence 47999999887543
No 184
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.62 E-value=33 Score=27.75 Aligned_cols=17 Identities=29% Similarity=0.659 Sum_probs=13.4
Q ss_pred eeeCCCCCCCccHhhhh
Q 027247 48 EYPCPFCSEDFDLVGLC 64 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~ 64 (226)
...||-||+.|+-..+.
T Consensus 49 ~t~CP~Cg~~~e~~fvv 65 (115)
T COG1885 49 STSCPKCGEPFESAFVV 65 (115)
T ss_pred cccCCCCCCccceeEEE
Confidence 57899999998866543
No 185
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=25.48 E-value=32 Score=25.70 Aligned_cols=8 Identities=38% Similarity=1.547 Sum_probs=5.3
Q ss_pred eeCCCCCC
Q 027247 49 YPCPFCSE 56 (226)
Q Consensus 49 f~CPfC~e 56 (226)
+.||+||.
T Consensus 2 m~CP~Cg~ 9 (72)
T PRK09678 2 FHCPLCQH 9 (72)
T ss_pred ccCCCCCC
Confidence 46777766
No 186
>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=25.30 E-value=41 Score=31.34 Aligned_cols=26 Identities=35% Similarity=0.708 Sum_probs=17.2
Q ss_pred hhhcccccCCCCCccccCCccccCcc
Q 027247 63 LCCHIDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 63 L~~H~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
|.|.|......+++.-|||+|...||
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 34445555555788899999999988
No 187
>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=25.16 E-value=44 Score=36.82 Aligned_cols=47 Identities=19% Similarity=0.415 Sum_probs=31.4
Q ss_pred cCCccCCCcchhhhccCcceeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 29 CIDFEDIEEDDYEEVKGEYEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 29 ~~~~e~~~~d~d~e~~~~~~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
.+|+-|++ + ++ +-|.||-|.- +|...+- -.--++--.-.||.|....
T Consensus 671 ~lgITeVd---P--L~--phy~c~~c~~~ef~~~~~-----~~sg~dlp~k~cp~c~~~~ 718 (1213)
T TIGR01405 671 MTGITEVN---P--LP--PHYLCPNCKYSEFITDGS-----VGSGFDLPDKDCPKCGAPL 718 (1213)
T ss_pred HhcCCCcC---C--Cc--ccccCccccccccccccc-----ccccccCccccCccccccc
Confidence 55776666 4 77 8999999987 7754431 1112455567899998854
No 188
>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=24.94 E-value=39 Score=33.42 Aligned_cols=15 Identities=33% Similarity=0.789 Sum_probs=13.6
Q ss_pred CCccccCCccccCcc
Q 027247 74 EAKSGVCPVCVTRVT 88 (226)
Q Consensus 74 e~~~vvCPVC~~~v~ 88 (226)
+++..|||||...||
T Consensus 34 ~PNt~v~pvclg~PG 48 (478)
T TIGR00133 34 PPNTNVCPVCLGLPG 48 (478)
T ss_pred CCCcccCccccCCCC
Confidence 678899999999988
No 189
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.81 E-value=20 Score=34.68 Aligned_cols=42 Identities=21% Similarity=0.498 Sum_probs=25.0
Q ss_pred ceeeCCCCCCCccHh--hhhhcccccCCCC---CccccCCccccCcc
Q 027247 47 YEYPCPFCSEDFDLV--GLCCHIDEEHPVE---AKSGVCPVCVTRVT 88 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~--~L~~H~~~eH~~e---~~~vvCPVC~~~v~ 88 (226)
..|.||.|.+.|... .=|.|..=..|.. .....||+|-..++
T Consensus 25 ~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 25 TSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred cccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 569999999866544 3344432222211 12347999988654
No 190
>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=24.77 E-value=36 Score=23.55 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=8.9
Q ss_pred ceeeCCCCCC
Q 027247 47 YEYPCPFCSE 56 (226)
Q Consensus 47 ~~f~CPfC~e 56 (226)
..|.||.|+.
T Consensus 33 ~~w~CP~C~a 42 (50)
T cd00730 33 DDWVCPVCGA 42 (50)
T ss_pred CCCCCCCCCC
Confidence 6799999987
No 191
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.91 E-value=32 Score=32.74 Aligned_cols=24 Identities=38% Similarity=0.870 Sum_probs=20.0
Q ss_pred eeeCCCCCCCccHhhhhhcccccCC
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHP 72 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~ 72 (226)
+.-||||.-.+.....|.|++ -|-
T Consensus 2 e~iCP~CkLsv~~~~m~~Hie-aHF 25 (393)
T KOG4696|consen 2 EIICPFCKLSVNYDEMCFHIE-AHF 25 (393)
T ss_pred cccccceecccCHHHHHHHHH-hhc
Confidence 356999999999999999996 443
No 192
>PHA02929 N1R/p28-like protein; Provisional
Probab=23.91 E-value=19 Score=32.48 Aligned_cols=41 Identities=24% Similarity=0.482 Sum_probs=24.3
Q ss_pred ceeeCCCCCCCccHh----------hhhhcccccCCC---CCccccCCccccCc
Q 027247 47 YEYPCPFCSEDFDLV----------GLCCHIDEEHPV---EAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~----------~L~~H~~~eH~~---e~~~vvCPVC~~~v 87 (226)
....||.|.+.+... .=|.|.--..+. -.....||+|...+
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~ 226 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF 226 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence 357899999965432 225664333322 12456899997654
No 193
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.62 E-value=41 Score=34.53 Aligned_cols=37 Identities=22% Similarity=0.383 Sum_probs=23.5
Q ss_pred ceeeCCCCCCCccH----hhhhhcccccCCCCCccccCCccccC
Q 027247 47 YEYPCPFCSEDFDL----VGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 47 ~~f~CPfC~e~~dv----~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
..+.||.|+-.+.. ..|.||-...+ ...-.||-|...
T Consensus 391 ~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~---~~p~~Cp~Cgs~ 431 (665)
T PRK14873 391 TPARCRHCTGPLGLPSAGGTPRCRWCGRA---APDWRCPRCGSD 431 (665)
T ss_pred CeeECCCCCCceeEecCCCeeECCCCcCC---CcCccCCCCcCC
Confidence 46899999985554 24644433332 236799999763
No 194
>PRK05978 hypothetical protein; Provisional
Probab=23.58 E-value=35 Score=28.76 Aligned_cols=28 Identities=21% Similarity=0.441 Sum_probs=16.9
Q ss_pred eeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccC
Q 027247 48 EYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (226)
Q Consensus 48 ~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~ 86 (226)
.-+||-||+ .+=. .+-.-+-.||+|-..
T Consensus 33 ~grCP~CG~G~LF~-----------g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 33 RGRCPACGEGKLFR-----------AFLKPVDHCAACGED 61 (148)
T ss_pred cCcCCCCCCCcccc-----------cccccCCCccccCCc
Confidence 468999999 4311 222334567777663
No 195
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.56 E-value=30 Score=27.87 Aligned_cols=8 Identities=38% Similarity=1.281 Sum_probs=4.3
Q ss_pred eeCCCCCC
Q 027247 49 YPCPFCSE 56 (226)
Q Consensus 49 f~CPfC~e 56 (226)
|.||.||.
T Consensus 93 ~~CP~Cgs 100 (124)
T PRK00762 93 IECPVCGN 100 (124)
T ss_pred CcCcCCCC
Confidence 45555553
No 196
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=23.41 E-value=39 Score=31.19 Aligned_cols=18 Identities=33% Similarity=0.730 Sum_probs=15.7
Q ss_pred ccCcceeeCCCCCCCccH
Q 027247 43 VKGEYEYPCPFCSEDFDL 60 (226)
Q Consensus 43 ~~~~~~f~CPfC~e~~dv 60 (226)
+||..+|.||-|+..|.-
T Consensus 150 mwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 150 MWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred ccceeeeecccccccchh
Confidence 888899999999988763
No 197
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=23.37 E-value=53 Score=25.30 Aligned_cols=29 Identities=21% Similarity=0.439 Sum_probs=0.0
Q ss_pred CCccccCCccccCcc-hhhHhhhhhccccc
Q 027247 74 EAKSGVCPVCVTRVT-MDMVDHITTQHGNI 102 (226)
Q Consensus 74 e~~~vvCPVC~~~v~-~d~i~Hl~~qH~~~ 102 (226)
+.+.+||-.|-..|+ ..+.+|+..+|..+
T Consensus 8 ~~~vlIC~~C~~av~~~~v~~HL~~~H~~~ 37 (109)
T PF12013_consen 8 EYRVLICRQCQYAVQPSEVESHLRKRHHIL 37 (109)
T ss_pred cCCEEEeCCCCcccCchHHHHHHHHhcccc
No 198
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=22.99 E-value=36 Score=36.29 Aligned_cols=34 Identities=21% Similarity=0.563 Sum_probs=23.1
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCcccc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~ 85 (226)
+.|.||.|+..+..-+= .--.|.+-.+.||-|.-
T Consensus 244 ~~~acp~~g~~~~elep-----rlFSFNsP~GaCp~C~G 277 (935)
T COG0178 244 ENFACPVCGFSIPELEP-----RLFSFNSPFGACPTCDG 277 (935)
T ss_pred cccCCCccCcccCCCCc-----ccccCCCCCCCCCcCCC
Confidence 57999999875543221 22245677799999976
No 199
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=22.92 E-value=50 Score=23.06 Aligned_cols=30 Identities=33% Similarity=0.810 Sum_probs=21.0
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
..|.|--||..|+.. .....+.||-|..++
T Consensus 5 ~~Y~C~~Cg~~~~~~-----------~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVELD-----------QETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeehh-----------hccCceeCCCCCcEE
Confidence 579999999987322 124457899997655
No 200
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=22.85 E-value=28 Score=35.49 Aligned_cols=49 Identities=27% Similarity=0.555 Sum_probs=30.2
Q ss_pred ceeeCCCCCC-Ccc-Hhhhhhcc-----cc---cCCCCCccccCCccccCcchhhHhhh
Q 027247 47 YEYPCPFCSE-DFD-LVGLCCHI-----DE---EHPVEAKSGVCPVCVTRVTMDMVDHI 95 (226)
Q Consensus 47 ~~f~CPfC~e-~~d-v~~L~~H~-----~~---eH~~e~~~vvCPVC~~~v~~d~i~Hl 95 (226)
...-|-+|.+ -=| +..=|.|. .. +--.+..+|.||+|...+.-|+..|-
T Consensus 535 ~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~a 593 (791)
T KOG1002|consen 535 GEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPA 593 (791)
T ss_pred CceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchh
Confidence 5678999988 222 33333332 11 22347778999999988776655543
No 201
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.53 E-value=33 Score=26.32 Aligned_cols=46 Identities=24% Similarity=0.530 Sum_probs=32.0
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcchhhHhhhhhcccccccc
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHITTQHGNISNS 105 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~i~Hl~~qH~~~~K~ 105 (226)
..|.|--|+..+||.. |+ .+.-.+.||-|.+++.+- ..+-|..||.
T Consensus 11 Y~Y~c~~cg~~~dvvq---~~-----~ddplt~ce~c~a~~kk~-----l~~vgi~fKG 56 (82)
T COG2331 11 YSYECTECGNRFDVVQ---AM-----TDDPLTTCEECGARLKKL-----LNAVGIVFKG 56 (82)
T ss_pred eEEeecccchHHHHHH---hc-----ccCccccChhhChHHHHh-----hccceEEEec
Confidence 4689999999998764 33 345568999999866542 2345667774
No 202
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=22.53 E-value=52 Score=36.88 Aligned_cols=47 Identities=23% Similarity=0.484 Sum_probs=30.9
Q ss_pred cCCccCCCcchhhhccCcceeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 29 CIDFEDIEEDDYEEVKGEYEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 29 ~~~~e~~~~d~d~e~~~~~~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
.+|+-|++ + +. +-|.||-|.- +|...+= -.--++--.-.||.|...+
T Consensus 896 ~lgITeVd---P--L~--phy~C~~C~~~ef~~~~~-----~~sG~Dlpdk~Cp~Cg~~~ 943 (1437)
T PRK00448 896 MIGITEVN---P--LP--PHYVCPNCKYSEFFTDGS-----VGSGFDLPDKDCPKCGTKL 943 (1437)
T ss_pred HhcCCCcC---C--CC--ccccCccccccccccccc-----ccccccCccccCccccccc
Confidence 56777766 4 77 8999999977 7644331 0112344556899998854
No 203
>cd03021 DsbA_GSTK DsbA family, Glutathione (GSH) S-transferase Kappa (GSTK) subfamily; GSTK is a member of the GST family of enzymes which catalyzes the transfer of the thiol of GSH to electrophilic substrates. It is specifically located in the mitochondria and peroxisomes, unlike other members of the canonical GST family, which are mainly cytosolic. The biological substrates of GSTK are not yet known. It is presumed to have a protective role during respiration when large amounts of reactive oxygen species are generated. GSTK has the same general fold as DsbA, consisting of a thioredoxin domain interrupted by an alpha-helical domain and its biological unit is a homodimer. GSTK is closely related to the bacterial enzyme, 2-hydroxychromene-2-carboxylate (HCCA) isomerase. It shows little sequence similarity to the other members of the GST family.
Probab=22.38 E-value=19 Score=30.54 Aligned_cols=12 Identities=25% Similarity=0.625 Sum_probs=10.1
Q ss_pred ceeeCCCCCCCc
Q 027247 47 YEYPCPFCSEDF 58 (226)
Q Consensus 47 ~~f~CPfC~e~~ 58 (226)
..|.||||+.+.
T Consensus 7 ~D~vcPwcylg~ 18 (209)
T cd03021 7 YDVVSPYSYLAF 18 (209)
T ss_pred EeCCChHHHHHH
Confidence 689999999853
No 204
>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=22.38 E-value=37 Score=22.57 Aligned_cols=8 Identities=50% Similarity=1.447 Sum_probs=4.0
Q ss_pred eeCCCCCC
Q 027247 49 YPCPFCSE 56 (226)
Q Consensus 49 f~CPfC~e 56 (226)
-|||.|+-
T Consensus 4 ~pCP~CGG 11 (40)
T PF08273_consen 4 GPCPICGG 11 (40)
T ss_dssp E--TTTT-
T ss_pred CCCCCCcC
Confidence 47999976
No 205
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.23 E-value=36 Score=29.94 Aligned_cols=37 Identities=24% Similarity=0.585 Sum_probs=23.2
Q ss_pred CCCCCC-CccHhhh-hhcccccCCCCCccccCCccccCc
Q 027247 51 CPFCSE-DFDLVGL-CCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 51 CPfC~e-~~dv~~L-~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
|=.|++ +..|.-| |.|+--=-.-+...-+||||-..+
T Consensus 161 Cr~C~~~~~~VlllPCrHl~lC~~C~~~~~~CPiC~~~~ 199 (207)
T KOG1100|consen 161 CRKCGEREATVLLLPCRHLCLCGICDESLRICPICRSPK 199 (207)
T ss_pred ceecCcCCceEEeecccceEecccccccCccCCCCcChh
Confidence 999999 8887665 555422112232266799996543
No 206
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=22.22 E-value=51 Score=32.08 Aligned_cols=56 Identities=20% Similarity=0.290 Sum_probs=32.2
Q ss_pred eeeCCC--CCC-CccHhhhhhcccccC-CCCCccccCCcccc--CcchhhHhhhhhcccccc
Q 027247 48 EYPCPF--CSE-DFDLVGLCCHIDEEH-PVEAKSGVCPVCVT--RVTMDMVDHITTQHGNIS 103 (226)
Q Consensus 48 ~f~CPf--C~e-~~dv~~L~~H~~~eH-~~e~~~vvCPVC~~--~v~~d~i~Hl~~qH~~~~ 103 (226)
.|.|-+ |-+ -=....+..|..+.| .+..-.-.|-+|.. .-|.++.+||+-+|++-.
T Consensus 319 ~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~ 380 (467)
T KOG3608|consen 319 VYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRL 380 (467)
T ss_pred ceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccC
Confidence 345544 444 222334445555544 22333345777765 356799999999999743
No 207
>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=21.70 E-value=42 Score=22.98 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=6.9
Q ss_pred ceeeCCCCCC
Q 027247 47 YEYPCPFCSE 56 (226)
Q Consensus 47 ~~f~CPfC~e 56 (226)
..|.||-|+.
T Consensus 33 ~~w~CP~C~a 42 (47)
T PF00301_consen 33 DDWVCPVCGA 42 (47)
T ss_dssp TT-B-TTTSS
T ss_pred CCCcCcCCCC
Confidence 6799999986
No 208
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=21.53 E-value=46 Score=31.09 Aligned_cols=9 Identities=33% Similarity=0.929 Sum_probs=7.1
Q ss_pred eeeCCCCCC
Q 027247 48 EYPCPFCSE 56 (226)
Q Consensus 48 ~f~CPfC~e 56 (226)
.=.||.||.
T Consensus 184 ~~~CPvCGs 192 (305)
T TIGR01562 184 RTLCPACGS 192 (305)
T ss_pred CCcCCCCCC
Confidence 358999998
No 209
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=21.46 E-value=64 Score=27.83 Aligned_cols=39 Identities=18% Similarity=0.269 Sum_probs=22.4
Q ss_pred eCCCCCCCc---cHhhhhhcccccCCC-CCccccCCccccCcc
Q 027247 50 PCPFCSEDF---DLVGLCCHIDEEHPV-EAKSGVCPVCVTRVT 88 (226)
Q Consensus 50 ~CPfC~e~~---dv~~L~~H~~~eH~~-e~~~vvCPVC~~~v~ 88 (226)
.||+|+..+ .-.....-+...|.- ....-+||.|-..-|
T Consensus 99 RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 99 RCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred cCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccccc
Confidence 599999843 333333333333332 233467999988665
No 210
>PRK01546 hypothetical protein; Provisional
Probab=21.31 E-value=89 Score=23.88 Aligned_cols=29 Identities=21% Similarity=0.379 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHh---------HhhHHHHHHHhhhccC
Q 027247 196 SSLSNEDHLEKAN---------RSNFAQGLLFSTIMDD 224 (226)
Q Consensus 196 ~~ls~ed~eEk~~---------R~eFVQ~LllSTifdd 224 (226)
.-|+++|++|+.+ |..|-++|-.-.|.|+
T Consensus 20 ~gLT~eEk~Eq~~LR~eYl~~fR~~~~~~L~~i~vvD~ 57 (79)
T PRK01546 20 EGLTEEEQRERQSLREQYLKGFRQNMLNELKGIKVVNE 57 (79)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHhccceEECC
Confidence 5699999999854 6667677666666653
No 211
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=21.19 E-value=32 Score=36.61 Aligned_cols=38 Identities=26% Similarity=0.578 Sum_probs=0.0
Q ss_pred eeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcch
Q 027247 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (226)
Q Consensus 48 ~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~ 89 (226)
.+.||-||.. .....|..|- .|. ...-+||.|-..+..
T Consensus 655 ~r~Cp~Cg~~-t~~~~Cp~CG-~~T--~~~~~Cp~C~~~~~~ 692 (900)
T PF03833_consen 655 RRRCPKCGKE-TFYNRCPECG-SHT--EPVYVCPDCGIEVEE 692 (900)
T ss_dssp ------------------------------------------
T ss_pred cccCcccCCc-chhhcCcccC-Ccc--ccceeccccccccCc
Confidence 4677777762 2233343331 111 112356666555443
No 212
>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=21.17 E-value=50 Score=27.89 Aligned_cols=10 Identities=40% Similarity=0.823 Sum_probs=7.9
Q ss_pred ccccCCcccc
Q 027247 76 KSGVCPVCVT 85 (226)
Q Consensus 76 ~~vvCPVC~~ 85 (226)
+.+.||+|..
T Consensus 31 glv~CP~Cgs 40 (148)
T PF06676_consen 31 GLVSCPVCGS 40 (148)
T ss_pred CCccCCCCCC
Confidence 5578999965
No 213
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.17 E-value=61 Score=33.29 Aligned_cols=37 Identities=27% Similarity=0.538 Sum_probs=0.0
Q ss_pred eCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCcchh
Q 027247 50 PCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMD 90 (226)
Q Consensus 50 ~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d 90 (226)
.||-||. +-+-.-.|.+| -..-....||-|-+.+..+
T Consensus 3 ~Cp~Cg~~n~~~akFC~~C----G~~l~~~~Cp~CG~~~~~~ 40 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKC----GTSLTHKPCPQCGTEVPVD 40 (645)
T ss_pred cCCCCCCcCCCCCcccccc----CCCCCCCcCCCCCCCCCcc
No 214
>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=21.17 E-value=57 Score=28.15 Aligned_cols=40 Identities=23% Similarity=0.518 Sum_probs=25.9
Q ss_pred ceeeCCCCCCCccHhhhhhcccccCCCCCccccCCccccCcchhh
Q 027247 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDM 91 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v~~d~ 91 (226)
....|..|+..+....+..++. +...-.||.|...+..|+
T Consensus 108 ~~~~C~~C~~~~~~~~~~~~~~-----~~~~p~C~~Cg~~lrP~V 147 (218)
T cd01407 108 FRVRCTKCGKEYPRDELQADID-----REEVPRCPKCGGLLRPDV 147 (218)
T ss_pred CcceeCCCcCCCcHHHHhHhhc-----cCCCCcCCCCCCccCCCe
Confidence 3688999999877766553322 233457999976544443
No 215
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=21.13 E-value=31 Score=26.97 Aligned_cols=13 Identities=31% Similarity=0.887 Sum_probs=10.7
Q ss_pred ccCcceeeCCCCCCC
Q 027247 43 VKGEYEYPCPFCSED 57 (226)
Q Consensus 43 ~~~~~~f~CPfC~e~ 57 (226)
.+ +.+.||+|+..
T Consensus 32 ~~--~~~~Cp~C~~~ 44 (89)
T COG1997 32 QR--AKHVCPFCGRT 44 (89)
T ss_pred Hh--cCCcCCCCCCc
Confidence 55 78999999874
No 216
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=21.09 E-value=64 Score=31.58 Aligned_cols=44 Identities=27% Similarity=0.508 Sum_probs=25.6
Q ss_pred ceeeCCCCCC--CccHhhhhhcccccCCCCCccccCCcccc-CcchhhHhhhhhcccccc
Q 027247 47 YEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVT-RVTMDMVDHITTQHGNIS 103 (226)
Q Consensus 47 ~~f~CPfC~e--~~dv~~L~~H~~~eH~~e~~~vvCPVC~~-~v~~d~i~Hl~~qH~~~~ 103 (226)
..+.||-|+. +.+...| ++.+.||-|.. .+.. +.-|-+.|.+++
T Consensus 226 ~l~~C~~C~~s~n~e~~~~-----------sk~~~Cp~C~~~~L~~--~~~IEVgHtF~L 272 (457)
T KOG2324|consen 226 TLMSCPSCGYSKNSEDLDL-----------SKIASCPKCNEGRLTK--TKSIEVGHTFLL 272 (457)
T ss_pred ceeecCcCCccCchhhhcC-----------CccccCCcccCCCccc--ccceEEEEEEEe
Confidence 4689999975 3333222 44589999998 3322 222234455554
No 217
>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=20.97 E-value=51 Score=23.74 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=8.3
Q ss_pred eeCCCCCCCccH
Q 027247 49 YPCPFCSEDFDL 60 (226)
Q Consensus 49 f~CPfC~e~~dv 60 (226)
=-||+||+.+..
T Consensus 4 kHC~~CG~~Ip~ 15 (59)
T PF09889_consen 4 KHCPVCGKPIPP 15 (59)
T ss_pred CcCCcCCCcCCc
Confidence 358888886653
No 218
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=20.73 E-value=48 Score=23.74 Aligned_cols=10 Identities=50% Similarity=1.265 Sum_probs=8.3
Q ss_pred eeeCCCCCCC
Q 027247 48 EYPCPFCSED 57 (226)
Q Consensus 48 ~f~CPfC~e~ 57 (226)
..+||||+..
T Consensus 35 ~~pC~fCg~~ 44 (57)
T PF06221_consen 35 LGPCPFCGTP 44 (57)
T ss_pred cCcCCCCCCc
Confidence 5799999973
No 219
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=20.73 E-value=39 Score=25.69 Aligned_cols=14 Identities=29% Similarity=0.807 Sum_probs=7.6
Q ss_pred ceeeCCCCCCCccH
Q 027247 47 YEYPCPFCSEDFDL 60 (226)
Q Consensus 47 ~~f~CPfC~e~~dv 60 (226)
+.|.||-|++.+++
T Consensus 64 s~~~Cp~Cg~~~~i 77 (81)
T PF10609_consen 64 SYFVCPHCGERIYI 77 (81)
T ss_dssp -EEE-TTT--EEET
T ss_pred CccCCCCCCCeecC
Confidence 58999999985543
No 220
>TIGR00618 sbcc exonuclease SbcC. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.62 E-value=32 Score=36.62 Aligned_cols=34 Identities=15% Similarity=0.197 Sum_probs=19.5
Q ss_pred ceeeCCCCCC-CccHhhhhhcccccCCCCCccccCCccccCc
Q 027247 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (226)
Q Consensus 47 ~~f~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vvCPVC~~~v 87 (226)
+.=+||+||. ++=...... .....+.||.|....
T Consensus 500 ~~~~cplcgs~~hp~~~~~~-------~~~~~~~~~~~~~~~ 534 (1042)
T TIGR00618 500 QEEPCPLCGSCIHPNPARQD-------IDNPGPLTRRMQRGE 534 (1042)
T ss_pred CCCCCCCCCCCCCCChhhcc-------CCCCCHHHHHHHHHH
Confidence 4579999998 332121111 112357899986644
No 221
>PF05979 DUF896: Bacterial protein of unknown function (DUF896); InterPro: IPR009242 This family consists of several short, hypothetical bacterial proteins of unknown function. They may be involved in the bacterial SOS response [].; PDB: 2HEP_A 3BHP_C 2JVD_A.
Probab=20.62 E-value=49 Score=24.33 Aligned_cols=29 Identities=34% Similarity=0.479 Sum_probs=15.0
Q ss_pred CCCCHHHHHHHHh---------HhhHHHHHHHhhhccC
Q 027247 196 SSLSNEDHLEKAN---------RSNFAQGLLFSTIMDD 224 (226)
Q Consensus 196 ~~ls~ed~eEk~~---------R~eFVQ~LllSTifdd 224 (226)
..|+++|.+|+.. |..|-++|-.-.|.|+
T Consensus 17 ~gLT~eE~~Eq~~LR~eYl~~fR~~~~~~L~~i~ivD~ 54 (65)
T PF05979_consen 17 EGLTEEEKAEQAELRQEYLQNFRGNFRSQLENIKIVDP 54 (65)
T ss_dssp T---HHHHHHHHHHHHHHHHTTHHHHHHCSSTT-----
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcceeEECC
Confidence 5699999999854 6666666655555543
No 222
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=20.55 E-value=38 Score=31.54 Aligned_cols=42 Identities=19% Similarity=0.388 Sum_probs=29.9
Q ss_pred ceeeCCCCCCCccHhhhhhc---ccccCCCCCccccCCccccCcc
Q 027247 47 YEYPCPFCSEDFDLVGLCCH---IDEEHPVEAKSGVCPVCVTRVT 88 (226)
Q Consensus 47 ~~f~CPfC~e~~dv~~L~~H---~~~eH~~e~~~vvCPVC~~~v~ 88 (226)
..+.||.|.+.+......++ +.=.=+-......||.|...+|
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCcccceecCCCcEehhhhhhhhcccCCccccccc
Confidence 47899999999988887764 2222222345578999999877
No 223
>cd03024 DsbA_FrnE DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=20.47 E-value=26 Score=28.78 Aligned_cols=21 Identities=19% Similarity=0.422 Sum_probs=14.9
Q ss_pred ceeeCCCCCC-CccHhhhhhcc
Q 027247 47 YEYPCPFCSE-DFDLVGLCCHI 67 (226)
Q Consensus 47 ~~f~CPfC~e-~~dv~~L~~H~ 67 (226)
..|.||||+. .-.+..+....
T Consensus 5 ~D~~cP~cyl~~~~l~~~~~~~ 26 (201)
T cd03024 5 SDVVCPWCYIGKRRLEKALAEL 26 (201)
T ss_pred ecCcCccHHHHHHHHHHHHHhC
Confidence 5799999998 55565665443
No 224
>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=20.41 E-value=36 Score=27.18 Aligned_cols=18 Identities=28% Similarity=0.704 Sum_probs=12.9
Q ss_pred ceeeCCCCCC-CccHhhhh
Q 027247 47 YEYPCPFCSE-DFDLVGLC 64 (226)
Q Consensus 47 ~~f~CPfC~e-~~dv~~L~ 64 (226)
..|.||+|.. .-.+..+.
T Consensus 23 ~D~~Cp~C~~~~~~~~~~~ 41 (178)
T cd03019 23 FSYGCPHCYNFEPILEAWV 41 (178)
T ss_pred ECCCCcchhhhhHHHHHHH
Confidence 4699999998 55555554
No 225
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=20.35 E-value=36 Score=31.91 Aligned_cols=18 Identities=33% Similarity=0.647 Sum_probs=14.1
Q ss_pred ccccCCccccCcchhhHh
Q 027247 76 KSGVCPVCVTRVTMDMVD 93 (226)
Q Consensus 76 ~~vvCPVC~~~v~~d~i~ 93 (226)
+..+||||..+|-..||.
T Consensus 184 ~~~~CPvCGS~PvaSmV~ 201 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQ 201 (308)
T ss_pred ccccCCCcCCCCcceeee
Confidence 447999999998776663
No 226
>PRK02539 hypothetical protein; Provisional
Probab=20.13 E-value=95 Score=24.07 Aligned_cols=29 Identities=24% Similarity=0.395 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHHh---------HhhHHHHHHHhhhccC
Q 027247 196 SSLSNEDHLEKAN---------RSNFAQGLLFSTIMDD 224 (226)
Q Consensus 196 ~~ls~ed~eEk~~---------R~eFVQ~LllSTifdd 224 (226)
..|+++|++|+.+ |..|-++|---.|.|+
T Consensus 19 ~gLT~eEk~Eq~~LR~eYl~~fR~~~~~~L~~i~ivD~ 56 (85)
T PRK02539 19 EGLTGEEKVEQAKLREEYIEGYRRSVRHHIEGIKIVDE 56 (85)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHhccceEECC
Confidence 5699999999854 6666666655555543
Done!