Query 029557
Match_columns 191
No_of_seqs 153 out of 190
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 14:49:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029557.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029557hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05605 zf-Di19: Drought indu 99.8 2.1E-20 4.6E-25 127.3 3.6 54 47-100 1-54 (54)
2 PF14571 Di19_C: Stress-induce 99.8 6.9E-20 1.5E-24 141.3 4.1 59 119-177 1-61 (105)
3 KOG1280 Uncharacterized conser 98.6 2.1E-08 4.6E-13 91.8 3.6 57 25-88 63-120 (381)
4 COG5216 Uncharacterized conser 94.9 0.0096 2.1E-07 43.0 0.6 33 47-88 21-55 (67)
5 KOG2923 Uncharacterized conser 94.8 0.015 3.3E-07 42.3 1.6 46 31-88 8-55 (67)
6 PF13894 zf-C2H2_4: C2H2-type 94.6 0.023 5E-07 30.9 1.6 23 49-71 1-24 (24)
7 PF09237 GAGA: GAGA factor; I 93.4 0.038 8.3E-07 38.7 1.1 27 75-101 22-50 (54)
8 PLN03086 PRLI-interacting fact 92.6 0.11 2.5E-06 50.7 3.6 46 47-97 452-498 (567)
9 PF13913 zf-C2HC_2: zinc-finge 91.9 0.11 2.5E-06 30.5 1.6 21 48-68 2-22 (25)
10 PF00096 zf-C2H2: Zinc finger, 91.6 0.075 1.6E-06 29.5 0.6 21 49-69 1-22 (23)
11 COG5236 Uncharacterized conser 91.4 0.19 4.2E-06 47.3 3.4 55 43-105 217-311 (493)
12 PF12756 zf-C2H2_2: C2H2 type 90.2 0.12 2.6E-06 36.6 0.8 48 50-97 1-72 (100)
13 PHA00732 hypothetical protein 90.0 0.36 7.8E-06 35.6 3.2 43 49-96 2-45 (79)
14 KOG2462 C2H2-type Zn-finger pr 88.1 0.34 7.4E-06 43.8 2.3 35 47-85 160-195 (279)
15 PF14354 Lar_restr_allev: Rest 88.0 0.13 2.8E-06 35.0 -0.4 31 48-85 3-37 (61)
16 smart00531 TFIIE Transcription 87.4 0.45 9.8E-06 38.2 2.4 37 47-88 98-134 (147)
17 PHA00733 hypothetical protein 87.3 0.76 1.7E-05 36.5 3.6 50 47-100 72-124 (128)
18 PF13909 zf-H2C2_5: C2H2-type 87.3 0.3 6.4E-06 27.5 0.9 24 49-72 1-24 (24)
19 PF08271 TF_Zn_Ribbon: TFIIB z 87.1 0.18 4E-06 32.7 -0.0 34 49-92 1-34 (43)
20 PRK09710 lar restriction allev 87.0 0.22 4.7E-06 36.1 0.3 32 47-87 5-37 (64)
21 TIGR01206 lysW lysine biosynth 86.9 0.21 4.5E-06 34.8 0.2 30 48-86 2-31 (54)
22 smart00834 CxxC_CXXC_SSSS Puta 85.8 0.26 5.6E-06 30.8 0.2 33 47-87 4-36 (41)
23 PHA02768 hypothetical protein; 85.1 0.76 1.6E-05 32.3 2.2 34 48-85 5-39 (55)
24 PLN03086 PRLI-interacting fact 84.9 0.81 1.8E-05 45.0 3.1 38 47-87 477-514 (567)
25 PF09986 DUF2225: Uncharacteri 83.0 0.33 7.2E-06 41.4 -0.3 19 47-65 4-22 (214)
26 TIGR02098 MJ0042_CXXC MJ0042 f 82.5 1 2.2E-05 28.1 1.9 32 49-86 3-34 (38)
27 PF12756 zf-C2H2_2: C2H2 type 82.0 0.87 1.9E-05 32.2 1.6 26 48-73 50-76 (100)
28 PLN03208 E3 ubiquitin-protein 81.6 0.52 1.1E-05 40.5 0.4 43 47-89 17-80 (193)
29 COG1655 Uncharacterized protei 81.1 0.55 1.2E-05 42.0 0.4 14 46-59 17-30 (267)
30 KOG2462 C2H2-type Zn-finger pr 80.9 1.6 3.4E-05 39.6 3.2 85 48-139 187-275 (279)
31 PF12760 Zn_Tnp_IS1595: Transp 80.5 0.81 1.7E-05 30.1 0.9 14 43-56 13-26 (46)
32 TIGR02605 CxxC_CxxC_SSSS putat 80.1 1.1 2.3E-05 29.6 1.4 31 47-85 4-34 (52)
33 smart00734 ZnF_Rad18 Rad18-lik 79.7 1.4 3.1E-05 26.1 1.7 20 49-68 2-21 (26)
34 PF08274 PhnA_Zn_Ribbon: PhnA 79.1 0.67 1.4E-05 28.8 0.1 25 50-86 4-28 (30)
35 KOG1842 FYVE finger-containing 78.5 0.9 1.9E-05 43.9 0.9 34 42-77 11-45 (505)
36 PF14255 Cys_rich_CPXG: Cystei 78.4 0.67 1.5E-05 32.1 0.0 12 49-60 1-12 (52)
37 smart00504 Ubox Modified RING 78.1 2.2 4.7E-05 28.4 2.5 26 56-88 21-46 (63)
38 PRK14892 putative transcriptio 76.9 0.89 1.9E-05 35.2 0.3 34 47-89 20-54 (99)
39 cd00350 rubredoxin_like Rubred 76.4 1.2 2.6E-05 27.5 0.7 24 49-85 2-25 (33)
40 PRK00398 rpoP DNA-directed RNA 75.7 1.7 3.7E-05 28.4 1.4 29 48-87 3-31 (46)
41 PF04780 DUF629: Protein of un 73.6 1.9 4E-05 41.6 1.6 42 47-88 56-101 (466)
42 PF14206 Cys_rich_CPCC: Cystei 72.9 1.5 3.3E-05 32.7 0.7 24 49-83 2-26 (78)
43 PF13912 zf-C2H2_6: C2H2-type 72.7 2.3 5.1E-05 24.2 1.3 23 49-71 2-25 (27)
44 TIGR03655 anti_R_Lar restricti 71.8 1.7 3.6E-05 29.4 0.6 7 50-56 3-9 (53)
45 PHA00616 hypothetical protein 71.8 2 4.4E-05 28.9 1.0 25 49-73 2-27 (44)
46 KOG3623 Homeobox transcription 71.5 1.2 2.5E-05 45.7 -0.3 40 47-86 209-249 (1007)
47 PF05129 Elf1: Transcription e 70.9 1.6 3.4E-05 32.4 0.4 33 47-86 21-55 (81)
48 PF03470 zf-XS: XS zinc finger 70.9 2.9 6.3E-05 28.2 1.6 23 80-102 1-23 (43)
49 smart00355 ZnF_C2H2 zinc finge 70.8 3.8 8.2E-05 21.8 1.9 20 49-68 1-21 (26)
50 cd00729 rubredoxin_SM Rubredox 70.7 2.1 4.5E-05 26.9 0.8 26 48-86 2-27 (34)
51 PTZ00255 60S ribosomal protein 70.6 2 4.3E-05 33.0 0.8 13 47-59 35-48 (90)
52 PF05207 zf-CSL: CSL zinc fing 68.0 2 4.4E-05 29.6 0.4 47 31-89 4-52 (55)
53 PF07191 zinc-ribbons_6: zinc- 67.8 0.36 7.7E-06 35.5 -3.6 55 50-108 3-64 (70)
54 PF07754 DUF1610: Domain of un 67.5 3.1 6.7E-05 24.8 1.1 10 47-56 15-24 (24)
55 PRK03976 rpl37ae 50S ribosomal 66.0 2.7 5.8E-05 32.3 0.7 10 47-56 35-44 (90)
56 PF09723 Zn-ribbon_8: Zinc rib 65.7 3 6.4E-05 27.1 0.8 31 47-85 4-34 (42)
57 TIGR00280 L37a ribosomal prote 65.4 2.8 6E-05 32.3 0.7 10 47-56 34-43 (91)
58 PF12773 DZR: Double zinc ribb 65.3 4 8.7E-05 26.6 1.4 27 50-88 14-40 (50)
59 COG4888 Uncharacterized Zn rib 64.7 3 6.4E-05 32.9 0.8 35 47-86 21-55 (104)
60 PF15616 TerY-C: TerY-C metal 64.3 2.1 4.5E-05 34.8 -0.1 39 49-89 78-117 (131)
61 PRK12495 hypothetical protein; 64.2 4.3 9.3E-05 35.9 1.7 29 47-88 41-69 (226)
62 PRK14890 putative Zn-ribbon RN 63.8 4.7 0.0001 28.8 1.6 31 47-84 24-55 (59)
63 COG5175 MOT2 Transcriptional r 63.7 3.8 8.2E-05 38.8 1.4 36 51-87 17-63 (480)
64 PF02176 zf-TRAF: TRAF-type zi 63.2 2.5 5.5E-05 28.1 0.1 46 47-94 8-60 (60)
65 KOG2932 E3 ubiquitin ligase in 63.0 2.9 6.2E-05 39.1 0.5 57 49-105 91-177 (389)
66 PF05605 zf-Di19: Drought indu 62.9 4.3 9.4E-05 27.2 1.2 25 47-72 30-54 (54)
67 smart00659 RPOLCX RNA polymera 62.3 4.6 0.0001 26.8 1.2 28 48-87 2-29 (44)
68 PF07282 OrfB_Zn_ribbon: Putat 61.3 6.3 0.00014 27.2 1.9 38 47-96 27-65 (69)
69 PF03145 Sina: Seven in absent 61.1 5.5 0.00012 33.0 1.8 54 47-103 13-75 (198)
70 PF13465 zf-H2C2_2: Zinc-finge 61.0 2.4 5.1E-05 24.7 -0.3 11 48-58 14-24 (26)
71 PF01780 Ribosomal_L37ae: Ribo 60.8 3 6.4E-05 32.1 0.1 10 47-56 34-43 (90)
72 PRK06266 transcription initiat 59.4 7.5 0.00016 32.5 2.3 32 47-88 116-147 (178)
73 PF13395 HNH_4: HNH endonuclea 59.1 5.2 0.00011 27.0 1.1 14 51-64 1-14 (54)
74 TIGR00373 conserved hypothetic 58.7 7.4 0.00016 31.8 2.2 31 47-87 108-138 (158)
75 PF09538 FYDLN_acid: Protein o 58.5 6.1 0.00013 30.9 1.5 30 47-89 8-38 (108)
76 PF04564 U-box: U-box domain; 57.7 7.5 0.00016 27.6 1.8 36 47-88 3-50 (73)
77 KOG0320 Predicted E3 ubiquitin 57.6 5.3 0.00011 34.4 1.1 47 43-89 126-179 (187)
78 PF14616 DUF4451: Domain of un 57.4 6.6 0.00014 31.1 1.6 27 77-103 25-56 (124)
79 PF06957 COPI_C: Coatomer (COP 56.6 4.4 9.5E-05 38.6 0.5 36 44-92 376-412 (422)
80 COG4311 SoxD Sarcosine oxidase 55.8 5.3 0.00012 31.2 0.8 9 48-56 3-11 (97)
81 PRK12496 hypothetical protein; 53.6 8.5 0.00018 31.7 1.7 27 48-87 127-153 (164)
82 COG1592 Rubrerythrin [Energy p 52.6 9.5 0.00021 32.1 1.9 25 48-86 134-158 (166)
83 PF10571 UPF0547: Uncharacteri 52.6 8.4 0.00018 23.0 1.1 8 51-58 3-10 (26)
84 KOG0402 60S ribosomal protein 52.2 4.5 9.7E-05 31.1 -0.1 11 46-56 34-44 (92)
85 PRK00420 hypothetical protein; 52.2 9.9 0.00021 30.1 1.8 28 48-87 23-50 (112)
86 PF11672 DUF3268: Protein of u 51.0 7.5 0.00016 30.3 0.9 38 49-89 3-43 (102)
87 PF12230 PRP21_like_P: Pre-mRN 51.0 5.1 0.00011 34.1 0.0 21 77-97 168-189 (229)
88 PF08209 Sgf11: Sgf11 (transcr 50.5 8.1 0.00018 24.5 0.9 20 48-67 4-23 (33)
89 COG0675 Transposase and inacti 50.5 10 0.00022 32.0 1.7 35 47-97 308-342 (364)
90 PF10058 DUF2296: Predicted in 50.0 8.8 0.00019 26.5 1.1 9 48-56 44-52 (54)
91 PF13248 zf-ribbon_3: zinc-rib 49.8 11 0.00024 22.1 1.3 10 49-58 3-12 (26)
92 PRK03922 hypothetical protein; 48.4 8.8 0.00019 30.7 1.0 14 48-61 49-62 (113)
93 KOG2231 Predicted E3 ubiquitin 47.7 12 0.00025 37.8 1.9 27 48-74 182-209 (669)
94 PRK11088 rrmA 23S rRNA methylt 47.5 5.6 0.00012 34.2 -0.3 32 48-79 2-34 (272)
95 PF13719 zinc_ribbon_5: zinc-r 47.2 16 0.00034 23.1 1.8 29 49-85 3-33 (37)
96 PF04475 DUF555: Protein of un 47.0 9.4 0.0002 30.0 0.9 14 48-61 47-60 (102)
97 PF08996 zf-DNA_Pol: DNA Polym 46.0 3.1 6.7E-05 34.7 -2.0 39 48-88 18-56 (188)
98 TIGR00100 hypA hydrogenase nic 45.9 7.4 0.00016 30.2 0.2 27 47-86 69-95 (115)
99 smart00451 ZnF_U1 U1-like zinc 45.6 18 0.00038 21.4 1.8 22 48-69 3-25 (35)
100 PF02146 SIR2: Sir2 family; I 45.2 13 0.00029 30.0 1.6 40 48-92 105-144 (178)
101 PF14446 Prok-RING_1: Prokaryo 44.3 14 0.00031 25.9 1.4 25 49-86 6-30 (54)
102 smart00507 HNHc HNH nucleases. 43.8 5.1 0.00011 24.7 -0.8 21 49-69 11-31 (52)
103 PF04981 NMD3: NMD3 family ; 43.8 15 0.00033 31.5 1.8 35 51-85 1-43 (236)
104 PF14279 HNH_5: HNH endonuclea 43.7 5.5 0.00012 28.9 -0.8 40 51-95 1-48 (71)
105 TIGR00570 cdk7 CDK-activating 42.7 12 0.00026 34.5 1.0 38 48-86 3-52 (309)
106 PF12171 zf-C2H2_jaz: Zinc-fin 42.0 18 0.0004 20.7 1.4 20 49-68 2-22 (27)
107 TIGR00686 phnA alkylphosphonat 41.7 11 0.00025 29.9 0.7 25 50-86 4-28 (109)
108 TIGR02300 FYDLN_acid conserved 41.0 16 0.00035 29.8 1.5 28 47-87 8-36 (129)
109 KOG2879 Predicted E3 ubiquitin 40.9 7.8 0.00017 35.5 -0.4 41 47-87 238-286 (298)
110 KOG2817 Predicted E3 ubiquitin 40.9 17 0.00036 34.6 1.7 15 47-61 373-387 (394)
111 COG4049 Uncharacterized protei 40.4 9 0.00019 27.6 -0.1 27 78-104 18-46 (65)
112 PRK11595 DNA utilization prote 40.1 15 0.00032 31.2 1.2 33 50-84 7-41 (227)
113 KOG2177 Predicted E3 ubiquitin 40.0 9.8 0.00021 30.3 0.1 36 47-84 12-54 (386)
114 PF13824 zf-Mss51: Zinc-finger 39.9 14 0.0003 26.1 0.8 10 47-56 13-22 (55)
115 PF14353 CpXC: CpXC protein 39.5 15 0.00033 28.3 1.1 28 48-79 38-65 (128)
116 PF12013 DUF3505: Protein of u 38.9 21 0.00046 26.8 1.8 32 72-103 6-38 (109)
117 PF00097 zf-C3HC4: Zinc finger 38.5 16 0.00034 22.4 0.8 9 75-83 33-41 (41)
118 PRK12380 hydrogenase nickel in 37.8 13 0.00029 28.8 0.5 27 47-86 69-95 (113)
119 COG1499 NMD3 NMD protein affec 37.3 17 0.00037 33.9 1.2 39 47-85 5-51 (355)
120 PRK03824 hypA hydrogenase nick 37.0 15 0.00033 29.4 0.7 40 47-86 69-116 (135)
121 PF04423 Rad50_zn_hook: Rad50 36.6 12 0.00025 25.2 -0.0 14 50-63 22-35 (54)
122 smart00661 RPOL9 RNA polymeras 35.8 16 0.00034 23.7 0.5 27 50-85 2-28 (52)
123 KOG3576 Ovo and related transc 35.6 15 0.00033 32.7 0.6 61 49-112 146-213 (267)
124 PRK05477 gatB aspartyl/glutamy 35.3 18 0.00038 35.0 1.0 22 67-88 27-48 (474)
125 PF01155 HypA: Hydrogenase exp 35.1 9.2 0.0002 29.5 -0.8 27 47-86 69-95 (113)
126 COG5109 Uncharacterized conser 34.9 19 0.00041 33.9 1.1 11 47-57 375-385 (396)
127 COG5189 SFP1 Putative transcri 34.7 21 0.00045 33.8 1.3 40 48-87 349-408 (423)
128 PF04780 DUF629: Protein of un 34.6 16 0.00035 35.4 0.6 48 57-104 20-86 (466)
129 PRK04023 DNA polymerase II lar 34.4 19 0.00041 38.3 1.1 9 78-86 664-672 (1121)
130 COG2888 Predicted Zn-ribbon RN 33.9 22 0.00048 25.7 1.1 31 47-84 26-57 (61)
131 KOG3608 Zn finger proteins [Ge 33.5 37 0.00081 32.5 2.8 48 48-96 263-313 (467)
132 PF02892 zf-BED: BED zinc fing 33.4 17 0.00038 22.9 0.4 25 47-71 15-44 (45)
133 cd00730 rubredoxin Rubredoxin; 33.3 22 0.00047 24.3 0.9 12 43-56 31-42 (50)
134 PF12230 PRP21_like_P: Pre-mRN 33.1 14 0.00031 31.4 0.0 23 48-70 168-190 (229)
135 PF12660 zf-TFIIIC: Putative z 32.3 8.3 0.00018 29.4 -1.4 38 50-87 16-65 (99)
136 PRK00907 hypothetical protein; 31.8 22 0.00049 27.0 0.9 28 37-67 5-34 (92)
137 PHA00733 hypothetical protein 31.2 39 0.00085 26.7 2.2 25 48-72 99-124 (128)
138 COG2331 Uncharacterized protei 31.2 11 0.00025 28.4 -0.8 46 47-105 11-56 (82)
139 PF05876 Terminase_GpA: Phage 30.7 24 0.00052 34.3 1.1 40 47-88 199-240 (557)
140 TIGR00515 accD acetyl-CoA carb 30.7 28 0.00061 31.4 1.4 30 43-86 25-54 (285)
141 PF03966 Trm112p: Trm112p-like 30.5 28 0.00061 24.3 1.2 38 47-85 6-61 (68)
142 COG1675 TFA1 Transcription ini 30.2 28 0.00061 29.5 1.3 29 47-87 112-142 (176)
143 KOG4696 Uncharacterized conser 30.2 28 0.00062 32.6 1.4 23 49-72 3-25 (393)
144 PF09862 DUF2089: Protein of u 30.0 12 0.00026 29.7 -0.8 39 51-104 1-54 (113)
145 PF04267 SoxD: Sarcosine oxida 30.0 14 0.00031 27.9 -0.5 8 49-56 2-9 (84)
146 KOG3993 Transcription factor ( 29.8 15 0.00032 35.7 -0.5 33 47-79 457-490 (500)
147 PLN02751 glutamyl-tRNA(Gln) am 29.8 25 0.00053 34.7 1.0 21 68-88 84-104 (544)
148 PF01844 HNH: HNH endonuclease 29.7 7.4 0.00016 24.4 -1.8 11 51-61 1-11 (47)
149 PF14311 DUF4379: Domain of un 29.6 35 0.00075 22.8 1.4 29 47-83 27-55 (55)
150 cd03019 DsbA_DsbA DsbA family, 29.6 20 0.00043 27.7 0.3 19 47-65 23-42 (178)
151 PF11290 DUF3090: Protein of u 29.3 27 0.00059 29.7 1.1 13 49-61 155-167 (171)
152 TIGR01374 soxD sarcosine oxida 29.2 25 0.00054 26.7 0.7 8 49-56 2-9 (84)
153 PF00301 Rubredoxin: Rubredoxi 29.2 27 0.00058 23.6 0.8 10 47-56 33-42 (47)
154 PF10276 zf-CHCC: Zinc-finger 29.2 21 0.00045 23.5 0.2 9 48-56 29-37 (40)
155 PF12874 zf-met: Zinc-finger o 28.7 34 0.00074 18.8 1.1 16 80-95 3-20 (25)
156 PF09706 Cas_CXXC_CXXC: CRISPR 28.6 21 0.00046 25.5 0.3 10 47-56 4-13 (69)
157 TIGR03830 CxxCG_CxxCG_HTH puta 28.1 18 0.00038 27.2 -0.3 37 51-87 1-41 (127)
158 cd03021 DsbA_GSTK DsbA family, 28.1 13 0.00028 30.6 -1.1 13 43-57 5-17 (209)
159 PF09334 tRNA-synt_1g: tRNA sy 28.0 14 0.00031 34.1 -0.9 40 49-88 137-177 (391)
160 CHL00174 accD acetyl-CoA carbo 27.8 38 0.00081 31.0 1.8 29 43-85 37-65 (296)
161 TIGR00133 gatB glutamyl-tRNA(G 27.5 29 0.00062 33.6 1.0 15 74-88 34-48 (478)
162 COG4391 Uncharacterized protei 27.4 28 0.00061 25.2 0.7 13 74-86 45-57 (62)
163 PRK10220 hypothetical protein; 27.4 31 0.00068 27.5 1.0 13 74-86 17-29 (111)
164 COG4049 Uncharacterized protei 27.4 29 0.00062 25.1 0.7 27 47-73 16-43 (65)
165 PHA02565 49 recombination endo 27.4 26 0.00055 29.5 0.6 41 47-87 19-65 (157)
166 KOG2593 Transcription initiati 27.1 20 0.00043 34.5 -0.1 32 47-85 127-161 (436)
167 COG3058 FdhE Uncharacterized p 27.0 23 0.00051 32.6 0.3 18 76-93 184-201 (308)
168 PRK09678 DNA-binding transcrip 26.9 29 0.00063 25.5 0.7 8 49-56 2-9 (72)
169 PF14369 zf-RING_3: zinc-finge 26.8 31 0.00067 21.8 0.7 9 50-58 23-31 (35)
170 PRK14714 DNA polymerase II lar 26.8 32 0.0007 37.3 1.3 36 48-88 667-703 (1337)
171 PF13462 Thioredoxin_4: Thiore 26.3 6.1 0.00013 30.1 -3.1 21 47-67 20-41 (162)
172 PF13717 zinc_ribbon_4: zinc-r 26.3 50 0.0011 20.8 1.6 31 49-85 3-33 (36)
173 cd03024 DsbA_FrnE DsbA family, 26.1 18 0.00038 28.9 -0.6 21 47-67 5-26 (201)
174 PRK03681 hypA hydrogenase nick 26.0 22 0.00048 27.6 -0.1 12 47-58 69-80 (114)
175 PRK05654 acetyl-CoA carboxylas 25.7 39 0.00084 30.6 1.4 30 43-86 26-55 (292)
176 COG1997 RPL43A Ribosomal prote 25.6 23 0.0005 27.3 -0.0 13 43-57 32-44 (89)
177 PHA02929 N1R/p28-like protein; 25.4 13 0.00028 32.9 -1.6 41 47-87 173-226 (238)
178 PF02934 GatB_N: GatB/GatE cat 25.2 28 0.0006 31.7 0.4 23 66-88 21-43 (289)
179 smart00614 ZnF_BED BED zinc fi 24.3 39 0.00085 22.2 0.9 25 48-72 18-48 (50)
180 cd02972 DsbA_family DsbA famil 24.3 19 0.00041 24.1 -0.6 18 47-64 5-23 (98)
181 COG1198 PriA Primosomal protei 24.0 30 0.00066 35.2 0.5 38 47-86 443-484 (730)
182 cd03022 DsbA_HCCA_Iso DsbA fam 23.7 18 0.00038 28.5 -1.0 20 47-66 5-25 (192)
183 PRK00564 hypA hydrogenase nick 23.7 30 0.00066 26.9 0.3 28 47-86 70-97 (117)
184 PF03604 DNA_RNApol_7kD: DNA d 23.6 36 0.00077 21.3 0.6 11 77-87 17-27 (32)
185 PRK00423 tfb transcription ini 23.5 47 0.001 29.7 1.5 38 47-94 10-47 (310)
186 PF09889 DUF2116: Uncharacteri 23.5 44 0.00096 23.7 1.1 10 50-59 5-14 (59)
187 PRK00464 nrdR transcriptional 23.4 34 0.00074 28.3 0.6 31 50-86 2-37 (154)
188 PHA02540 61 DNA primase; Provi 23.0 37 0.00081 31.4 0.8 9 48-56 27-35 (337)
189 PF15135 UPF0515: Uncharacteri 22.9 39 0.00085 30.7 0.9 17 43-59 150-166 (278)
190 PF14634 zf-RING_5: zinc-RING 22.6 50 0.0011 21.0 1.2 20 63-84 24-43 (44)
191 COG2761 FrnE Predicted dithiol 22.3 29 0.00063 30.6 0.0 53 43-102 10-70 (225)
192 PF06676 DUF1178: Protein of u 22.0 41 0.00089 27.9 0.8 10 76-85 31-40 (148)
193 PF08273 Prim_Zn_Ribbon: Zinc- 22.0 38 0.00083 22.2 0.5 8 49-56 4-11 (40)
194 PF06221 zf-C2HC5: Putative zi 21.9 44 0.00096 23.6 0.8 9 48-56 35-43 (57)
195 PRK00762 hypA hydrogenase nick 21.9 30 0.00065 27.3 -0.0 8 49-56 93-100 (124)
196 COG1656 Uncharacterized conser 21.8 66 0.0014 27.3 2.0 39 50-88 99-141 (165)
197 TIGR01405 polC_Gram_pos DNA po 21.6 57 0.0012 35.1 2.0 47 28-86 670-717 (1213)
198 PF13453 zf-TFIIB: Transcripti 21.0 25 0.00054 22.4 -0.5 10 51-60 2-11 (41)
199 PRK11639 zinc uptake transcrip 20.8 72 0.0016 26.1 2.0 41 47-87 99-150 (169)
200 cd01407 SIR2-fam SIR2 family o 20.4 68 0.0015 26.9 1.8 35 48-87 109-143 (218)
201 KOG3608 Zn finger proteins [Ge 20.3 71 0.0015 30.7 2.1 56 48-103 319-380 (467)
202 smart00586 ZnF_DBF Zinc finger 20.3 41 0.00089 23.1 0.4 28 74-102 2-30 (49)
203 KOG3214 Uncharacterized Zn rib 20.2 43 0.00094 26.6 0.6 34 47-85 22-55 (109)
204 TIGR00244 transcriptional regu 20.2 43 0.00094 27.8 0.6 32 50-88 2-39 (147)
205 PF14968 CCDC84: Coiled coil p 20.2 44 0.00095 31.1 0.7 22 47-68 57-85 (336)
206 KOG4080 Mitochondrial ribosoma 20.1 44 0.00096 28.6 0.7 25 48-88 93-117 (176)
No 1
>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=99.80 E-value=2.1e-20 Score=127.32 Aligned_cols=54 Identities=37% Similarity=0.864 Sum_probs=52.0
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcccchHhhhhcccc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHITTQHG 100 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~d~v~Hl~~qH~ 100 (191)
++|+||||+++||+.+|+.|++++|..+.++||||||+.+++.||++||+.+|+
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 369999999999999999999999999999999999999999999999999996
No 2
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=99.79 E-value=6.9e-20 Score=141.32 Aligned_cols=59 Identities=49% Similarity=0.628 Sum_probs=53.8
Q ss_pred cchhhhHHHHhhhhhhhhcCC-CCCCCCCCCCCCCccc-cccCCCCCCCcCCcCccCCcCC
Q 029557 119 TISSLRKELQNAHFQSLLARS-SSSVSSSKKTSDPWLS-FIYNMPTADESESIQPALSTGE 177 (191)
Q Consensus 119 ~~s~l~k~lre~~lq~llgg~-s~~~~~s~~~pDPLLS-Fi~~~~~~~~~~~~~~~~~~e~ 177 (191)
|+|+|+|||||||||+||||+ +++++++|++|||||| ||||+|.++.++.+++..++++
T Consensus 1 tlsll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~~~~~~~~~~~~~~~~~ 61 (105)
T PF14571_consen 1 TLSLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFPAPEAEEPSKSSSSSEE 61 (105)
T ss_pred CcchhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCCCccccccCCccccccc
Confidence 689999999999999999998 6666789999999999 9999999999999998887663
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=98.63 E-value=2.1e-08 Score=91.77 Aligned_cols=57 Identities=26% Similarity=0.562 Sum_probs=51.7
Q ss_pred cccccCCCCCCCcchhhhccCcceecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 25 FADFCIDFEDIEEDDYEEVKGEYEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 25 ~d~~~~g~e~~e~d~d~e~~~~~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
||+ |+|+|-+--+++ ..|+||||++ +|....+.+|+..+|+.....+|||||+..+.
T Consensus 63 feL-~f~Ge~i~~y~~------qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~ 120 (381)
T KOG1280|consen 63 FEL-YFGGEPISHYDP------QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPE 120 (381)
T ss_pred eee-EecCcccccccc------ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcc
Confidence 676 778888888888 7899999999 99999999999999999999999999999754
No 4
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.86 E-value=0.0096 Score=42.99 Aligned_cols=33 Identities=33% Similarity=0.841 Sum_probs=23.9
Q ss_pred ceecCCCCCC--CcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 47 YEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 47 ~~F~CPfC~e--~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
-+|||| ||. ++.+..|.. .-..++||-|+-+|-
T Consensus 21 ftyPCP-CGDRFeIsLeDl~~--------GE~VArCPSCSLiv~ 55 (67)
T COG5216 21 FTYPCP-CGDRFEISLEDLRN--------GEVVARCPSCSLIVC 55 (67)
T ss_pred EEecCC-CCCEeEEEHHHhhC--------CceEEEcCCceEEEE
Confidence 489999 998 555555532 456789999988653
No 5
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.85 E-value=0.015 Score=42.25 Aligned_cols=46 Identities=33% Similarity=0.720 Sum_probs=29.2
Q ss_pred CCCCCCcchhhhccCcceecCCCCCC--CcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 31 DFEDIEEDDYEEVKGEYEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 31 g~e~~e~d~d~e~~~~~~F~CPfC~e--~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
.++|++-|+|. -. .+|||| ||. .+....|.. .-..+.||-|+-.+.
T Consensus 8 eiedfe~~~e~-~~--y~yPCp-CGDrf~It~edL~~--------ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 8 EIEDFEFDEEN-QT--YYYPCP-CGDRFQITLEDLEN--------GEDVARCPSCSLIIR 55 (67)
T ss_pred EeecceeccCC-Ce--EEcCCC-CCCeeeecHHHHhC--------CCeeecCCCceEEEE
Confidence 45565544331 22 589999 998 455555532 445689999988664
No 6
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=94.62 E-value=0.023 Score=30.88 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=17.2
Q ss_pred ecCCCCCC-CcCHHHHHhhhhhcC
Q 029557 49 YPCPFCSE-DFDLVGLCCHIDEEH 71 (191)
Q Consensus 49 F~CPfC~e-~~D~~~L~~H~~eeH 71 (191)
|.||+|+. --+...|..|+...|
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 78999999 667888888888766
No 7
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=93.36 E-value=0.038 Score=38.74 Aligned_cols=27 Identities=19% Similarity=0.575 Sum_probs=18.3
Q ss_pred CCcccccccccCcc--cchHhhhhccccc
Q 029557 75 AKSGVCPVCVTRVT--MDMVDHITTQHGN 101 (191)
Q Consensus 75 ~k~vVCPICa~~~~--~d~v~Hl~~qH~~ 101 (191)
.....||+|.+.+. +|+-+||-+.|+.
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 34679999998765 7999999988874
No 8
>PLN03086 PRLI-interacting factor K; Provisional
Probab=92.63 E-value=0.11 Score=50.75 Aligned_cols=46 Identities=24% Similarity=0.455 Sum_probs=36.6
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcc-cchHhhhhc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT-MDMVDHITT 97 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~-~d~v~Hl~~ 97 (191)
.-+.||+|++.|....|-.|....| +.+.|| |..... .+|..|++.
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 3468999999899999999999866 678999 965433 588888764
No 9
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.86 E-value=0.11 Score=30.51 Aligned_cols=21 Identities=33% Similarity=0.661 Sum_probs=18.8
Q ss_pred eecCCCCCCCcCHHHHHhhhh
Q 029557 48 EYPCPFCSEDFDLVGLCCHID 68 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~ 68 (191)
..+||+||..|....|-.|..
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 468999999999999999964
No 10
>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=91.61 E-value=0.075 Score=29.46 Aligned_cols=21 Identities=29% Similarity=0.611 Sum_probs=15.0
Q ss_pred ecCCCCCC-CcCHHHHHhhhhh
Q 029557 49 YPCPFCSE-DFDLVGLCCHIDE 69 (191)
Q Consensus 49 F~CPfC~e-~~D~~~L~~H~~e 69 (191)
|.||.|++ =-+...|..|+..
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 67888888 4556677777765
No 11
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.41 E-value=0.19 Score=47.35 Aligned_cols=55 Identities=27% Similarity=0.447 Sum_probs=42.1
Q ss_pred ccCcceecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccC-------------------------------cc--
Q 029557 43 VKGEYEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTR-------------------------------VT-- 88 (191)
Q Consensus 43 ~~~~~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~-------------------------------~~-- 88 (191)
.+|| =.|-||.. =+|-.+|..||...|- .|-||..+ ++
T Consensus 217 FKGH--P~C~FC~~~FYdDDEL~~HcR~~HE------~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~ 288 (493)
T COG5236 217 FKGH--PLCIFCKIYFYDDDELRRHCRLRHE------ACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKC 288 (493)
T ss_pred cCCC--chhhhccceecChHHHHHHHHhhhh------hhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcE
Confidence 5543 46999999 8899999999999884 46666442 11
Q ss_pred ------cchHhhhhcccccchhh
Q 029557 89 ------MDMVDHITTQHGNISNS 105 (191)
Q Consensus 89 ------~d~v~Hl~~qH~~~~K~ 105 (191)
..++.||+..|+..+|.
T Consensus 289 ~vf~~~~el~~h~~~~h~~~~~~ 311 (493)
T COG5236 289 YVFPYHTELLEHLTRFHKVNARL 311 (493)
T ss_pred EEeccHHHHHHHHHHHhhccccc
Confidence 46888999999999884
No 12
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.23 E-value=0.12 Score=36.64 Aligned_cols=48 Identities=25% Similarity=0.554 Sum_probs=14.0
Q ss_pred cCCCCCCC-cCHHHHHhhhhhcCCCCCC---------------------cccccccccCc--ccchHhhhhc
Q 029557 50 PCPFCSED-FDLVGLCCHIDEEHPVEAK---------------------SGVCPVCVTRV--TMDMVDHITT 97 (191)
Q Consensus 50 ~CPfC~e~-~D~~~L~~H~~eeH~~e~k---------------------~vVCPICa~~~--~~d~v~Hl~~ 97 (191)
-|+||+.. -++..|..|+...|.+... ...|++|.... ...+..||..
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 13499998764 3688999864
No 13
>PHA00732 hypothetical protein
Probab=90.04 E-value=0.36 Score=35.63 Aligned_cols=43 Identities=28% Similarity=0.652 Sum_probs=32.7
Q ss_pred ecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccCcccchHhhhh
Q 029557 49 YPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHIT 96 (191)
Q Consensus 49 F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~d~v~Hl~ 96 (191)
|.|+.|+. --....|..|....|.. ..|++|...-. ++..|+.
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 88999999 44788899999866653 26999977553 5777763
No 14
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=88.11 E-value=0.34 Score=43.81 Aligned_cols=35 Identities=20% Similarity=0.552 Sum_probs=24.0
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCCCCCccccccccc
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
..|.||+|++ .+.+..|--|+... . -.-+|+||-.
T Consensus 160 ka~~C~~C~K~YvSmpALkMHirTH-~---l~c~C~iCGK 195 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIRTH-T---LPCECGICGK 195 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhhcc-C---CCcccccccc
Confidence 4688888888 88888888887643 2 2346667654
No 15
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=87.96 E-value=0.13 Score=35.02 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=19.4
Q ss_pred eecCCCCCC-CcCHHHHHhhhhhcCCCCC---Cccccccccc
Q 029557 48 EYPCPFCSE-DFDLVGLCCHIDEEHPVEA---KSGVCPVCVT 85 (191)
Q Consensus 48 ~F~CPfC~e-~~D~~~L~~H~~eeH~~e~---k~vVCPICa~ 85 (191)
.-+|||||. .+.+.. ....+. -.|.|..|.+
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 458999997 554332 222222 4577999977
No 16
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.45 E-value=0.45 Score=38.18 Aligned_cols=37 Identities=22% Similarity=0.530 Sum_probs=25.4
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
..|.||.|+.-|+..+-....+ . ....+||.|-..+-
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 6899999999666554333322 1 34489999988653
No 17
>PHA00733 hypothetical protein
Probab=87.28 E-value=0.76 Score=36.47 Aligned_cols=50 Identities=38% Similarity=0.700 Sum_probs=35.7
Q ss_pred ceecCCCCCCCc-CHHHHHhhhhhcCCCCCCcccccccccCc--ccchHhhhhcccc
Q 029557 47 YEYPCPFCSEDF-DLVGLCCHIDEEHPVEAKSGVCPVCVTRV--TMDMVDHITTQHG 100 (191)
Q Consensus 47 ~~F~CPfC~e~~-D~~~L~~H~~eeH~~e~k~vVCPICa~~~--~~d~v~Hl~~qH~ 100 (191)
..|.|+.|+..| ....|..|... | .....|++|.... ..++..|+.--|+
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~-h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRY-T---EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhc-C---CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 369999999954 55668888874 2 1346999997653 3588889876665
No 18
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=87.26 E-value=0.3 Score=27.54 Aligned_cols=24 Identities=38% Similarity=0.778 Sum_probs=16.0
Q ss_pred ecCCCCCCCcCHHHHHhhhhhcCC
Q 029557 49 YPCPFCSEDFDLVGLCCHIDEEHP 72 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~eeH~ 72 (191)
|.||+|.-.-....|..|++..|+
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 678888883337788888887764
No 19
>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=87.09 E-value=0.18 Score=32.66 Aligned_cols=34 Identities=24% Similarity=0.556 Sum_probs=21.2
Q ss_pred ecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcccchH
Q 029557 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMV 92 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~d~v 92 (191)
|.||.|+... + +.+ ......||+.|-..+..+.+
T Consensus 1 m~Cp~Cg~~~-~------~~D---~~~g~~vC~~CG~Vl~e~~i 34 (43)
T PF08271_consen 1 MKCPNCGSKE-I------VFD---PERGELVCPNCGLVLEENII 34 (43)
T ss_dssp ESBTTTSSSE-E------EEE---TTTTEEEETTT-BBEE-TTB
T ss_pred CCCcCCcCCc-e------EEc---CCCCeEECCCCCCEeecccc
Confidence 6899999843 2 122 34566899999777655444
No 20
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=86.99 E-value=0.22 Score=36.14 Aligned_cols=32 Identities=25% Similarity=0.523 Sum_probs=21.9
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
..=||||||. .+.+. |....-.++|.-|.+..
T Consensus 5 ~lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 5 NVKPCPFCGCPSVTVK---------AISGYYRAKCNGCESRT 37 (64)
T ss_pred cccCCCCCCCceeEEE---------ecCceEEEEcCCCCcCc
Confidence 3459999999 66554 22223359999998853
No 21
>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=86.86 E-value=0.21 Score=34.82 Aligned_cols=30 Identities=20% Similarity=0.574 Sum_probs=21.5
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
.|.||-||+.+.+.... . .-.+.||.|.+.
T Consensus 2 ~~~CP~CG~~iev~~~~-------~--GeiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPE-------L--GELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCc-------c--CCEEeCCCCCCE
Confidence 48999999977654332 1 336899999774
No 22
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=85.82 E-value=0.26 Score=30.79 Aligned_cols=33 Identities=30% Similarity=0.735 Sum_probs=23.0
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
.+|.||-||..|++..-. .+...++||.|.+.+
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 579999999977643211 125678999998743
No 23
>PHA02768 hypothetical protein; Provisional
Probab=85.07 E-value=0.76 Score=32.29 Aligned_cols=34 Identities=21% Similarity=0.501 Sum_probs=25.5
Q ss_pred eecCCCCCC-CcCHHHHHhhhhhcCCCCCCccccccccc
Q 029557 48 EYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 48 ~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
.|.||.||+ =.....|..|....+ ++-.|..|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~----k~~kc~~C~k 39 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN----TNLKLSNCKR 39 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC----CcccCCcccc
Confidence 489999999 556778999999844 4556777744
No 24
>PLN03086 PRLI-interacting factor K; Provisional
Probab=84.92 E-value=0.81 Score=44.96 Aligned_cols=38 Identities=18% Similarity=0.314 Sum_probs=27.9
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
..+.|| |+..+....|..|.. .|+-. +...|+.|...+
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~-thCp~-Kpi~C~fC~~~v 514 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQA-STCPL-RLITCRFCGDMV 514 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhh-ccCCC-CceeCCCCCCcc
Confidence 457888 888778888888874 45553 667888887655
No 25
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=82.95 E-value=0.33 Score=41.43 Aligned_cols=19 Identities=21% Similarity=0.642 Sum_probs=14.8
Q ss_pred ceecCCCCCCCcCHHHHHh
Q 029557 47 YEYPCPFCSEDFDLVGLCC 65 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~ 65 (191)
.+++||+|+..|....+..
T Consensus 4 k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CceECCCCCCeeeeeEEEc
Confidence 4689999999998765443
No 26
>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=82.53 E-value=1 Score=28.05 Aligned_cols=32 Identities=22% Similarity=0.422 Sum_probs=19.9
Q ss_pred ecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
+.||.|+.-|.+..-. .......+.||.|-..
T Consensus 3 ~~CP~C~~~~~v~~~~------~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ------LGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHH------cCCCCCEEECCCCCCE
Confidence 7899999955443211 1223346889999654
No 27
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=82.05 E-value=0.87 Score=32.17 Aligned_cols=26 Identities=27% Similarity=0.737 Sum_probs=21.2
Q ss_pred eecCCCCCCCc-CHHHHHhhhhhcCCC
Q 029557 48 EYPCPFCSEDF-DLVGLCCHIDEEHPV 73 (191)
Q Consensus 48 ~F~CPfC~e~~-D~~~L~~H~~eeH~~ 73 (191)
.|.|++|++.| +...|..|+...|..
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~ 76 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHK 76 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCC
Confidence 59999999965 899999999987543
No 28
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=81.59 E-value=0.52 Score=40.53 Aligned_cols=43 Identities=26% Similarity=0.624 Sum_probs=27.4
Q ss_pred ceecCCCCCCCcC--HHHHHhh-----hhhcCC--------------CCCCcccccccccCccc
Q 029557 47 YEYPCPFCSEDFD--LVGLCCH-----IDEEHP--------------VEAKSGVCPVCVTRVTM 89 (191)
Q Consensus 47 ~~F~CPfC~e~~D--~~~L~~H-----~~eeH~--------------~e~k~vVCPICa~~~~~ 89 (191)
..|.||.|.+.+. +...|.| |..... ...+...||+|...+..
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 5799999999333 3445666 233211 12345689999998864
No 29
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.11 E-value=0.55 Score=41.98 Aligned_cols=14 Identities=29% Similarity=0.888 Sum_probs=10.7
Q ss_pred cceecCCCCCCCcC
Q 029557 46 EYEYPCPFCSEDFD 59 (191)
Q Consensus 46 ~~~F~CPfC~e~~D 59 (191)
..++.||+|+--|-
T Consensus 17 kk~ieCPvC~tkFk 30 (267)
T COG1655 17 KKTIECPVCNTKFK 30 (267)
T ss_pred hceeccCcccchhh
Confidence 36899999986553
No 30
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=80.94 E-value=1.6 Score=39.60 Aligned_cols=85 Identities=26% Similarity=0.377 Sum_probs=53.5
Q ss_pred eecCCCCCCCcCHHHHH-hhhhhcCCCCCCcccccccccCcc--cchHhhhhcccccchhhhhhhcccCC-CCCccchhh
Q 029557 48 EYPCPFCSEDFDLVGLC-CHIDEEHPVEAKSGVCPVCVTRVT--MDMVDHITTQHGNISNSWHKLKLHKG-NSNSTISSL 123 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~-~H~~eeH~~e~k~vVCPICa~~~~--~d~v~Hl~~qH~~~~K~~rrrk~~k~-~s~s~~s~l 123 (191)
-+.|++||+-|+..=|. -|++ .|-.| |+-.||.|..--. .|+-.||+. |+.. | +-+..+= .+-+-.|+|
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiR-THTGE-KPF~C~hC~kAFADRSNLRAHmQT-HS~~-K---~~qC~~C~KsFsl~SyL 259 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIR-THTGE-KPFSCPHCGKAFADRSNLRAHMQT-HSDV-K---KHQCPRCGKSFALKSYL 259 (279)
T ss_pred CcccccccccccchHHhhcccc-cccCC-CCccCCcccchhcchHHHHHHHHh-hcCC-c---cccCcchhhHHHHHHHH
Confidence 58999999999987654 4554 46554 5679999966433 699999964 5554 2 1122221 133445677
Q ss_pred hHHHHhhhhhhhhcCC
Q 029557 124 RKELQNAHFQSLLARS 139 (191)
Q Consensus 124 ~k~lre~~lq~llgg~ 139 (191)
-|-+..|=+..+.|++
T Consensus 260 nKH~ES~C~~~~~g~~ 275 (279)
T KOG2462|consen 260 NKHSESACLKYLAGVM 275 (279)
T ss_pred HHhhhhccccccccCC
Confidence 7766665555554444
No 31
>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=80.49 E-value=0.81 Score=30.07 Aligned_cols=14 Identities=21% Similarity=0.764 Sum_probs=12.3
Q ss_pred ccCcceecCCCCCC
Q 029557 43 VKGEYEYPCPFCSE 56 (191)
Q Consensus 43 ~~~~~~F~CPfC~e 56 (191)
+||...|.||+||.
T Consensus 13 ~RW~~g~~CP~Cg~ 26 (46)
T PF12760_consen 13 IRWPDGFVCPHCGS 26 (46)
T ss_pred hcCCCCCCCCCCCC
Confidence 78888899999996
No 32
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=80.09 E-value=1.1 Score=29.61 Aligned_cols=31 Identities=29% Similarity=0.845 Sum_probs=22.0
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCccccccccc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
.+|.|+-|+..|++. .... +...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~---~~~~-----~~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVL---QKMS-----DDPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEE---EecC-----CCCCCCCCCCCC
Confidence 579999999988743 1111 245578999987
No 33
>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=79.75 E-value=1.4 Score=26.15 Aligned_cols=20 Identities=25% Similarity=0.572 Sum_probs=12.1
Q ss_pred ecCCCCCCCcCHHHHHhhhh
Q 029557 49 YPCPFCSEDFDLVGLCCHID 68 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~ 68 (191)
..||.|++.+....+-.|++
T Consensus 2 v~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREVPENLINSHLD 21 (26)
T ss_pred CcCCCCcCcccHHHHHHHHH
Confidence 35666666666666666655
No 34
>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=79.07 E-value=0.67 Score=28.83 Aligned_cols=25 Identities=28% Similarity=0.870 Sum_probs=13.3
Q ss_pred cCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 50 ~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
+||.|+.++.. .+....|||-|...
T Consensus 4 ~Cp~C~se~~y------------~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY------------EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E------------E-SSSEEETTTTEE
T ss_pred CCCCCCCccee------------ccCCEEeCCccccc
Confidence 68999886655 57778899999653
No 35
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=78.51 E-value=0.9 Score=43.85 Aligned_cols=34 Identities=35% Similarity=0.609 Sum_probs=29.1
Q ss_pred hccCcceecCCCCCCCc-CHHHHHhhhhhcCCCCCCc
Q 029557 42 EVKGEYEYPCPFCSEDF-DLVGLCCHIDEEHPVEAKS 77 (191)
Q Consensus 42 e~~~~~~F~CPfC~e~~-D~~~L~~H~~eeH~~e~k~ 77 (191)
+++ +-|-||+|.++| ++..|-+|++.+|..+-+.
T Consensus 11 ~i~--egflCPiC~~dl~~~~~L~~H~d~eH~~ed~~ 45 (505)
T KOG1842|consen 11 EIL--EGFLCPICLLDLPNLSALNDHLDVEHFEEDEK 45 (505)
T ss_pred hhh--hcccCchHhhhhhhHHHHHHHHhhhccccchh
Confidence 366 789999999977 4788999999999998764
No 36
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=78.38 E-value=0.67 Score=32.06 Aligned_cols=12 Identities=33% Similarity=1.237 Sum_probs=9.4
Q ss_pred ecCCCCCCCcCH
Q 029557 49 YPCPFCSEDFDL 60 (191)
Q Consensus 49 F~CPfC~e~~D~ 60 (191)
+.|||||+.+++
T Consensus 1 i~CPyCge~~~~ 12 (52)
T PF14255_consen 1 IQCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCCeeEE
Confidence 469999996654
No 37
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=78.10 E-value=2.2 Score=28.41 Aligned_cols=26 Identities=15% Similarity=0.192 Sum_probs=17.9
Q ss_pred CCcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 56 EDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 56 e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
.-|+...+..++.. ...||+|.....
T Consensus 21 ~v~~~~~i~~~~~~-------~~~cP~~~~~~~ 46 (63)
T smart00504 21 QTYERRAIEKWLLS-------HGTDPVTGQPLT 46 (63)
T ss_pred CEEeHHHHHHHHHH-------CCCCCCCcCCCC
Confidence 34677777777755 358999977654
No 38
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=76.94 E-value=0.89 Score=35.22 Aligned_cols=34 Identities=15% Similarity=0.405 Sum_probs=21.1
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccCccc
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~ 89 (191)
..|.||||++ -+. +.-.+ ..--++||+|-..-+.
T Consensus 20 t~f~CP~Cge~~v~-------v~~~k--~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKVSIS-------VKIKK--NIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCeEee-------eecCC--CcceEECCCCCCccCE
Confidence 5799999995 221 11112 2334899999876543
No 39
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=76.42 E-value=1.2 Score=27.53 Aligned_cols=24 Identities=42% Similarity=0.888 Sum_probs=15.4
Q ss_pred ecCCCCCCCcCHHHHHhhhhhcCCCCCCccccccccc
Q 029557 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
|.|+.||--++... ..-+||+|.+
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCC
Confidence 67888886433322 4568888865
No 40
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=75.69 E-value=1.7 Score=28.37 Aligned_cols=29 Identities=31% Similarity=0.751 Sum_probs=19.5
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
+|.||-||..|+.... .....||.|..++
T Consensus 3 ~y~C~~CG~~~~~~~~-----------~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY-----------GTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC-----------CCceECCCCCCeE
Confidence 6889999986665211 1167899997654
No 41
>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=73.62 E-value=1.9 Score=41.60 Aligned_cols=42 Identities=29% Similarity=0.420 Sum_probs=33.6
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCCCCCc---ccccccccCcc
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKS---GVCPVCVTRVT 88 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~---vVCPICa~~~~ 88 (191)
.--.||+|.+ -.|..++..|+..+|...-.+ -+.|-+....|
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~~w 101 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDDDW 101 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCHHH
Confidence 4678999999 999999999999999986543 46677666443
No 42
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=72.86 E-value=1.5 Score=32.66 Aligned_cols=24 Identities=46% Similarity=1.233 Sum_probs=17.1
Q ss_pred ecCCCCCC-CcCHHHHHhhhhhcCCCCCCccccccc
Q 029557 49 YPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVC 83 (191)
Q Consensus 49 F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPIC 83 (191)
|+||-||. -|+..+ +...-|||||
T Consensus 2 ~~CPCCg~~Tl~~~~-----------~~~ydIC~VC 26 (78)
T PF14206_consen 2 YPCPCCGYYTLEERG-----------EGTYDICPVC 26 (78)
T ss_pred ccCCCCCcEEeccCC-----------CcCceECCCC
Confidence 89999998 655322 2236699999
No 43
>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=72.66 E-value=2.3 Score=24.16 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=16.9
Q ss_pred ecCCCCCC-CcCHHHHHhhhhhcC
Q 029557 49 YPCPFCSE-DFDLVGLCCHIDEEH 71 (191)
Q Consensus 49 F~CPfC~e-~~D~~~L~~H~~eeH 71 (191)
|.|..|++ =-+...|..|.+..|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 77888888 556778888876554
No 44
>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=71.82 E-value=1.7 Score=29.38 Aligned_cols=7 Identities=71% Similarity=2.128 Sum_probs=6.6
Q ss_pred cCCCCCC
Q 029557 50 PCPFCSE 56 (191)
Q Consensus 50 ~CPfC~e 56 (191)
+|||||-
T Consensus 3 PCPfCGg 9 (53)
T TIGR03655 3 PCPFCGG 9 (53)
T ss_pred CCCCCCC
Confidence 7999998
No 45
>PHA00616 hypothetical protein
Probab=71.80 E-value=2 Score=28.92 Aligned_cols=25 Identities=20% Similarity=0.236 Sum_probs=19.5
Q ss_pred ecCCCCCC-CcCHHHHHhhhhhcCCC
Q 029557 49 YPCPFCSE-DFDLVGLCCHIDEEHPV 73 (191)
Q Consensus 49 F~CPfC~e-~~D~~~L~~H~~eeH~~ 73 (191)
|.||-||. =....+|..|+...|.-
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 67888888 55677888888777765
No 46
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=71.47 E-value=1.2 Score=45.65 Aligned_cols=40 Identities=25% Similarity=0.457 Sum_probs=35.0
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
+..+||||.. .-.+..|..|+.-.|---.-+.-|+.|...
T Consensus 209 qlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsyt 249 (1007)
T KOG3623|consen 209 QLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYT 249 (1007)
T ss_pred hhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhh
Confidence 4689999999 667889999999999987778899999874
No 47
>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=70.90 E-value=1.6 Score=32.41 Aligned_cols=33 Identities=24% Similarity=0.566 Sum_probs=13.6
Q ss_pred ceecCCCCC-C-CcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 47 YEYPCPFCS-E-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 47 ~~F~CPfC~-e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
..|.||||+ + -+.+ .-......-.+.|-+|-..
T Consensus 21 ~~F~CPfC~~~~sV~v-------~idkk~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSV-------KIDKKEGIGILSCRVCGES 55 (81)
T ss_dssp S----TTT--SS-EEE-------EEETTTTEEEEEESSS--E
T ss_pred ceEcCCcCCCCCeEEE-------EEEccCCEEEEEecCCCCe
Confidence 579999999 3 2222 1122233345789999653
No 48
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=70.87 E-value=2.9 Score=28.16 Aligned_cols=23 Identities=26% Similarity=0.418 Sum_probs=13.4
Q ss_pred ccccccCcccchHhhhhcccccc
Q 029557 80 CPVCVTRVTMDMVDHITTQHGNI 102 (191)
Q Consensus 80 CPICa~~~~~d~v~Hl~~qH~~~ 102 (191)
||.|..+.+.|+.=+-.+||..-
T Consensus 1 CP~C~~kkk~~Y~~~~LlqHA~g 23 (43)
T PF03470_consen 1 CPFCPGKKKQDYKYRELLQHASG 23 (43)
T ss_pred CCCCCCCCCcceehhHHHHHHHh
Confidence 78887776644444444555443
No 49
>smart00355 ZnF_C2H2 zinc finger.
Probab=70.85 E-value=3.8 Score=21.81 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=13.6
Q ss_pred ecCCCCCC-CcCHHHHHhhhh
Q 029557 49 YPCPFCSE-DFDLVGLCCHID 68 (191)
Q Consensus 49 F~CPfC~e-~~D~~~L~~H~~ 68 (191)
|.|+.|+. =-....|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 56788877 445567777766
No 50
>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=70.70 E-value=2.1 Score=26.88 Aligned_cols=26 Identities=23% Similarity=0.617 Sum_probs=16.9
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
.|.|+.||.-++... ..-+||||-+.
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 478999987433221 23599999764
No 51
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=70.64 E-value=2 Score=33.02 Aligned_cols=13 Identities=38% Similarity=1.088 Sum_probs=10.7
Q ss_pred ceecCCCCCC-CcC
Q 029557 47 YEYPCPFCSE-DFD 59 (191)
Q Consensus 47 ~~F~CPfC~e-~~D 59 (191)
+.|+||||+. .+.
T Consensus 35 a~y~CpfCgk~~vk 48 (90)
T PTZ00255 35 AKYFCPFCGKHAVK 48 (90)
T ss_pred CCccCCCCCCCcee
Confidence 7899999987 443
No 52
>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=67.97 E-value=2 Score=29.58 Aligned_cols=47 Identities=28% Similarity=0.553 Sum_probs=31.2
Q ss_pred CCCCCCcchhhhccCcceecCCCCCC--CcCHHHHHhhhhhcCCCCCCcccccccccCccc
Q 029557 31 DFEDIEEDDYEEVKGEYEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (191)
Q Consensus 31 g~e~~e~d~d~e~~~~~~F~CPfC~e--~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~ 89 (191)
.++|++.+++++. -+|+|+ ||. .+....|-.+ .-.|-|+-|+-.+..
T Consensus 4 ~l~d~~~~~~~~~---~~y~CR-CG~~f~i~e~~l~~~--------~~iv~C~sCSL~I~V 52 (55)
T PF05207_consen 4 SLDDMEFDEEEGV---YSYPCR-CGGEFEISEEDLEEG--------EVIVQCDSCSLWIRV 52 (55)
T ss_dssp ETTTSEEETTTTE---EEEEET-TSSEEEEEHHHHHCT----------EEEETTTTEEEEE
T ss_pred EhhhceecCCCCE---EEEcCC-CCCEEEEcchhccCc--------CEEEECCCCccEEEE
Confidence 3566666554334 389995 998 7777777666 445789999876643
No 53
>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=67.83 E-value=0.36 Score=35.52 Aligned_cols=55 Identities=22% Similarity=0.394 Sum_probs=24.0
Q ss_pred cCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcc-------cchHhhhhcccccchhhhhh
Q 029557 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT-------MDMVDHITTQHGNISNSWHK 108 (191)
Q Consensus 50 ~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~-------~d~v~Hl~~qH~~~~K~~rr 108 (191)
.||-|...++..+-.-||..=+..=.+.+.||-|...+- .|+.= +|++-+|+++|
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC----~~c~gLiSKkr 64 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFC----NHCHGLISKKR 64 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-----TTTT-EE-TTT
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceee----ccCCceeecce
Confidence 455555555555422222222222234588999988643 36653 47888876433
No 54
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=67.47 E-value=3.1 Score=24.76 Aligned_cols=10 Identities=40% Similarity=1.168 Sum_probs=8.9
Q ss_pred ceecCCCCCC
Q 029557 47 YEYPCPFCSE 56 (191)
Q Consensus 47 ~~F~CPfC~e 56 (191)
..|+||-||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 6799999986
No 55
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=66.04 E-value=2.7 Score=32.30 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=9.2
Q ss_pred ceecCCCCCC
Q 029557 47 YEYPCPFCSE 56 (191)
Q Consensus 47 ~~F~CPfC~e 56 (191)
+.|+||||+.
T Consensus 35 a~y~CpfCgk 44 (90)
T PRK03976 35 AKHVCPVCGR 44 (90)
T ss_pred cCccCCCCCC
Confidence 7899999987
No 56
>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=65.72 E-value=3 Score=27.06 Aligned_cols=31 Identities=32% Similarity=0.785 Sum_probs=22.1
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCccccccccc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
.+|.|+=||..|++..- ..+...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~~--------~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQS--------ISEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEE--------cCCCCCCcCCCCCC
Confidence 47999999987765321 12356789999977
No 57
>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=65.38 E-value=2.8 Score=32.27 Aligned_cols=10 Identities=50% Similarity=1.471 Sum_probs=9.2
Q ss_pred ceecCCCCCC
Q 029557 47 YEYPCPFCSE 56 (191)
Q Consensus 47 ~~F~CPfC~e 56 (191)
+.|+||||+.
T Consensus 34 a~y~CpfCgk 43 (91)
T TIGR00280 34 AKYVCPFCGK 43 (91)
T ss_pred cCccCCCCCC
Confidence 7899999987
No 58
>PF12773 DZR: Double zinc ribbon
Probab=65.28 E-value=4 Score=26.55 Aligned_cols=27 Identities=26% Similarity=0.767 Sum_probs=18.8
Q ss_pred cCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 50 ~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
.||.||..+. ..+...++||.|.+.+.
T Consensus 14 fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 14 FCPHCGTPLP------------PPDQSKKICPNCGAENP 40 (50)
T ss_pred CChhhcCChh------------hccCCCCCCcCCcCCCc
Confidence 5777777655 44556688999977654
No 59
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=64.67 E-value=3 Score=32.90 Aligned_cols=35 Identities=20% Similarity=0.415 Sum_probs=20.7
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
-+|+||||+...-..-+ -.-....-+++|-+|-..
T Consensus 21 k~FtCp~Cghe~vs~ct-----vkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 21 KTFTCPRCGHEKVSSCT-----VKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred ceEecCccCCeeeeEEE-----EEecCceeEEEcccCcce
Confidence 58999999984332222 111122335889999663
No 60
>PF15616 TerY-C: TerY-C metal binding domain
Probab=64.32 E-value=2.1 Score=34.81 Aligned_cols=39 Identities=15% Similarity=0.398 Sum_probs=28.4
Q ss_pred ecCCCCCCCcCHHHHHhhhhhcCCC-CCCcccccccccCccc
Q 029557 49 YPCPFCSEDFDLVGLCCHIDEEHPV-EAKSGVCPVCVTRVTM 89 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~eeH~~-e~k~vVCPICa~~~~~ 89 (191)
=.||+||..+-.+-. =|-.-|+. ....++||-|-....-
T Consensus 78 PgCP~CGn~~~fa~C--~CGkl~Ci~g~~~~~CPwCg~~g~~ 117 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC--GCGKLFCIDGEGEVTCPWCGNEGSF 117 (131)
T ss_pred CCCCCCcChhcEEEe--cCCCEEEeCCCCCEECCCCCCeeee
Confidence 579999995544432 58888884 5567999999876543
No 61
>PRK12495 hypothetical protein; Provisional
Probab=64.21 E-value=4.3 Score=35.89 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=22.2
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
..|.||.||..+- .. ...++||+|-..+.
T Consensus 41 sa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 41 TNAHCDECGDPIF------------RH-DGQEFCPTCQQPVT 69 (226)
T ss_pred chhhcccccCccc------------CC-CCeeECCCCCCccc
Confidence 4699999999554 22 55688999988765
No 62
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=63.84 E-value=4.7 Score=28.82 Aligned_cols=31 Identities=26% Similarity=0.667 Sum_probs=21.9
Q ss_pred ceecCCCCCCC-cCHHHHHhhhhhcCCCCCCcccccccc
Q 029557 47 YEYPCPFCSED-FDLVGLCCHIDEEHPVEAKSGVCPVCV 84 (191)
Q Consensus 47 ~~F~CPfC~e~-~D~~~L~~H~~eeH~~e~k~vVCPICa 84 (191)
..|.||-||+. +-. |..|.. .++.-+||-|-
T Consensus 24 ~~F~CPnCG~~~I~R---C~~CRk----~~~~Y~CP~CG 55 (59)
T PRK14890 24 VKFLCPNCGEVIIYR---CEKCRK----QSNPYTCPKCG 55 (59)
T ss_pred CEeeCCCCCCeeEee---chhHHh----cCCceECCCCC
Confidence 67999999994 544 444443 35678899884
No 63
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=63.70 E-value=3.8 Score=38.83 Aligned_cols=36 Identities=28% Similarity=0.770 Sum_probs=21.5
Q ss_pred CCCCCCCcCHHH-----------HHhhhhhcCCCCCCcccccccccCc
Q 029557 51 CPFCSEDFDLVG-----------LCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 51 CPfC~e~~D~~~-----------L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
||.|-|.+|+.. +|..|- .|.-+.-++.||.|..+-
T Consensus 17 cplcie~mditdknf~pc~cgy~ic~fc~-~~irq~lngrcpacrr~y 63 (480)
T COG5175 17 CPLCIEPMDITDKNFFPCPCGYQICQFCY-NNIRQNLNGRCPACRRKY 63 (480)
T ss_pred CcccccccccccCCcccCCcccHHHHHHH-HHHHhhccCCChHhhhhc
Confidence 777777666542 333332 222334789999998753
No 64
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=63.18 E-value=2.5 Score=28.11 Aligned_cols=46 Identities=35% Similarity=0.685 Sum_probs=29.4
Q ss_pred ceecCCC--CCCCcCHHHHHhhhhhcCCCCCCcccccc----cccCcc-cchHhh
Q 029557 47 YEYPCPF--CSEDFDLVGLCCHIDEEHPVEAKSGVCPV----CVTRVT-MDMVDH 94 (191)
Q Consensus 47 ~~F~CPf--C~e~~D~~~L~~H~~eeH~~e~k~vVCPI----Ca~~~~-~d~v~H 94 (191)
....||+ |.+.+-...|-.|+..+=+ .+.+.||. |..++. .+|..|
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 3578999 6667888999999985433 35789999 987765 356554
No 65
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=62.95 E-value=2.9 Score=39.07 Aligned_cols=57 Identities=26% Similarity=0.549 Sum_probs=36.6
Q ss_pred ecCCCCCCCcCHHH---HHhhhhhcCCCCCC-cccccccccCcc--------------------------cchHhhhhcc
Q 029557 49 YPCPFCSEDFDLVG---LCCHIDEEHPVEAK-SGVCPVCVTRVT--------------------------MDMVDHITTQ 98 (191)
Q Consensus 49 F~CPfC~e~~D~~~---L~~H~~eeH~~e~k-~vVCPICa~~~~--------------------------~d~v~Hl~~q 98 (191)
-.|--|+.-+-+-+ =|+|+-=.-|.-+. --+||.|..+|- +||-.||+.+
T Consensus 91 HfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~VqrIeq~~~g~iFmC~~~~GC~RTyLsqrDlqAHInhr 170 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQRIEQIMMGGIFMCAAPHGCLRTYLSQRDLQAHINHR 170 (389)
T ss_pred EeecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHHHHHHhcccceEEeecchhHHHHHhhHHHHHHHhhhh
Confidence 45666666444433 25554433332221 358999998641 7999999999
Q ss_pred cccchhh
Q 029557 99 HGNISNS 105 (191)
Q Consensus 99 H~~~~K~ 105 (191)
|+.++|-
T Consensus 171 H~~~~~p 177 (389)
T KOG2932|consen 171 HGSLLQP 177 (389)
T ss_pred hccccCC
Confidence 9988764
No 66
>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=62.93 E-value=4.3 Score=27.20 Aligned_cols=25 Identities=28% Similarity=0.598 Sum_probs=20.5
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCC
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHP 72 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~ 72 (191)
..+.||.|...+.. .|..|+...|.
T Consensus 30 ~~v~CPiC~~~~~~-~l~~Hl~~~H~ 54 (54)
T PF05605_consen 30 KNVVCPICSSRVTD-NLIRHLNSQHR 54 (54)
T ss_pred CCccCCCchhhhhh-HHHHHHHHhcC
Confidence 36999999996653 99999998884
No 67
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=62.29 E-value=4.6 Score=26.82 Aligned_cols=28 Identities=21% Similarity=0.489 Sum_probs=21.4
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
.|.|.-||.++++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 58899999977754 34568999997665
No 68
>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=61.34 E-value=6.3 Score=27.19 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=28.2
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccCcccchHhhhh
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHIT 96 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~d~v~Hl~ 96 (191)
.+=+||.||. .-+ ....+..+||.|-....+|+.+=++
T Consensus 27 TSq~C~~CG~~~~~------------~~~~r~~~C~~Cg~~~~rD~naA~N 65 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK------------RRSGRVFTCPNCGFEMDRDVNAARN 65 (69)
T ss_pred CccCccCccccccc------------ccccceEEcCCCCCEECcHHHHHHH
Confidence 5678999998 333 5566778999998887777776543
No 69
>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=61.12 E-value=5.5 Score=32.97 Aligned_cols=54 Identities=24% Similarity=0.503 Sum_probs=32.4
Q ss_pred ceecCCC----CCCCcCHHHHHhhhhhcCCCCCCcccccc----cccC-cccchHhhhhcccccch
Q 029557 47 YEYPCPF----CSEDFDLVGLCCHIDEEHPVEAKSGVCPV----CVTR-VTMDMVDHITTQHGNIS 103 (191)
Q Consensus 47 ~~F~CPf----C~e~~D~~~L~~H~~eeH~~e~k~vVCPI----Ca~~-~~~d~v~Hl~~qH~~~~ 103 (191)
-.|||+| |.+.+-......|-..= .-+...||+ |.-. ...++..|+...|+...
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE~~C---~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHEEEC---PFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHHHT----TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhHhccC---CCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 4699999 99988888888887442 345678999 7322 23699999999998754
No 70
>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=60.98 E-value=2.4 Score=24.72 Aligned_cols=11 Identities=45% Similarity=1.558 Sum_probs=9.0
Q ss_pred eecCCCCCCCc
Q 029557 48 EYPCPFCSEDF 58 (191)
Q Consensus 48 ~F~CPfC~e~~ 58 (191)
.|.||+|+..|
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 59999998754
No 71
>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=60.80 E-value=3 Score=32.05 Aligned_cols=10 Identities=50% Similarity=1.534 Sum_probs=8.5
Q ss_pred ceecCCCCCC
Q 029557 47 YEYPCPFCSE 56 (191)
Q Consensus 47 ~~F~CPfC~e 56 (191)
..|.||||+.
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 72
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.40 E-value=7.5 Score=32.53 Aligned_cols=32 Identities=22% Similarity=0.402 Sum_probs=23.0
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
..|.||-|+.-|+..+-.. ..-.||+|-...-
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 6899999999555554332 2579999977653
No 73
>PF13395 HNH_4: HNH endonuclease
Probab=59.11 E-value=5.2 Score=26.98 Aligned_cols=14 Identities=29% Similarity=1.013 Sum_probs=12.1
Q ss_pred CCCCCCCcCHHHHH
Q 029557 51 CPFCSEDFDLVGLC 64 (191)
Q Consensus 51 CPfC~e~~D~~~L~ 64 (191)
|||||+.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 99999999988764
No 74
>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=58.74 E-value=7.4 Score=31.80 Aligned_cols=31 Identities=19% Similarity=0.344 Sum_probs=23.5
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
..|.||-|+.-++..+-.. ..-.||+|-...
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME----------LNFTCPRCGAML 138 (158)
T ss_pred CeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEe
Confidence 6799999999666655554 267999997764
No 75
>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=58.47 E-value=6.1 Score=30.91 Aligned_cols=30 Identities=33% Similarity=0.686 Sum_probs=22.7
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccCccc
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~ 89 (191)
....||-||. =+|+ ...++|||-|.+..-.
T Consensus 8 tKR~Cp~CG~kFYDL-------------nk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL-------------NKDPIVCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhccC-------------CCCCccCCCCCCccCc
Confidence 7789999999 5554 2467999999775543
No 76
>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=57.66 E-value=7.5 Score=27.55 Aligned_cols=36 Identities=17% Similarity=0.450 Sum_probs=22.6
Q ss_pred ceecCCCCCC------------CcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 47 YEYPCPFCSE------------DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 47 ~~F~CPfC~e------------~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
..|.||.|++ -||...+-.++.. ...+||+|...+.
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~ 50 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLS 50 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-S
T ss_pred cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCC
Confidence 3577887765 3667777777766 6789999977665
No 77
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.60 E-value=5.3 Score=34.41 Aligned_cols=47 Identities=23% Similarity=0.564 Sum_probs=29.1
Q ss_pred ccCcceecCCCCCCCcCHHH----HHhhhhhcCCC---CCCcccccccccCccc
Q 029557 43 VKGEYEYPCPFCSEDFDLVG----LCCHIDEEHPV---EAKSGVCPVCVTRVTM 89 (191)
Q Consensus 43 ~~~~~~F~CPfC~e~~D~~~----L~~H~~eeH~~---e~k~vVCPICa~~~~~ 89 (191)
.+....|.||.|=+.+.... =|-|+-=.-+. =.+.++||+|..++..
T Consensus 126 ~~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 126 LRKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred cccccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 33346899999988666554 23443322222 1234789999987763
No 78
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=57.44 E-value=6.6 Score=31.11 Aligned_cols=27 Identities=30% Similarity=0.478 Sum_probs=22.1
Q ss_pred cccccccccCcc-----cchHhhhhcccccch
Q 029557 77 SGVCPVCVTRVT-----MDMVDHITTQHGNIS 103 (191)
Q Consensus 77 ~vVCPICa~~~~-----~d~v~Hl~~qH~~~~ 103 (191)
.+.||+|....| ..+..||+.-||-.-
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~s 56 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGISS 56 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhcccccc
Confidence 789999987655 468999999998764
No 79
>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=56.56 E-value=4.4 Score=38.58 Aligned_cols=36 Identities=36% Similarity=0.999 Sum_probs=17.7
Q ss_pred cCcceecCCCCCCCcCHHHHHhhhhhcCCCCCCccccccc-ccCcccchH
Q 029557 44 KGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVC-VTRVTMDMV 92 (191)
Q Consensus 44 ~~~~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPIC-a~~~~~d~v 92 (191)
+|.+.-.||||+.-+ |+ +-+--+|||| ...||.+-+
T Consensus 376 ~G~~~v~CP~cgA~y------------~~-~~kG~lC~vC~l~~IG~~a~ 412 (422)
T PF06957_consen 376 RGSPSVKCPYCGAKY------------HP-EYKGQLCPVCELSEIGADAS 412 (422)
T ss_dssp TTS-EEE-TTT--EE------------EG-GGTTSB-TTTTTBBTT---S
T ss_pred CCCCCeeCCCCCCcc------------Ch-hhCCCCCCCCcceeeCCcce
Confidence 445677899999743 22 2345699999 456775543
No 80
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=55.83 E-value=5.3 Score=31.15 Aligned_cols=9 Identities=56% Similarity=1.619 Sum_probs=7.8
Q ss_pred eecCCCCCC
Q 029557 48 EYPCPFCSE 56 (191)
Q Consensus 48 ~F~CPfC~e 56 (191)
-++|||||+
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 478999998
No 81
>PRK12496 hypothetical protein; Provisional
Probab=53.59 E-value=8.5 Score=31.74 Aligned_cols=27 Identities=22% Similarity=0.584 Sum_probs=19.2
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
.|.|+-|+..|+. ....-+||||-..+
T Consensus 127 ~~~C~gC~~~~~~-------------~~~~~~C~~CG~~~ 153 (164)
T PRK12496 127 RKVCKGCKKKYPE-------------DYPDDVCEICGSPV 153 (164)
T ss_pred eEECCCCCccccC-------------CCCCCcCCCCCChh
Confidence 5999999987753 12235899996554
No 82
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=52.62 E-value=9.5 Score=32.10 Aligned_cols=25 Identities=32% Similarity=0.848 Sum_probs=17.6
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
.+.||.||- .|.. -.+.+||||-+.
T Consensus 134 ~~vC~vCGy-------------~~~g-e~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGY-------------THEG-EAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCC-------------cccC-CCCCcCCCCCCh
Confidence 689999974 1222 446899999753
No 83
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=52.61 E-value=8.4 Score=23.01 Aligned_cols=8 Identities=38% Similarity=1.244 Sum_probs=3.9
Q ss_pred CCCCCCCc
Q 029557 51 CPFCSEDF 58 (191)
Q Consensus 51 CPfC~e~~ 58 (191)
||-|+..+
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 55555443
No 84
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=52.17 E-value=4.5 Score=31.13 Aligned_cols=11 Identities=36% Similarity=1.189 Sum_probs=9.8
Q ss_pred cceecCCCCCC
Q 029557 46 EYEYPCPFCSE 56 (191)
Q Consensus 46 ~~~F~CPfC~e 56 (191)
|+.|.|+|||+
T Consensus 34 haky~CsfCGK 44 (92)
T KOG0402|consen 34 HAKYTCSFCGK 44 (92)
T ss_pred hhhhhhhhcch
Confidence 37899999998
No 85
>PRK00420 hypothetical protein; Validated
Probab=52.16 E-value=9.9 Score=30.13 Aligned_cols=28 Identities=25% Similarity=0.431 Sum_probs=18.9
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
.-.||.||..+-. .....++||+|...+
T Consensus 23 ~~~CP~Cg~pLf~------------lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLFE------------LKDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCccee------------cCCCceECCCCCCee
Confidence 4689999974311 124568999998754
No 86
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=50.96 E-value=7.5 Score=30.34 Aligned_cols=38 Identities=24% Similarity=0.467 Sum_probs=21.8
Q ss_pred ecCCCCCCCcCH---HHHHhhhhhcCCCCCCcccccccccCccc
Q 029557 49 YPCPFCSEDFDL---VGLCCHIDEEHPVEAKSGVCPVCVTRVTM 89 (191)
Q Consensus 49 F~CPfC~e~~D~---~~L~~H~~eeH~~e~k~vVCPICa~~~~~ 89 (191)
-.|||||....+ ..+.-|-.+.+ +-.-+|+-|-+.||.
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 469999993322 22222222211 112689999999884
No 87
>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=50.96 E-value=5.1 Score=34.09 Aligned_cols=21 Identities=19% Similarity=0.453 Sum_probs=0.0
Q ss_pred cccccccccCcc-cchHhhhhc
Q 029557 77 SGVCPVCVTRVT-MDMVDHITT 97 (191)
Q Consensus 77 ~vVCPICa~~~~-~d~v~Hl~~ 97 (191)
.++||||-.+|- ..|-.||++
T Consensus 168 ~~~cPitGe~IP~~e~~eHmRi 189 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMRI 189 (229)
T ss_dssp ----------------------
T ss_pred cccccccccccccccccccccc
Confidence 379999999865 689999975
No 88
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=50.53 E-value=8.1 Score=24.48 Aligned_cols=20 Identities=20% Similarity=0.469 Sum_probs=8.2
Q ss_pred eecCCCCCCCcCHHHHHhhh
Q 029557 48 EYPCPFCSEDFDLVGLCCHI 67 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~ 67 (191)
+|.||-|+..+-..-+..|+
T Consensus 4 ~~~C~nC~R~v~a~RfA~HL 23 (33)
T PF08209_consen 4 YVECPNCGRPVAASRFAPHL 23 (33)
T ss_dssp EEE-TTTSSEEEGGGHHHHH
T ss_pred eEECCCCcCCcchhhhHHHH
Confidence 34444444444444444443
No 89
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.47 E-value=10 Score=31.98 Aligned_cols=35 Identities=20% Similarity=0.441 Sum_probs=27.3
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcccchHhhhhc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHITT 97 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~d~v~Hl~~ 97 (191)
..=.||.||. ...+...||.|-...-+|..+=+++
T Consensus 308 tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~Ni 342 (364)
T COG0675 308 TSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALNI 342 (364)
T ss_pred CcccccccCC----------------ccceeEECCCCCCeehhhHHHHHHH
Confidence 4477999998 3467789999988877888777653
No 90
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=50.02 E-value=8.8 Score=26.54 Aligned_cols=9 Identities=44% Similarity=1.652 Sum_probs=8.0
Q ss_pred eecCCCCCC
Q 029557 48 EYPCPFCSE 56 (191)
Q Consensus 48 ~F~CPfC~e 56 (191)
.|.||+|+.
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 599999986
No 91
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.79 E-value=11 Score=22.06 Aligned_cols=10 Identities=30% Similarity=0.919 Sum_probs=6.2
Q ss_pred ecCCCCCCCc
Q 029557 49 YPCPFCSEDF 58 (191)
Q Consensus 49 F~CPfC~e~~ 58 (191)
-.||.||..+
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 3577777643
No 92
>PRK03922 hypothetical protein; Provisional
Probab=48.40 E-value=8.8 Score=30.70 Aligned_cols=14 Identities=43% Similarity=0.786 Sum_probs=11.4
Q ss_pred eecCCCCCCCcCHH
Q 029557 48 EYPCPFCSEDFDLV 61 (191)
Q Consensus 48 ~F~CPfC~e~~D~~ 61 (191)
.-.||+||++|+-.
T Consensus 49 ~~~cP~cge~~~~a 62 (113)
T PRK03922 49 LTICPKCGEPFDSA 62 (113)
T ss_pred cccCCCCCCcCCcE
Confidence 56899999998743
No 93
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.68 E-value=12 Score=37.82 Aligned_cols=27 Identities=30% Similarity=0.415 Sum_probs=24.3
Q ss_pred eecCCCCCC-CcCHHHHHhhhhhcCCCC
Q 029557 48 EYPCPFCSE-DFDLVGLCCHIDEEHPVE 74 (191)
Q Consensus 48 ~F~CPfC~e-~~D~~~L~~H~~eeH~~e 74 (191)
---|+||-+ -||..+|..|+..+|.+.
T Consensus 182 hp~C~~C~~~fld~~el~rH~~~~h~~c 209 (669)
T KOG2231|consen 182 HPLCKFCHERFLDDDELYRHLRFDHEFC 209 (669)
T ss_pred CccchhhhhhhccHHHHHHhhccceehe
Confidence 467999999 999999999999999873
No 94
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=47.52 E-value=5.6 Score=34.17 Aligned_cols=32 Identities=28% Similarity=0.616 Sum_probs=20.0
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCC-CCccc
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVE-AKSGV 79 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e-~k~vV 79 (191)
.|.||.|+..+.+..=-=+|...|.+| ++.+.
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~fd~a~~Gy 34 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQFDCAKEGY 34 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCCccccCce
Confidence 389999999764332223466778874 34443
No 95
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=47.19 E-value=16 Score=23.07 Aligned_cols=29 Identities=31% Similarity=0.764 Sum_probs=18.4
Q ss_pred ecCCCCCCCcCHH--HHHhhhhhcCCCCCCccccccccc
Q 029557 49 YPCPFCSEDFDLV--GLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 49 F~CPfC~e~~D~~--~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
..||-|+..|.+. .| +...+.|.||-|..
T Consensus 3 i~CP~C~~~f~v~~~~l--------~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKL--------PAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEcCHHHc--------ccCCcEEECCCCCc
Confidence 5788888855443 22 22456788888854
No 96
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=46.98 E-value=9.4 Score=30.03 Aligned_cols=14 Identities=36% Similarity=0.878 Sum_probs=11.4
Q ss_pred eecCCCCCCCcCHH
Q 029557 48 EYPCPFCSEDFDLV 61 (191)
Q Consensus 48 ~F~CPfC~e~~D~~ 61 (191)
.-.||+|+++|+-.
T Consensus 47 ~~~cP~Cge~~~~a 60 (102)
T PF04475_consen 47 DTICPKCGEELDSA 60 (102)
T ss_pred cccCCCCCCccCce
Confidence 56899999988743
No 97
>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=46.03 E-value=3.1 Score=34.72 Aligned_cols=39 Identities=26% Similarity=0.698 Sum_probs=19.4
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
.|+||.|+..+...++.. .+.-........||-|.....
T Consensus 18 ~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~~ 56 (188)
T PF08996_consen 18 KLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPLS 56 (188)
T ss_dssp EEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B--
T ss_pred EeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcCC
Confidence 699999999777777544 111112344578999988544
No 98
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=45.87 E-value=7.4 Score=30.25 Aligned_cols=27 Identities=30% Similarity=0.386 Sum_probs=20.4
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
..+.|+-|+..+..... ...||-|...
T Consensus 69 ~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 69 VECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred cEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 57999999987766532 4679999763
No 99
>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=45.63 E-value=18 Score=21.42 Aligned_cols=22 Identities=18% Similarity=0.608 Sum_probs=14.9
Q ss_pred eecCCCCCCCcC-HHHHHhhhhh
Q 029557 48 EYPCPFCSEDFD-LVGLCCHIDE 69 (191)
Q Consensus 48 ~F~CPfC~e~~D-~~~L~~H~~e 69 (191)
.|.|.+|+..|. ...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 477888888555 6667777653
No 100
>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=45.19 E-value=13 Score=30.01 Aligned_cols=40 Identities=33% Similarity=0.670 Sum_probs=28.9
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcccchH
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMV 92 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~d~v 92 (191)
.+.|.-|+..++...+.......... .||.|...+-.|.+
T Consensus 105 ~~~C~~C~~~~~~~~~~~~~~~~~~~-----~C~~C~~~lrp~vv 144 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVDSIDEEEPP-----RCPKCGGLLRPDVV 144 (178)
T ss_dssp EEEETTTSBEEEGHHHHHHHHTTSSC-----BCTTTSCBEEEEE-
T ss_pred eeeecCCCccccchhhcccccccccc-----cccccCccCCCCee
Confidence 68999999988888777665544322 99999886554444
No 101
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=44.31 E-value=14 Score=25.86 Aligned_cols=25 Identities=32% Similarity=0.773 Sum_probs=17.5
Q ss_pred ecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
-.||.|++.|.. +.-.||||.|.+.
T Consensus 6 ~~C~~Cg~~~~~-------------~dDiVvCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFKD-------------GDDIVVCPECGAP 30 (54)
T ss_pred ccChhhCCcccC-------------CCCEEECCCCCCc
Confidence 578999886621 2345899999774
No 102
>smart00507 HNHc HNH nucleases.
Probab=43.83 E-value=5.1 Score=24.68 Aligned_cols=21 Identities=19% Similarity=0.175 Sum_probs=13.5
Q ss_pred ecCCCCCCCcCHHHHHhhhhh
Q 029557 49 YPCPFCSEDFDLVGLCCHIDE 69 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~e 69 (191)
+.|+||+..++..--+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 799999996654233444443
No 103
>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=43.79 E-value=15 Score=31.51 Aligned_cols=35 Identities=26% Similarity=0.553 Sum_probs=21.3
Q ss_pred CCCCCC--CcCHHHHHhhhhhcCCC------CCCccccccccc
Q 029557 51 CPFCSE--DFDLVGLCCHIDEEHPV------EAKSGVCPVCVT 85 (191)
Q Consensus 51 CPfC~e--~~D~~~L~~H~~eeH~~------e~k~vVCPICa~ 85 (191)
||.||. +-.+.+||.=|--+... .....+||.|-+
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~ 43 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGR 43 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCC
Confidence 888887 33345677666544432 224577888865
No 104
>PF14279 HNH_5: HNH endonuclease
Probab=43.65 E-value=5.5 Score=28.87 Aligned_cols=40 Identities=20% Similarity=0.556 Sum_probs=24.6
Q ss_pred CCCCCCCcCHHHHHhhhhhcCCC--------CCCcccccccccCcccchHhhh
Q 029557 51 CPFCSEDFDLVGLCCHIDEEHPV--------EAKSGVCPVCVTRVTMDMVDHI 95 (191)
Q Consensus 51 CPfC~e~~D~~~L~~H~~eeH~~--------e~k~vVCPICa~~~~~d~v~Hl 95 (191)
|.||.++++....- .||-. ..+. ||--|-...+...-+++
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 89999977654322 45544 2233 88888887774444433
No 105
>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=42.67 E-value=12 Score=34.46 Aligned_cols=38 Identities=34% Similarity=0.552 Sum_probs=24.0
Q ss_pred eecCCCCCC--Cc--CHH--------HHHhhhhhcCCCCCCcccccccccC
Q 029557 48 EYPCPFCSE--DF--DLV--------GLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 48 ~F~CPfC~e--~~--D~~--------~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
.+.||.|.. .+ +.. .+|..|.+..-.. ....||+|...
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~-~~~~CP~C~~~ 52 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR-GSGSCPECDTP 52 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcC-CCCCCCCCCCc
Confidence 478999988 22 211 2466676666433 44699999764
No 106
>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=42.03 E-value=18 Score=20.75 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=13.3
Q ss_pred ecCCCCCC-CcCHHHHHhhhh
Q 029557 49 YPCPFCSE-DFDLVGLCCHID 68 (191)
Q Consensus 49 F~CPfC~e-~~D~~~L~~H~~ 68 (191)
|.|+.|+. =-+...|..|+.
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 67777777 446666666664
No 107
>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=41.75 E-value=11 Score=29.91 Aligned_cols=25 Identities=28% Similarity=0.984 Sum_probs=16.3
Q ss_pred cCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 50 ~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
+||-|+.++.-. +....|||-|+.-
T Consensus 4 ~CP~C~seytY~------------dg~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCPKCNSEYTYH------------DGTQLICPSCLYE 28 (109)
T ss_pred cCCcCCCcceEe------------cCCeeECcccccc
Confidence 588877654321 4556889999764
No 108
>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=40.98 E-value=16 Score=29.79 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=21.6
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
....||-||. =+|+ ...++|||-|-...
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 7789999999 5553 34679999997654
No 109
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.91 E-value=7.8 Score=35.49 Aligned_cols=41 Identities=29% Similarity=0.511 Sum_probs=26.1
Q ss_pred ceecCCCCCC--CcCHHHH-HhhhhhcCCCCCCc-----ccccccccCc
Q 029557 47 YEYPCPFCSE--DFDLVGL-CCHIDEEHPVEAKS-----GVCPVCVTRV 87 (191)
Q Consensus 47 ~~F~CPfC~e--~~D~~~L-~~H~~eeH~~e~k~-----vVCPICa~~~ 87 (191)
.+-.||+||+ -+--... |.|+-=+-|.-++. -.||-|.+.+
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 4444444 78865555544433 3788887654
No 110
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.87 E-value=17 Score=34.62 Aligned_cols=15 Identities=20% Similarity=0.691 Sum_probs=10.2
Q ss_pred ceecCCCCCCCcCHH
Q 029557 47 YEYPCPFCSEDFDLV 61 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~ 61 (191)
.+|.||||-.+-+..
T Consensus 373 ~sfKCPYCP~e~~~~ 387 (394)
T KOG2817|consen 373 QSFKCPYCPVEQLAS 387 (394)
T ss_pred eeeeCCCCCcccCHH
Confidence 468888887755443
No 111
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=40.42 E-value=9 Score=27.64 Aligned_cols=27 Identities=26% Similarity=0.481 Sum_probs=19.7
Q ss_pred ccccccccC--cccchHhhhhcccccchh
Q 029557 78 GVCPVCVTR--VTMDMVDHITTQHGNISN 104 (191)
Q Consensus 78 vVCPICa~~--~~~d~v~Hl~~qH~~~~K 104 (191)
..||-|.+. -..|.++|.+-.|+++|.
T Consensus 18 lrCPRC~~~FR~~K~Y~RHVNKaH~~~~~ 46 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHVNKAHGWLFG 46 (65)
T ss_pred eeCCchhHHHHHhHHHHHHhhHHhhhhhc
Confidence 456666552 346899999999999873
No 112
>PRK11595 DNA utilization protein GntX; Provisional
Probab=40.14 E-value=15 Score=31.22 Aligned_cols=33 Identities=24% Similarity=0.565 Sum_probs=18.6
Q ss_pred cCCCCCCCcCH--HHHHhhhhhcCCCCCCcccccccc
Q 029557 50 PCPFCSEDFDL--VGLCCHIDEEHPVEAKSGVCPVCV 84 (191)
Q Consensus 50 ~CPfC~e~~D~--~~L~~H~~eeH~~e~k~vVCPICa 84 (191)
.|+.|++.+.. ..||.+|.+.=..- ...||.|.
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~--~~~C~~Cg 41 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTL--KTCCPQCG 41 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcc--cCcCccCC
Confidence 48888874432 35788886552221 23566654
No 113
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.00 E-value=9.8 Score=30.27 Aligned_cols=36 Identities=36% Similarity=0.579 Sum_probs=22.6
Q ss_pred ceecCCCCCCCcCHH-HH-Hhh-----hhhcCCCCCCcccccccc
Q 029557 47 YEYPCPFCSEDFDLV-GL-CCH-----IDEEHPVEAKSGVCPVCV 84 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~-~L-~~H-----~~eeH~~e~k~vVCPICa 84 (191)
..+.||+|.+.|... -| |-| |...... ....||+|.
T Consensus 12 ~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~--~~~~Cp~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFREPVLLPCGHNFCRACLTRSWE--GPLSCPVCR 54 (386)
T ss_pred ccccChhhHHHhhcCccccccchHhHHHHHHhcC--CCcCCcccC
Confidence 468999999966655 22 223 3322222 348999998
No 114
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=39.87 E-value=14 Score=26.06 Aligned_cols=10 Identities=30% Similarity=0.939 Sum_probs=8.8
Q ss_pred ceecCCCCCC
Q 029557 47 YEYPCPFCSE 56 (191)
Q Consensus 47 ~~F~CPfC~e 56 (191)
..|+||.||.
T Consensus 13 v~~~Cp~cGi 22 (55)
T PF13824_consen 13 VNFECPDCGI 22 (55)
T ss_pred cCCcCCCCCC
Confidence 7899999986
No 115
>PF14353 CpXC: CpXC protein
Probab=39.47 E-value=15 Score=28.28 Aligned_cols=28 Identities=29% Similarity=0.413 Sum_probs=18.7
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCccc
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGV 79 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vV 79 (191)
.|+||.||..+-+ .+--.+|-.+.+.++
T Consensus 38 ~~~CP~Cg~~~~~----~~p~lY~D~~~~~~i 65 (128)
T PF14353_consen 38 SFTCPSCGHKFRL----EYPLLYHDPEKKFMI 65 (128)
T ss_pred EEECCCCCCceec----CCCEEEEcCCCCEEE
Confidence 7999999996543 445556665655543
No 116
>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=38.94 E-value=21 Score=26.81 Aligned_cols=32 Identities=19% Similarity=0.371 Sum_probs=25.8
Q ss_pred CCCCCcccccccccCcc-cchHhhhhcccccch
Q 029557 72 PVEAKSGVCPVCVTRVT-MDMVDHITTQHGNIS 103 (191)
Q Consensus 72 ~~e~k~vVCPICa~~~~-~d~v~Hl~~qH~~~~ 103 (191)
..+.+.+||-.|-.-|+ ..+.+||..+|..+.
T Consensus 6 ~~~~~vlIC~~C~~av~~~~v~~HL~~~H~~~~ 38 (109)
T PF12013_consen 6 NPEYRVLICRQCQYAVQPSEVESHLRKRHHILK 38 (109)
T ss_pred cCcCCEEEeCCCCcccCchHHHHHHHHhccccc
Confidence 34678899999987665 799999998888763
No 117
>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=38.53 E-value=16 Score=22.45 Aligned_cols=9 Identities=44% Similarity=1.095 Sum_probs=4.7
Q ss_pred CCccccccc
Q 029557 75 AKSGVCPVC 83 (191)
Q Consensus 75 ~k~vVCPIC 83 (191)
...+.||+|
T Consensus 33 ~~~~~CP~C 41 (41)
T PF00097_consen 33 SGSVKCPLC 41 (41)
T ss_dssp TSSSBTTTT
T ss_pred cCCccCCcC
Confidence 344456665
No 118
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=37.85 E-value=13 Score=28.82 Aligned_cols=27 Identities=22% Similarity=0.438 Sum_probs=19.1
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
..+.|+-|+..|.+.. ....||-|-..
T Consensus 69 ~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred cEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 5699999998665533 33469999753
No 119
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=37.28 E-value=17 Score=33.92 Aligned_cols=39 Identities=31% Similarity=0.598 Sum_probs=28.7
Q ss_pred ceecCCCCCCCcC--HHHHHhhhhhc-CCC-----CCCccccccccc
Q 029557 47 YEYPCPFCSEDFD--LVGLCCHIDEE-HPV-----EAKSGVCPVCVT 85 (191)
Q Consensus 47 ~~F~CPfC~e~~D--~~~L~~H~~ee-H~~-----e~k~vVCPICa~ 85 (191)
.+-.||.||...| +.+||.=|--+ |+. +.+..+|+-|-+
T Consensus 5 ~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 5 STILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGA 51 (355)
T ss_pred cccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCC
Confidence 5678999999887 88888877665 544 233477888864
No 120
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.96 E-value=15 Score=29.35 Aligned_cols=40 Identities=23% Similarity=0.426 Sum_probs=22.0
Q ss_pred ceecCCCCCCCcCHHHHHhhhh-----hcCCCC---CCcccccccccC
Q 029557 47 YEYPCPFCSEDFDLVGLCCHID-----EEHPVE---AKSGVCPVCVTR 86 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~-----eeH~~e---~k~vVCPICa~~ 86 (191)
..+.|+-||..+...+--.++. .-|-.. .....||.|-..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 5799999998665542111111 112111 244679999754
No 121
>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=36.65 E-value=12 Score=25.15 Aligned_cols=14 Identities=29% Similarity=0.667 Sum_probs=7.3
Q ss_pred cCCCCCCCcCHHHH
Q 029557 50 PCPFCSEDFDLVGL 63 (191)
Q Consensus 50 ~CPfC~e~~D~~~L 63 (191)
.||.|+.+||...-
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 89999998876543
No 122
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=35.75 E-value=16 Score=23.70 Aligned_cols=27 Identities=26% Similarity=0.429 Sum_probs=14.9
Q ss_pred cCCCCCCCcCHHHHHhhhhhcCCCCCCccccccccc
Q 029557 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 50 ~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
.||-||.-+-..+ .+ +....+||.|..
T Consensus 2 FCp~Cg~~l~~~~------~~---~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKE------GK---EKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCcccccc------CC---CCCEEECCcCCC
Confidence 4888887332221 11 123678999964
No 123
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=35.63 E-value=15 Score=32.75 Aligned_cols=61 Identities=23% Similarity=0.364 Sum_probs=0.0
Q ss_pred ecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccCccc--chHhhhh----cccccchhhhhhhccc
Q 029557 49 YPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTM--DMVDHIT----TQHGNISNSWHKLKLH 112 (191)
Q Consensus 49 F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~--d~v~Hl~----~qH~~~~K~~rrrk~~ 112 (191)
+.|-|||+ =.|.-.|..|....- .-++-.|-+|..-.+. .+-.|+. .+|.+-+| +||-|+.
T Consensus 146 ~lct~cgkgfndtfdlkrh~rtht--gvrpykc~~c~kaftqrcsleshl~kvhgv~~~yayk-err~kl~ 213 (267)
T KOG3576|consen 146 HLCTFCGKGFNDTFDLKRHTRTHT--GVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYK-ERRAKLY 213 (267)
T ss_pred HHHhhccCcccchhhhhhhhcccc--CccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHH-Hhhhhee
No 124
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=35.32 E-value=18 Score=34.97 Aligned_cols=22 Identities=27% Similarity=0.607 Sum_probs=16.3
Q ss_pred hhhcCCCCCCcccccccccCcc
Q 029557 67 IDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 67 ~~eeH~~e~k~vVCPICa~~~~ 88 (191)
|..+.-.+++.-|||||...||
T Consensus 27 c~~~~~~~PNt~vcpv~lg~PG 48 (474)
T PRK05477 27 CSTDFGAEPNTNVCPVCLGLPG 48 (474)
T ss_pred CCcccCCCCCCCcCccccCCCC
Confidence 3333444678899999999987
No 125
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=35.06 E-value=9.2 Score=29.54 Aligned_cols=27 Identities=22% Similarity=0.475 Sum_probs=17.7
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
..+.|+-|+..|++.... ..||-|-..
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 579999999987766543 239999764
No 126
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=34.88 E-value=19 Score=33.89 Aligned_cols=11 Identities=36% Similarity=1.253 Sum_probs=9.3
Q ss_pred ceecCCCCCCC
Q 029557 47 YEYPCPFCSED 57 (191)
Q Consensus 47 ~~F~CPfC~e~ 57 (191)
.+|.||||-++
T Consensus 375 ~~FKCPYCP~~ 385 (396)
T COG5109 375 LSFKCPYCPEM 385 (396)
T ss_pred EEeeCCCCCcc
Confidence 57999999883
No 127
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=34.74 E-value=21 Score=33.77 Aligned_cols=40 Identities=33% Similarity=0.600 Sum_probs=31.8
Q ss_pred eecCCC--CCC-CcCHHHHHhhhhhcCCC-----------------CCCcccccccccCc
Q 029557 48 EYPCPF--CSE-DFDLVGLCCHIDEEHPV-----------------EAKSGVCPVCVTRV 87 (191)
Q Consensus 48 ~F~CPf--C~e-~~D~~~L~~H~~eeH~~-----------------e~k~vVCPICa~~~ 87 (191)
-|.||. |.+ .-.+-+|.-|...-|+. +.|+-+|+||..+-
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 499997 777 77889999999888832 33567899998875
No 128
>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=34.64 E-value=16 Score=35.35 Aligned_cols=48 Identities=17% Similarity=0.279 Sum_probs=34.1
Q ss_pred CcCHHHHHhhhhhcCCCCC-----------------CcccccccccCcc--cchHhhhhcccccchh
Q 029557 57 DFDLVGLCCHIDEEHPVEA-----------------KSGVCPVCVTRVT--MDMVDHITTQHGNISN 104 (191)
Q Consensus 57 ~~D~~~L~~H~~eeH~~e~-----------------k~vVCPICa~~~~--~d~v~Hl~~qH~~~~K 104 (191)
.+++..|..|+...|..++ +.-+||+|..+-. .++..|+...|-.-++
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 4566777777776665332 2356999997643 6899999999977764
No 129
>PRK04023 DNA polymerase II large subunit; Validated
Probab=34.43 E-value=19 Score=38.28 Aligned_cols=9 Identities=22% Similarity=0.589 Sum_probs=4.7
Q ss_pred ccccccccC
Q 029557 78 GVCPVCVTR 86 (191)
Q Consensus 78 vVCPICa~~ 86 (191)
..||-|-..
T Consensus 664 y~CPKCG~E 672 (1121)
T PRK04023 664 DECEKCGRE 672 (1121)
T ss_pred CcCCCCCCC
Confidence 346666543
No 130
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=33.86 E-value=22 Score=25.65 Aligned_cols=31 Identities=29% Similarity=0.750 Sum_probs=20.0
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccc
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCV 84 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa 84 (191)
..|+||-||+ .+-.-.-|.- ..+.-+||-|-
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 5544333321 24556888883
No 131
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=33.47 E-value=37 Score=32.54 Aligned_cols=48 Identities=31% Similarity=0.578 Sum_probs=32.6
Q ss_pred eecCCCCCCC-cCHHHHHhhhhhcCCCCCCcccccccccCcc--cchHhhhh
Q 029557 48 EYPCPFCSED-FDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT--MDMVDHIT 96 (191)
Q Consensus 48 ~F~CPfC~e~-~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~--~d~v~Hl~ 96 (191)
.|+||.|+-. =-..+|-.|+.-.|.- .|.-.|--|...-- .|+..|+.
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 3456788888888876 66777887766422 35555554
No 132
>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=33.35 E-value=17 Score=22.89 Aligned_cols=25 Identities=20% Similarity=0.535 Sum_probs=15.4
Q ss_pred ceecCCCCCCCcCH-----HHHHhhhhhcC
Q 029557 47 YEYPCPFCSEDFDL-----VGLCCHIDEEH 71 (191)
Q Consensus 47 ~~F~CPfC~e~~D~-----~~L~~H~~eeH 71 (191)
....|-||+..+.. ..|..|+...|
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 45788888885544 47788876665
No 133
>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=33.28 E-value=22 Score=24.30 Aligned_cols=12 Identities=25% Similarity=0.958 Sum_probs=10.2
Q ss_pred ccCcceecCCCCCC
Q 029557 43 VKGEYEYPCPFCSE 56 (191)
Q Consensus 43 ~~~~~~F~CPfC~e 56 (191)
+- .+|.||-|+.
T Consensus 31 Lp--~~w~CP~C~a 42 (50)
T cd00730 31 LP--DDWVCPVCGA 42 (50)
T ss_pred CC--CCCCCCCCCC
Confidence 55 6899999997
No 134
>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=33.10 E-value=14 Score=31.36 Aligned_cols=23 Identities=22% Similarity=0.239 Sum_probs=0.0
Q ss_pred eecCCCCCCCcCHHHHHhhhhhc
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEE 70 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~ee 70 (191)
...||+||+-+-+..+-.|++-+
T Consensus 168 ~~~cPitGe~IP~~e~~eHmRi~ 190 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMRIE 190 (229)
T ss_dssp -----------------------
T ss_pred ccccccccccccccccccccccc
Confidence 47999999999999999998743
No 135
>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=32.27 E-value=8.3 Score=29.37 Aligned_cols=38 Identities=29% Similarity=0.630 Sum_probs=11.8
Q ss_pred cCCCCCCCcCHHHHH-hhhhhcCCC-----------CCCcccccccccCc
Q 029557 50 PCPFCSEDFDLVGLC-CHIDEEHPV-----------EAKSGVCPVCVTRV 87 (191)
Q Consensus 50 ~CPfC~e~~D~~~L~-~H~~eeH~~-----------e~k~vVCPICa~~~ 87 (191)
.||+|++.+....+. .=|..-|.+ +++.-+|++|..+.
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 599999977765543 446777755 55567899997654
No 136
>PRK00907 hypothetical protein; Provisional
Probab=31.79 E-value=22 Score=27.03 Aligned_cols=28 Identities=18% Similarity=0.218 Sum_probs=19.2
Q ss_pred cchhhhccCcceecCCCCCC--CcCHHHHHhhh
Q 029557 37 EDDYEEVKGEYEYPCPFCSE--DFDLVGLCCHI 67 (191)
Q Consensus 37 ~d~d~e~~~~~~F~CPfC~e--~~D~~~L~~H~ 67 (191)
.|++|++. +|||.|..+ |.+..+|...+
T Consensus 5 ~~~~~~li---EFPc~fpiKVmG~a~~~l~~~V 34 (92)
T PRK00907 5 SDNPDHGF---QFPGTFELSAMGTAERGLETEL 34 (92)
T ss_pred cCCCCccE---ecCCCCeEEEEEcCchhHHHHH
Confidence 34444455 799999988 87777766544
No 137
>PHA00733 hypothetical protein
Probab=31.22 E-value=39 Score=26.73 Aligned_cols=25 Identities=20% Similarity=0.453 Sum_probs=21.5
Q ss_pred eecCCCCCCC-cCHHHHHhhhhhcCC
Q 029557 48 EYPCPFCSED-FDLVGLCCHIDEEHP 72 (191)
Q Consensus 48 ~F~CPfC~e~-~D~~~L~~H~~eeH~ 72 (191)
.|.|+.|++. -....|..|+...|.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 5999999994 566889999999985
No 138
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.19 E-value=11 Score=28.45 Aligned_cols=46 Identities=24% Similarity=0.525 Sum_probs=31.4
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcccchHhhhhcccccchhh
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDHITTQHGNISNS 105 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~d~v~Hl~~qH~~~~K~ 105 (191)
..|.|--|+..+|+.. |-.|.-...||-|.+++.+-| .+=|..||+
T Consensus 11 Y~Y~c~~cg~~~dvvq--------~~~ddplt~ce~c~a~~kk~l-----~~vgi~fKG 56 (82)
T COG2331 11 YSYECTECGNRFDVVQ--------AMTDDPLTTCEECGARLKKLL-----NAVGIVFKG 56 (82)
T ss_pred eEEeecccchHHHHHH--------hcccCccccChhhChHHHHhh-----ccceEEEec
Confidence 4689999999888753 334566789999988654322 344556664
No 139
>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=30.74 E-value=24 Score=34.28 Aligned_cols=40 Identities=30% Similarity=0.620 Sum_probs=25.3
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhc--CCCCCCcccccccccCcc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEE--HPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~ee--H~~e~k~vVCPICa~~~~ 88 (191)
-..+||-||+.+.+. ..++.-. ...+.-..+||-|-..+.
T Consensus 199 ~~vpCPhCg~~~~l~--~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLE--WENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EEccCCCCCCCcccc--ccceeecCCCCccceEEECCCCcCCCC
Confidence 468999999955443 2223222 133444578999988775
No 140
>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=30.71 E-value=28 Score=31.37 Aligned_cols=30 Identities=30% Similarity=0.509 Sum_probs=22.7
Q ss_pred ccCcceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 43 VKGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 43 ~~~~~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
+| ..||-|++-+-..+|.. +.-|||-|...
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 78999999776666543 34699999763
No 141
>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=30.46 E-value=28 Score=24.33 Aligned_cols=38 Identities=29% Similarity=0.488 Sum_probs=24.3
Q ss_pred ceecCCCCCCCcCHHHHHhhh------------------hhcCCCCCCccccccccc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHI------------------DEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~------------------~eeH~~e~k~vVCPICa~ 85 (191)
..-.||+|.-.+|...|..=. .+.|..+ ...+||.|..
T Consensus 6 niL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~e-g~L~Cp~c~r 61 (68)
T PF03966_consen 6 NILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVE-GELICPECGR 61 (68)
T ss_dssp GTBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTT-TEEEETTTTE
T ss_pred hhhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccC-CEEEcCCCCC
Confidence 467899998888767766622 2234444 4579999953
No 142
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=30.22 E-value=28 Score=29.53 Aligned_cols=29 Identities=31% Similarity=0.561 Sum_probs=21.2
Q ss_pred ceecCCCCCC--CcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 47 YEYPCPFCSE--DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 47 ~~F~CPfC~e--~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
..|.||-|.. .||.+-+.. -.||.|-+.+
T Consensus 112 ~~y~C~~~~~r~sfdeA~~~~------------F~Cp~Cg~~L 142 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAMELG------------FTCPKCGEDL 142 (176)
T ss_pred CceeCCCCCCcccHHHHHHhC------------CCCCCCCchh
Confidence 5799999998 555554433 6899997754
No 143
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.16 E-value=28 Score=32.60 Aligned_cols=23 Identities=35% Similarity=0.856 Sum_probs=19.9
Q ss_pred ecCCCCCCCcCHHHHHhhhhhcCC
Q 029557 49 YPCPFCSEDFDLVGLCCHIDEEHP 72 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~eeH~ 72 (191)
.-||||.-.+...++|.|++ .|-
T Consensus 3 ~iCP~CkLsv~~~~m~~Hie-aHF 25 (393)
T KOG4696|consen 3 IICPFCKLSVNYDEMCFHIE-AHF 25 (393)
T ss_pred ccccceecccCHHHHHHHHH-hhc
Confidence 56999999999999999998 454
No 144
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=30.04 E-value=12 Score=29.68 Aligned_cols=39 Identities=23% Similarity=0.716 Sum_probs=24.1
Q ss_pred CCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcc---------------cchHhhhhcccccchh
Q 029557 51 CPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT---------------MDMVDHITTQHGNISN 104 (191)
Q Consensus 51 CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~---------------~d~v~Hl~~qH~~~~K 104 (191)
||.||..+-+.. ..||-|...+- .+|+.-+-...|++=.
T Consensus 1 CPvCg~~l~vt~---------------l~C~~C~t~i~G~F~l~~~~~L~~E~~~Fi~~Fi~~rGnlKe 54 (113)
T PF09862_consen 1 CPVCGGELVVTR---------------LKCPSCGTEIEGEFELPWFARLSPEQLEFIKLFIKNRGNLKE 54 (113)
T ss_pred CCCCCCceEEEE---------------EEcCCCCCEEEeeeccchhhcCCHHHHHHHHHHHHhcCCHHH
Confidence 899988776544 45666655432 4666666666666533
No 145
>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=30.00 E-value=14 Score=27.93 Aligned_cols=8 Identities=50% Similarity=1.551 Sum_probs=5.3
Q ss_pred ecCCCCCC
Q 029557 49 YPCPFCSE 56 (191)
Q Consensus 49 F~CPfC~e 56 (191)
.+|||||.
T Consensus 2 I~CP~CG~ 9 (84)
T PF04267_consen 2 IPCPHCGP 9 (84)
T ss_dssp EEETTTEE
T ss_pred ccCCCCCc
Confidence 46777776
No 146
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=29.78 E-value=15 Score=35.70 Aligned_cols=33 Identities=27% Similarity=0.614 Sum_probs=28.9
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCCCCCccc
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGV 79 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vV 79 (191)
+.|+|-||-. =+...+|-.|++..|+.+.++|.
T Consensus 457 q~f~~ky~~atfyss~~ltrhin~~Hpse~rqv~ 490 (500)
T KOG3993|consen 457 QGFTCKYCPATFYSSPGLTRHINKCHPSELRQVA 490 (500)
T ss_pred hccccccchHhhhcCcchHhHhhhcChHHhhhhH
Confidence 6799999988 77888999999999999988864
No 147
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=29.77 E-value=25 Score=34.70 Aligned_cols=21 Identities=29% Similarity=0.504 Sum_probs=16.8
Q ss_pred hhcCCCCCCcccccccccCcc
Q 029557 68 DEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 68 ~eeH~~e~k~vVCPICa~~~~ 88 (191)
..+...+++.-|||||...||
T Consensus 84 ~~~~g~~PNt~vcpvclg~PG 104 (544)
T PLN02751 84 PYNYGAEPNTTVCPVCMGLPG 104 (544)
T ss_pred CcccCCCCccCcCccccCCCC
Confidence 334455788999999999988
No 148
>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=29.73 E-value=7.4 Score=24.40 Aligned_cols=11 Identities=18% Similarity=0.543 Sum_probs=4.1
Q ss_pred CCCCCCCcCHH
Q 029557 51 CPFCSEDFDLV 61 (191)
Q Consensus 51 CPfC~e~~D~~ 61 (191)
|++|++.+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 78888865554
No 149
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=29.59 E-value=35 Score=22.84 Aligned_cols=29 Identities=21% Similarity=0.594 Sum_probs=17.9
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCccccccc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVC 83 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPIC 83 (191)
.-+.||.|+-++...-= .++ .+...||.|
T Consensus 27 v~W~C~~Cgh~w~~~v~-------~R~-~~~~~CP~C 55 (55)
T PF14311_consen 27 VWWKCPKCGHEWKASVN-------DRT-RRGKGCPYC 55 (55)
T ss_pred EEEECCCCCCeeEccHh-------hhc-cCCCCCCCC
Confidence 45899999875543211 111 456789988
No 150
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=29.57 E-value=20 Score=27.74 Aligned_cols=19 Identities=26% Similarity=0.618 Sum_probs=13.4
Q ss_pred ceecCCCCCC-CcCHHHHHh
Q 029557 47 YEYPCPFCSE-DFDLVGLCC 65 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~ 65 (191)
..|.||+|.. .=.+..|..
T Consensus 23 ~D~~Cp~C~~~~~~~~~~~~ 42 (178)
T cd03019 23 FSYGCPHCYNFEPILEAWVK 42 (178)
T ss_pred ECCCCcchhhhhHHHHHHHH
Confidence 4699999998 555555544
No 151
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=29.26 E-value=27 Score=29.69 Aligned_cols=13 Identities=46% Similarity=1.099 Sum_probs=10.4
Q ss_pred ecCCCCCCCcCHH
Q 029557 49 YPCPFCSEDFDLV 61 (191)
Q Consensus 49 F~CPfC~e~~D~~ 61 (191)
=+||+||.-+|-.
T Consensus 155 P~CPlCg~PlDP~ 167 (171)
T PF11290_consen 155 PPCPLCGEPLDPE 167 (171)
T ss_pred CCCCCCCCCCCCC
Confidence 4799999987754
No 152
>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=29.19 E-value=25 Score=26.68 Aligned_cols=8 Identities=50% Similarity=1.767 Sum_probs=6.0
Q ss_pred ecCCCCCC
Q 029557 49 YPCPFCSE 56 (191)
Q Consensus 49 F~CPfC~e 56 (191)
.+||+||.
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 47888885
No 153
>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=29.18 E-value=27 Score=23.58 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=7.0
Q ss_pred ceecCCCCCC
Q 029557 47 YEYPCPFCSE 56 (191)
Q Consensus 47 ~~F~CPfC~e 56 (191)
..|.||-|+.
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 6799999987
No 154
>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=29.18 E-value=21 Score=23.49 Aligned_cols=9 Identities=33% Similarity=1.206 Sum_probs=7.3
Q ss_pred eecCCCCCC
Q 029557 48 EYPCPFCSE 56 (191)
Q Consensus 48 ~F~CPfC~e 56 (191)
.-.||||+.
T Consensus 29 ~~~CpYCg~ 37 (40)
T PF10276_consen 29 PVVCPYCGT 37 (40)
T ss_dssp EEEETTTTE
T ss_pred eEECCCCCC
Confidence 378999985
No 155
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=28.71 E-value=34 Score=18.79 Aligned_cols=16 Identities=19% Similarity=0.698 Sum_probs=6.8
Q ss_pred ccccccCcc--cchHhhh
Q 029557 80 CPVCVTRVT--MDMVDHI 95 (191)
Q Consensus 80 CPICa~~~~--~d~v~Hl 95 (191)
|.||-.... ..|..|+
T Consensus 3 C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQHL 20 (25)
T ss_dssp ETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCcCCHHHHHHHH
Confidence 555533322 2444444
No 156
>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=28.58 E-value=21 Score=25.52 Aligned_cols=10 Identities=50% Similarity=1.245 Sum_probs=8.2
Q ss_pred ceecCCCCCC
Q 029557 47 YEYPCPFCSE 56 (191)
Q Consensus 47 ~~F~CPfC~e 56 (191)
..+.|-+||+
T Consensus 4 ~~~~C~~Cg~ 13 (69)
T PF09706_consen 4 KKYNCIFCGE 13 (69)
T ss_pred CCCcCcCCCC
Confidence 5689999994
No 157
>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=28.08 E-value=18 Score=27.21 Aligned_cols=37 Identities=16% Similarity=0.343 Sum_probs=18.9
Q ss_pred CCCCCCCcCHHHHHhhhhhcCC----CCCCcccccccccCc
Q 029557 51 CPFCSEDFDLVGLCCHIDEEHP----VEAKSGVCPVCVTRV 87 (191)
Q Consensus 51 CPfC~e~~D~~~L~~H~~eeH~----~e~k~vVCPICa~~~ 87 (191)
||+|+.+--+.....+.....- .+....+||.|-...
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
Confidence 9999863333333332211111 133346799997754
No 158
>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=28.06 E-value=13 Score=30.65 Aligned_cols=13 Identities=15% Similarity=0.391 Sum_probs=10.8
Q ss_pred ccCcceecCCCCCCC
Q 029557 43 VKGEYEYPCPFCSED 57 (191)
Q Consensus 43 ~~~~~~F~CPfC~e~ 57 (191)
+. ..|.||||+.+
T Consensus 5 ~~--~D~vcPwcylg 17 (209)
T cd03021 5 LY--YDVVSPYSYLA 17 (209)
T ss_pred EE--EeCCChHHHHH
Confidence 55 78999999984
No 159
>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=28.03 E-value=14 Score=34.11 Aligned_cols=40 Identities=25% Similarity=0.524 Sum_probs=26.2
Q ss_pred ecCCCCCCCcCHHHHHhhhhhcC-CCCCCcccccccccCcc
Q 029557 49 YPCPFCSEDFDLVGLCCHIDEEH-PVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~eeH-~~e~k~vVCPICa~~~~ 88 (191)
=.||+|+.+---...|++|-... +.+..+.+|.+|...+.
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 57999996555556777776544 36778899999987664
No 160
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=27.81 E-value=38 Score=30.99 Aligned_cols=29 Identities=21% Similarity=0.200 Sum_probs=22.6
Q ss_pred ccCcceecCCCCCCCcCHHHHHhhhhhcCCCCCCccccccccc
Q 029557 43 VKGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 43 ~~~~~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
+| ..||-|++-+-...|-. +.-|||-|..
T Consensus 37 lw----~kc~~C~~~~~~~~l~~----------~~~vcp~c~~ 65 (296)
T CHL00174 37 LW----VQCENCYGLNYKKFLKS----------KMNICEQCGY 65 (296)
T ss_pred Ce----eECCCccchhhHHHHHH----------cCCCCCCCCC
Confidence 67 78999999777777643 3469999976
No 161
>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=27.52 E-value=29 Score=33.56 Aligned_cols=15 Identities=33% Similarity=0.789 Sum_probs=13.8
Q ss_pred CCCcccccccccCcc
Q 029557 74 EAKSGVCPVCVTRVT 88 (191)
Q Consensus 74 e~k~vVCPICa~~~~ 88 (191)
+++..|||||...||
T Consensus 34 ~PNt~v~pvclg~PG 48 (478)
T TIGR00133 34 PPNTNVCPVCLGLPG 48 (478)
T ss_pred CCCcccCccccCCCC
Confidence 688899999999988
No 162
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.40 E-value=28 Score=25.17 Aligned_cols=13 Identities=46% Similarity=0.963 Sum_probs=8.0
Q ss_pred CCCcccccccccC
Q 029557 74 EAKSGVCPVCVTR 86 (191)
Q Consensus 74 e~k~vVCPICa~~ 86 (191)
+.+.|+||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 4556777777553
No 163
>PRK10220 hypothetical protein; Provisional
Probab=27.37 E-value=31 Score=27.54 Aligned_cols=13 Identities=23% Similarity=0.715 Sum_probs=8.5
Q ss_pred CCCcccccccccC
Q 029557 74 EAKSGVCPVCVTR 86 (191)
Q Consensus 74 e~k~vVCPICa~~ 86 (191)
+....|||-|+.-
T Consensus 17 d~~~~vCpeC~hE 29 (111)
T PRK10220 17 DNGMYICPECAHE 29 (111)
T ss_pred CCCeEECCcccCc
Confidence 3445788888663
No 164
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=27.36 E-value=29 Score=25.10 Aligned_cols=27 Identities=19% Similarity=0.218 Sum_probs=22.7
Q ss_pred ceecCCCCCC-CcCHHHHHhhhhhcCCC
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHIDEEHPV 73 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~~eeH~~ 73 (191)
.-|.||-|+. =-+...-..|++..|-.
T Consensus 16 ~~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 16 EFLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred eeeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 3589999999 66788899999998865
No 165
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=27.35 E-value=26 Score=29.53 Aligned_cols=41 Identities=22% Similarity=0.464 Sum_probs=26.5
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcC-----CCCC-CcccccccccCc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEH-----PVEA-KSGVCPVCVTRV 87 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH-----~~e~-k~vVCPICa~~~ 87 (191)
+--.||.|+..++..--..|++=.| .... +-+.|+-|-...
T Consensus 19 Q~G~CaiC~~~l~~~~~~~~vDHDH~l~g~~TG~VRGLLC~~CN~~l 65 (157)
T PHA02565 19 QNGICPLCKRELDGDVSKNHLDHDHELNGPNAGRVRGLLCNLCNALE 65 (157)
T ss_pred hCCcCCCCCCccCCCccccccCCCCCCCCcccccccccCchhhhhhh
Confidence 4578999999776432234777777 3322 446799995533
No 166
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=27.07 E-value=20 Score=34.54 Aligned_cols=32 Identities=25% Similarity=0.513 Sum_probs=21.6
Q ss_pred ceecCCCCCC---CcCHHHHHhhhhhcCCCCCCccccccccc
Q 029557 47 YEYPCPFCSE---DFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 47 ~~F~CPfC~e---~~D~~~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
+.|.||+|.. .||+..|..- +...-.|-.|-.
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~~-------~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLDN-------ETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHhhcc-------cCceEEEecCCC
Confidence 6899999999 4555555542 234456777755
No 167
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=26.98 E-value=23 Score=32.58 Aligned_cols=18 Identities=33% Similarity=0.647 Sum_probs=14.1
Q ss_pred CcccccccccCcccchHh
Q 029557 76 KSGVCPVCVTRVTMDMVD 93 (191)
Q Consensus 76 k~vVCPICa~~~~~d~v~ 93 (191)
+..+||||..+|...||.
T Consensus 184 ~~~~CPvCGS~PvaSmV~ 201 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQ 201 (308)
T ss_pred ccccCCCcCCCCcceeee
Confidence 457999999998766663
No 168
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=26.94 E-value=29 Score=25.46 Aligned_cols=8 Identities=38% Similarity=1.547 Sum_probs=5.3
Q ss_pred ecCCCCCC
Q 029557 49 YPCPFCSE 56 (191)
Q Consensus 49 F~CPfC~e 56 (191)
|.||+||.
T Consensus 2 m~CP~Cg~ 9 (72)
T PRK09678 2 FHCPLCQH 9 (72)
T ss_pred ccCCCCCC
Confidence 46777766
No 169
>PF14369 zf-RING_3: zinc-finger
Probab=26.79 E-value=31 Score=21.78 Aligned_cols=9 Identities=44% Similarity=1.250 Sum_probs=7.7
Q ss_pred cCCCCCCCc
Q 029557 50 PCPFCSEDF 58 (191)
Q Consensus 50 ~CPfC~e~~ 58 (191)
.||.|+-+|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 699999876
No 170
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.76 E-value=32 Score=37.32 Aligned_cols=36 Identities=28% Similarity=0.659 Sum_probs=20.3
Q ss_pred eecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 48 EYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 48 ~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
.|.||-||. .+. ..|..|-.. .++ ..+||.|-+.+.
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CGs~--te~-vy~CPsCGaev~ 703 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCGTH--TEP-VYVCPDCGAEVP 703 (1337)
T ss_pred EEECCCCCCcccc--ccCcccCCc--CCC-ceeCccCCCccC
Confidence 588999988 332 356555543 111 236777766543
No 171
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=26.25 E-value=6.1 Score=30.08 Aligned_cols=21 Identities=24% Similarity=0.719 Sum_probs=17.0
Q ss_pred ceecCCCCCC-CcCHHHHHhhh
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHI 67 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~ 67 (191)
..|.||+|.. .-.+..|..+.
T Consensus 20 ~d~~Cp~C~~~~~~~~~~~~~~ 41 (162)
T PF13462_consen 20 FDFQCPHCAKFHEELEKLLKKY 41 (162)
T ss_dssp E-TTSHHHHHHHHHHHHHHHHH
T ss_pred ECCCCHhHHHHHHHHhhhhhhc
Confidence 4699999999 77777888885
No 172
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=26.25 E-value=50 Score=20.75 Aligned_cols=31 Identities=19% Similarity=0.546 Sum_probs=18.1
Q ss_pred ecCCCCCCCcCHHHHHhhhhhcCCCCCCccccccccc
Q 029557 49 YPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 49 F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
+.||-|+..|++.+=. =+.....|-||.|..
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 6788888855443211 123455677888854
No 173
>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=26.10 E-value=18 Score=28.88 Aligned_cols=21 Identities=19% Similarity=0.422 Sum_probs=16.0
Q ss_pred ceecCCCCCC-CcCHHHHHhhh
Q 029557 47 YEYPCPFCSE-DFDLVGLCCHI 67 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~~H~ 67 (191)
..|.||||+. .-.+..+....
T Consensus 5 ~D~~cP~cyl~~~~l~~~~~~~ 26 (201)
T cd03024 5 SDVVCPWCYIGKRRLEKALAEL 26 (201)
T ss_pred ecCcCccHHHHHHHHHHHHHhC
Confidence 6799999998 55666676555
No 174
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.97 E-value=22 Score=27.62 Aligned_cols=12 Identities=25% Similarity=0.429 Sum_probs=6.9
Q ss_pred ceecCCCCCCCc
Q 029557 47 YEYPCPFCSEDF 58 (191)
Q Consensus 47 ~~F~CPfC~e~~ 58 (191)
..+.|+-|+..|
T Consensus 69 ~~~~C~~Cg~~~ 80 (114)
T PRK03681 69 AECWCETCQQYV 80 (114)
T ss_pred cEEEcccCCCee
Confidence 346666666633
No 175
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=25.65 E-value=39 Score=30.56 Aligned_cols=30 Identities=27% Similarity=0.525 Sum_probs=22.4
Q ss_pred ccCcceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 43 VKGEYEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 43 ~~~~~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
+| -.||-|++-+-...|-. +.-|||-|-..
T Consensus 26 ~~----~~c~~c~~~~~~~~l~~----------~~~vc~~c~~h 55 (292)
T PRK05654 26 LW----TKCPSCGQVLYRKELEA----------NLNVCPKCGHH 55 (292)
T ss_pred Ce----eECCCccchhhHHHHHh----------cCCCCCCCCCC
Confidence 77 89999999776666543 23699999763
No 176
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=25.60 E-value=23 Score=27.29 Aligned_cols=13 Identities=31% Similarity=0.887 Sum_probs=10.7
Q ss_pred ccCcceecCCCCCCC
Q 029557 43 VKGEYEYPCPFCSED 57 (191)
Q Consensus 43 ~~~~~~F~CPfC~e~ 57 (191)
.+ +.+.||+|+..
T Consensus 32 ~~--~~~~Cp~C~~~ 44 (89)
T COG1997 32 QR--AKHVCPFCGRT 44 (89)
T ss_pred Hh--cCCcCCCCCCc
Confidence 55 78999999873
No 177
>PHA02929 N1R/p28-like protein; Provisional
Probab=25.42 E-value=13 Score=32.90 Aligned_cols=41 Identities=24% Similarity=0.482 Sum_probs=23.5
Q ss_pred ceecCCCCCCCcCHH----------HHHhhhhhcCCC---CCCcccccccccCc
Q 029557 47 YEYPCPFCSEDFDLV----------GLCCHIDEEHPV---EAKSGVCPVCVTRV 87 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~----------~L~~H~~eeH~~---e~k~vVCPICa~~~ 87 (191)
....||.|.+.+... .=|.|.--..+. -.....||+|...+
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 125553222221 12346899997754
No 178
>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=25.23 E-value=28 Score=31.74 Aligned_cols=23 Identities=30% Similarity=0.587 Sum_probs=15.4
Q ss_pred hhhhcCCCCCCcccccccccCcc
Q 029557 66 HIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 66 H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
.|......+++.-|||+|...||
T Consensus 21 ~c~~~~~~~pNt~v~~~~lg~PG 43 (289)
T PF02934_consen 21 SCPNEFGAEPNTNVCPVCLGLPG 43 (289)
T ss_dssp SSBSSTTSCTTSSB-TTTTT-TT
T ss_pred CCCCCCCCCCccccCceeccCCC
Confidence 34444444788899999999987
No 179
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=24.32 E-value=39 Score=22.19 Aligned_cols=25 Identities=24% Similarity=0.670 Sum_probs=14.8
Q ss_pred eecCCCCCCCcCHH------HHHhhhhhcCC
Q 029557 48 EYPCPFCSEDFDLV------GLCCHIDEEHP 72 (191)
Q Consensus 48 ~F~CPfC~e~~D~~------~L~~H~~eeH~ 72 (191)
.-.|-+|+..+... .|..|+...|+
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 45677777755443 56666665554
No 180
>cd02972 DsbA_family DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins.
Probab=24.28 E-value=19 Score=24.14 Aligned_cols=18 Identities=28% Similarity=0.713 Sum_probs=12.3
Q ss_pred ceecCCCCCC-CcCHHHHH
Q 029557 47 YEYPCPFCSE-DFDLVGLC 64 (191)
Q Consensus 47 ~~F~CPfC~e-~~D~~~L~ 64 (191)
..|.||||.. .-.+..+.
T Consensus 5 ~d~~Cp~C~~~~~~l~~~~ 23 (98)
T cd02972 5 FDPLCPYCYLFEPELEKLL 23 (98)
T ss_pred ECCCCHhHHhhhHHHHHHH
Confidence 4689999998 44444444
No 181
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=23.96 E-value=30 Score=35.19 Aligned_cols=38 Identities=29% Similarity=0.587 Sum_probs=25.2
Q ss_pred ceecCCCCCCCcC----HHHHHhhhhhcCCCCCCcccccccccC
Q 029557 47 YEYPCPFCSEDFD----LVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 47 ~~F~CPfC~e~~D----~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
..+.||.|+..+. ...|.||-=..+ +...-.||=|-..
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 4689999998443 345555433333 5667899999775
No 182
>cd03022 DsbA_HCCA_Iso DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is unique to bacteria that degrade polycyclic aromatic compounds. It is closely related to the eukaryotic protein, GSH transferase kappa (GSTK).
Probab=23.69 E-value=18 Score=28.50 Aligned_cols=20 Identities=15% Similarity=0.486 Sum_probs=13.6
Q ss_pred ceecCCCCCCCc-CHHHHHhh
Q 029557 47 YEYPCPFCSEDF-DLVGLCCH 66 (191)
Q Consensus 47 ~~F~CPfC~e~~-D~~~L~~H 66 (191)
..|.||||+... -+..+...
T Consensus 5 ~D~~cP~cy~~~~~l~~~~~~ 25 (192)
T cd03022 5 FDFSSPYSYLAHERLPALAAR 25 (192)
T ss_pred EeCCChHHHHHHHHHHHHHHH
Confidence 679999999943 33445543
No 183
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.66 E-value=30 Score=26.95 Aligned_cols=28 Identities=36% Similarity=0.699 Sum_probs=19.2
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
..+.|+-|+..+..... ....||-|...
T Consensus 70 ~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 70 VELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred CEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 57999999976655422 22459999763
No 184
>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=23.62 E-value=36 Score=21.30 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=5.8
Q ss_pred cccccccccCc
Q 029557 77 SGVCPVCVTRV 87 (191)
Q Consensus 77 ~vVCPICa~~~ 87 (191)
.+.||-|..++
T Consensus 17 ~irC~~CG~RI 27 (32)
T PF03604_consen 17 PIRCPECGHRI 27 (32)
T ss_dssp TSSBSSSS-SE
T ss_pred cEECCcCCCeE
Confidence 35677775443
No 185
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=23.48 E-value=47 Score=29.73 Aligned_cols=38 Identities=26% Similarity=0.524 Sum_probs=26.2
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcccchHhh
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVTMDMVDH 94 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~~d~v~H 94 (191)
....||.|+.. + -+.+ .+...+||.-|-.-+..+++.+
T Consensus 10 ~~~~Cp~Cg~~-~------iv~d---~~~Ge~vC~~CG~Vl~e~~iD~ 47 (310)
T PRK00423 10 EKLVCPECGSD-K------LIYD---YERGEIVCADCGLVIEENIIDQ 47 (310)
T ss_pred cCCcCcCCCCC-C------eeEE---CCCCeEeecccCCccccccccc
Confidence 34679999961 1 1222 2577899999999887777655
No 186
>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=23.46 E-value=44 Score=23.67 Aligned_cols=10 Identities=30% Similarity=1.026 Sum_probs=7.0
Q ss_pred cCCCCCCCcC
Q 029557 50 PCPFCSEDFD 59 (191)
Q Consensus 50 ~CPfC~e~~D 59 (191)
-||+||+.++
T Consensus 5 HC~~CG~~Ip 14 (59)
T PF09889_consen 5 HCPVCGKPIP 14 (59)
T ss_pred cCCcCCCcCC
Confidence 4888887554
No 187
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=23.40 E-value=34 Score=28.30 Aligned_cols=31 Identities=29% Similarity=0.709 Sum_probs=18.4
Q ss_pred cCCCCCCCcCHHHHHhhhhhcCCCCCCc-----ccccccccC
Q 029557 50 PCPFCSEDFDLVGLCCHIDEEHPVEAKS-----GVCPVCVTR 86 (191)
Q Consensus 50 ~CPfC~e~~D~~~L~~H~~eeH~~e~k~-----vVCPICa~~ 86 (191)
.|||||.... |+.+.-.....+ --||-|.-.
T Consensus 2 ~cp~c~~~~~------~~~~s~~~~~~~~~~~~~~c~~c~~~ 37 (154)
T PRK00464 2 RCPFCGHPDT------RVIDSRPAEDGNAIRRRRECLACGKR 37 (154)
T ss_pred cCCCCCCCCC------EeEeccccCCCCceeeeeeccccCCc
Confidence 6999998431 333444333333 349999764
No 188
>PHA02540 61 DNA primase; Provisional
Probab=23.02 E-value=37 Score=31.42 Aligned_cols=9 Identities=33% Similarity=1.472 Sum_probs=8.2
Q ss_pred eecCCCCCC
Q 029557 48 EYPCPFCSE 56 (191)
Q Consensus 48 ~F~CPfC~e 56 (191)
.+.||||++
T Consensus 27 ~~~CPf~~d 35 (337)
T PHA02540 27 NFRCPICGD 35 (337)
T ss_pred EecCCCCCC
Confidence 599999998
No 189
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=22.88 E-value=39 Score=30.71 Aligned_cols=17 Identities=35% Similarity=0.858 Sum_probs=15.5
Q ss_pred ccCcceecCCCCCCCcC
Q 029557 43 VKGEYEYPCPFCSEDFD 59 (191)
Q Consensus 43 ~~~~~~F~CPfC~e~~D 59 (191)
+||..+|.||-|+..|.
T Consensus 150 mwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 150 MWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccceeeeecccccccch
Confidence 88899999999998776
No 190
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=22.57 E-value=50 Score=20.96 Aligned_cols=20 Identities=30% Similarity=0.642 Sum_probs=12.1
Q ss_pred HHhhhhhcCCCCCCcccccccc
Q 029557 63 LCCHIDEEHPVEAKSGVCPVCV 84 (191)
Q Consensus 63 L~~H~~eeH~~e~k~vVCPICa 84 (191)
+|.-+..... .+.++||+|.
T Consensus 24 ~C~~C~~~~~--~~~~~CP~C~ 43 (44)
T PF14634_consen 24 FCEKCLKKLK--GKSVKCPICR 43 (44)
T ss_pred HHHHHHHhhc--CCCCCCcCCC
Confidence 3344444443 6678999994
No 191
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.30 E-value=29 Score=30.55 Aligned_cols=53 Identities=19% Similarity=0.271 Sum_probs=33.7
Q ss_pred ccCcceecCCCCCC-CcCHHHHHhhhh-------hcCCCCCCcccccccccCcccchHhhhhcccccc
Q 029557 43 VKGEYEYPCPFCSE-DFDLVGLCCHID-------EEHPVEAKSGVCPVCVTRVTMDMVDHITTQHGNI 102 (191)
Q Consensus 43 ~~~~~~F~CPfC~e-~~D~~~L~~H~~-------eeH~~e~k~vVCPICa~~~~~d~v~Hl~~qH~~~ 102 (191)
++ ..+.||+|+. .-.+..+..-.. .-|+++.....||- +.|...++...-|..
T Consensus 10 v~--sD~vCPwC~ig~~rL~ka~~~~~~~~~v~i~w~pf~l~p~~~~~-----g~~~~~~l~~k~g~~ 70 (225)
T COG2761 10 VF--SDVVCPWCYIGKRRLEKALAEYPQEVRVEIRWRPFELDPDLPPE-----GLDRKEYLAQKYGIS 70 (225)
T ss_pred EE--eCCcCchhhcCHHHHHHHHHhcCcceeEEEEecccccCCCCCcc-----cccHHHHHHHHhCcc
Confidence 56 7899999998 555555444333 34667777777775 566666665444443
No 192
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=22.03 E-value=41 Score=27.85 Aligned_cols=10 Identities=40% Similarity=0.823 Sum_probs=8.1
Q ss_pred Cccccccccc
Q 029557 76 KSGVCPVCVT 85 (191)
Q Consensus 76 k~vVCPICa~ 85 (191)
+.+.||+|-.
T Consensus 31 glv~CP~Cgs 40 (148)
T PF06676_consen 31 GLVSCPVCGS 40 (148)
T ss_pred CCccCCCCCC
Confidence 5688999965
No 193
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=21.97 E-value=38 Score=22.18 Aligned_cols=8 Identities=50% Similarity=1.447 Sum_probs=3.6
Q ss_pred ecCCCCCC
Q 029557 49 YPCPFCSE 56 (191)
Q Consensus 49 F~CPfC~e 56 (191)
=+||.|+-
T Consensus 4 ~pCP~CGG 11 (40)
T PF08273_consen 4 GPCPICGG 11 (40)
T ss_dssp E--TTTT-
T ss_pred CCCCCCcC
Confidence 36888875
No 194
>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=21.93 E-value=44 Score=23.56 Aligned_cols=9 Identities=56% Similarity=1.431 Sum_probs=8.0
Q ss_pred eecCCCCCC
Q 029557 48 EYPCPFCSE 56 (191)
Q Consensus 48 ~F~CPfC~e 56 (191)
..+||||+.
T Consensus 35 ~~pC~fCg~ 43 (57)
T PF06221_consen 35 LGPCPFCGT 43 (57)
T ss_pred cCcCCCCCC
Confidence 579999998
No 195
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.90 E-value=30 Score=27.25 Aligned_cols=8 Identities=38% Similarity=1.281 Sum_probs=5.1
Q ss_pred ecCCCCCC
Q 029557 49 YPCPFCSE 56 (191)
Q Consensus 49 F~CPfC~e 56 (191)
|.||.||-
T Consensus 93 ~~CP~Cgs 100 (124)
T PRK00762 93 IECPVCGN 100 (124)
T ss_pred CcCcCCCC
Confidence 56777764
No 196
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=21.85 E-value=66 Score=27.26 Aligned_cols=39 Identities=18% Similarity=0.265 Sum_probs=25.5
Q ss_pred cCCCCCC---CcCHHHHHhhhhhcCCCC-CCcccccccccCcc
Q 029557 50 PCPFCSE---DFDLVGLCCHIDEEHPVE-AKSGVCPVCVTRVT 88 (191)
Q Consensus 50 ~CPfC~e---~~D~~~L~~H~~eeH~~e-~k~vVCPICa~~~~ 88 (191)
.||+|+. .+.-.+-..-+...|... ...-+||.|-..-|
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 5999998 445555554555555543 33467999988766
No 197
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=21.60 E-value=57 Score=35.07 Aligned_cols=47 Identities=19% Similarity=0.386 Sum_probs=31.0
Q ss_pred ccCCCCCCCcchhhhccCcceecCCCCCC-CcCHHHHHhhhhhcCCCCCCcccccccccC
Q 029557 28 FCIDFEDIEEDDYEEVKGEYEYPCPFCSE-DFDLVGLCCHIDEEHPVEAKSGVCPVCVTR 86 (191)
Q Consensus 28 ~~~g~e~~e~d~d~e~~~~~~F~CPfC~e-~~D~~~L~~H~~eeH~~e~k~vVCPICa~~ 86 (191)
|.+|+-|++ + ++ +-|.||-|.- +|...+- -.--++--.-.||.|-..
T Consensus 670 y~lgITeVd---P--L~--phy~c~~c~~~ef~~~~~-----~~sg~dlp~k~cp~c~~~ 717 (1213)
T TIGR01405 670 TMTGITEVN---P--LP--PHYLCPNCKYSEFITDGS-----VGSGFDLPDKDCPKCGAP 717 (1213)
T ss_pred HHhcCCCcC---C--Cc--ccccCccccccccccccc-----ccccccCccccCcccccc
Confidence 466776654 4 77 8899999987 7754431 111234455689999875
No 198
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=21.01 E-value=25 Score=22.36 Aligned_cols=10 Identities=30% Similarity=1.092 Sum_probs=5.5
Q ss_pred CCCCCCCcCH
Q 029557 51 CPFCSEDFDL 60 (191)
Q Consensus 51 CPfC~e~~D~ 60 (191)
||-|+..+..
T Consensus 2 CP~C~~~l~~ 11 (41)
T PF13453_consen 2 CPRCGTELEP 11 (41)
T ss_pred cCCCCcccce
Confidence 6666554443
No 199
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=20.75 E-value=72 Score=26.06 Aligned_cols=41 Identities=15% Similarity=0.360 Sum_probs=28.7
Q ss_pred ceecCCCCCC--CcCH---HHHHhhhhhcCCCCCC------cccccccccCc
Q 029557 47 YEYPCPFCSE--DFDL---VGLCCHIDEEHPVEAK------SGVCPVCVTRV 87 (191)
Q Consensus 47 ~~F~CPfC~e--~~D~---~~L~~H~~eeH~~e~k------~vVCPICa~~~ 87 (191)
.-|.|=-||. +|+. ..+...+...|.+... .++||-|....
T Consensus 99 ~H~iC~~CGki~~i~~~~l~~~~~~~~~~~gf~i~~~~l~~~GiC~~C~~~~ 150 (169)
T PRK11639 99 AMFICDRCGAVKEECAEGVEDIMHTLAAKMGFALRHNVIEAHGLCAACVEVE 150 (169)
T ss_pred CeEEeCCCCCEEEecccHHHHHHHHHHHHcCCEEeccEEEEEEEChhhcCcc
Confidence 3599999999 7763 3456667677766433 37899997763
No 200
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=20.36 E-value=68 Score=26.91 Aligned_cols=35 Identities=23% Similarity=0.508 Sum_probs=24.0
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCc
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRV 87 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~ 87 (191)
...|.-|+..+....+..++. +...-.||.|...+
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~-----~~~~p~C~~Cg~~l 143 (218)
T cd01407 109 RVRCTKCGKEYPRDELQADID-----REEVPRCPKCGGLL 143 (218)
T ss_pred cceeCCCcCCCcHHHHhHhhc-----cCCCCcCCCCCCcc
Confidence 688999999887776653332 23345799997653
No 201
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=20.28 E-value=71 Score=30.69 Aligned_cols=56 Identities=20% Similarity=0.290 Sum_probs=35.2
Q ss_pred eecCCC--CCC-CcCHHHHHhhhhhcC-CCCCCccccccccc--CcccchHhhhhcccccch
Q 029557 48 EYPCPF--CSE-DFDLVGLCCHIDEEH-PVEAKSGVCPVCVT--RVTMDMVDHITTQHGNIS 103 (191)
Q Consensus 48 ~F~CPf--C~e-~~D~~~L~~H~~eeH-~~e~k~vVCPICa~--~~~~d~v~Hl~~qH~~~~ 103 (191)
-|.|-+ |-+ -=....|..|..+.| .+.+-.-.|-+|.. .-|.++.+||+-+||.-+
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 355655 555 223445566666666 33344456777765 346799999999998754
No 202
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=20.26 E-value=41 Score=23.07 Aligned_cols=28 Identities=29% Similarity=0.595 Sum_probs=21.4
Q ss_pred CCCcccccccccCcccchHhhhh-cccccc
Q 029557 74 EAKSGVCPVCVTRVTMDMVDHIT-TQHGNI 102 (191)
Q Consensus 74 e~k~vVCPICa~~~~~d~v~Hl~-~qH~~~ 102 (191)
+++.+.|-+|..+- .||..||. -+|+.+
T Consensus 2 ~~k~GYCE~Cr~kf-d~l~~Hi~s~~Hr~F 30 (49)
T smart00586 2 EKKPGYCENCREKY-DDLETHLLSEKHRRF 30 (49)
T ss_pred CCCCcccccHhHHH-hhHHHHhccHHHHHH
Confidence 67899999998876 58999995 344444
No 203
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=20.22 E-value=43 Score=26.59 Aligned_cols=34 Identities=24% Similarity=0.802 Sum_probs=18.8
Q ss_pred ceecCCCCCCCcCHHHHHhhhhhcCCCCCCccccccccc
Q 029557 47 YEYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVT 85 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~ 85 (191)
..|.||||.-+- ..-+-++..|. ...+-|-||..
T Consensus 22 t~FnClfcnHek---~v~~~~Dk~~~--iG~~sC~iC~e 55 (109)
T KOG3214|consen 22 TQFNCLFCNHEK---SVSCTLDKKHN--IGKASCRICEE 55 (109)
T ss_pred eeeccCcccccc---ceeeeehhhcC--cceeeeeehhh
Confidence 459999997632 11111222222 23467999965
No 204
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=20.21 E-value=43 Score=27.84 Aligned_cols=32 Identities=31% Similarity=0.667 Sum_probs=18.7
Q ss_pred cCCCCCC-CcCHHHHHhhhhhcCCCCCCc-----ccccccccCcc
Q 029557 50 PCPFCSE-DFDLVGLCCHIDEEHPVEAKS-----GVCPVCVTRVT 88 (191)
Q Consensus 50 ~CPfC~e-~~D~~~L~~H~~eeH~~e~k~-----vVCPICa~~~~ 88 (191)
.||||+. +-- +.+.-..+..+ =-|+.|..+-+
T Consensus 2 ~CP~C~~~dtk-------ViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTR-------VLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCE-------eeeccccCCCCeeeecccCCccCCccc
Confidence 5999998 432 22333333333 34999988643
No 205
>PF14968 CCDC84: Coiled coil protein 84
Probab=20.16 E-value=44 Score=31.09 Aligned_cols=22 Identities=23% Similarity=0.490 Sum_probs=16.1
Q ss_pred ceecCCCCCCCcCHH-------HHHhhhh
Q 029557 47 YEYPCPFCSEDFDLV-------GLCCHID 68 (191)
Q Consensus 47 ~~F~CPfC~e~~D~~-------~L~~H~~ 68 (191)
..|=|+||+.++... ++..|+-
T Consensus 57 ~~fWC~fC~~ev~~~~s~~~~~~ai~HLa 85 (336)
T PF14968_consen 57 NRFWCVFCDCEVREHDSSFACGGAIEHLA 85 (336)
T ss_pred ceeEeeCccchhhhccchhhhccHHhhcC
Confidence 679999999877654 5555553
No 206
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=20.15 E-value=44 Score=28.59 Aligned_cols=25 Identities=28% Similarity=0.752 Sum_probs=17.0
Q ss_pred eecCCCCCCCcCHHHHHhhhhhcCCCCCCcccccccccCcc
Q 029557 48 EYPCPFCSEDFDLVGLCCHIDEEHPVEAKSGVCPVCVTRVT 88 (191)
Q Consensus 48 ~F~CPfC~e~~D~~~L~~H~~eeH~~e~k~vVCPICa~~~~ 88 (191)
.=+||-||- +. ...+.|+-|..+|-
T Consensus 93 l~~CP~CGh----------~k------~a~~LC~~Cy~kV~ 117 (176)
T KOG4080|consen 93 LNTCPACGH----------IK------PAHTLCDYCYAKVH 117 (176)
T ss_pred cccCcccCc----------cc------cccccHHHHHHHHH
Confidence 458999984 22 23478899988764
Done!